Hostname: page-component-76fb5796d-dfsvx Total loading time: 0 Render date: 2024-04-25T11:38:06.565Z Has data issue: false hasContentIssue false
  • English
  • Français

Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMRspectroscopy

Published online by Cambridge University Press:  17 March 2009

Axel T. Brünger  and
Michael Nilges
Axel T. Brünger
Affiliation:
Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven CT 06511, USA
Michael Nilges
Affiliation:
European Molecular Biology Laboratory, Meyerhofstr. 1, D-6900 Heidelberg, FRG
Get access Rights & Permissions [Opens in a new window]

Extract

Macromolecular structure determination by X-ray crystallography and solution NMR spectroscopy has experienced unprecedented growth during the past decade.

Type
Research Article
Information
Quarterly Reviews of Biophysics , Volume 26 , Issue 1 , February 1993 , pp. 49 - 125
Copyright
Copyright © Cambridge University Press 1993

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abagyan, R. A. & Mazur, A. K. (1989). New methodology for computer aided modelling of biomolecular structure and dynamics. (2) Local deformation and cycles. J. Biomolec. Struct. Dyn. 4, 833–845.CrossRefGoogle Scholar
Agarwal, R. C. & Isaacs, N. W. (1977). Method for obtaining a high resolution protein map starting from a low resolution map. Proc. natn. Acad. Sci. U.S.A. 74, 2835–2839.CrossRefGoogle ScholarPubMed
Allen, F. H., Kennard, O & Taylor, R (1983). Systematic analysis of structural data as a researh technique in organic chemistry. Acct. chem. Res. 16, 146–153.CrossRefGoogle Scholar
Altman, R. B. & Jardetzky, O (1986). New strategies for the determination of macromolecular structure in solution. J. Biochem. 100, 1403–1423.CrossRefGoogle ScholarPubMed
Altman, R. B. & Jardetzky, O. (1989). Heuristic refinement method for determination of solution structure of proteins from nuclear magnetic resonance data. Methods Enzymol. 177, 218–246.CrossRefGoogle ScholarPubMed
Arnold, E. & Rossmann, M. G. (1988). The use of molecular-replacement phases for the refinement of the human rhinovirus 14 structure. Acta crystallogr. A 44, 270–282.CrossRefGoogle ScholarPubMed
Arnold, E., Vriend, G., Luo, M., Griffith, J. P.., Kamer, G., Erickson, J. W.., Johnson, J. E. & Rossman, M. G. (1987). The structure determination of a common cold virus, human rhinovirus 14. Ada crystallogr. A 43, 346–361.CrossRefGoogle Scholar
Badger, J. & Caspar, D. L. D. (1991). Water structure, in cubic insulin crystals. Proc. natn. Acad. Sci. U.S.A. 88, 622–626.CrossRefGoogle ScholarPubMed
Bae, D.-S. & Haug, E. J. (1987). A recursive formulation for constrained mechanical system dynamics: Part I. Open loop systems. Mech. Struct. & Mach. 15, 359–382.CrossRefGoogle Scholar
Bae, D.-S. & Haug, E. J. (1988). A recursive formulation for constrained mechanical system dynamics: Part II. Closed loop systems. Mech. Struct. & Mach. 15, 481–506.CrossRefGoogle Scholar
Baker, D., Krukowski, A. E. & Agard, D. A. (1993 a). Uniqueness and the Ab Initio phase problem in macromolecular crystallography. Ada crystallogr. D 49, 186–192.CrossRefGoogle ScholarPubMed
Baker, D., Bystroff, C., Fletterick, R. J. & Agard, D. A. (1993b). PRISM: Topologically constrained phase refinement for macromolecular crystallography. Ada Cryst. D 49, in pressGoogle ScholarPubMed
Baldwin, E. T., Weber, I. T., St. Charles, R., Xuan, J. C., Appella, E., Yamada, M., Matsushima, K., Edwards, B. F. P., Clore, G. M., Gronenborn, A. M. & Wlodawer, A. (1991). Crystal structure of interleukin-8 – symbiosis of NMR and crystallography. Proc. natn. Acad. Set. U.S.A. 88, 502–506.CrossRefGoogle ScholarPubMed
Baleja, J. D. (1992). NOE-based structure determination without the use of NMR derived interproton distances. J. magn. Reson. 96, 619–623.Google Scholar
Baleja, J. D., Moult, J. & Sykes, B. D. (1990a). Distance measurement and structure refinement with NOE data. J. magn. Resort. 87, 375–384.Google Scholar
Baleja, J. D., Germann, M. W., Van De Sande, J. H. & Sykes, B. D. (1990b). Solution conformation of purine-pyrimidine DNA octamers using nuclear magnetic resonance, restrained molecular dynamics and NOE-based refinement. J. molec. Biol. 215, 411–428.CrossRefGoogle ScholarPubMed
Banks, K. M., Hare, D. R. & Reid, B. R. (1989). Three-dimensional solution structure of a DNA duplex containing the Bcll restriction sequence: two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the Noesy Spectrum. Biochemistry 28, 6996–7010.CrossRefGoogle Scholar
Bassolino, D. A., Hirata, F., Kitchen, D., Kominos, D., Pardi, A. & Levy, R. M. (1988). Determination of protein structures in solution using NMR data and Impact. Int. J. Supercomput. Appl. 2, 41–61.Google Scholar
Bates, R. H. T. (1982). Fourier phase problems are uniquely solvable in more than onedimension. I: Underlying theory. Optik 61, 247–262.Google Scholar
Bax, A. & Davis, D. G. (1985). Practical aspects of two-dimensional transverse NOE spectroscopy. J. magn. Reson. 63, 207–213.Google Scholar
Bax, A., Sklenář, V. & Summers, M. (1986). Direct identification of relayed nuclear overhauser effects. J. magn. Reson. 70, 327–331.Google Scholar
Bentley, G. A. & Houdusse, A. (1992). Some applications of the phased translation function in macromolecular structure determination. Acta crystallogr. A 48, 312–322.CrossRefGoogle ScholarPubMed
Berendsen, H. J. C.Postma, J. P. M., Van Gunsteren, W. F.Dinola, A. & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. J. chem. Phys. 81, 3684–3690.CrossRefGoogle Scholar
Berndt, K. D., Güntert, P., Orbons, L. P. M. & Wüthrich, K. (1992). Determination of a high-quality nuclear magnetic resonance solution structure of the bovine pancreatic trypsin inhibitor and comparison with three crystal structures. J. molec. Biol. 227, 757–775.CrossRefGoogle ScholarPubMed
Beurskens, P. T., Gould, R. O., Bruins Slot, H. J. & Bosman, W. P. (1987). Translation functions for the positioning of a well oriented molecular fragment. Z. Kristallogr. Kristallgeom. 179, 127–159.CrossRefGoogle Scholar
Bhat, T. N. (1990). A metropolis-like algorithm to improve phases: some preliminary results. Acta crystallogr. A 46, 735–742.CrossRefGoogle Scholar
Billeter, M. (1992). Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals. Q. Rev. Biophys. 25, 325–377.CrossRefGoogle ScholarPubMed
Billeter, M., Kline, A. D., Braun, W., Huber, R. & Wüthrich, K. (1990). Comparison of the high resolution structures of the α amylase inhibitor tendamistat determined by nuclear magnetic resonance in solution and by X-ray diffraction in single crystals. J. molec. Biol. 206, 677–687.CrossRefGoogle Scholar
Blow, D. M. & Crick, F. H. C. (1959). The treatment of errors in the isomorphous replacement method. Acta crystallogr. 12, 794–802.CrossRefGoogle Scholar
Blumenthal, L. (1953). Theory and Applications of Distance Geometry. Cambridge, UK: Cambridge University Press.Google Scholar
Bode, W., Greyling, H. J., Huber, R., Otlewski, J. & Wilusz, T. (1989). The refined 2'0 Å X-ray crystal structure of the complex formed between bovine β-Trypsin and CMTI-I, a trypsin inhibitor from squash seeds. FEBS Lett. 242, 285–292.CrossRefGoogle ScholarPubMed
Boelens, R., Koning, T. M. G. & Kaptein, R. (1988). Determination of biomolecular structures from proton–proton NOEs using a relaxation matrix approach. J. molec. Struct. 173, 299–311.CrossRefGoogle Scholar
Boelens, R., Koning, T. M. G., Van Der Marel, G. A., Van Boom, J. H. & Kaptein, R. (1989). Iterative procedure for structure determination from proton–proton NOEs using a full relaxation matrix approach. Application to a DNA octamer. J. magn. Reson. 82, 290–308.Google Scholar
Bonvin, A. M. J. J., Boelens, R. & Kaptein, R. (1991a). Direct NOE refinement of biomolecular structures using 2D NMR data. J. biomol. NMR 1, 305–309.CrossRefGoogle ScholarPubMed
Bonvin, A. M. J. J., Boelens, R. & Kaptein, R. (1991b). Direct structure refinement using 3D NOE-NOE spectra of biomolecules. j. magn. Reson. 87, 646–651.Google Scholar
Borgias, B. A. & James, T. L. (1988). Comatose: A method for constrained refinement of macromolecular structure based on two-dimensional nuclear overhauser effect spectra. J. magn. Reson. 79, 493–512.Google Scholar
Borgias, B. A. & James, T. L. (1990). Mardigras: a procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure. J. magn. Reson. 87, 475–487.Google Scholar
Borgias, B. A., Gochin, M., Kerwood, D. J. & James, T. L. (1990). Relaxation matrix analysis of 2D NMR data. Progr. nucl. magn. Reson. Spectrosc. 22, 83–100.CrossRefGoogle Scholar
Bothner-By, A. A., Stevens, R., Lee, J.-M., Warren, C. D. & Jeancoz, R. W. (1984). Structure determination of a tetrasaccharide: transient nuclear overhauser effects in the rotating frame. J. Am. chem. Soc. 106, 811–813.CrossRefGoogle Scholar
Bounds, D. G. (1987). New optimization methods from physics and biology. Nature Lond. 329, 215–219.CrossRefGoogle Scholar
Bowie, J. U., Lüthy, R. & Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science N. Y. 253, 164–170.CrossRefGoogle ScholarPubMed
Brady, R. L., Edwards, D. J., Hubbard, R. E., Jiang, J.-S., Lange, G., Robertsc, S. M., Todd, R. J., Adair, J. R., Emtage, J. S., King, D. J. & Low, D. C. (1992). Crystal structure of a chimeric fab’ fragment of an antibody binding tumor cells. J. molec. Biol. 227, 253–264.CrossRefGoogle Scholar
Brändén, C. I. & Jones, A. (1990). Between objectivity and subjectivity. Nature Lond. 343, 687–689.CrossRefGoogle Scholar
Brändén, C. & Tooze, J. (1991). Introduction to Protein Structure, p. 302. New York N.Y.: Garland Publishing Inc.Google Scholar
Braun, W. (1987). Distance geometry and related methods for protein structure determination from NMR data. Q. Rev. Biophys. 19, 115–157.CrossRefGoogle ScholarPubMed
Braun, W. & Gō, N. (1985). Calculation of protein conformations by proton–proton distance constraints. A new efficient algorithm. J. molec. Biol. 186, 611–626.CrossRefGoogle ScholarPubMed
Braun, W., Epp, O., Wüthrich, K. & Huber, R. (1989). Solution of the phase problem in the X-ray diffraction method for proteins with the nuclear magnetic resonance solution structure as initial model. Patterson search and refinement for the α-amylase inhibitor tendamistat. J. molec. Biol. 206, 669–676.CrossRefGoogle ScholarPubMed
Breg, J. N., Van Opheusden, J. H. J., Burgering, M. J. M., Boelens, R. & Kaptein, R. (1990). Structure of arc repressor in solution: evidence for a family of β-Sheet DNA binding proteins. Nature Lond. 346, 586–589.CrossRefGoogle ScholarPubMed
Bricogne, G. (1984). Maximum entropy and the foundation of direct methods. Acta crystallogr. A 40, 410–445.CrossRefGoogle Scholar
Bricogne, G. (1988). Maximum entropy methods in the X-ray phase problem. In Crystallographic Computing 4 (ed. Isaacs, N. W. & Taylor, M. R.), pp. 60–79, New York: Oxford Univ. Press.Google Scholar
Bricogne, G. (1991). Maximum entropy as a common statistical basis for all phase determination methods. In Crystallogr aphic Computing 5, From Chemistry to Biology (ed. Moras, D., Podjarny, A. D. and Thierry, J. C.), pp. 257–297. New York: Oxford University Press.Google Scholar
Bricogne, G. (1993). Direct phase determination by entropy maximization and likelihood ranking: status report and perspectives. Acta crystallogr. D 49, 37–60.Google Scholar
Bricogne, G. & Gilmore, C. J. (1990). A multisolution method of phase determination by combined maximization of entropy and likelihood. I. Theory, algorithms and strategy. Acta crystallogr. A 46, 284–297.CrossRefGoogle Scholar
Brinkley, J. F., Altmann, R. B., Duncan, B. S., Buchanan, B. G. & Jardetzky, O. (1988). Heuristic refinement method for the derivation of protein solution structures: validation on cytochrome b562. J. chem. Inf. Comput. Sci. 28, 194.CrossRefGoogle ScholarPubMed
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983). Charmm: A program for macromolecular energy, minimization, and dynamics calculations. J. comp. Chem. 4, 187–217.CrossRefGoogle Scholar
Brünger, A. T. (1988). Crystallographic refinement by simulated annealing: application to a 28 Å resolution structure of aspartate aminotransferase. J. molec. Biol. 203, 803–816.CrossRefGoogle ScholarPubMed
Brünger, A. T. (1989). A memory-efficient fast fourier transformation algorithm for crystallographic refinement on supercomputer. Acta crystallogr. A 45, 42–50.CrossRefGoogle Scholar
Brünger, A. T. (1990). Extension of molecular replacement: a new search strategy based on Patterson correlation refinement. Acta crystallogr. A 46, 46–57.CrossRefGoogle Scholar
Brünger, A. T. (1991a). Solution of a Fab (26–10)/Digoxin complex by generalized molecular replacement. Acta crystallogr. A 47, 195–204.CrossRefGoogle ScholarPubMed
Brünger, A. T. (1991 b). Simulated annealing in crystallography. Ann. Rev. phys. Chem. 42, 197–223.CrossRefGoogle Scholar
Brünger, A. T. (1992a). The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature Lond. 355, 472–474.CrossRefGoogle Scholar
Brünger, A. T. (1992b). X-PLOR. Version 3.1. A System for X-ray Crystallography and NMR. New Haven: Yale University Press.Google Scholar
Brunger, A. T. (1993a). Assessment of phase accuracy by cross validation: the free Rvalue. Methods and applications. Acta crystallogr. D 49, 24–36.Google Scholar
Brünger, A. T. (1993b). Structure determination of antibodies and antibody-antigen complexes by molecular replacement. In Immunomethods (ed. Wilson, I. A.) (In the press).Google Scholar
Brünger, A. T., Clore, G. M., Gronenborn, A. M. & Karplus, M. (1986). Threedimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc. natn. Acad. Sci. U.S.A. 83, 3801–3805.CrossRefGoogle ScholarPubMed
Brünger, A. T., Kuriyan, J. & Karplus, M. (1987a). Crystallographic R factor refinement by molecular dynamics. Science N. Y. 235, 458–460.CrossRefGoogle ScholarPubMed
Brünger, A. T., Campbell, R. L., Clore, G. M., Gronenborn, A. M., Karplus, M., Petsko, G. A. & Teeter, M. M. (1987b). Solution of a protein crystal structure with a model obtained from NMR interproton distance restraints. ScienceN. Y. 235, 1049–1053.CrossRefGoogle Scholar
Brünger, A. T., Clore, G. M., Gronenborn, A. M. & Karplus, M. (1987 c). Solution conformations of human growth hormone releasing factor: comparison of the restrained molecular dynamics and distance geometry methods for a system without long-range distance data. Protein Eng. 1, 399–406.CrossRefGoogle ScholarPubMed
Brünger, A. T., Krukowski, A. & Erickson, J. (1990a). Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta crystallogr. A 46, 585–593.CrossRefGoogle ScholarPubMed
Brünger, A. T., Milburn, M. V., Tong, L., De Vos, A. M., Jancarik, J., Yamaizumi, Z., Nishimura, S., Ohtsuka, E. & Kim, S.-H. (1990b). Crystal structure of an active form of ras protein, a complex of GTP analog and c-H-ras P21 catalytic domain. Proc. natn. Acad. Set. U.S.A. 87, 4849–4853.CrossRefGoogle ScholarPubMed
Brünger, A. T., Leavy, D. J., Hynes, T. R. & Fox, R. O. (1991). The 29 Å resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody fab fragment with bound hapten. J. molec. Biol. 221, 239–256.Google ScholarPubMed
Brüschweiler, R., Roux, B., Blackledge, M., Griesinger, C., Karplus, M. & Ernst, R. R. (1992). Influence of rapid intramolecular motion of NMR cross-relaxation rates. A molecular dynamics study of antanamide in solution. J. Am. chem. Soc. 114, 2289–2302.CrossRefGoogle Scholar
Bystroff, C., Baker, D., Fletterick, R. J. & Agard, D. (1993). Prism: Application to the experimental solution of two protein structures. Acta Cryst. D 49 (in press).Google Scholar
Carter, C. W., Crumley, K. V., Coleman, D. E. & Hage, F. (1990). Direct phase determination for the molecular envelope of tryptophanyl-tRNA synthetase from Bacillus stearothermophilus by X-ray contrast variation. Acta crystallogr. A 46, 57–68.CrossRefGoogle ScholarPubMed
Chapman, M. S., Tsao, J. & Rossmann, M. G. (1992). Ab Initio phase determination for spherical viruses: parameter determination for spherical shell models. Acta crystallogr. A 48, 301–312.CrossRefGoogle ScholarPubMed
Cheng, X. & Schoenborn, B. P. (1990). Hydration in protein crystals. A neutron diffraction analysis of carbonmonoxymyoglobin. Acta crystallogr. B 46, 195–208.CrossRefGoogle Scholar
Chiche, L., Gaboriaud, C., Heitz, A., Mornon, J.-P., Castro, B. & Kollmann, P. A. (1989). Use of restrained molecular dynamics in water to determine threedimensional protein structure: prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II. Proteins 6, 405–417.CrossRefGoogle ScholarPubMed
Chiche, L., Gregoret, L. M., Cohen, F. E. & Kollman, P. A. (1990). Protein model structure evaluation using the solvation free energy of folding. Proc. natn. Acad. Set. U.S.A. 87, 3240–3243.CrossRefGoogle ScholarPubMed
Chothia, C. (1992). One thousand families for the molecular biologist. Nature Lond. 357, 543–544.CrossRefGoogle ScholarPubMed
Chothia, C. & Lesk, A. (1987). Canonical structures for the hypervariable regions of immunoglobulins. J. molec. Biol. 196, 901–917.CrossRefGoogle ScholarPubMed
Clore, G. M. & Gronenborn, A. M. (1985). Assessment of errors involved in the determination of interproton distance ratios and distances by means of one- and twodimensional NOE measurements, j. magn. Reson. 61, 158–164.Google Scholar
Clore, G. M. & Gronenborn, A. M. (1989a). Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resinance spectroscopy. CRC Crit. Rev. Biochem. 24, 479–564.CrossRefGoogle ScholarPubMed
Clore, G. M. & Gronenborn, A. M. (1989b). How accurately can interproton distances in macromolecules really be determined by full relaxation matrix analysis of nuclear overhauser enhancement data ? J. magn. Reson. 84, 398–409.Google Scholar
Clore, G. M. & Gronenborn, A. M. (1991 a). Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy. Science N.Y. 252, 1390–1399.CrossRefGoogle ScholarPubMed
Clore, G. M. & Gronenborn, A. M. (1991b). Comparison of the solution nuclear magnetic resonance and crystal structures of interleukin-8. Possible implications for the mechanism of receptor binding. J. molec. Biol. 217, 611–620.CrossRefGoogle ScholarPubMed
Clore, G. M. & Gronenborn, A. M. (1991c). Comparison of the solution nuclear magnetic resonance and X-ray crystal structures of human recombinant interleukin- 1β J. molec. Biol. 221, 47–53.CrossRefGoogle Scholar
Clore, G. M. & Gronenborn, A. M. (1991d). Two-, three-, and four-dimensional NMR methods for obtaining larger and more precise three-dimensional structures of proteins in solution. Ann. Rev. Biophys. Biophys. Chem. 20, 29–63.CrossRefGoogle ScholarPubMed
Clore, G. M., Gronenborn, A. M., Brünger, A. T. & Karplus, M. (1985). The solution conformation of a heptadecapetide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli: combined use of 1H-nuclear magnetic resonance and restrained molecular dynamics. J. molec. Biol. 186, 435–455.CrossRefGoogle Scholar
Clore, G. M., Brünger, A. T., Karplus, M. & Gronenborn, A. M. (1986 a). Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination: a model study of crambin. J. molec. Biol. 191. 523–551.CrossRefGoogle Scholar
Clore, G. M., Nilges, M., Sukumaran, D. K., Brünger, A. T., Karplus, M. & Gronenborn, A. M. (1986 b). The three-dimensional structure of α-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry, and restrained molecular dynamics. EMBO J. 5, 2729–2735.CrossRefGoogle ScholarPubMed
Clore, G. M., Gronenborn, A. M., Nilges, M. & Ryan, C. A. (1987). The three-dimensional structure of potato carboxypeptidase inhibitor in solution: a study using nuclear magnetic resonance, distance geometry and restrained molecular dynamics. Biochemistry. 26, 8012–8023.CrossRefGoogle ScholarPubMed
Clore, G. M., Szabo, A., Bax, A., Lewis, E., Driscoll, P. C. & Gronenborn, A. M. (1990 a). Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J. Am. chem. Soc. 112, 4989–4991.CrossRefGoogle Scholar
Clore, G. M., Driscoll, P. C., Wingfield, P. T. & Gronenborn, A. M. (1990 b). Analysis of the backbone dynamics of interleukin-1β using two-dimensional inverse detected heteronuclear nitrogen-15-proton NMR spectroscopy. Biochemistr. 32, 7387–7401.CrossRefGoogle Scholar
Clore, G. M., Wingfield, P. T. & Gronenborn, A. M. (1991 e). High-resolution three-dimensional structure of interleukin 1β in solution by three- and four-dimensional nuclear magnetic resonance spectroscopy. Biochemistr. 30, 2315–2323.CrossRefGoogle Scholar
Cochran, W. & Woolfson, M. M. (1955). The theory of sign relations between structure factors. Acta crystallogr. 8, 1–12.CrossRefGoogle Scholar
Collins, D. M. (1982). Electron density images from imperfect data by iterative entropy maximization. Nature Lond. 298, 49–51.CrossRefGoogle Scholar
Collins, D. M. (1993). Entropy on charge density: making the quantum mechanical connection. Acta crystallogr. D 49, 86–89.Google ScholarPubMed
Cowtan, K. D. & Main, P. (1993). Improvement of macromolecular electron-density maps by the simultaneous application of real and reciprocal space constraints. Acta crystallogr. D 49, 148–157.Google ScholarPubMed
Crippen, G. M. (1977). A novel approach to the calculation of conformation: distance geometry. J. comp. Physiol.. 24, 96–107.CrossRefGoogle Scholar
Crippen, G. M. (1989). Linearized embedding: a new metric matrix method for calculating molecular conformations subject to geometric constraints. J. comp. Chem.. 10, 896–902.CrossRefGoogle Scholar
Crippen, G. M. & Havel, T. F. (1978). Stable Calculation of Coordinates from Distance Information. Acta crystallogr. A 34, 282–284.CrossRefGoogle Scholar
Crippen, G. M. & Havel, T. F. (1988). Distance Geometry and Molecular Conformation. Taunton, Somerset, England: Research Studies Press.Google Scholar
Crowther, R. A. (1972). Fast rotation function. In The Molecular Replacement Method, Int. Sci. Rev. No. 13 (Rossmann, M. G. ed.), pp. 173–178. New York: Gordon & Breach.Google Scholar
Cura, V., Krishnaswamy, S. & Podjarny, A. D. (1992). Heavy-atom refinement against solvent-flattened phases. Acta crystallogr. A 48, 756–764.CrossRefGoogle ScholarPubMed
Dainty, J. C. & Fienup, J. R. (1987). Phase retrieval and image reconstruction for astronomy. In Image Recovery. Theory and Applications (ed. Stark, H.), pp. 231–272. San Diego: Academic Press.Google Scholar
de Vlieg, J., Scheek, R. M., van Gunsteren, W. F., Berendsen, H. J., Kaptein, R. & Thomason, J. (1988). Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: Application to the DNA binding domain of lac repressor from Escherichia coli. Proteins 3, 209–218.CrossRefGoogle Scholar
de Vlieg, J., Berendsen, H. J. & van Gunsteren, W. F. (1989). An NMR-based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solutionr. Proteins 6, 104–127.CrossRefGoogle Scholar
de Vlieg, J. & van Gunsteren, W. F. (1991). Combined procedures of distance geometry and molecular dynamics for determining protein structure from nuclear magnetic resonance data. Methods Enzymol. 202, 268–300.CrossRefGoogle ScholarPubMed
Diamond, R. (1990). On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor. Acta crystallogr. A 46, 425–435.CrossRefGoogle Scholar
Dobson, C. M. & Karplus, M. (1986). Internal motion of proteins: nuclear magnetic resonance measurements and dynamics simulations. Methods Enzymol. 131, 362–389.CrossRefGoogle Scholar
Driscoll, P. C., Gronenborn, A. M. & Clore, G. M. (1989). The influence of stereospecific assignments on the determination of three-dimensional structures of proteins by nuclear magnetic resonance spectroscopy. FEBS Lett. 243, 223–233.CrossRefGoogle ScholarPubMed
Easthorpe, P. L. & Havel, T. F. (1989). Computation experience with an algorithm for tetrangle inequality bound smoothing. Bull. Math. Bio. 51, 173–194.CrossRefGoogle Scholar
Eisenberg, D. & McLachlan, A. D. (1986). Solvation energy in protein folding and binding. Nature Lond. 319, 199–203.CrossRefGoogle ScholarPubMed
Endo, S., Wako, H., Nagayama, K. & Gō, N. (1991). A new version of DADAS (distance analysis in dihedral angle space) and its performance. In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy (ed. Hoch, J. C., Poulsen, F. M., Redfield, C.), pp. 233–251. New York: Plenum Press.CrossRefGoogle Scholar
Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray structure refinement. Acta crystallogr. A 47, 392–400.CrossRefGoogle Scholar
Ernst, R. R., Bodenhausen, G. & Wokaun, A. (1987). Principles of Nuclear Magnetic Resonance in One and Two Dimensions. Oxford: Clarendon Press.Google Scholar
Fan, H.-F., Hao, Q. & Woolfson, M. M. (1991). Proteins and direct methods. Z. Kristallogr. Kristallgeom. 197, 197–208.Google Scholar
Fejzo, J., Krezel, A. M., Westler, W. M., Macura, S. & Markley, J. L. (1991). Refinement of the NMR solution structure of a protein to remove distortions arising from neglect of internal motion. Biochemistry 30, 3807–3811.CrossRefGoogle ScholarPubMed
Fitzgerald, P. M. D. (1991). Molecular replacement. In Crystallographic Computing 5, From Chemistry to Biology (ed. Moras, D., Podjarny, A. D. and Thierry, J. C.), pp. 333–347. New York: Oxford University Press.Google Scholar
Forman-Kay, J. D., Clore, G. M. & Gronenborn, A. M. (1992). Relationship between electrostatics and redox function in human thioredoxin: characterization of pH titration shifts using two-dimensional homo- and heteronuclear NMR. Biochemistry 31, 3442–3452.CrossRefGoogle ScholarPubMed
Forster, M. J. (1991). Comparison of computational methods for simulating nuclear overhauser effects in NMR spectroscopy. J. comp. Chem. 12, 292–300.CrossRefGoogle Scholar
Fortier, S., Castleden, J., Glasgow, J., Conklin, D., Walmsley, C, Leherte, L. & Allen, F. H. (1993). Molecular scene analysis: the integration of direct methods and artificial intelligence strategies for solving protein crystal structures. Acta crystallogr. D49, 168–178.Google Scholar
Fraser, R. D. B., Macrae, T. P. & Suzuki, E. (1978). An improved method for calculating the contribution of solvent to the X-ray diffraction pattern of biological molecules. J. Appl. Cryst. 11, 693–694.CrossRefGoogle Scholar
Fujinaga, M. & Read, R. J. (1987). Experiences with a new translation-function program, j. appl. Crystallogr. 20, 517–521.CrossRefGoogle Scholar
Fujinaga, M., Gros, P. & van Gunsteren, W. F. (1989). Testing the method of crystallographic refinement using molecular dynamics. J. appl. Crystallogr. 22, 1–8.CrossRefGoogle Scholar
Garcia, K. C., Ronco, P. M., Verroust, P. J., Brunger, A. T. & Amzel, L. M. (1992). Three-dimensional structure of an angiotensin II-Fab complex at 3 Å: hormone recognition by an anti-idiotypic antibody. Science N. Y. 257, 502–507.CrossRefGoogle ScholarPubMed
Giacovazzo, C, Guagliardi, A., Ravelli, R. & Siliqi, D. (1993). At initio direct phasing of proteins: the limits. Z. Kristallographie (In the press).Google Scholar
Gilmore, C. J. (1992). Novel phasing techniques in macromolecular crystallography. Curr. Opin. Struct. Biol. 2, 806–810.CrossRefGoogle Scholar
Gilmore, C. J., Bricogne, G. & Bannister, C. (1990). A multisolution method of phase determination by combined maximization of entropy and likelihood. II. Application to small molecules. Acta crystallogr. A 46, 297–308.CrossRefGoogle Scholar
Gilmore, C. J., Henderson, A. N. & Bricogne, G. (1991 a). A multisolution method of phase determination by combined maximization of entropy and likelihood. V. The use of likelihood as a discriminator of phase sets produced by the saytan program for a small protein. Acta crystallogr. A 47, 842–846.CrossRefGoogle ScholarPubMed
Gilmore, C. J., Henderson, K. & Bricogne, G. (1991 b). A multisolution method of phase determination by combined maximization of entropy and likelihood. IV. The ab initio solution of crystal structures from the X-ray powder data. Acta crystallogr. A 47, 830–841.CrossRefGoogle Scholar
Gonzalez, C, Rullmann, J. A. C., Bonvin, A. M. J. J., Boelens, R. & Kaptein, R. (1991). Toward an NMR R-factor. J. magn. Reson. 91, 659–664.Google Scholar
Greer, J. (1985). Computer skeletonization and automatic electron density map analysis. Meth. Enzymol. 115, 206–226.CrossRefGoogle ScholarPubMed
Griewank, A. O. (1981). Generalized descent for global optimization. J. Optimization Theory and Applications 34, 11–39.CrossRefGoogle Scholar
Gronenborn, A. M. & Clore, G. M. (1989). Analysis of the relative contributions of the nuclear overhauser interproton distance restraints and the empirical energy function in the calculation of oligonucleotide structures using restrained molecular dynamics. Biochemistry 28, 5978–5984.CrossRefGoogle ScholarPubMed
Gronenborn, A. M., Filpula, D. R., Essig, N. Z., Achari, A., Whitlow, M., Wingfield, P. T. & Clore, G. M. (1991). The immunoglobulin binding domain of streptococcal protein G has a novel and highly stable polypeptide fold. Science N. Y. 253, 657–661.CrossRefGoogle Scholar
Gros, P., Betzel, Ch., Dauter, Z., Wilson, K. S. & Hol, W. G. J. (1989). Molecular dynamics refinement of a thermitase – Eglin-c complex at 1–98 Å resolution and comparison of two crystal forms that differ in calcium content. J. molec. Biol. 210, 347–367.CrossRefGoogle ScholarPubMed
Gros, P., van Gunsteren, W. F. & Hol, W. G. J. (1990). Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics. Science N. Y. 249, 1149–1152.CrossRefGoogle ScholarPubMed
Guesnet, J.-L., Vovelle, F., Thuong, N. T. & Lancelot, G. (1990). 2D-NMR studies and 3D-structure of the parallel-stranded duplex oligonucleotide acrm5-αd(TCTAAACTC)-β-d(AGATTTGAG) via complete relaxation matrix analysis of the NOE effects and molecular mechanics calculations. Biochemistry 29, 4982–4991.CrossRefGoogle Scholar
Güntert, P. & Wüthrich, K. (1991). Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J. Biomolec. NMR I, 447–456.CrossRefGoogle Scholar
Güntert, P., Braun, W., Billeter, M. & Wüthrich, K. (1989). Automated stereospecific lH NMR assignments and their impact on the precision of protein structure determination in solution. J. Am. chetn. Soc. 111, 3997–4004.CrossRefGoogle Scholar
Güntert, P., Braun, W. & Wüthrich, K. (1991). Efficient computation of threedimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. molec. Biol. 217, 517–530.CrossRefGoogle ScholarPubMed
Guo, H.-C, Jardetzky, T. S., Garrett, T. P.J., Lane, S. W., Strominger, J. L. & Wiley, D. C. (1992). Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle. Nature Lond. 360, 364–366.CrossRefGoogle ScholarPubMed
Habazettl, J., Cieslar, C, Oschkinat, H. & Holak, T. A. (1990). iH NMR assignments of sidechain conformations in proteins using a high-dimensional potential in the simulated annealing calculations. FEBS Lett. 268, 141–145.CrossRefGoogle Scholar
Habazettl, J., Gondol, D., Wiltscheck, R., Otlewski, J., Schleicher, M. & Holak, T. A. (1992 a). Structure of hisactophilin is similar to interleukin-iβ and fibroblast growth factor. J. molec. Biol. 359, 855–858.Google Scholar
Habazettl, J., Schleicher, M., Otlewski, J. & Holak, T. A. (1992b). Homonuclear three-dimensional NOE-NOE nuclear magnetic resonance spectra for structure determination of proteins in solutions. J. molec. Biol. 228, 156–169.CrossRefGoogle Scholar
Hamilton, W. C. (1965). Significance tests on the crystallographic R factor Acta crystallogr. 18, 502–510.Google Scholar
Harrison, R. W. (1988). Histogram specification as a method of density modification. J. appl Crystallogr. 21, 949–952.CrossRefGoogle Scholar
Harrison, R. W. (1989). Minimization of cross entropy: a tool for solving crystal structures. Acta crystallogr. A 45, 4–10.CrossRefGoogle Scholar
Hauptman, H. A. (1982). On integrating the techniques of direct methods and isomorphous replacement. I. The theoretical basis. Acta crystallogr. A 38, 289–294.CrossRefGoogle Scholar
Hauptman, H. A. (1988). A minimal principle and its role in direct methods. Abstracts of the American Crystallographic Association. Philadelphia, Abstract R4, pp. 53, Pennsylvania.Google Scholar
Hauptman, H. A. (1989). The phase problem of X-ray crystallography. Physics Today 42, No. 11, 24–29.CrossRefGoogle Scholar
Hauptman, H. A. (1991). A minimal principle in the phase problem. In Crystallographic Computing 5, From Chemistry to Biology (ed. Podjarny, D. A. D. and Thierry, J. C.), pp. 324–332. New York: Oxford University Press.Google Scholar
Hauptman, H. A. & Han, F. (1993). Phasing macromolecular structures via structure invariant algebra. Acta crystallogr. D 49, 3–8.Google ScholarPubMed
Havel, T. F. (1990). The sampling properties of some distance geometry algorithms applied to unconstrained polypeptide chains: A study of 1830 independently computed conformations. Biopolymers 29, 1565–1585.CrossRefGoogle ScholarPubMed
Havel, T. F. (1991). An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance. Prog. Biophys. molec. Biol. 56, 43–78.CrossRefGoogle ScholarPubMed
Havel, T. F. & Wüthrick, K. (1984). A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of intramolecular 1H1H proximities in solution. Bull. math. Bio. 46, 673–698.Google Scholar
Havel, T. F. & Wüthrich, K. (1985). An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformation in solution. J. molec. Biol. 182, 281–294.CrossRefGoogle Scholar
Havel, T. F., Kuntz, I. D. & Crippen, G. M. (1983). The theory and practice of distance geometry. Bull. math. Bio. 45, 665–720.CrossRefGoogle Scholar
Hayes, M. H. (1982). The reconstruction of a multidimensional sequence from the phase or magnitude of its fourier transform. IEEE Trans. Acoustics, Speech, and Signal Processing ASSP-30, 140–154.CrossRefGoogle Scholar
He, X.-M. & Craven, B. M. (1993). Internal vibrations of a molecule consisting of rigid segments. I. Non-interacting internal vibrations. Acta crystallogr. A 49, 10–22.CrossRefGoogle ScholarPubMed
Helliwell, J. R., Ealick, S., Doing, P., Irving, T. & Szebenyi, M. (1993). Towards the measurement of ideal data for macromolecular crystallography using synchrotron sources such as the ESRF. Acta crystallogr. D 49, 120–128.Google Scholar
Hendrickson, W. A. (1985). Stereochemically restrained refinement of macromolecular structures. Meth. Enzymol. 11, 252–270.CrossRefGoogle Scholar
Hendrickson, W. A. (1991). Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science N. Y. 254, 51–58.CrossRefGoogle ScholarPubMed
Hendrickson, W. A. & Lattman, E. E. (1970). Representation of phase probability distributions for simplified combination of independent phase information. Acta crystallogr. B 26, 136–143.CrossRefGoogle Scholar
Hendrickson, W. A., Wüthrich, K. (1991). Macromolecular Structures 1991, Atomic Structures of Biological Macromolecules Reported During 1990. London: Current Biology Ltd.Google Scholar
Hoch, J. C. (1991). An amateur looks at error analysis in the determination of protein structure by NMR. In Computational aspects of the study of biological macromolecules by nuclear magnetic resonance spectroscopy (ed. Hoch, J. C., Poulson, F. M. and Redfield, C.), pp. 253–267. New York: Plenum Press.CrossRefGoogle Scholar
Hoch, J. C. & Stern, A. S. (1992). A method for determining overall protein fold from NMR distance restraints. J. Biomolecular NMR 2, 535–543.CrossRefGoogle Scholar
Hoch, J. C., Redfield, C. & Stern, A. S. (1991). Computer-aided analysis of protein NMR spectra. Curr. Opinion. Struct. Biol. 1, 1036–1041.CrossRefGoogle Scholar
Hodel, A., Kim, S.-H. & Brunger, A. T. (1992). Model bias in macromolecular crystal structures. Acta crystallogr. 48, 851–859.CrossRefGoogle Scholar
Holak, T. A., Kearsley, S. K., Kim, Y. & Prestegard, J. H. (1988). Threedimensional structure of acyl carrier protein determined by NMR pseudoenergy and distance geometry calculations. Biochemistry 27, 6135–6142.CrossRefGoogle ScholarPubMed
Holak, T. A., Nilges, M. & Oschkinat, H. (1989 a). Improved strategies for the determination of protein structures from NMR data. The solution structure of acyl carrier protein. FEBS Lett. 242, 649–654.CrossRefGoogle ScholarPubMed
Holak, T. A., Gondol, D., Otlewski, J. & Wilusz, T. (1989 b). Determination of the complete three-dimensional structure of the trypsin inhibitor from squash seeds in aqueous solution by nuclear magnetic resonance and a combination of distance geometry and dynamical simulated annealing. J. molec. Biol. 210, 635–648.CrossRefGoogle Scholar
Holak, T. A., Bode, W., Huber, R., Otlewski, J. & Wilusz, T. (1989c). Nuclear magnetic resonance solution and X-ray structures of squash trypsin inhibitor exhibit the same conformation of the proteinase binding loop. J. molec. Biol. 210, 649–654.CrossRefGoogle ScholarPubMed
Hoppe, W. (1957). Die Faltmolekiilmethode - eine neue Methode zur Bestimmung der Kristallstruktur bei Ganz oder Teilweise bekannter Molekiilstruktur. Acta crystallogr. 10, 750–751.Google Scholar
Howlin, B., Moss, D. S. & Harris, G. W. (1989). Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model. Acta crystallogr. A 45, 851–861.CrossRefGoogle ScholarPubMed
Huber, R. (1965). Die automatisierte Faltmolekiilmethode. Acta crystallogr. A 19, 353–356.CrossRefGoogle Scholar
Hyberts, S. G., Mäarki, W. & Wagner, G. (1987). Stereospecific assignments of side chain protons and characterization of torsion angles. Eur. J. Biochem. 164, 625–635.CrossRefGoogle ScholarPubMed
Hyberts, S. G., Goldberg, M. S., Havel, T. F. & Wagner, G. (1992). The solution structure of Eglin c based on measurements of many NOEs and coupling constants and its comparison with X-ray structures. Protein Science 1, 736–751.CrossRefGoogle ScholarPubMed
Ikura, M., Clore, G. M., Gronenborn, A. M., Zhu, G., Klee, C. B. & Bax, A. (1992). Solution structure of a calmodulin-target peptide complex by multidimensional NMR. Science N. Y. 256, 632–638.CrossRefGoogle ScholarPubMed
Jack, A. & Levitt, M. (1978). Refinement of large structures by simultaneous minimization of energy and R factor. Acta crystallogr. A 34, 931–935.CrossRefGoogle Scholar
James, M. N. G. & Sielecki, A. R. (1983). Structure and refinement of penicillopepsin at 18 Å resolution. J. molec. Biol. 163, 299–361.CrossRefGoogle ScholarPubMed
James, T. L. (1991). Relaxation matrix analysis of two-dimensional nuclear overhauser effect spectra. Curr. Opinion Struct. Biol. 1, 1042–1053.CrossRefGoogle Scholar
James, T. L., Gochin, M., Kerwood, D. J., Pearlman, D. A., Schmitz, U. & Thomas, P. D. (1991). Refinement of three-dimensional protein and DNA structures in solution from NMR data. In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spedroscopy (ed. Hoch, J. C., Poulsen, F. M. and Redfield, C.), pp. 331–347. New York: Plenum Press.CrossRefGoogle Scholar
Jaynes, E. T. (1978). Where do we stand on maximum entropy? In Papers on Probability, Statistics, and Statistical Physics (ed. Rosenkrantz, R. D.), pp. 211–314. Reidel: Dordrecht Holland.Google Scholar
Jones, T. A., Zou, J.-Y., COWAN, S. W. & KJELDGAARD, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta crystallogr. A 47, 110–119.CrossRefGoogle ScholarPubMed
Kalk, A. & Berendsen, J. C. (1976). Proton magnetic relaxation and spin diffusion in proteins. J. magn. Reson. 24, 343–366.Google Scholar
Kaptein, R., Zuiderweg, E. R. P., Scheek, R. M., Boelens, R. & van Gunsteren, W. F. (1985). A protein structure from nuclear magnetic resonance data, lac repressor headpiece. J. molec. Biol. 182, 179–182.CrossRefGoogle ScholarPubMed
Karle, J. (1991). Direct calculation of atomic coordinates from diffraction intensities: space group P1. Proc. natn. Acad. Sci. U.S.A. 88, 10099–10103.CrossRefGoogle ScholarPubMed
Karle, J. & Hauptman, H. (1950). The phases and magnitudes of the structure factors. Acta crystallogr. 3, 181–187.CrossRefGoogle Scholar
Karle, J. & Hauptman, H. (1956). A theory of phase determination for the four types of non-centrosymmetric space groups 1P222, 2P22, 3P 12, 3P 22. Acta crystallogr. 9, 635–651.CrossRefGoogle Scholar
Karle, J. & Hauptman, H. (1956). A theory of phase determination for the four types of non-centrosymmetric space groups 1P222, 2P22, 3P 12, 3P 22. Acta crystallogr. 9, 635–651.CrossRefGoogle Scholar
Karplus, M. (1963). Vicinal proton coupling in nuclear magnetic resonance. J. Am. chem. Soc. 85, 2870–2871.CrossRefGoogle Scholar
Karplus, M. & Petsko, G. A. (1990). Molecular-dynamics simulations in biology. Nature, Land. 347, 631–639.CrossRefGoogle ScholarPubMed
Kay, L. E., Torchia, D. A. & Bax, A. (1989). Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry 28, 8972–8979.CrossRefGoogle ScholarPubMed
Kay, L. E., Forman-Kay, J. D., McCubbin, W. D. & Kay, C. M. (1991). Solution structure of a polypeptide dimer comprising the fourth Ca(2+)-binding site of troponin C by nuclear magnetic resonance spectroscopy. Biochemistry 30, 4323–4333.CrossRefGoogle ScholarPubMed
Keepers, J. W. & James, T. L. (1984). A theoretical study of distance determinations from NMR. Two dimensional nuclear overhauser effect spectra. J. magn. Reson. 57, 404–426.Google Scholar
Kidera, A. & Gō, N. (1990). Refinement of protein dynamic structure: normal mode refinement. Proc. natn. Acad. Sci. U.S.A. 87, 3718–3722.CrossRefGoogle ScholarPubMed
Kidera, A., Inaka, K., Matsushima, M. & Gō, N. (1992). Normal mode refinement: crystallographic refinement of protein dynamic structure applied to human lysozyme. Biopolymers 32, 315–319.CrossRefGoogle ScholarPubMed
Kim, Y. & Prestegard, J. H. (1989). A dynamic model for the structure of acyl carrier protein in solution. Biochemistry 28, 8792–8797.CrossRefGoogle ScholarPubMed
Kim, Y. & Prestegard, J. H. (1990). Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Proteins 8, 377–385.CrossRefGoogle ScholarPubMed
Kirkpatrick, S., Gelatt, C. D. Jr., & Vecchi, M. P. (1983). Optimization by simulated annealing. Science, N.Y. 220, 671–680.CrossRefGoogle ScholarPubMed
Kline, A. D., Braun, W. & Wüthrich, K. (1988). Determination of the complete three-dimensional structure of the α-amylase inhibitor tendamistat in aqueous solution by nuclear magnetic resonance and distance geometry. J. molec. Biol. 204, 675–724.CrossRefGoogle ScholarPubMed
Koehl, P. & Lefèvre, J. F. (1990). The reconstruction of the relaxation matrix from an incomplete set of nuclear overhauser effects. J. magn. Reson. 86, 565–583.Google Scholar
Kohlstaedt, L. A., Wang, J., Friedman, J. M., Rice, P. A. & Steitz, T. A. (1992). Crystal structure at 35 Å resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science, N.Y. 256, 1783–1790.CrossRefGoogle ScholarPubMed
Koning, T. M. G., Boelens, R. & Kaptein, R. (1990). Calculation of the nuclear overhauser effect and the determination of proton–proton distances in the presence of internal motion. magn. Reson. 90, 111–123.Google Scholar
Koning, T. M. G., Boelens, R., van der Marel, G. A., van Boom, J. H. & Kaptein, R. (1991). Structure determination of a DNA octamer in solution by NMR spectroscopy. Effect of fast local motions. Biochemistry 30, 3787–3797.CrossRefGoogle ScholarPubMed
Konnert, J. H. & Hendrickson, W. A. (1980). A restrained-parameter thermal-factor refinement procedure. Acta crystallogr. A 36, 344–349.CrossRefGoogle Scholar
Kraulis, P. (1991). Molscript: a program to produce both detailed and schematic plots of protein structures. J. appl. Crystallogr. 24, 946–950.CrossRefGoogle Scholar
Kuntz, I. D., Thomason, J. F. & Oshiro, C. M. (1989). Distance geometry. Methods. Enzym. 177, 159–204.CrossRefGoogle ScholarPubMed
Kuriyan, J. & Weis, W. I. (1991). Rigid protein motion as a model for crystallographic temperature factors. Proc. natn. Acad. Set. U.S.A. 88, 2773–2777.CrossRefGoogle Scholar
Kuriyan, J., Petsko, G. A., Levy, R. M. & Karplus, M. (1986). Effect of anisotropy and anharmonicity on protein crystallographic refinement. J. molec. Biol. 190, 227–254.CrossRefGoogle ScholarPubMed
Kuriyan, J., Brünger, A. T., Karplus, M. & Hendrickson, W. A. (1989). X-ray refinement of protein structures by simulated annealing: test of the method on myohemerythrin. Acta crystallogr. A 45, 396–409.CrossRefGoogle ScholarPubMed
Kuriyan, J., Ösapay, K., Burley, S. K., Brünger, A. T., Hendrickson, W. A. & Karplus, M. (1991). Exploration of disorder in protein structures by X-ray restrained molecular dynamics. Proteins 10, 340–358.CrossRefGoogle ScholarPubMed
Kuszewski, J., Nilges, M. & Brünger, A. T. (1992). Sampling and efficiency of metric matrix distance geometry: a novel partial metrization algorithm. J. Biomolec. NMR 2, 33–56.CrossRefGoogle ScholarPubMed
Laarhoven, P. J. M. & Aarts, E. H. L. (eds). (1987). Simulated Annealing: Theory and Applications, pp. 187. Dordrecht: D. Reidel Publishing Company.CrossRefGoogle Scholar
Lamzin, V. S. & Wilson, K. S. (1993). Automated refinement of protein models. Acta crystallogr. D 49, 129–147.Google ScholarPubMed
Landy, S. B. & Rao, B. D. N. (1989 a). Influence of molecular geometry on uncertainty in NOE determined distances. J. magn. Reson. 83, 267–278.Google Scholar
Landy, S. B. & Rao, B. D. N. (1989 b). Dynamical NOE in multiple-spin systems undergoing chemical exchange. J. magn. Reson. 81, 371–377.Google Scholar
Langs, D. A. (1988). Three-dimensional structure at o·86 Å of the uncomplexed form of the transmembrane ion channel peptide Gramicidin A. Science, N. Y. 241, 188–191.CrossRefGoogle Scholar
Lattman, E. E. (1985). Use of the rotation and translation functions. Meth. Enzymol. 115, 55–77CrossRefGoogle ScholarPubMed
Lawrence, M. C. (1991). The application of the molecular replacement method to the de novo determination of protein structure. Q. Rev. Biophysics 24, 399–424.CrossRefGoogle Scholar
Leahy, D. J., Hynes, T. R., McConnell, H. M. & Fox, R. O. (1988). Crystallization of an anti-tempo-dinitrophenyl monoclonal antibody fab fragment with and without bound hapten. J. molec. Biol. 203, 829–830.CrossRefGoogle ScholarPubMed
Leahy, D. J., Axel, R. & Hendrickson, W. A. (1992). Crystal structure of a soluble form of the human T cell coreceptor CD8 at 2·6 Å resolution. Cell 68, 1145–1162.CrossRefGoogle Scholar
Lefévre, J.-F., Lane, A. N. & Jardetzky, O. (1987). Solution structure of the Trp operator of Escherichia coli determined by NMR. Biochemistry 26, 5076–5090.CrossRefGoogle ScholarPubMed
LeMaster, D. M., Kay, L. E., Brünger, A. T. & Prestegard, J. H. (1988). Protein dynamics and distance determination by NOE measurements. FEBS Lett. 236, 71–76.CrossRefGoogle ScholarPubMed
Lesk, A. M. & Boswell, D. R. (1992). It's déjà vu all over again. Current Biology 2, 491–493.CrossRefGoogle Scholar
Levinthal, Z. (1968). Are there pathways for protein folding? J. Chim. phys. 65, 44–45.CrossRefGoogle Scholar
Levitt, M. (1983). Protein folding by restrained energy minimization and molecular dynamics. J. molec. Biol. 170, 723–764.CrossRefGoogle ScholarPubMed
Levy, R. M., Bassolino, D. A., Kitchen, D. B. & Pardi, A. (1989). Solution structures of proteins from NMR data and modeling: Alternative folds for neutrophil peptide 5. Biochemistry 28, 9361–9372.CrossRefGoogle ScholarPubMed
Lichtarge, O., Cornelius, C. W., Buchanan, B. G. & Jardetzky, O. (1987). Validation of the first step of the heuristic refinement method for the derivation of solution structures of proteins from NMR data. Proteins 2, 340–358.CrossRefGoogle ScholarPubMed
Lipari, G. & Szabo, A. (1982). Model-free approach to the interpretation of nuclear magnetic resonance in macromolecules. 1. Theory and range of validity. J. Am. chem. Soc. 104, 4546–4559.CrossRefGoogle Scholar
Liu, H., Thomas, P. D. & James, T. L. (1992). Averaging of cross-relaxation rates and distances for methyl, methylene and aromatic ring protons due to motion or overlap: extraction of accurate distances iteratively via relaxation matrix analysis of 2D NOE Spectra. J. magn. Reson. 98, 163–175.Google Scholar
Lunin, V. Y. (1988). Use of the information on electron density distribution in macromolecules. Acta crystallogr. A 44, 144–150.CrossRefGoogle Scholar
Lunin, V. Y. (1993). Electron-density histograms and the phase problem. Acta crystallogr. D 49, 90–99.Google ScholarPubMed
Lüthy, R., Bowie, J. U. & Eisenberg, D.Assessment of protein models with threedimensional profiles. (1992). Nature, Lond. 356, 83–85.CrossRefGoogle ScholarPubMed
Macura, S. & Ernst, R. R. (1980). Elucidation of cross relaxation in liquids by 2D NMR Spectroscopy. Molec. Phys. 41, 95–117.CrossRefGoogle Scholar
Madrid, M. & Jardetzky, O. (1988). Comparison of experimentally determined protein structures by solution of the bloch equations. Biochim. Biophys. Acta 953, 61–69.CrossRefGoogle ScholarPubMed
Madrid, M., Llinas, E. & Llinas, M. (1991). Model-independent refinement of interproton distances generated from 1H-NMR overhauser intensities. J. magn. Reson. 93. 329–346.Google Scholar
Main, P. (1990). A formula for electron density histograms for equal-atom structures. Acta crystallogr. A 46, 507–509.CrossRefGoogle Scholar
Marion, D., Genest, M. & Ptak, M. (1987). Reconstruction of NOESY Maps. A requirement for a reliable conformational analysis of biomolecules using 2D NMR. Byophys. Chem. 28, 235–244.CrossRefGoogle Scholar
Matthews, B. W. (1968). Solvent content of protein crystals. J. molec. Biol. 33, 491–497.CrossRefGoogle ScholarPubMed
Mazur, A. K. & Abagyan, R. A. (1989). New methodology for computer aided modelling of biomolecular structure and dynamics. (1) Non-cyclic structures. J. Biomolec. Struct. Dyn. 4, 815–832.CrossRefGoogle Scholar
McLachlan, A. D. (1993). Entropy phase dynamics. Acta crystallogr. D 49, 75–85.Google ScholarPubMed
Mertz, J. E., Güntert, P., Wüthrich, K. & Braun, W. (1991). Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities. J. Biomolec. NMR 1, 257–269.CrossRefGoogle ScholarPubMed
Metropolis, N., Rosenbluth, M., Rosenbluth, A., Teller, A. & Teller, E. (1953). Equation of state calculations by fast computing machines. J. chem. Phys. 21, 1087–1092.CrossRefGoogle Scholar
Metzler, W. J., Hare, D. R. & Pardi, A. (1989). Limited sampling of conformational space by the distance geometry algorithm: implications for structures generated from NMR data. Biochemistry 28, 7045–7052.CrossRefGoogle ScholarPubMed
Millane, R. P. (1990). Phase retrieval in crystallography and optics. J. opt. Soc. Am. A 7. 394–411.CrossRefGoogle Scholar
Miller, R., DeTitta, G. T., Langs, D. A., Weeks, C. M. & Hauptman, H. A. (1993). On the Application of the Minimal Principle to Solve Unknown Structures. Science, N.Y. 259, 1431–1433.CrossRefGoogle ScholarPubMed
Moews, P. C. & Kretsinger, R. H. (1975). Refinement of the structure of the carp muscle calcium-binding parvalbumin by model building and difference fourier analysis. J. molec. Biol. 91, 201–228.CrossRefGoogle ScholarPubMed
Morris, A. L., MacArthur, M. W., Hutchinson, E. G. & Thornton, J. M. (1992). Stereochemical quality of protein structure coordinates. Proteins 12, 345–364.CrossRefGoogle ScholarPubMed
Mukherjee, M. & Woolfson, M. M. (1993). On the application of phase relationships to complex structures. XXXII. A small protein at low resolution. Acta crystallogr. D 49 9–12.Google ScholarPubMed
Musacchio, A., Noble, M., Pauptit, R., Wierenga, R. & Saraste, M. (1992). Crystal Structure of a Src-homology 3 (SH3) Domain. Nature, Lond. 359, 851–855.CrossRefGoogle ScholarPubMed
Nerdal, W., Hare, D. R. & Reid, B. R. (1989). Solution structure of the EcoRI DNA sequence: refinement of NMR-derived distance geometry structures by NOESY spectrum back-calculations. Biochemistry 28, 10008–10021.CrossRefGoogle ScholarPubMed
Nikonowicz, E. P., Meadows, R. P. & Gorenstein, D. G. (1990). NMR structural refinement of an extrahelical adenosine tridecamer d(CGCAGAATTCGCG)2 via a hybrid relaxation matrix procedure. Biochemistry 29, 4193–4204.CrossRefGoogle Scholar
Nilges, M. & Brünger, A. T. (1991 c). Automated assignment of ambiguous crosspeaks in symmetric dimers. J. cell. Biochem. 15G, Abstract CG 422.Google Scholar
Nilges, M., Clore, G. M. & Gronenborn, A. M. (1988 a). Determination of threedimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett. 229, 317–324.CrossRefGoogle ScholarPubMed
Nilges, M., Gronenborn, A. M., Brünger, A. T. & Clore, G. M. (1988 b). Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng. 2, 27–38.CrossRefGoogle ScholarPubMed
Nilges, M., Clore, G. M. & Gronenborn, A. M. (1988 c). Determination of threedimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms. FEBS Lett. 239, 129–136.CrossRefGoogle ScholarPubMed
Nilges, M., Clore, G. M. & Gronenborn, A. M. (1990). 1H-NMR stereospecific assignments by conformational data-base searches. Biopolymers 29, 813–822.CrossRefGoogle ScholarPubMed
Nilges, M., Kuszewski, J. & Brunger, A. T. (1991 a). Sampling properties of simulated annealing and distance geometry. In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy (ed.Hoch, J. C., Poulsen, F. M., Redfield, C.), pp. 451–455. New York: Plenum Press.CrossRefGoogle Scholar
Nilges, M., Habazettl, J., Brünger, A. T. & Holak, T. A. (1991 b). Relaxation matrix refinement of the solution structure of squash trypsin inhibitor. J. molec. Biol. 219, 499–510.CrossRefGoogle ScholarPubMed
Nilsson, L., Clore, G. M., Gronenborn, A. M., Brünger, A. T. & Karplus, M. (1986). Structure refinement of oligonucleotides by molecular dynamics with nuclear overhauser effect interproton distance restraints: application to 5'd(CGTACG)2. J. molec. Biol. 188, 455–475.CrossRefGoogle Scholar
Novotný, J., Rashin, A. A. & Bruccoleri, R. E. (1988). Criteria that discriminate between native proteins and incorrectly folded models. Proteins 4, 19–30.CrossRefGoogle ScholarPubMed
Olejniczak, E. T. (1989). Including methyl rotation in simulation of spin-Lattice relaxation experiments. J. magn. Reson. 81, 392–394.Google Scholar
Olejniczak, E. T., Gampe, R. T. Jr., & Fesik, S. W. (1986). Accounting for spin diffusion in the analysis of 2D NOE Data. J. magn. Reson. 67, 28–41.Google Scholar
Ösapay, K. & Case, D. (1991). A new analysis of proton chemical shifts in proteins. J. Am. chem. Soc. 113, 9436–9444.CrossRefGoogle Scholar
Pai, E. F. (1992). Time-resolved macromolecular crystallography. Curr. Opin. Struct. Biol. 2, 821–827.CrossRefGoogle Scholar
Pardi, A., Billeter, M. & Wüthrich, K. (1984). Calibration of the angular dependence of the amide proton-Cα proton coupling constants, 3JHNα, in a globular protein. J. molec. Biol. 180, 741–751.CrossRefGoogle Scholar
Pardi, A., Hare, D. R., Selsted, M. E., Morrison, R. D., Bassolino, D. A. & Bach, A. C. (1988). Solution structures of the rabbit neutophil defensin NP-5. J. molec. Biol. 201, 625–636.CrossRefGoogle Scholar
Pearlman, D. A. & Kollman, P. A. (1991). Are time-averaged restraints necessary for nuclear magnetic resonance refinement? A model study for DNA. J. molec. Biol. 220, 457–479.CrossRefGoogle Scholar
Peng, J. W. & Wagner, G. (1992). Mapping the spectral densities of N–H Bond motions in eglin c using heternuclear relaxation experiments. Biochemistry 31, 8571–8586.CrossRefGoogle Scholar
Phillips, S. E. W. (1980). Structure and refinement of oxymyoglobin at 1·6 Å resolution. J. molec. Biol. 142, 531–554.CrossRefGoogle ScholarPubMed
Podjarny, A. D., Bhat, T. N. & Zwick, M. (1987). Improving crystallographic macromolecular images: The real-space approach. Ann. Rev. Biophys. Biophys. Chem. 16, 351–373.CrossRefGoogle ScholarPubMed
Post, C. B. (1992). Internal motional averaging and three-dimensional structure determination by nuclear magnetic resonance. J. molec. Biol. 224, 1087–1101.CrossRefGoogle ScholarPubMed
Post, C. B., Meadows, R. P. & Gorenstein, D. G. (1990). On the evaluation of interproton distances for three-dimensional structure determination by NMR using a relaxation matrix analysis. J. Am. chem. Soc. 112, 6796–6803.CrossRefGoogle Scholar
Powers, R., Garrett, D. S., March, C. J., Frieden, E. A., Gronenborn, A. M. & Clore, G. M. (1992 a). Three-dimensional solution structure of human interleukin- 4 by multidimensional heteronuclear magnetic resonance spectroscopy. Science, N. Y. 256, 1673–1677.CrossRefGoogle ScholarPubMed
Powers, R., Garrett, R., Daniel, S., March, C. J., Frieden, E. A., Gronenborn, A. M. & Clore, G. M. (1992 b). Proton, nitrogen-15, carbon-13, carbon-13 monoxide assignments of human interleukin-4 using three-dimensional double- and tripleresonance heteronuclear magnetic resonance spectroscopy. Biochemistry 31, 4334–4346.CrossRefGoogle Scholar
Press, W. H., Flannery, B. P., Teukolosky, S. A. & Vetterling, W. T. (eds) (1986). Numerical Recipes, pp. 498–546. Cambridge: Cambridge University Press.Google Scholar
Prince, E. (1993). Construction of maximum entropy density maps, and their use in phase determination and extension. Acta crystallogr. D 49, 61–65.Google ScholarPubMed
Prince, E., Sjülin, L. & Alenljung, R. (1988). Phase extension by combined entropy maximization and solvent flattening. Acta crystallogr. A 44, 216–222.CrossRefGoogle Scholar
Ramachandran, G. N. & Sasisekharan, V. (1968). Conformation of polypeptides and proteins. Adv. Protein Chem. 23, 283–438.CrossRefGoogle ScholarPubMed
Read, R. J. (1986). Improved fourier coefficients for maps using phases from partial structures with errors. Acta crystallogr. A 42, 140–149.CrossRefGoogle Scholar
Read, R. J. (1990). Structure-factor probabilities for related structures. Acta crystallogr. A 46, 900–912.CrossRefGoogle Scholar
Read, R. J. & Moult, J. (1992). Fitting electron density by systematic search. Acta crystallogr. A 48, 104–113.CrossRefGoogle ScholarPubMed
Read, R. J. & Schierbeek, A. J. (1988). A phased translation function. J. appl. Crystallogr. 21, 490–495.CrossRefGoogle Scholar
Redfield, C., Boyd, J., Smith, L. J., Smith, R. A. G. & Dobson, C. M. (1992). Loop mobility in a four helix bundle protein: 15N-NMR relaxation measurements on human interleukin-4. Biochemistry 31, 10431–10437.CrossRefGoogle Scholar
Rini, J. M., Stanfield, R. L., Stura, E. A., Profy, A. T. & Wilson, I. A.Crystal structure of an HIV-1 neutralizing antibody 50.1 in complex with V3 loop peptide antigen. Proc. Natl. Acad. Sci. USA, in press (1993).CrossRefGoogle ScholarPubMed
Robinson, H. & Wang, A. H. (1992). A simple spectral-driven procedure for the refinement of DNA structures by NMR spectroscopy. Biochemistry 31, 3524–3533.CrossRefGoogle ScholarPubMed
Rossmann, M. G. (1972). The Molecular Replacement Method. International Science Review No. 13. New York: Gordon & Breach.Google Scholar
Rossmann, M. G. & Blow, D. M. (1962). The detection of sub-units within the crystallographic asymmetric unit. Acta crystallogr. A 15, 24–31.CrossRefGoogle Scholar
Roth, M. (1991). Phasing at low resolution. In Crystallographic Computing 5, From Chemistry to Biology (ed. Moras, D., Podjarny, A. D. and Thierry, J. C.), pp. 227–248. New York: Oxford University Press.Google Scholar
Rould, M. A., Perona, J. J. & Steitz, T. A. (1992). Improving multiple isomorphous replacement phasing by heavy-atom refinement using solvent-flattened phases. Acta crystallogr. A 48, 751–756.CrossRefGoogle ScholarPubMed
Sato, T. (1992). Maximum-entropy method: phase refinement, Acta crystallogr. A 48, 842–850.CrossRefGoogle Scholar
Sayre, D. (1952). The squaring method: a new method for phase determination. Acta crystallogr. 5, 60–65.CrossRefGoogle Scholar
Sayre, D. (1993). Discussion after talk by J. M. Stewart. Acta crystallogr. D 49, 107.Google Scholar
Scheek, R. M., van Gunsteren, W. F. & Kaptein, R. (1989). Molecular dynamics simulation techniques for determination of molecular structures from nuclear magnetic resonance data. Methods Enzymol. 177, 204–218.CrossRefGoogle ScholarPubMed
Scheek, R. M., Torda, A. E., Kemmink, J. & van Gunsteren, W. F. (1991). Structure determination by NMR: The modelling of NMR parameters as ensemble averages. In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy (ed. Hoch, J. C., Poulsen, F. M., Redfield, C.), pp. 209–217. New York: Plenum Press.CrossRefGoogle Scholar
Schmitz, U., Kumar, A. & James, T. L. (1992). Dynamic interpretation of NMR data: molecular dynamics with weighted time-averaged restraints and ensemble R-factor. J. Am. Chem. Soc. 114, 10654–10656.CrossRefGoogle Scholar
Schomaker, V. & Trueblood, K. N. (1968). On the rigid-body motion of molecules in crystals. Acta crystallogr. B 24, 63–76.CrossRefGoogle Scholar
Shaanan, B., Gronenborn, A. M., Cohen, G. H., Gilliland, G. L., Veerapandian, B., Davies, D. R. & Clore, G. M. (1992). Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Science, N.Y. 257, 961–964.CrossRefGoogle ScholarPubMed
Sheldrick, G. M. (1990). Phase annealing in SHELX-90: Direct methods for larger structures. Acta crystallogr. A 46, 467–473.CrossRefGoogle Scholar
Sheldrick, G. M. (1992). Tutorial on automated patterson interpretation to find heavy atoms. In Crystallographic Computing 5, From Chemistry to Biology (ed. Moras, D., Podjarny, A. D. and Thierry, J. C.), pp. 143–157. New York: Oxford University Press.Google Scholar
Sheldrick, G. M., Dauter, Z., Wilson, K. S., Hope, H. & Sieker, L. C. (1993). The application of direct methods and Patterson interpretation to high-resolution native protein data. Acta crystallogr. D 49, 18–23.Google ScholarPubMed
Shiono, M. & Woolfson, M. M. (1991). On the application of phase relationships to complex structures: XXI. Properties and limitations of Sayre's equation. Acta crystallogr. A 47, 526–533.CrossRefGoogle Scholar
Shiono, M. & Woolfson, M. M. (1992). Direct-space methods in phase extension and phase determination. I. Low-density elimination. Acta crystallogr. A 48, 451–456.CrossRefGoogle Scholar
Sjolin, L. & Svensson, L. A. (1993). Experience with phase extension and ab initio phase determination in macromolecular crystallography using maximum entropy methods. Acta crystallogr. D 49, 66–74.Google ScholarPubMed
Sjülin, L., Prince, E., Svensson, L. A. & Gilliland, G. L. (1991). Ab initio phase determination for X-ray diffraction data from crystals of a native protein. Acta crystallogr. A 47, 216–222.CrossRefGoogle Scholar
Smith, J. L. (1991). Determination of three-dimensional structure by multiwavelength anomalous diffraction. Curr. Opin. Struct. Biol. 1, 1002–1011.CrossRefGoogle Scholar
Smith, L. J., Redfield, C., Boyd, J., Lawrence, G. M. P., Edwards, R. G., Smith, R. A. G. & Dobson, C. M. (1992). The solution structure of a four-helix bundle protein. J. molec. Biol. 224, 899–904.CrossRefGoogle ScholarPubMed
Solomon, I. (1955). Relaxation processes in a system of two spins. Phys. Rev. 99, 559–565.CrossRefGoogle Scholar
Spera, S. & Bax, A. (1991). Empirical correlation between protein backbone conformation and Cα and Cβ 13C nuclear magnetic resonance chemical shifts. J. Am. chem. Soc. 113, 5490–5492.CrossRefGoogle Scholar
Steigemann, W. (1974). Ph.D. Thesis, Technische Universität München.Google Scholar
Stickle, D. G., Presta, L. G., Dill, K. A. & Rose, G. D. (1992). Hydrogen bonding in globular proteins. J. molec. Biol. 226, 1143–1159.CrossRefGoogle ScholarPubMed
Stout, G. H. & Jensen, L. H. (eds) (1989). X-ray Structure Determination, A Practical Guide, pp. 341–419. New York: John Wiley & Sons.Google Scholar
Subbiah, S. (1991). Low-resolution real-space envelopes: an approach to the ab initio macromolecular phase problem. Science, N.Y. 252, 128–133.CrossRefGoogle Scholar
Subbiah, S. (1993). Low-resolution real-space envelopes: improvements of the condensing protocol approach and a new method to fix the sign of such envelopes. Acta crystallogr. D 49, 108–119.Google Scholar
Summers, M. F., South, T. L., Kim, B. & Hare, D. R. (1990). High resolution structure of an HIV zinc fingerlike domain via a new NMR-based distance geometry approach. Biochemistry 29, 329–340.CrossRefGoogle Scholar
Sussman, J. L., Holbrook, S. R., Church, G. M. & Kim, S. H. (1977). Structurefactor least-squares refinement procedure for macromolecular structure using constrained and restrained parameters. Acta crystallogr. A 33, 800–804.CrossRefGoogle Scholar
Swaminathan, S., Furey, W., Pletcher, J. & Sax, M. (1992). Crystal structure of staphylococcal enterotoxin B, a superantigen. Nature, Lond. 359, 801–806.CrossRefGoogle ScholarPubMed
Swanson, R. & Swanson, S. M. (1993). The effect of noise on entropy. Acta crystallogr. D49, 182–185.Google Scholar
Ten Eyck, L. F. (1973). Crystallographic fast Fourier transforms. Acta crystallogr. A 29, 183–191.CrossRefGoogle Scholar
Ten Eyck, L. F. (1977). Efficient structure-factor calculation for large molecules by the fast fourier transform. Acta crystallogr. A 33, 486–492.CrossRefGoogle Scholar
Thériault, Y., Logan, T. M., Meadows, R., Yu, L., Olejneczak, E. T., Holzmann, T. F., Simmer, R. L. & Fesik, S. W. (1992). Solution structure of a decameric cyclophilin-cyclosporin crystal complex. Nature, Lond. 361, 88–91.CrossRefGoogle Scholar
Thomas, P. D., Basus, V. J. & James, T. L. (1991). Protein solutin structure determination using distances from 2D NOE experiments: Effects of approximations on the accuracy of derived structures. Proc. natn. Acad. Sci. U.S.A. 88, 1237–1241.CrossRefGoogle Scholar
Torda, A. E., Scheek, R. M. & van Gunsteren, W. F. (1989). Time-dependent 124 A. T. Briinger and M. Nilges distance restraints in molecular dynamics simulations. Chem. Phys. Lett. 157, 289–294.CrossRefGoogle Scholar
Torda, A. E., Scheek, R. M. & van Gunsteren, W. F. (1990). Time-averaged nuclear overhauser effect distance restraints applied to tendamistat. J. molec. Biol. 214, 223–235.CrossRefGoogle ScholarPubMed
Torda, A. E., Brunne, R. M., Huber, T., Kessler, H. & van Gunsteren, W. F. (1993). Structure refinement using time-averaged J-coupling constant restraints. J. Biomolec. NMR 3, 55–66.CrossRefGoogle ScholarPubMed
Tronrud, D. E., Ten Eyck, L. F. & Matthews, B. W. (1987). An efficient generalpurpose least-squares refinement program for macromolecular structures Acta crystallogr. A 43, 489–500.CrossRefGoogle Scholar
Tronrud, D. E. (1992). Conjugate-direction minimization: an improved method for the refinement of macromolecules. Acta crystallogr. A 48, 912–916.CrossRefGoogle ScholarPubMed
Tsao, J., Chapman, M. S. & Rossmann, M. G. (1992). Ab initio Phase determination for viruses with high symmetry: a feasibility study. Acta crystallogr. A 48, 293–301.CrossRefGoogle ScholarPubMed
van de Ven, F. J. M., Blommers, M. J. J., Schouten, R. E. & Hilbers, C. W. (1991). Calculation of interproton distances from NOE intensities. A relaxation matrix approach without requirement of a molecular model. j. magn. Reson. 94, 140–151.Google Scholar
van Schaik, R. C., van Gunsteren, W. F. & Berendsen, H. J. C. (1992). Conformational search by potential energy annealing: algorithm and application to cyclosporin A. J. comp.-aided molec. Design, 6, 97–112.CrossRefGoogle ScholarPubMed
Venkatesan, R. (1991). The phase problem and its relation to the spin-glass problem. Acta crystallogr. A 47, 400–404.CrossRefGoogle Scholar
Verlet, L. (1967). Computer ‘Experiments’ on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159, 98–105.CrossRefGoogle Scholar
Verwer, P., Krabbendam, H. & Kroon, J. (1991). The concept of sparse electron density as a tool in structure-factor phase determination. Acta crystallogr. A 47, 143–144.CrossRefGoogle Scholar
Vriend, G. & Sander, C. (1993). Quality control of protein models: directional atomic contact analysis. J. appl. Crystallogr. 26, 47–60.CrossRefGoogle Scholar
Wang, B. C. (1985). Resolution of phase ambiguity in macromolecular crystallography. Meth. Enzymol. 115, 90–112.CrossRefGoogle ScholarPubMed
Weber, P. L., Morrison, R. & Hare, D. (1988). Determining stereo-specific 1H nuclear magnetic resonance assignments from distance geometry calculations. J. molec. Biol. 204, 483–487.CrossRefGoogle ScholarPubMed
Weeks, C. M., DeTitta, G. T., Miller, R. & Hauptman, H. A. (1993). Applications of the minimal principle to peptide structures. Acta crystallogr. D 49, 179–181.Google ScholarPubMed
White, S. A., Nilges, M., Huang, A., Brünger, A. T. & Moore, P. B. (1992). NMR Analysis of Helix I from the 5S RNA of Escherichia coli. Biochemistry 31, 1610–1621.CrossRefGoogle ScholarPubMed
Wilson, I. A., Rini, J. M., Fremont, D. H., Fieser, G. G. & Stura, E. A. (1991). Xray crystallographic analysis of free and antigen-complexed fab fragments to investigate structural basis of immune recognition. Meth. Enzymol. 203, 153–176.CrossRefGoogle ScholarPubMed
Wilson, C. & Agard, D. A. (1993). PRISM: automated crystallographic phase refinement by iterative skeletonization. Acta crystallogr. A 49, 97–104.CrossRefGoogle Scholar
Withka, J. M., Swaminathan, S., Srinivasan, J., Beveridge, D. L. & Bolton, P. H. (1992 a). Toward a dynamical structure of DNA: comparison of theoretical and experimental NOE intensities. Science, N. Y. 255, 597–599.CrossRefGoogle Scholar
Withka, J. M., Srinivasan, J. & Bolton, P. H. (1992 b). Problems with, and alternatives to, an NMR R-factor. J. magn. Reson. 98, 611–617.Google Scholar
Wlodawer, A. & Sjölin, L. (1983). Structure of ribonuclease A: results from joint neutron and X-ray refinement at 2·0 Å resolution. Biochemistry 22, 2720–2728.CrossRefGoogle ScholarPubMed
Wlodawer, A., Walter, J., Huber, R. & Sjölin, L. (1984). Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form. II. J. molec. Biol. 180, 301–329.CrossRefGoogle ScholarPubMed
Woolfson, M. M. (1987). Direct methods – from birth to maturity. Acta crystallogr. A 43. 593–612.CrossRefGoogle Scholar
Woolfson, M. M. & Yao, Jia-Xing (1990). On the application of phase relationships to complex structures. XXX. Ab initio solution of a small protein by SAYTAN. Acta crystallogr. A 46, 409–413.CrossRefGoogle Scholar
Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids. New York: Wiley.CrossRefGoogle Scholar
Wüthrjch, K., Billeter, M. & Braun, W. (1983). Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance. J. molec. Biol. 169, 949–961.CrossRefGoogle Scholar
Xiang, S., Carter, C. W. Jr., Bricogne, G. & Gilmore, C. J. (1993). Entropy maximization constrained by solvent flatness: a new method for macromolecular phase extension and map improvement. Acta crystallogr. D 49, 193–212.Google ScholarPubMed
Yeates, T. O. & Rini, J. M. (1990). Intensity-based domain refinement of oriented but unpositioned molecular replacement models. Acta crystallogr. A 46, 352–359.CrossRefGoogle ScholarPubMed
Yip, P. (1989). Calculating NOESY intensities by perturbation expansion. Chem. Phys. Lett. 161, 50–54.CrossRefGoogle Scholar
Yip, P. & Case, D. A. (1989). A new method for refinement of macromolecular structures based on nuclear overhauser effect spectra. J. magn. Reson. 83, 643–648.Google Scholar
Yip, P. & Case, D. A. (1991). Incorporation of internal motion in NMR refinement based on NOESY data. In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy (ed. Hoch, J. C., Poulsen, F. M. and Redfield, C.), pp. 317–330. New York: Plenum Press.CrossRefGoogle Scholar
Zhang, K. Y. J. (1993). SQUASH –combining constraints for macromolecular phase refinement and extension. Acta crystallogr. D 49, 213–222.Google ScholarPubMed
Zhang, K. Y. J. & Main, P. (1990 a). Histogram matching as a new density modification technique for phase refinement and extension of protein molecules. Acta crystallogr. A 46, 41–46.CrossRefGoogle Scholar
Zhang, K. Y. J. & Main, P. (1990 b). The use of Sayre's equation with solvent flattening and histogram matching for phase extension and refinement of protein structures. Acta crystallogr. A 46, 377–381.CrossRefGoogle Scholar