Strategy for supplementing structure calculations using limited data with hydrophobic distance restraints

Proteins: Structure, Function and Genetics

Volumn 56, Issue 1, 2004, Pages 117-129

  Alexandrescu, Andrei T ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

angle; Long range restraints; Protein folding; Structure modeling; Torsion angles

Indexed keywords

BACTERIAL PROTEIN; COLD SHOCK PROTEIN; NUCLEASE; PEPTIDE; PROTEIN; PROTEIN G; STAPHYLOCOCCAL NUCLEASE; UNCLASSIFIED DRUG;

ARTICLE; CALCULATION; HYDROPHOBICITY; MODEL; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; HYDROPHOBICITY; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SENSITIVITY AND SPECIFICITY;

EID: 2642586515     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20134     Document Type: Article

References (50)

1. Lamzin VS, Perrakis A. Current state of automated crystallographic data analysis. Nature Struct Biol 2000;7(Suppl):978-981.
2. Edison AS, Abildgaard F, Westler WM, Mooberry ES, Markley JL. Practical introduction to theory and implementation of multinuclear, multidimensional nuclear magnetic resonance experiments. Methods Enzymol 1994;239:3-79.
3. Wuthrich K. NMR studies of structure and function of biological macromolecules (Nobel lecture). Angew Chem Int Ed Engl 2003;42: 3340-3363.
4. Tjandra N, Bax A. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 1997;278:1111-1114.
5. Rohl CA, Baker D. De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J Am Chem Soc 2000;124:2723-2729.
6. Kuszewski J, Gronenborn AM, Clore GM. Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration. J Am Chem Soc 1999;121:2337-2338.
7. Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
8. Baldwin RL, Rose GD. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem Sci 1999;24:26-33.
9. Dill KA. Dominant forces in protein folding. Biochemistry 1990;29: 7133-7155.
10. Viguera AR, Serrano L, Wilmanns M. Different folding transition states may result in the same native structure. Nature Struct Biol 1996;3:874-880.
11. Alexandrescu AT, Hinck AP, Markley JL. Coupling between local structure and global stability of a protein: mutants of staphylococcal nuclease. Biochemistry 1990;29:4516-4525.
12. Kabsch W, Sander C. On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc Natl Acad Sci USA 1984;81:1075-1078.
13. Derrick JP, Wigley DB. The third IgG-binding domain from streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with Fab. J Mol Biol 1994;243:906-918.
14. Edison AS, Weinhold F, Westler WM, Markley JL. Estimates of phi and psi torsion angles in proteins from one-, two- and three-bond nuclear spin-spin couplings: application to staphylococcal nuclease. J Biomol NMR 1994;4:543-551.
15. Wang AC, Bax A. Determination of the backbone dihedral angles phi in human ubiquitin from reparametrized empirical Karplus equations. J Am Chem Soc 1996; 118:2483-2494.
16. Skolnick J, Kolinski A, Ortiz AR. MONSSTER: a method for folding globular proteins with a small number of distance restraints. J Mol Biol 1997;265:217-241.
17. Bonvin AM, Houben K, Guenneugues M, Kaptein R, Boelens R. Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N 13C′ scalar couplings (3hbJNC′). J Biomol NMR 2001;21:221-233.
18. Beger RD, Bolton PH. Protein phi and psi dihedral restraints determined from multidimensional hypersurface correlations of backbone chemical shifts and their use in the determination of protein tertiary structures. J Biomol NMR 1997;10:129-142.
19. Cordier F, Grzesiek S. Direct observation of hydrogen-bonds in proteins by interresidue 3hJNC′ scalar couplings. J Am Chem Soc 1999;121:1601-1602.
20. Wang YX, Jacob J, Cordier F, Wingfield P, Stahl SJ, Lee-Huang S, Torchia D, Grzesiek S, Bax A. Measurement of 3hJNC′ connectivities across hydrogen bonds in a 30 kDa protein. J Biomol NMR 1999;14:181-184.
21. Guntert P, Mumenthaler C, Wuthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 1997;273:283-298.
22. Brunger AT. A system for X-ray crystallography and NMR. X-PLOR version 3.1. New Haven, CT: Yale University Press; 1992.
23. Cornilescu G, Delaglio F, Bax A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 1999;13:289-302.
24. Creighton TE. Proteins: structures and molecular properties. New York: W.H. Freeman; 1993.
25. Koradi R, Billeter M, Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996;14:29-32, 51-55.
26. Cornilescu G, Ramirez BE, Frank MK, Clore GM, Gronenborn AM, Bax A. Correlation between 3hJNC′ and hydrogen-bond length in proteins. J Am Chem Soc 1999;121:6275-6279.
27. MacArthur MW, Thornton JM. Deviations from planarity of the peptide bond in peptides and proteins. J Mol Biol 1996;264:1180-1195.
28. Edison AS. Linus Pauling and the planar peptide bond. Nature Struct Biol 2001;8:201-202.
29. Gronenborn AM, Filpula DR, Essig NZ, Achari A, Whitlow M, Wingfield PT, Clore GM. A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science 1991;253:657-661.
30. Delaglio F, Kontaxis G, Bax A. Protein structure determination using molecular fragment replacement and NMR dipolar couplings. J Am Chem Soc 2000;122:2142-2143.
31. Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 1996;8:477-486.
32. Schindelin H, Jiang W, Inouye M, Heinemann U. Crystal structure of CspA, the major cold shock protein of Escherichia coli. Proc Natl Acad Sci USA 1994;91:5119-5123.
33. Feng W, Tejero R, Zimmerman DE, Inouye M, Montelione GT. Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA binding site. Biochemistry 1998;37:10881-10896.
34. Hynes TR, Fox RO. The crystal structure of staphylococcal nuclease refined at 1.7 Å resolution. Proteins 1991;10:92-105.
35. Ramachandran GN, Sasisekharan V. Conformation of polypeptides and proteins. Adv Protein Chem 1968;23:283-438.
36. Gunasekaran K, Ramakrishnan C, Balaram P. Disallowed Ramachandran conformations of amino acid residues in protein structures. J Mol Biol 1996;264:191-198.
37. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH-a hierarchic classification of protein domain structures. Structure 1997;5:1093-1108.
38. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
39. Ruczinski I, Kooperberg C, Bonneau R, Baker D. Distributions of beta sheets in proteins with application to structure prediction. Proteins 2002;48:85-97.
40. Mo H, Moore RC, Cohen FE, Westaway D, Prusiner SB, Wright PE, Dyson HJ. Two different neurodegenerative diseases caused by proteins with similar structures. Proc Natl Acad Sci USA 2001;98:2352-2357.
41. Shortle D. Composites of local structure propensities: evidence for local encoding of long-range structure. Protein Sci 2002;11:18-26.
42. Shortle D. Staphylococcal nuclease: a showcase of m-value effects. Adv Protein Chem 1995;46:217-247.
43. Alexandrescu AT, Gittis AG, Abeygunawardana C, Shortle D. NMR structure of a stable "OB-fold" sub-domain isolated from staphylococcal nuclease. J Mol Biol 1995;250:134-143.
44. Green SM, Gittis AG, Meeker AK, Lattman EE. One-step evolution of a dimer from a monomeric protein. Nature Struct Biol 1995;2:746-751.
45. Alexandrescu AT, Jahnke W, Wiltscheck R, Blommers MJ. Accretion of structure in staphylococcal nuclease: an 15N NMR relaxation study. J Mol Biol 1996;260:570-587.
46. Alexandrescu AT, Snyder DR, Abildgaard F. NMR of hydrogen bonding in cold shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths. Protein Sci 2001;10:1856-1868.
47. Dosset P, Hus JC, Marion D, Blackledge M. A novel interactive tool for rigid body modeling of multi-domain macromolecules using residual dipolar couplings. J Biomol NMR 2001;20:223-231.
48. Bowers PM, Strauss CE, Baker D. De novo protein structure determination using sparse NMR data. J Biomol NMR 2000;18: 311-318.
49. Cahill M, Cahill S, Cahill K. Proteins wriggle. Biophys J 2002;82: 2665-2670.
50. Kraulis PJ. MOLSCRIPT-a program to produce both detailed and schematic plots of protein structure. J Appl Crystallogr 1991;24:946-950.