Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates

Proteins: Structure, Function and Genetics

Volumn 29, Issue 1, 1997, Pages 1-14

  Wriggers, Willy ^a   Schulten, Klaus ^a  

^a University of Illinois at Urbana Champaign   (United States)

Author keywords

Actin; Binge bend ing; Hexokinase; Human growth factor; Human tissue factor; Lactoferrin; Protein architecture

Indexed keywords

ALGORITHM; ARTICLE; CONFORMATIONAL TRANSITION; HUMAN; MATHEMATICAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ACTINS; ALGORITHMS; CRYSTALLOGRAPHY, X-RAY; HEXOKINASE; HUMAN GROWTH HORMONE; HUMANS; LACTOFERRIN; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, SOMATOTROPIN; THROMBOPLASTIN;

EID: 0030883755     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199709)29:1<1::AID-PROT1>3.0.CO;2-J     Document Type: Article

References (51)

1. Lesk, A.M. "Protein Architecture." New York: Oxford University Press, 1991.
2. Gerstein, M., Lesk, A.M., Chothia, C. Structural mechanisms for domain movements in proteins. Biochemistry 33:6739-6749, 1994.
3. Sandak, B., Nussinov, R., Wolfson, H.J. An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching. Comp. Appl. Biosci. 11:87-99, 1995.
4. Sandak, B., Nussinov, R., Wolfson, H.J. Docking of conformationally flexible proteins. In: "Proceedings of the 1996 Symposium on Combinatorial Pattern Matching." Dan Hirschberg, Gene Myers, eds. Lecture Notes in Computer Science. Vol. 1075. Springer Verlag, 1996.
5. Brünger, A.T. "X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR." The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, 1992.
6. Rossman, M.G., Argos, P. Exploring structural homology of proteins. J. Mol. Biol. 105:75-95, 1976.
7. Rao, S.T., Rossman, M.G. Comparison of super-secondary structures in proteins. J. Mol. Biol. 76:241-256, 1973.
8. Remington, S.J., Mathews, B.W. A general method to assess similarity of protein structures, with applications to T4 bacteriophage lysozyme. Proc. Natl. Acad. Sci. U.S.A. 75:2180-2184, 1978.
9. Levine, M., Stuart, D., Williams, J. A method for the systematic comparison of three-dimensional structures of proteins and some results. Acta Cryst. A 40:600-610, 1984.
10. Barton, G.J., Sternberg, M.J.E. LOPAL and SCAMP: Techniques for the comparison and display of protein structures. J. Mol. Graphics 6:190-196, 1988.
11. Zuker, M., Somorjai, R.L. The alignment of protein structures in three dimensions. Bull. Math. Biol. 51:55-78, 1989.
12. Taylor, W.R., Orango, C.A. Protein structure alignment. J. Mol. Biol. 208:1-22, 1989.
13. Šali, A., Blundell, T.L. Definition of general topological equivalence in protein structures. J. Mol. Biol. 212:403-428, 1990.
14. Brint, A.T., Davies, H.M., Mitchell, E.M., Willett, P. Rapid geometric searching in protein structures. J. Mol. Graphics 7:48-53, 1989.
15. Holm, L., Sander, C. Structure comparison by alignment of distance matrices. J. Mol. Biol. 233:123-138, 1993.
16. Abagyan, R.A., Maiorov, V.N. A simple qualitative representation of polypeptide chain folds: Comparison of protein tertiary structures. J. Biomed. Struct. Dyn. 5:1267-1279, 1988.
17. Abagyan, R.A., Maiorov, V.N. An automatic search for similar spatial arrangements of α-helices and β-strands in globular proteins. J. Biomed. Struct. Dyn. 6:1045-1060, 1989.
18. Lesk, A.M. Detection of 3D patterns of atoms in chemical structures. Communications A.C.M. 22:219-224, 1979.
19. Vriend, G., Sander, C. Detection of common three-dimensional substructures in proteins. Proteins 11:52-58, 1991.
20. Freer, S.T., Kraut, J., Robertus, J.D., Wright, H.T., Xuong, N.H. Chymotrypsinogen: 2.5-Å crystal structure, comparison with α-chymotrypsin, and implications for zymogen activation. Biochemistry 9:1997-2009, 1970.
21. Chothia, C., Lesk, A.M. The relation between the divergence of sequence and structure in proteins. EMBO J 5:823-826, 1986.
22. Nichols, W.L., Rose, G., Eyck, L.F.T., Zimm, B.H. Rigid domains in proteins: An algorithmic approach to their identification. Proteins 23:38-48, 1995.
23. Kabsch, W. A solution for the best rotation to relate two sets of vectors. Acta Cryst. A 32:922-923, 1976.
24. Kabsch, W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Cryst. A 34:827-828, 1978.
25. Browner, M.F., Fauman, E.B., Fletterick, R.J. Tracking conformational states in allosteric transitions of phosphorylase. Biochemistry 31:11297-11304, 1992.
26. Gerstein, M., Altman, R.B. Average core structures and variability measures for protein families: Application to the immunoglobulins. J. Mol. Biol. 251:161-175, 1995.
27. Lesk, A.M., Fordham, W.D. Conservation and variability in the structures of serine proteinases of the chymotrypsin family. J. Mol. Biol. 258:501-537, 1996.
28. Goldstein, H. "Classical Mechanics." Reading, MA: Addison-Wesley Pub. Co., 1980.
29. Diamond, R. On the factorization of rotations with examples in diffractometry. Proc. R. Soc. Lond. A (Math. Phys. Sci.) 428:451-472, 1990.
30. Gerstein, M., Anderson, B.F., Norris, G.E., Baker, E.N., Lesk, A.M., Chothia, C. Domain closure in lactoferrin. J. Mol. Biol. 234:357-372, 1993.
31. Chasles, M. Note sur les propriétés générales du s̀ystème de deux corps semblables entre'eus et placés d'une manière quelconque dans l'espace; et sur la deplacement fini ou infinement petit d'un corps solide libre. Férusac, Bull. Sci. Math. 14:321-326, 1830.
32. Babcock, M.S., Pednault, E.P.D., Olson, W.K. Nucleic acid structure analysis. J. Mol. Biol. 237:125-156, 1994.
33. Anderson, B.F., Baker, H.M., Norris, G.E., Rice, D.W., Baker, E.N. Structure of human lactoferrin. J. Mol. Biol. 209:711-734, 1989.
34. Anderson, B.F., Baker, H.M., Norris, G.E., Rumball, S.V., Baker, E.N. Apolactoferrin structure demonstrates ligand-induced conformational change in transferrins. Nature 344:784-787, 1990.
35. Wriggers, W., Schulten, K. Stability and dynamics of G-actin: Back door water diffusion and behavior of a subdomain 3/4 loop. Biophys. J., in press.
36. Kabsch, W., Mannherz, H., Suck, D., Pai, E., Holmes, K. Atomic structure of the actin: DNase I complex. Nature 347:37-44, 1990.
37. Bennett, W.S., Steitz, T.A. Structure of a complex between yeast hexokinase A and glucose II. J. Mol. Biol. 140:211-230, 1980.
38. Bennett, W.S., Steitz, T.A. Structure of a complex between yeast hexokinase A and glucose I. J. Mol. Biol. 140:183-209, 1980.
39. Anderson, C.M., Stenkamp, R.E., Steitz, T.A. Sequencing a protein by X-ray crystallography. J. Mol. Biol. 123:1-13, 1978.
40. Schutt, C.E., Myslik, J.C., Rozycki, M.D., Goonesekere, N.C.W., Lindberg, U. The structure of crystalline profilin-β-actin. Nature 365:810-816, 1993.
41. McLaughlin, P.J., Gooch, J.T., Mannherz, H.-G., Weeds, A.G. Structure of gelsolin segment 1-actin complex and the mechanism of filament severing. Nature 364:685-692, 1993.
42. Chik, J., Lindberg, U., Schutt, C. The structure of an open state of beta actin at 2.65 A resolution. J. Mol. Biol. 263:607-623, 1996.
43. Muller, Y.A., Ultsch, M.H., Kelley, R.F., de Vos, A.M. Structure of the extracellular domain of human tissue factor: Location of the factor Vila binding site. Biochemistry 33:10864-10870, 1994.
44. Harlos, K., Martin, D.M.A., O'Brien, D.P., Jones, E.Y., Stuart, D.I., Polikarpov, I., Miller, A., Tuddenham, E.G.D., Boys, C.W.G. Crystal structure of the extracellular region of human tissue factor. Nature 370:662-666, 1994.
45. de Vos, A.M., Ultsch, M., Kossiakoff, A.A. Human growth hormone and extra-cellular domain of its receptor: Crystal structure of the complex. Science 255:306-312, 1992.
46. Bazan, J.F. Structural design and molecular evolution of a cytokine receptor superfamily. Proc. Natl. Acad. Sci. U.S.A. 87:6934-6938, 1990.
47. Humphrey, W.F., Dalke, A., Schulten, K. VMD - Visual molecular dynamics. J. Mol. Graphics 14(1):33-38, 1996.
48. Anderson, C.M., Stenkamp, R.E., McDonald, R.C., Steitz, T.A. A refined model of the sugar binding site of yeast hexokinase B. J. Mol. Biol. 123:207-219, 1978.
49. Bennett, W.S., Steitz, T.A. Glucose-induced conformational change in yeast hexokinase. Biochemistry 75:4848-4852, 1978.
50. Lesk, A.M., Chothia, C. Mechanisms of domain closure in proteins. J. Mol. Biol. 174:175-191, 1984.
51. Balsera, M.A., Wriggers, W., Oono, Y., Schulten, K. Principal component analysis and long time protein dynamics. J. Phys. Chem. 100:2567-2572, 1996.