How orientational order governs collectivity of folded proteins

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 16, 2010, Pages 3363-3375

  Atilgan, Canan ^a   Okan, Osman Burak ^a   Atilgan, Ali Rana ^a  

^a SABANCI UNIVERSITY   (Turkey)

Author keywords

Cooperative motions; Elastic network models; Mean square fluctuations; Network construction; Normal mode analysis; Packing regularity; Spectral properties

Indexed keywords

ANISOTROPY; ARTICLE; CONTROLLED STUDY; MOTION; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN POLYMORPHISM; PROTEIN STABILITY; PROTEIN STRUCTURE;

ALGORITHMS; AMINO ACIDS; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 78349302991     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22843     Document Type: Article

References (50)

1. Soyer A, Chomilier J, Mornon JP, Jullien R, Sadoc JF. Voronoi tessellation reveals the condensed matter character of folded proteins. Phys Rev Lett 2000; 85: 3532-3535.
2. Raghunathan G, Jernigan RL. Ideal architecture of residue packing and its observation in protein structures. Prot Sci 1997; 6: 2072-2083.
3. Atilgan AR, Akan P, Baysal C. Small-world communication of residues and significance for protein dynamics. Biophys J 2004; 86: 85-91.
4. Liang J, Dill KA. Are proteins well packed? Biophys J 2001; 81: 751-766.
5. Zhang JF, Chen R, Tang C, Liang J. Origin of scaling behavior of protein packing density: a sequential Monte Carlo study of compact long chain polymers. J Chem Phys 2003; 118: 6102-6109.
6. ben-Avraham D. Vibrational normal-mode spectrum of globular-proteins. Phys Rev B 1993; 47: 14559-14560.
7. Bahar I, Atilgan AR, Demirel MC, Erman B. Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability. Phys Rev Lett 1998; 80: 2733-2736.
8. Bahar I, Rader AJ. Coarse-grained normal mode analysis in structural biology. Curr Opin Struc Biol 2005; 15: 586-592.
9. Cui Q. Normal mode analysis: theory and applications to biological and chemical systems. Florida: Chapman & Hall/CRC; 2006.
10. Tirion MM. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 1996; 77: 1905-1908.
11. Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 1997; 2: 173-181.
12. Yilmaz LS, Atilgan AR. Identifying the adaptive mechanism in globular proteins: fluctuations in densely packed regions manipulate flexible parts. Journal of Chemical Physics 2000; 113: 4454-4464.
13. Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys Journal 2001; 80: 505-515.
14. Gerek ZN, Keskin O, Ozkan SB. Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior. Proteins 2009; 77: 796-811.
15. Song G, Jernigan RL. vGNM: a better model for understanding the dynamics of proteins in crystals. J Mol Biol 2007; 369: 880-893.
16. Atilgan C, Ozkan SB, Gerek ZN, Atilgan AR. Perturbation-response scanning as a methodology for determining how conformational change is manipulated in proteins upon ligand binding. Biophys J 2010; 99: 933-943.
17. Delarue M, Sanejouand YH. Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the Elastic Network Model. J Mol Biol 2002; 320: 1011-1024.
18. Doruker P, Atilgan AR, Bahar I. Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor. Proteins-Structure Function and Genetics 2000; 40: 512-524.
19. Haliloglu T, Bahar I. Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data. Proteins 1999; 37: 654-667.
20. Temiz NA, Meirovitch E, Bahar I. Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling N-15-NMR relaxation data. Proteins 2004; 57: 468-480.
21. Petrone P, Pande VS. Can conformational change be described by only a few normal modes? Biophys J 2006; 90: 1583-1593.
22. Yang L, Song G, Jernigan RL. How well can we understand large-scale protein motions using normal modes of elastic network models? Biophys J 2007; 93: 920-929.
23. Yang L, Song G, Jernigan RL. Protein elastic network models and the ranges of cooperativity. Proc Natl Acad Sci U S A 2009; 106: 12347-12352.
24. Dupuis F, Sadoc JF, Jullien R, Angelov B, Mornon JP. Voro3D: 3D Voronoi tessellations applied to protein structures. Bioinformatics 2005; 21: 1715-1716.
25. Bode C, Kovacs IA, Szalay MS, Palotai R, Korcsmaros T, Csermely P. Network analysis of protein dynamics. FEBS Lett 2007; 581: 2776-2782.
26. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000; 28: 235-242.
27. Steinhardt PJ, Nelson DR, Ronchetti M. Bond-orientational order in liquids and glasses. Phys Rev B 1983; 28: 784.
28. Torquato S. Random heterogenous materials: microstructure and macroscopic properties. Berling: Springer-Verlag; 2002.
29. Truskett TM, Torquato S, Debenedetti PG. Towards a quantification of disorder in materials: distinguishing equilibrium and glassy sphere packings. Phys Rev E 2000; 62: 993.
30. Demmel JW. Applied numerical linear algebra. Society for Industrial and Applied Mathematics (SIAM): Philadelphia; 1997.
31. Covell DG, Jernigan RL. Conformations of folded proteins in restricted spaces. Biochemistry 1990; 29: 3287-3294.
32. Bagci Z, Jernigan RL, Bahar I. Residue packing in proteins: uniform distribution on a coarse-grained scale. J Chem Phys 2002; 116: 2269-2276.
33. Kolinski A, Skolnick J. Monte carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 1994; 18: 338-352.
34. Feng Y, Jernigan RL, Kloczkowski A. Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron. Proteins 2008; 73: 730-741.
35. Golub GH, van Loan CF. Matrix computations. Baltimore: Johns Hopkins University Press; 1996.
36. Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998; 33: 417-429.
37. Baysal C, Atilgan AR. Elucidating the structural mechanisms for biological activity of the chemokine family. Proteins 2001; 43: 150-160.
38. Keskin O. Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies. BMC Struct Biol 2007; 7: 31.
39. Tama F, Sanejouand YH. Conformational change of proteins arising from normal mode calculations. Prot Eng 2001; 14: 1-6.
40. Zen A, Carnevale V, Lesk AM, Micheletti C. Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families. Prot Sci 2008; 17: 918-929.
41. Zheng WJ, Brooks BR, Thirumalai D. Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks. Curr Protein Pept Sci 2009; 10: 128-132.
42. Zheng W, Brooks BR, Thirumalai D. Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys J 2007; 93: 2289-2299.
43. Zheng WJ, Brooks B. Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model. J Mol Biol 346: 745-759.
44. Sacquin-Mora S, Lavery R. Modeling the mechanical response of proteins to anisotropic deformation. Chemphyschem 2009; 10: 115-118.
45. Atilgan C, Atilgan AR. Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein. PLoS Comput Biol 2009; 5: 14.
46. da Silveira CH, Pires DEV, Minardi RC, Ribeiro C, Veloso CJM, Lopes JCD, Meira W, Neshich G, Ramos CHI, Habesch R, Santoro MM. Protein cutoff scanning: a comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins. Proteins 2009; 74: 727-743.
47. Hafner J, Zheng WJ. Optimal modeling of atomic fluctuations in protein crystal structures for weak crystal contact interactions. J Chem Phys 2010; 132: 014111.
48. Riccardi D, Cui Q, Phillips GN. Application of elastic network models to proteins in the crystalline state. Biophys J 2009; 96: 464-475.
49. Okan OB, Atilgan AR, Atilgan C. Nanosecond motions in proteins impose bounds on the timescale distributions of local dynamics. Biophys J 2009; 97: 2080-2088.
50. Miyashita O, Onuchic JN, Wolynes PG. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci U S A 2003; 100: 12570-12575.