Anisotropy of fluctuation dynamics of proteins with an elastic network model

Biophysical Journal

Volumn 80, Issue 1, 2001, Pages 505-515

  Atilgan, A R ^a   Durell, S R ^b,c   Jernigan, R L ^b,c   Demirel, M C ^a   Keskin, O ^b,c   Bahar, I ^a,b,c  

^a BOGAZICI UNIVERSITY   (Turkey)

^b NATIONAL CANCER INSTITUTE   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; M PROTEIN; RETINOIC ACID BINDING PROTEIN;

ANISOTROPY; ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; ELASTICITY; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR MODEL; PROTEIN CONFORMATION; PROTEIN STRUCTURE;

EID: 0035132230     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(01)76033-X     Document Type: Article

References (49)

1. Essential dynamics of proteins
2. Vibrational dynamics of folded proteins. Significance of slow and fast modes in relation to function and stability
3. Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential
4. Examination of collective motions in HIV-1 reverse transcriptase. Examination of flexibility and enzyme function
5. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
6. Vibrational dynamics of transfer RNAs: Comparison of the free and synthetase bound forms
7. Cooperative fluctuations and subunit communication in tryptophan synthase
8. Correlation between native state hydrogen exchange and cooperative residue fluctuations from a simple model
9. Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: The central helix is flexible
10. Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor
11. A theoretical perspective of dynamics, structure, and thermodynamics
12. Locally accessible conformations of proteins: Multiple molecular dynamics simulations of proteins
13. Functional concerted motions in the bovine serum retinol-binding protein
14. Proteins can adopt totally different folded conformations
15. Identification of kinetically hot residues in proteins
16. Predicting the ensemble of unfolding pathways for proteins: An updated incremental Lagrangian model
17. The Theory of Polymer Dynamics
18. Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α-amylase inhibitor
19. Low frequency modes in proteins: Use of effective-medium approximation to interpret the fractal dimension observed in electron-spin relaxation measurements
20. Statistical thermodynamics of random networks
21. Dynamics and function of proteins: The search for general concepts
22. The energy landscapes and motions of proteins
23. Large-amplitude nonlinear motions in proteins
24. Simulations of CRP:(cAMP)2 in noncrystalline environments show a subunit transition from the open to the closed conformation
25. Dynamics of a small globular protein in terms of low-frequency vibrational modes
26. Structure-based analysis of protein dynamics. Comparison of theoretical results for hen lysozyme with x-ray diffraction and NMR relaxation data
27. Gaussian dynamics of folded proteins
28. Harmonicity and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis
29. Harmonicity and anharmonicity in protein dynamics: A normal-mode analysis and principal component analysis
30. Analysis of domain motions by approximate normal mode calculations
31. A simplified force field for describing the vibrational protein dynamics over the whole frequency range
32. Analysis of domain motions in large proteins
33. Anisotropy and anharmonicity of atomic fluctuations in proteins: Analysis of a molecular dynamics simulations
34. Relating structure to function through the dominant modes of motion of DNA topoisomerase II
35. Proteins with similar architecture exhibit common large scale dynamics
36. Investigating protein dynamics in collective coordinate space
37. Mechanical property of a TIM-barrel protein
38. Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics
39. Dynamics of Proteins and Nucleic Acids
40. Crystals of the haemoglobin with the T quarternary structure bind oxygen noncooperatively with the Bohr effect
41. SCOP: A structural classification of protein databases for the investigation of sequences and structures
42. The structure of human retinol-binding protein (RBP) with its carrier protein transthyretin reveals an interaction with the carboxy terminus of RBP
43. A theory of the linear viscoelastic properties of dilute solutions of coiling polymers
44. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
45. Protein dynamics derived from clusters of crystal structures
46. Engineering protein mechanics: Inhibition of concerted motions of the cellular retinol binding protein by site-directed mutagenesis
47. How soft is a protein? A protein dynamics force constant measured by neutron scattering
48. Structure of pig plasma retinol-binding protein at 1.65 Å resolution
49. Native proteins are surface-molten solids: Application of the Lindemann criterion for the solid versus liquid state