Dynamics of proteins predicted by molecular simulations and analytical approaches: Application to α-amylase inhibitor

Proteins: Structure, Function and Genetics

Volumn 40, Issue 3, 2000, Pages 512-524

  Doruker, Pemra ^a   Atilgan, Ali Rana ^a   Bahar, Ivet ^a  

^a BOGAZICI UNIVERSITY   (Turkey)

Author keywords

proteins; Anisotropic effects; Correlated fluctuations; Gaussian network model; Molecular dynamics simulations; Principal component analysis

Indexed keywords

AMYLASE INHIBITOR;

ANISOTROPY; ARTICLE; MODEL; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN STRUCTURE; SIMULATION;

ALPHA-AMYLASE; COMPUTER SIMULATION; ENZYME INHIBITORS; FLUORESCENCE POLARIZATION; MODELS, MOLECULAR; MOTION; NEURAL NETWORKS (COMPUTER); NORMAL DISTRIBUTION; PEPTIDES; PROTEIN CONFORMATION; SUPPORT, NON-U.S. GOV'T;

EID: 0034663710     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0134(20000815)40:3<512::AID-PROT180>3.0.CO;2-M     Document Type: Article

References (55)

1. Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: Human lysozyme
2. Simulations of CRP:(cAMP)2 in noncrystalline environments show a subunit transition from the open to the closed conformation
3. Analysis of domain motions by approximate normal mode calculations
4. Dynamics and function of proteins: The search for general concepts
5. Investigating protein dynamics in collective coordinate space
6. Dynamics of a small protein in terms of low-frequency vibrational modes
7. Method for estimating the configurational entropy of macromolecules
8. Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
9. Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme
10. 2
11. Extraction of the energetics of selected types of motion from molecular dynamics trajectories by filtering
12. Real-time interactive frequency filtering of molecular dynamics trajectories
13. Partitioning the motion in molecular dynamics simulations into characteristic modes of motion
14. Essential dynamics of proteins
15. The essential dynamics of thermolysin: Confirmation of the hinge-bending motion and comparison of simulations in vacuum and water
16. Coupling between different modes in local chain dynamics: A modal correlation analysis
17. Automatic identification of discrete substates in proteins: Singular value decomposition analysis of time-averaged crystallographic refinements
18. Vibrational approach to the dynamics of an α-helix
19. Molecular dynamics of an α-helical polypeptide: Temperature dependence and deviation from harmonic behavior
20. Evaluation of the configurationaI entropy for proteins: Application to molecular dynamics simulations of an α-helix
21. Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
22. Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data
23. The effects of solvent on the conformation and the collective motions of a protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum
24. A sampling problem in molecular dynamics simulations of macromolecules
25. Locally accessible conformations of proteins: Multiple molecular dynamics simulations of proteins
26. Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential
27. Structure-derived potentials and protein simulations
28. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
29. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
30. Correlation between native state hydrogen exchange and cooperative residue fluctuations from a simple model
31. Structure-based analysis of protein dynamics near the folded state. Results for hen Iysozyme, and comparison with X-ray diffraction and NMR relaxation data
32. Collective dynamics of HIV-1 reverse transcriptase: Examination of flexibility and enzyme function
33. Vibrational dynamics of transfer RNAs: Comparison of the free and enzyme bound forms
34. Cooperative fluctuations and subunit communication in tryptophan synthase
35. Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics
36. SCOP: A structural classification of proteins database
37. Harmonicity and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis
38. Crystal structure determination, refinement and the molecular model of the α-amylase inhibitor Hoe-467A
39. Determination of the complete three-dimensional structure of the α-amylase inhibitor tendamistat in aqueous solution by nuclear magnetic resonance and distance geometry
40. Restrained energy refinement with two different algorithms and force fields of the structure of the α-amylase inhibitor tendamistat determined by NMR solution
41. Numerical integration of cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
42. Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry
43. The protein data bank: A computer based Archival file for macromolecular structures
44. Molecular dynamics with coupling to an external bath
45. Energy landscape of a native protein: Jumping-among-minima model
46. Predicting the ensemble of unfolding pathways for proteins: An updated incremental Lagrangian model
47. Dynamic information from protein crystallography. An analysis of temperature factors from refinement of the hen egg-white lysozyme structure
48. Crystallographic studies of the dynamic properties of lysozyme
49. Temperature-dependent X-ray diffraction as a probe of protein structural dynamics
50. Vibrational dynamics of folded proteins. Significance of slow and fast modes in relation to function and stability
51. Investigation of shape variations m the antibody binding site by molecular dynamics computer simulation
52. Effect of solvent on collective motions in globular protein
53. Role of water on unfolding kinetics of polypeptides studied by molecular dynamics simulations