Efficient generation of feasible pathways for protein conformational transitions

Biophysical Journal

Volumn 83, Issue 3, 2002, Pages 1620-1630

  Kim, Moon K ^a,b   Jernigan, Robert L ^a,b   Chirikjian, Gregory S ^a,b,c  

^a Departments of Orthopaedic Surgery   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CITRATE SYNTHASE; LACTATE DEHYDROGENASE; LACTOFERRIN;

ARTICLE; CHEMICAL STRUCTURE; CONFORMATIONAL TRANSITION; GEOMETRY; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR MODEL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION; STEREOCHEMISTRY; STEREOSPECIFICITY; STRUCTURE ACTIVITY RELATION; BIOPHYSICS; CHEMISTRY; COMPUTER SIMULATION; THEORETICAL MODEL;

BIOPHYSICS; CITRATE (SI)-SYNTHASE; COMPUTER SIMULATION; L-LACTATE DEHYDROGENASE; LACTOFERRIN; MODELS, MOLECULAR; MODELS, THEORETICAL; PROTEIN CONFORMATION;

EID: 0036708474     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)73931-3     Document Type: Article

References (30)

1. Anisotropy of fluctuation dynamics of proteins with an elastic network model
2. Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential
3. Examination of collective motions in HIV-1 reverse transcriptase. Examination of flexibility and enzyme function
4. Vibrational dynamics of transfer RNAs: Comparison of the free and synthetase bound forms
5. Following protein-folding in real-time using NMR-spectroscopy
6. The Protein Data Bank
7. Visualizing protein conformational changes on a personal computer-alpha carbon pseudo bonding as a constraint for interpolation in internal coordinates space
8. Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic typsin inhibitor
9. Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme
10. Grabbing the cat by the tail: Manipulating molecules one by one
11. Reaction path study of conformational transitions in flexible systems: Applications to peptides
12. Transition path sampling and the calculation of rate constants
13. Insights into protein folding from NMR
14. A method for determining reaction paths in large molecules: Application to myoglobins
15. A database of macromolecular motions
16. The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at finite temperature
17. Conformational change in the activation of lipase: An analysis in terms of low-frequency normal modes
18. Nudged elastic band method for finding minimum energy paths of transitions
19. Where freedom is given, liberties are taken
20. Phi/Psi-chology: Ramachandran revisited
21. Calculation of classical trajectories with a very large time step: Formalism and numerical examples
22. Conformational change of proteins arising from normal mode calculations
23. Normal mode analysis of G-actin
24. Normal modes analyses of macromolecules
25. Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases
26. Resonance energy transfer: Methods and applications
27. 7 chaperonin complex
28. GroEL/GroES: Structure and function of a two-stroke folding machine