Free energy landscapes of peptides by enhanced conformational sampling

Journal of Molecular Biology

Volumn 296, Issue 1, 2000, Pages 197-216

  Nakajima, Nobuyuki ^a   Higo, Junichi ^a   Kidera, Akinori ^b   Nakamura, Haruki ^a  

^a BIOMOL ENG RESEARCH INSTITUTE   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

Free energy landscape; Hydration energy; Multicanonical molecular dynamics; Structural ensemble; turns

Indexed keywords

ALANINE; ASPARTIC ACID; DIMER; GLYCINE; PEPTIDE DERIVATIVE; PROLINE; SERINE;

AMINO ACID SEQUENCE; ARTICLE; CONFORMATIONAL TRANSITION; HYDRATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STABILITY; PROTEIN STRUCTURE; THERMODYNAMICS;

EID: 0034635351     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3440     Document Type: Article

References (66)

1. Microfolding: Conformational probability map for the alanine dipeptide in water from molecular dynamics simulations
2. Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations
3. Characterization of flexible molecules in solution: The RGDW peptide
4. Multicanonical algorithms for first order phase transitions
5. Multicanonical ensemble: A new approach to simulate first-order phase transitions
6. The Protein Data Bank. A computer-based archival file for macromolecular structures
7. Constant-temperature free energy surfaces for physical and chemical processes
8. The meaning of component analysis: Decomposition of the free energy in terms of specific interactions
9. Decomposition of interaction free energies in proteins and other complex systems
10. Simulations of peptide conformational dynamics and thermodynamics
11. Conformational analysis and forces that determine protein structure
12. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
13. An NMR-based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution
14. Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions
15. Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn
16. Solvation energy of protein folding and binding
17. The isothermal/isobaric molecular dynamics ensemble
18. New Monte Carlo technique for studying phase transitions
19. Why do protein architectures have Boltzmann-like statistics?
20. Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problem
21. Molecular dynamics, Langevin, and hybrid Monte Carlo simulations in multicanonical ensemble
22. Molecular dynamics simulations of helix and turn propensities in model peptides
23. Two-component multicanonical Monte Carlo method for effective conformation sampling
24. Enlarged representative set of protein structure
25. Selection of representative protein data sets
26. High-strain-rate plastic flow studied via nonequilibrium molecular dynamics
27. A revised set of potentials for β-turn formation in proteins
28. Structural study of mutants of Escherichia coli ribonuclease HI with enhanced thermostability
29. Comparison of simple potential functions for simulating liquid water
30. On the use of sequence homologies to predict protein structure: Identical pentapeptides can have completely different conformations
31. Statistical clustering techniques for the analysis of long molecular dynamics trajectories: Analysis of 2.2-ns trajectories of YPGDV
32. Enhanced conformational sampling in Monte Carlo simulations of proteins: Application to a constrained peptide
33. First-principle determination of peptide conformations in solvents: Combination of Monte Carlo simulated annealing and RISM theory
34. The development/application of a 'minimalist' organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data
35. New Monte Carlo algorithm: Entropic sampling
36. Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering
37. Contribution of hydration to protein folding thermodynamics I. The enthalpy of hydration
38. Decomposition of the free energy of a system in terms of specific interactions
39. Satisfying hydrogen bonding potential in proteins
40. Chameleon sequences in the PDB
41. Context-depending secondary structure formation of a designed protein sequence
42. PRESTO: A vectorized molecular mechanics program for biopolymers
43. A selectively enhanced multicanonical molecular dynamics method for conformational sampling of peptides in realistic water molecules
44. Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides
45. Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation
46. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
47. Contribution of hydration to protein folding thermodynamics II. The entropy and Gibbs energy of hydration
48. The anatomy and taxonomy of protein structure
49. Principles and patterns of protein conformation
50. Turns in peptides and proteins
51. Modern computational methodology applied to the simulation of blocked trialanine peptide in vacuo, water clusters, and bulk water
52. Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model
53. Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics
54. Environment and exposure to solvent of protein atoms. Lysozyme and insulin
55. Conformation of β-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering
56. Structural diversity of sequentially identical subsequences of proteins: Identical octapeptides can have different conformations
57. Crystal structure of the yeast MATα2/MCM1/DNA ternary complex
58. Analysis, design and modification of loop regions in proteins
59. Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution: A comparison of theoretical results
60. Reverse turns in blocked dipeptides are intrinsically unstable in water
61. Nanosecond time scale folding dynamics of a peptapeptide in water
62. β-turns and their distortions: A proposed new nomenclature
63. Conformation of peptide fragments of proteins in aqueous solution: Implications for initiation of protein folding
64. Free energies for refolding of the common β-turn into the inverse-common β-turn: Simulation of the role of D/L chirality
65. Free energy determinants of secondary structure formation: III. β-Turns and their role in protein folding
66. A thermodynamic analysis of solvation