Characterization of internal motions of Escherichia coli ribonuclease H by Monte Carlo simulation

Proteins: Structure, Function and Genetics

Volumn 34, Issue 4, 1999, Pages 533-539

  Haliloǧlu, Türkan ^a  

^a BOGAZICI UNIVERSITY   (Turkey)

Author keywords

Auto and cross correlation; Conformational dynamics; E. coli; Hydrogen exchange; Monte Carlo simulation technique; NMR; RNase; Virtual bonds

Indexed keywords

CARBON; HYDROGEN; RIBONUCLEASE H;

ARTICLE; CHEMICAL BOND; CRYSTALLOGRAPHY; ENZYME ANALYSIS; ESCHERICHIA COLI; MOTION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; ROTATION; SIMULATION; SYSTEM ANALYSIS;

AMINO ACIDS; COMPUTER SIMULATION; ESCHERICHIA COLI; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; MONTE CARLO METHOD; RIBONUCLEASE H, CALF THYMUS; TIME FACTORS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0033104694     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990301)34:4<533::AID-PROT12>3.0.CO;2-A     Document Type: Article

References (22)

1. Bahar I, Erman B, Haliloǧlu T, Jernigan RL. Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations. Biochemistry 1997;36: 13512-13523.
2. Haliloǧlu T, Bahar I. Coarse-grained simulations of conformational dynamics of proteins: application to apomyoglobin. Proteins 1998;31:271-281.
3. Haliloǧlu T. Coarse-grained simulations of conformational dynamics of proteins. Computational and Theoretical Polymer Science, 1998; submitted.
4. Bahar I, Jernigan RL. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 1997;266:195-214.
5. Bahar I, Kaplan M, Jernigan RL. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins 1997;29:292-308.
6. Ueda Y, Taketomi H, Go N. Studies on protein folding, unfolding, and fluctuations by computer simulations. II. A three dimensional lattice model of lysozyme. Biopolymers 1978;17:1531-1548.
7. Karplus M, Sali A. Theoretical studies of protein folding and unfolding. Curr Opin Struct Biol 1995;5:58-73.
8. Elofsson A, Le Grand SM, Eisenberg D. Local moves: an efficient algorithm for simulation of protein folding. Proteins 1995;23: 73-82.
9. Sun S. Reduced representation model of protein structure prediction: statistical potential and genetic algorithms. Protein Sci 1993;2:762-785.
10. Park BH, Levitt M. The complexity and accuracy of discrete state models of protein structure. J Mol Biol 1995;249:493-507.
11. Sun S, Thomas PD, Dill KA. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng 1995;8:769-778.
12. Park BH, Levitt M. Energy functions that discriminate X-ray and near-native folds from well-constructed decoys. J Mol Biol 1996; 258:367-392.
13. Chamberlein AK, Hande TM, Marqusee S. Detection of rare partially folded molecules in equilibrium with the native conformation of Rnase H. Nature Struct Biol 1996;3:782-787.
14. Powers R, Clore GM, Stahl SJ, Wingfield PT, Gronenborn A. Analysis of the backbone dynamics of the ribonuclease-H domain of the human-immunodeficiency-virus reverse-transcriptase using N-15 relaxation measurements. Biochemistry 1992;31:9150-9157.
15. Bahar I, Jernigan RL. Angular distributions of non-bonded residues around central residues in globular proteins. Fold Design 1996; 1:357-370.
16. Katayanagi K, Miyagawa M, Matushima M, Ishikawa M, Kanaya S, Nakamura H, Ikehara M, Matsuzaki T, Morikawa K. Sructural details of ribonuclease H from Escherichia coli as refined to an atomic resolution. J Mol Biol 1992;223:1029-1052.
17. Bernstein F, Koetzle T, Williams G, Meyer E, Brice M, Rodgers J, Kennard O, Shimanouchi T, Tasumi M. The protein databank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
18. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller EJ. Equation of state calculations by fast computing machines. J Chem Phys 1953;21:1087-1092.
19. Kanaya S, Kohara A, Miura Y, Sekiguchi A, Iwai S, Inoue H, Ohtsuka E, Ikehara M. Identification of the amino-acid-residues involved in an active-site of Escherichia-coli ribonuclease-H by site-directed mutagenesis. J Biol Chem 1990;265:4615-4621.
20. Oda Y, Yoshida M, Kanaya S. Role of histidine-124 in the catalytic function of ribonuclease-III from Escherichia-coli. J Biol Chem 1993;268:88-92.
21. Bahar I, Wallqvist DG, Covell DG, Jernigan RL. Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry 1998;37:1067-1075.
22. Haliloǧlu T, Bahar I, Erman B, Kim E-G, Mattice WL. A dynamic rotational isomeric state approach for extension of the time scale of the local dynamics observed in fully atomistic molecular dynamic simulations. J Chem Phys 1996;104:4828-4834.