Molecular dynamics simulations of ribonuclease T1: Comparison of the free enzyme and 2′ GMP–enzyme complex

Molecular dynamics simulations were performed on free RNase T1 and the 2′GMP–RNase T1 complex in vacuum and with water in the active site along with crystallographically identified waters, allowing analysis of both active site and overall structural and dynamics changes due to the presence of 2′GMP. Difference in the active site include a closing in the presence of 2′GMP, which is accompanied by a decrease in mobility of active site residues. The functional relevance of the active site fluctuations is discussed. 2′GMP alters the motion of Tyr‐45, suggesting a role for that residue in providing a hydrophobic environment for the protein–nucleic acid interactions responsible for the specificity of RNase T1. The presence of 2′GMP causes a structural change of the C‐terminus of the α‐helix, indicating the transmission of structural changes from the active site through the protein matrix. Overall fluctuations of both the free and 2′GMP enzyme forms are in good agreement with X‐ray temperature factors. The motion of Trp‐59 is influenced by 2′GMP, indicating difference in enzyme dynamics away from the active site, with the calculated changes following those previously seen in time‐resolved fluorescence experiments.

[1]  T. Uchida,et al.  9 Microbial Ribonucleases with Special Reference to RNases T1, T2, N1, and U2 , 1971 .

[2]  W. Bennett,et al.  Structural and functional aspects of domain motions in proteins. , 1984, CRC critical reviews in biochemistry.

[3]  Alexander D. MacKerell,et al.  Molecular dynamics simulations of ribonuclease T1: analysis of the effect of solvent on the structure, fluctuations, and active site of the free enzyme. , 1988, Biochemistry.

[4]  W. F. van Gunsteren,et al.  Effect of constraints on the dynamics of macromolecules , 1982 .

[5]  M. Karplus,et al.  Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study. , 1983, Biochemistry.

[6]  T. Oshima,et al.  Specific interaction of base-specific nucleases with nucleosides and nucleotides. , 1980, Molecular biology, biochemistry, and biophysics.

[7]  W. Saenger,et al.  Three‐dimensional structure of the ribonuclease t1 · 3'‐guanylic acid complex at 2.6 Å resolution , 1985, FEBS letters.

[8]  U Heinemann,et al.  Three-dimensional structure of the ribonuclease T1 2'-GMP complex at 1.9-A resolution. , 1988, The Journal of biological chemistry.

[9]  A. Warshel,et al.  Calculations of electrostatic interactions in biological systems and in solutions , 1984, Quarterly Reviews of Biophysics.

[10]  O. Tapia,et al.  Molecular dynamics simulations of the holo and apo forms of retinol binding protein. Structural and dynamical changes induced by retinol removal. , 1986, Journal of molecular biology.

[11]  M. Karplus,et al.  Molecular dynamics simulations of native and substrate-bound lysozyme. A study of the average structures and atomic fluctuations. , 1986, Journal of molecular biology.

[12]  Arieh Warshel,et al.  Calculations of chemical processes in solutions , 1979 .

[13]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[14]  S. Forsén,et al.  Molecular Dynamics Simulation of Parvalbumin in Aqueous Solution , 1987 .

[15]  O. Pongs,et al.  On the mechanism of action of ribonuclease T1. Nuclear magnetic resonance study on the active site. , 1971, European journal of biochemistry.

[16]  H. Matsuo,et al.  Proton and phosphorus nuclear magnetic resonance studies of ribonuclease T1. , 1979, Biochemistry.

[17]  M. Karplus,et al.  Stochastic boundary conditions for molecular dynamics simulations of ST2 water , 1984 .

[18]  S. Adelman Generalized Langevin theory for many‐body problems in chemical dynamics: Reactions in liquids , 1980 .

[19]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[20]  M. Karplus,et al.  Deformable stochastic boundaries in molecular dynamics , 1983 .

[21]  J. A. McCammon,et al.  REVIEW ARTICLE: Protein dynamics , 1984 .

[22]  H. J. Kim,et al.  Two histidine residues are essential for ribonuclease T1 activity as is the case for ribonuclease A. , 1987, Biochemistry.

[23]  A. Warshel Dynamics of enzymatic reactions. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[24]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[25]  Alexander D. MacKerell,et al.  Protein dynamics. A time-resolved fluorescence, energetic and molecular dynamics study of ribonuclease T1. , 1987, Biophysical chemistry.

[26]  Udo Heinemann,et al.  Restrained least‐squares refinement of the crystal structure of the ribonuclease T1*2'‐guanylic acid complex at 1·9 Å resolution , 1987 .

[27]  M Karplus,et al.  Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode. , 1979, The Journal of biological chemistry.

[28]  M Karplus,et al.  The internal dynamics of globular proteins. , 1981, CRC critical reviews in biochemistry.

[29]  U. Heinemann,et al.  Specific protein-nucleic acid recognition in ribonuclease T1–2′-guanylic acid complex: an X-ray study , 1982, Nature.

[30]  U. Heinemann,et al.  pH‐induced change in nucleotide binding geometry in the ribonuclease T1‐2'‐guanylic acid complex , 1985 .

[31]  M Karplus,et al.  Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics. , 1986, Journal of molecular biology.

[32]  J. Mccammon,et al.  Molecular dynamics with stochastic boundary conditions , 1982 .