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Molecular dynamics simulations of ribonuclease T 1 : Comparison of the free enzyme and 2′ GMP–enzyme complex
Author(s) -
MacKerell Alexander D,
Nilsson Lennart,
Rigler Rudolf,
Heinemann Udo,
Saenger Wolfram
Publication year - 1989
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340060103
Subject(s) - active site , molecular dynamics , rnase p , ribonuclease , chemistry , enzyme , rnase h , conformational change , protein dynamics , biophysics , nucleic acid , stereochemistry , crystallography , biochemistry , rna , biology , computational chemistry , gene
Molecular dynamics simulations were performed on free RNase T 1 and the 2′GMP–RNase T 1 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 T 1 . 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.