ISSN:
1432-1017
Keywords:
Ribonuclease T1
;
protein dynamics
;
molecular dynamics
;
protein-nucleic acid interaction
Source:
Springer Online Journal Archives 1860-2000
Topics:
Biology
,
Physics
Notes:
Abstract Molecular dynamics simulations in vacuum and with a water sphere around the active site were performed on the 2′GMP-RNase T1 complex. The presence of water led to the maintenance of the 2′-GMP-RNase T1 interactions as compared to the X-ray structure, including the hydrogen bonds implicated in the enzyme-inhibitor recognition process. The sidechain of His92 in the molecular dynamics water simulation, however, hydrogen bonds directly to the phosphate of 2′GMP in contrast to the X-ray structure but in support of the role of that residue in the enzyme's catalytic mechanism. Fluctuations of activesite residues are not strongly influenced by water, possibly owing to the exclusion of water by the bound 2′GMP, which did show an increase in mobility. Analysis of the 2′GMP-RNase T1 interactions versus time reveal an equilibrium fluctuation in the presence of water, leading to a less favorable 2′GMP-RNase T1 interaction energy, suggesting a possible relationship between picosecond fluctuations and inhibitor dissociation occurring in the millisecond time domain.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1007/BF00254065
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