Molecular dynamics simulations of ribonuclease T1 View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1988-12

AUTHORS

A. D. MacKerell, R. Rigler, L. Nilsson, U. Heinemann, W. Saenger

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. More... »

PAGES

287-297

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/bf00254065

DOI

http://dx.doi.org/10.1007/bf00254065

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1019223257

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/2853669


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