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Effects of substrate binding on the dynamics of RNase A: Molecular dynamics simulations of UpA bound and native RNase A

✍ Scribed by Gautham Nadig; Saraswathi Vishveshwara

Publisher: Wiley (John Wiley & Sons)
Year: 1997
Tongue: English
Weight: 358 KB
Volume: 42
Category: Article
ISSN: 0006-3525
DOI: 10.1002/(sici)1097-0282(19971015)42:5<505::aid-bip2>3.0.co;2-u

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✦ Synopsis

RNase A has been extensively used as a model protein in several biophysical and biochemical studies. Using the available structural and biochemical results, RNase A-UpA interaction has been computationally modeled at an atomic level. In this study, the molecular dynamics (MD) simulations of native and UpA bound RNase A have been carried out. The gross dynamical behavior and atomic fluctuations of the free and UpA bound RNase A have been characterized. Principal component analysis is carried out to identify the important modes of collective motion and to analyze the changes brought out in these modes of RNase A upon

UpA binding. The hydrogen bonds are monitored to study the atomic details of RNase A-UpA interactions and RNase A-water interactions. Based on these analysis, the stability of the free and UpA bound RNase A are discussed.

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