PMID: 9194161Apr 1, 1997Paper

Protein dynamics determined by backbone conformation and atom packing

Protein Engineering
J Higo, H Umeyama

Abstract

To study the factors determining the collective motions in thermal, conformational fluctuations of a globular protein, molecular dynamics simulations were performed with a backbone model and an atomic-level model. In the backbone model, only the C alpha atoms were explicitly treated with two types of pairwise interactions assigned between the C alpha atoms; atom-packing interactions to take into account the effect of tight atom packing in the protein interior and chain-restoring interactions to maintain the backbone around the native conformation. A quasi-harmonic method was used to decompose the overall fluctuations into independent, collective modes. The modes assigned to large conformational fluctuations showed a good correlation between the backbone and atomic-level models. From this study, it was suggested that the collective modes were motions in which a protein fluctuates, keeping the tertiary structure around the native one and avoiding backbone overlap and, hence, rough aspects of the collective modes can be derived without details of the atomic interactions. The backbone model is useful in obtaining the overall backbone motions of a protein without heavy simulations, even though the simulation starts from a poorly det...Continue Reading

Citations

Feb 19, 2000·Journal of Molecular Graphics & Modelling·T YonedaH Umeyama
Sep 19, 2002·Protein Science : a Publication of the Protein Society·Narutoshi KamiyaHaruki Nakamura
May 23, 2001·Protein Science : a Publication of the Protein Society·J HigoH Nakamura
Oct 19, 2012·PloS One·Markus DüttmannAlexander S Mikhailov
Oct 26, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Georgina MircevaDanco Davcev
Feb 14, 2012·Biophysical Journal·Markus DüttmannAlexander S Mikhailov
Jun 11, 2004·Biophysical Journal·Sibsankar Kundu, Robert L Jernigan
Jul 19, 2002·Biophysical Journal·Sibsankar KunduGeorge N Phillips
Oct 13, 2004·Proteins·Sibsankar KunduGeorge N Phillips
May 13, 2018·Amino Acids·Oliviero Carugo
Dec 20, 2018·International Journal of Molecular Sciences·Yuichi Togashi, Holger Flechsig

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