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Normal-mode analysis of the glycine alpha1 receptor by three separate methods
Stanford University.
Stanford University.
Stockholm University.ORCID iD: 0000-0002-2734-2794
2007 (English)In: Journal of Chemical Information and Modeling, ISSN 1549-9596, Vol. 47, no 4, 1572-1579 p.Article in journal (Refereed) Published
Abstract [en]

Predicting collective dynamics and structural changes in biological macromolecules is pivotal toward a better understanding of many biological processes. Limitations due to large system sizes and inaccessible time scales have prompted the development of alternative techniques for the calculation of such motions. In this work, we present the results of a normal-mode analysis technique based on molecular mechanics that enables the calculation of accurate force-field based vibrations of extremely large molecules and compare it with two elastic network approximate models. When applied to the glycine alpha1 receptor, all three normal-mode analysis algorithms demonstrate an "iris-like" gating motion. Such gating motions have implications for understanding the effects of anesthetic and other ligand binding sites and for the means of transducing agonist binding into ion channel opening. Unlike the more approximate methods, molecular mechanics based analyses can also reveal approximate vibrational frequencies. Such analyses may someday allow the use of protein dynamics elucidated via normal-mode calculations as additional endpoints for future drug design.

Place, publisher, year, edition, pages
2007. Vol. 47, no 4, 1572-1579 p.
National Category
Biophysics Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:kth:diva-82624DOI: 10.1021/ci600566jISI: 000248192200029PubMedID: 17602605OAI: oai:DiVA.org:kth-82624DiVA: diva2:498450
Note
QC 20120309Available from: 2012-02-12 Created: 2012-02-12 Last updated: 2012-03-09Bibliographically approved

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Lindahl, Erik

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