Normal-mode analysis of the glycine alpha1 receptor by three separate methods.

Normal-mode analysis of the glycine alpha1 receptor by three separate methods. Research Abstract Details 

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Normal-mode analysis of the glycine alpha1 receptor by three separate methods. Abstract Text:

Edward J Bertaccini,James R Trudell,Erik Lindahl,

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.

Normal-mode analysis of the glycine alpha1 receptor by three separate methods. Publishing Authors By Initials

EJ Bertaccini,JR Trudell,E Lindahl,

For similar proteins: membrane proteins: receptors, cell surface: receptors, neurotransmitter: receptors, amino acid: receptors, glycine research abstracts see: proteins: membrane proteins: receptors, cell surface: receptors, neurotransmitter: receptors, amino acid: receptors, glycine research

PUBMED ID PMID:

MEDLINE DATE: 2007 Jul-Aug

Normal-mode analysis of the glycine alpha1 receptor by three separate methods. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Journal of chemical information and modeling

VOLUME: 47

Page Numbers: 1572-9

Journal Abbreviation:

ISSN: 1549-9596

DAY: 30

MONTH: 06

YEAR: 2007

Normal-mode analysis of the glycine alpha1 receptor by three separate methods. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 101230060

Normal-mode analysis of the glycine alpha1 receptor by three separate methods. Keywords Mesh Terms:

KEYWORDS: Receptors, Glycine

MESH TERMS: chemistry

Chemical & Substance for Abstract: Normal-mode analysis of the glycine alpha1 receptor by three separate methods. Information

Substance Name: glycine receptor alpha1

Registry Number: 0

Grant and Affiliation Information for Normal-mode analysis of the glycine alpha1 receptor by three separate methods.

AFFILIATION: Department of Anesthesia, Stanford University School of Medicine and Beckman Center for Molecular and Genetic Medicine, Stanford, California 94305-5117, USA. edwardb@stanford.edu

Country: United States

AGENCY: United States NIGMS

GRANT: GM064371

ACRONYM: GM

MEDLINETA: J Chem Inf Model

REFSOURCE:

DATABASENAME:

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