Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models.

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. Abstract Text:

Eran Eyal,Chakra Chennubhotla,Lee-Wei Yang,Ivet Bahar,

MOTIVATION: A common practice in X-ray crystallographic structure refinement has been to model atomic displacements or thermal fluctuations as isotropic motions. Recent high-resolution data reveal, however, significant departures from isotropy, described by anisotropic displacement parameters (ADPs) modeled for individual atoms. Yet, ADPs are currently reported for a limited set of structures, only. RESULTS: We present a comparative analysis of the experimentally reported ADPs and those theoretically predicted by the anisotropic network model (ANM) for a representative set of structures. The relative sizes of fluctuations along different directions are shown to agree well between experiments and theory, while the cross-correlations between the (x-, y- and z-) components of the fluctuations show considerable deviations. Secondary structure elements and protein cores exhibit more robust anisotropic characteristics compared to disordered or flexible regions. The deviations between experimental and theoretical data are comparable to those between sets of experimental ADPs reported for the same protein in different crystal forms. These results draw attention to the effects of crystal form and refinement procedure on experimental ADPs and highlight the potential utility of ANM calculations for consolidating experimental data or assessing ADPs in the absence of experimental data. AVAILABILITY: The ANM server at http://www.ccbb.pitt.edu/anm is upgraded to permit users to compute and visualize the theoretical ADPs for any PDB structure, thus providing insights into the anisotropic motions intrinsically preferred by equilibrium structures. SUPPLEMENTARY INFORMATION: Two Supplementary Material files can be accessed at the journal website. The first presents the tabulated results from computations (Pearson correlations and KL distances with respect to experimental ADPs) reported for each of the 93 proteins in Set I (the averages over all proteins are presented above in Table 3). The second file consists of three sections: (A) detailed derivation of Equation (7), (B) analysis of the effect of ANM parameters on computed ADPs and identification of parameters that achieve optimal correlation with experiments and (C) description of the method for computing the tangential and radial components of equilibrium fluctuations.

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. Publishing Authors By Initials

E Eyal,C Chennubhotla,LW Yang,I Bahar,

For similar investigative techniques: genetic techniques: sequence analysis: sequence analysis, protein research abstracts see: investigative techniques: genetic techniques: sequence analysis: sequence analysis, protein research

PUBMED ID PMID:

MEDLINE DATE:

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Bioinformatics (Oxford, England)

VOLUME: 23

Page Numbers: i175-84

Journal Abbreviation: Bioinformatics

ISSN: 1460-2059

DAY: 1

MONTH: Jul

YEAR: 2007

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 9808944

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. Keywords Mesh Terms:

KEYWORDS: Sequence Analysis, Protein

MESH TERMS: methods

Chemical & Substance for Abstract: Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. Information

Substance Name: Proteins

Registry Number: 0

Grant and Affiliation Information for Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models.

AFFILIATION: Department of Computational Biology, School of Medicine, University of Pittsburgh, Suite 3064, Biomedical Science Tower 3, 3051 Fifth Ave., Pittsburgh, PA 15213, USA.

Country: England

AGENCY: United States NIGMS

GRANT: R33 GM068400-01A2

ACRONYM: GM

MEDLINETA: Bioinformatics

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models Related Publications

• Amino acids partitioning in aqueous two-phase system of polypropylene glycol and magnesium sulfate.
• Amniotic fluid embolism: a plea for better brain protection.
• Analysis of correlated mutations in HIV-1 protease using spectral clustering.
• Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models.
• Anisotropic network model: systematic evaluation and a new web interface.
• Cervical cerclage for prevention of preterm birth in women with twin pregnancy.
• Chapter 34 Spinal strokes.
• Computational insights on the competing effects of nitric oxide in regulating apoptosis.
• Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL.
• Emergency cervical cerclage. Does the gestational age make a difference?
• Fluid preload before spinal anaesthesia in Caesarean section: the effect on neonatal acid-base status.
• Frustration, drift, and antiphase coupling in a neural array.
• Imaging cortical electrical stimulation in vivo: fast intrinsic optical signal versus voltage-sensitive dyes.
• Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions.
• Investigation on mitochondrial tRNA(Leu/Lys), NDI and ATPase 6/8 in Iranian multiple sclerosis patients.
• Markov methods for hierarchical coarse-graining of large protein dynamics.
• Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes.
• Mining frequent patterns in protein structures: a study of protease families.
• Molecular and histological changes following central retinal artery occlusion in a mouse model.
• Predisposition of the dark state of rhodopsin to functional changes in structure.
• Recruitment of rare 3-grams at functional sites: is this a mechanism for increasing enzyme specificity?
• Signal propagation in proteins and relation to equilibrium fluctuations.
• The relationship between n-gram patterns and protein secondary structure.
• Time-resolved Mechanism of Extracellular Gate Opening and Substrate Binding in a Glutamate Transporter.
• Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models.
• Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening.