TITLE

Tracing conformational changes in proteins

AUTHOR(S)
Haspel, Nurit; Moll, Mark; Baker, Matthew L.; Chiu, Wah; Kavraki, Lydia E.
PUB. DATE
January 2010
SOURCE
BMC Structural Biology;2010 Supplement 1, Vol. 10, Special section p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Many proteins undergo extensive conformational changes as part of their functionality. Tracing these changes is important for understanding the way these proteins function. Traditional biophysics-based conformational search methods require a large number of calculations and are hard to apply to large-scale conformational motions. Results: In this work we investigate the application of a robotics-inspired method, using backbone and limited side chain representation and a coarse grained energy function to trace large-scale conformational motions. We tested the algorithm on four well known medium to large proteins and we show that even with relatively little information we are able to trace low-energy conformational pathways efficiently. The conformational pathways produced by our methods can be further filtered and refined to produce more useful information on the way proteins function under physiological conditions. Conclusions: The proposed method effectively captures large-scale conformational changes and produces pathways that are consistent with experimental data and other computational studies. The method represents an important first step towards a larger scale modeling of more complex biological systems.
ACCESSION #
51197249

 

Related Articles

  • A tale of two tails: why are terminal residues of proteins exposed? Ron Unger // Bioinformatics;Jan2007, Vol. 23 Issue 2, pe225 

    Motivation: It is widely known that terminal residues of proteins (i.e. the N- and C-termini) are predominantly located on the surface of proteins and exposed to the solvent. However, there is no good explanation as to the forces driving this phenomenon. The common explanation that terminal...

  • A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers. Dorfman, Roman J.; Smith, Karl M.; Masek, Brian B.; Clark, Robert D. // Journal of Computer-Aided Molecular Design;Sep2008, Vol. 22 Issue 9, p681 

    This paper describes a new and efficient stochastic conformational sampling method for generating a range of low-energy molecule conformations. Sampling can be tailored to a specific structural domain (e.g., peptides) by extracting torsional profiles from specific datasets and subsequently...

  • Interactions of Primary Amphipathic Cell Penetrating Peptides with Model Membranes: Consequences on the Mechanisms of Intracellular Delivery of Therapeutics. Deshayes, S�; Morris, May C.; Divita, Gilles; Heitz, Fr�d�ric // Current Pharmaceutical Design;Oct2005, Vol. 11 Issue 28, p3629 

    This review focuses on two peptides, MPG and Pep-1, which facilitate the transfer of nucleic acids and proteins, respectively, into subcellular compartments. We have investigated the interactions between these two carrier peptides and model membrane systems as well as the conformational...

  • Direct measurement of protein energy landscape roughness. Nevo, Reinat; Brumfeld, Vlad; Kapon, Ruti; Hinterdorfer, Peter; Reich, Ziv // EMBO Reports;May2005, Vol. 6 Issue 5, p482 

    The energy landscape of proteins is thought to have an intricate, corrugated structure. Such roughness should have important consequences on the folding and binding kinetics of proteins, as well as on their equilibrium fluctuations. So far, no direct measurement of protein energy landscape...

  • Multiscale Coarse-Graining of the Protein Energy Landscape. Hills Jr., Ronald D.; Lanyuan Lu; Voth, Gregory A. // PLoS Computational Biology;Jun2010, Vol. 6 Issue 6, p1 

    A variety of coarse-grained (CG) models exists for simulation of proteins. An outstanding problem is the construction of a CG model with physically accurate conformational energetics rivaling all-atom force fields. In the present work, atomistic simulations of peptide folding and aggregation...

  • Molecular biology: Triggering positive competition. Yonath, Ada // Nature;11/23/2006, Vol. 444 Issue 7118, p435 

    The article focuses on a study describing how a molecule known as trigger factor prevents misfolding of newly made proteins emerging from their ribosome. The study also provides insight into its protective mechanisms using fluorescence spectroscopy. It found that when trigger factor binds to the...

  • G-Protein-Coupled Receptors: from Structural Insights to Functional Mechanisms. Chini, Bice; Parenti, Marco; Poyner, David R.; Wheatley, Mark // Biochemical Society Transactions;Feb2013, Vol. 41 Issue 1, p135 

    The papers resulting from the recent Biochemical Society Focused Meeting 'G-Protein-Coupled Receptors: from Structural Insights to Functional Mechanisms' held in Prato in September 2012 are introduced in the present overview. A number of future goals for GPCR (G-protein-coupled receptor)...

  • The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics. Lanucara, Francesco; Holman, Stephen W.; Gray, Christopher J.; Eyers, Claire E. // Nature Chemistry;Apr2014, Vol. 6 Issue 4, p281 

    Mass spectrometry is a vital tool for molecular characterization, and the allied technique of ion mobility is enhancing many areas of (bio)chemical analysis. Strong synergy arises between these two techniques because of their ability to ascertain complementary information about gas-phase ions....

  • Dynamics and Conformational Studies of TOAC Spin Labeled Analogues of Ctx(Ile21)-Ha Peptide from Hypsiboas albopunctatus. Vicente, Eduardo F.; Basso, Luis Guilherme M.; Cespedes, Graziely F.; Lorenzón, Esteban N.; Castro, Mariana S.; Mendes-Giannini, Maria José S.; Costa-Filho, Antonio José; Cilli, Eduardo M. // PLoS ONE;Apr2013, Vol. 8 Issue 4, p1 

    Antimicrobial peptides (AMPs) isolated from several organisms have been receiving much attention due to some specific features that allow them to interact with, bind to, and disrupt cell membranes. The aim of this paper was to study the interactions between a membrane mimetic and the cationic...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics