Literature DB >> 17910943

Mapping folding energy landscapes with theory and experiment.

Silvina Matysiak1, Cecilia Clementi.   

Abstract

The detailed characterization of the overall free energy landscape associated with the folding process of a protein is the ultimate goal in protein folding studies. Modern experimental techniques and all-atom simulations provide a way to obtain accurate thermodynamic and kinetic measurements, but they are oftentimes restricted to probe limited regions of a protein landscape. Although simplified protein models can access larger regions of the landscape, they are built on assumptions and approximations that can affect the accuracy of the results. We review here recent promising approaches that allow to combine the complementary strengths of theory and experiment for a more complete characterization of a protein folding landscape at multiple resolutions. Recent results and possible applications are discussed.

Mesh:

Year:  2007        PMID: 17910943     DOI: 10.1016/j.abb.2007.08.019

Source DB:  PubMed          Journal:  Arch Biochem Biophys        ISSN: 0003-9861            Impact factor:   4.013


  6 in total

Review 1.  Experimentally-driven protein structure modeling.

Authors:  Nikolay V Dokholyan
Journal:  J Proteomics       Date:  2020-04-05       Impact factor: 4.044

2.  Characterization of the unfolded state of repeat proteins.

Authors:  Amit Mor; Gilad Haran; Yaakov Levy
Journal:  HFSP J       Date:  2008-11-12

3.  Malleability of the folding mechanism of the outer membrane protein PagP: parallel pathways and the effect of membrane elasticity.

Authors:  Gerard H M Huysmans; Sheena E Radford; Stephen A Baldwin; David J Brockwell
Journal:  J Mol Biol       Date:  2012-01-08       Impact factor: 5.469

4.  COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids.

Authors:  Casey T Andrews; Adrian H Elcock
Journal:  J Chem Theory Comput       Date:  2014-10-07       Impact factor: 6.006

5.  Multiscale approach to the determination of the photoactive yellow protein signaling state ensemble.

Authors:  Mary A Rohrdanz; Wenwei Zheng; Bradley Lambeth; Jocelyne Vreede; Cecilia Clementi
Journal:  PLoS Comput Biol       Date:  2014-10-30       Impact factor: 4.475

6.  Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins.

Authors:  Sai J Ganesan; S Matysiak
Journal:  J Chem Theory Comput       Date:  2014-05-09       Impact factor: 6.006

  6 in total

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