Literature DB >> 16526672

Electron density redistribution accounts for half the cooperativity of alpha helix formation.

Alexandre V Morozov, Kiril Tsemekhman, David Baker.   

Abstract

The energy of alpha helix formation is well known to be highly cooperative, but the origin and relative importance of the contributions to helical cooperativity have been unclear. Here we separate the energy of helix formation into short range and long range components by using two series of helical dimers of variable length. In one dimer series two monomeric helices interact by forming hydrogen bonds, while in the other they are coupled only through long range, primarily electrostatic interactions. Using Density Functional Theory, we find that approximately half of the cooperativity of helix formation is due to electrostatic interactions between residues, while the other half is due to nonadditive many-body effects brought about by redistribution of electron density with helix length.

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Year:  2006        PMID: 16526672     DOI: 10.1021/jp057161f

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  14 in total

1.  Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures.

Authors:  Andrew M Wollacott; Kenneth M Merz
Journal:  J Chem Theory Comput       Date:  2007       Impact factor: 6.006

Review 2.  Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors:  A T Hagler
Journal:  J Comput Aided Mol Des       Date:  2018-11-30       Impact factor: 3.686

3.  Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide.

Authors:  Jing Huang; Alexander D MacKerell
Journal:  Biophys J       Date:  2014-08-19       Impact factor: 4.033

4.  Observation of α-Helical Hydrogen-Bond Cooperativity in an Intact Protein.

Authors:  Jingwen Li; Yefei Wang; Jingfei Chen; Zhijun Liu; Ad Bax; Lishan Yao
Journal:  J Am Chem Soc       Date:  2016-02-08       Impact factor: 15.419

5.  Challenges in protein folding simulations: Timescale, representation, and analysis.

Authors:  Peter L Freddolino; Christopher B Harrison; Yanxin Liu; Klaus Schulten
Journal:  Nat Phys       Date:  2010-10-01       Impact factor: 20.034

6.  Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.

Authors:  Robert B Best; Gerhard Hummer
Journal:  J Phys Chem B       Date:  2009-07-02       Impact factor: 2.991

7.  Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation.

Authors:  Robert B Best; Jeetain Mittal; Michael Feig; Alexander D MacKerell
Journal:  Biophys J       Date:  2012-09-05       Impact factor: 4.033

8.  The origins of femtomolar protein-ligand binding: hydrogen-bond cooperativity and desolvation energetics in the biotin-(strept)avidin binding site.

Authors:  Jason DeChancie; K N Houk
Journal:  J Am Chem Soc       Date:  2007-04-07       Impact factor: 15.419

9.  Density functional study of molecular interactions in secondary structures of proteins.

Authors:  Yu Takano; Ayumi Kusaka; Haruki Nakamura
Journal:  Biophys Physicobiol       Date:  2016-02-13

10.  Strong Short-Range Cooperativity in Hydrogen-Bond Chains.

Authors:  Nicholas Dominelli-Whiteley; James J Brown; Kamila B Muchowska; Ioulia K Mati; Catherine Adam; Thomas A Hubbard; Alex Elmi; Alisdair J Brown; Ian A W Bell; Scott L Cockroft
Journal:  Angew Chem Int Ed Engl       Date:  2017-06-01       Impact factor: 15.336

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