Literature DB >> 15506785

Calculation of trans-hydrogen-bond 13C-15N three-bond and other scalar J-couplings in cooperative peptide models. A density functional theory study.

Pedro Salvador1, Nadya Kobko, Robert Wieczorek, J J Dannenberg.   

Abstract

We report B3LYP DFT calculations on peptide models that consider the effects of cooperative interactions with proximate H-bonds and local geometry at the H-bonding site upon trans-H-bond (13)C-(15)N three-bond scalar J-couplings. The calculations predict that cooperative interactions with other H-bonds within a H-bonding chain can significantly increase the magnitude of these couplings. Such increases are due to a combination of the presence of the neighboring H-bonds and the slight increase in C=O distances expected for peptide H-bonds near the centers of H-bonding chains. The energies of H-bonds inferred from H-bonding distances, alone, could be significantly in error if the effects of neighboring H-bonds are ignored.

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Year:  2004        PMID: 15506785     DOI: 10.1021/ja0492788

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  7 in total

1.  Structural dependencies of protein backbone 2JNC' couplings.

Authors:  Nenad Juranić; J J Dannenberg; Gabriel Cornilescu; Pedro Salvador; Elena Atanasova; Hee-Chul Ahn; Slobodan Macura; John L Markley; Franklyn G Prendergast
Journal:  Protein Sci       Date:  2008-02-27       Impact factor: 6.725

2.  J-coupling constants for a trialanine peptide as a function of dihedral angles calculated by density functional theory over the full Ramachandran space.

Authors:  Pedro Salvador; I-Hsien Midas Tsai; J J Dannenberg
Journal:  Phys Chem Chem Phys       Date:  2011-09-06       Impact factor: 3.676

3.  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

4.  Evidences for Cooperative Resonance-Assisted Hydrogen Bonds in Protein Secondary Structure Analogs.

Authors:  Yu Zhou; Geng Deng; Yan-Zhen Zheng; Jing Xu; Hamad Ashraf; Zhi-Wu Yu
Journal:  Sci Rep       Date:  2016-11-16       Impact factor: 4.379

5.  Experimental and theoretical investigation of intramolecular cooperativity in cyclic benzene trimer motif.

Authors:  Chakka Kiran Kumar; Shankar Deval Sathiyashivan; Dhanraj T Masram; K V Jovan Jose; Malaichamy Sathiyendiran
Journal:  RSC Adv       Date:  2019-01-04       Impact factor: 4.036

6.  Capping parallel β-sheets of acetyl(Ala)6NH2 with an acetyl(Ala)5ProNH2 can arrest the growth of the sheet, suggesting a potential for curtailing amyloid growth. An ONIOM and density functional theory study.

Authors:  Gabor Pohl; Amparo Asensio; J J Dannenberg
Journal:  Biochemistry       Date:  2014-01-23       Impact factor: 3.162

Review 7.  Viroid research and its significance for RNA technology and basic biochemistry.

Authors:  Gerhard Steger; Detlev Riesner
Journal:  Nucleic Acids Res       Date:  2018-11-16       Impact factor: 16.971

  7 in total

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