Literature DB >> 33148530

Low barrier hydrogen bonds in protein structure and function.

M Trent Kemp1, Eric M Lewandowski1, Yu Chen2.   

Abstract

Low-barrier hydrogen bonds (LBHBs) are a special type of short hydrogen bond (HB) that is characterized by the equal sharing of a hydrogen atom. The existence and catalytic role of LBHBs in proteins has been intensely contested. Advancements in X-ray and neutron diffraction methods has revealed delocalized hydrogen atoms involved in potential LBHBs in a number of proteins, while also demonstrating that short HBs are not necessarily LBHBs. More importantly, a series of experiments on ketosteroid isomerase (KSI) have suggested that LBHBs are significantly stronger than standard HBs in the protein microenvironment in terms of enthalpy, but not free energy. The discrepancy between the enthalpy and free energy of LBHBs offers clues to the challenges, and potential solutions, of the LBHB debate, where the unique strength of LBHBs plays a special role in the kinetic processes of enzyme function and structure, together with other molecular forces in a pre-organized environment.
Copyright © 2020 Elsevier B.V. All rights reserved.

Entities:  

Keywords:  Enzyme catalysis; LBHB; NMR downfield shift; Neutron diffraction; Short HB; Sub-angstrom resolution X-ray crystallography

Mesh:

Substances:

Year:  2020        PMID: 33148530      PMCID: PMC7736181          DOI: 10.1016/j.bbapap.2020.140557

Source DB:  PubMed          Journal:  Biochim Biophys Acta Proteins Proteom        ISSN: 1570-9639            Impact factor:   3.036


  86 in total

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Authors:  E Lolis; G A Petsko
Journal:  Biochemistry       Date:  1990-07-17       Impact factor: 3.162

2.  Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons.

Authors:  Jiusheng Lin; Edwin Pozharski; Mark A Wilson
Journal:  Biochemistry       Date:  2016-12-30       Impact factor: 3.162

3.  Neutral imidazole is the electrophile in the reaction catalyzed by triosephosphate isomerase: structural origins and catalytic implications.

Authors:  P J Lodi; J R Knowles
Journal:  Biochemistry       Date:  1991-07-16       Impact factor: 3.162

4.  Mechanism of proton transfer in class A β-lactamase catalysis and inhibition by avibactam.

Authors:  Orville A Pemberton; Radwan E Noor; Vasantha Kumar M V; Ruslan Sanishvili; M Trent Kemp; Fiona L Kearns; H Lee Woodcock; Ioannis Gelis; Yu Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2020-03-02       Impact factor: 11.205

5.  Ab initio QM/MM study of class A beta-lactamase acylation: dual participation of Glu166 and Lys73 in a concerted base promotion of Ser70.

Authors:  Samy O Meroueh; Jed F Fisher; H Bernhard Schlegel; Shahriar Mobashery
Journal:  J Am Chem Soc       Date:  2005-11-09       Impact factor: 15.419

6.  Energetics of short hydrogen bonds in photoactive yellow protein.

Authors:  Keisuke Saito; Hiroshi Ishikita
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-15       Impact factor: 11.205

7.  Crystallographic analysis of transition-state mimics bound to penicillopepsin: phosphorus-containing peptide analogues.

Authors:  M E Fraser; N C Strynadka; P A Bartlett; J E Hanson; M N James
Journal:  Biochemistry       Date:  1992-06-09       Impact factor: 3.162

8.  Are there really low-barrier hydrogen bonds in proteins? The case of photoactive yellow protein.

Authors:  Marc Nadal-Ferret; Ricard Gelabert; Miquel Moreno; José M Lluch
Journal:  J Am Chem Soc       Date:  2014-02-19       Impact factor: 15.419

9.  A low-barrier hydrogen bond in the catalytic triad of serine proteases.

Authors:  P A Frey; S A Whitt; J B Tobin
Journal:  Science       Date:  1994-06-24       Impact factor: 47.728

10.  Short Hydrogen Bonds and Proton Delocalization in Green Fluorescent Protein (GFP).

Authors:  Luke M Oltrogge; Steven G Boxer
Journal:  ACS Cent Sci       Date:  2015-06-05       Impact factor: 14.553

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  2 in total

1.  Effective prediction of short hydrogen bonds in proteins via machine learning method.

Authors:  Shengmin Zhou; Yuanhao Liu; Sijian Wang; Lu Wang
Journal:  Sci Rep       Date:  2022-01-10       Impact factor: 4.996

2.  Structural insights into the catalytic and inhibitory mechanisms of the flavin transferase FmnB in Listeria monocytogenes.

Authors:  Yanhui Zheng; Weizhu Yan; Chao Dou; Dan Zhou; Yunying Chen; Ying Jin; Lulu Yang; Xiaotao Zeng; Wei Cheng
Journal:  MedComm (2020)       Date:  2022-01-10
  2 in total

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