Literature DB >> 25503367

Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site.

Lu Wang1, Stephen D Fried1, Steven G Boxer1, Thomas E Markland2.   

Abstract

Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.

Entities:  

Keywords:  ab initio path integral molecular dynamics; enzyme; hydrogen bonding; nuclear quantum effects; proton delocalization

Mesh:

Substances:

Year:  2014        PMID: 25503367      PMCID: PMC4284547          DOI: 10.1073/pnas.1417923111

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  33 in total

1.  Detection of large pKa perturbations of an inhibitor and a catalytic group at an enzyme active site, a mechanistic basis for catalytic power of many enzymes.

Authors:  N C Ha; M S Kim; W Lee; K Y Choi; B H Oh
Journal:  J Biol Chem       Date:  2000-12-29       Impact factor: 5.157

2.  A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

Authors:  Yong Duan; Chun Wu; Shibasish Chowdhury; Mathew C Lee; Guoming Xiong; Wei Zhang; Rong Yang; Piotr Cieplak; Ray Luo; Taisung Lee; James Caldwell; Junmei Wang; Peter Kollman
Journal:  J Comput Chem       Date:  2003-12       Impact factor: 3.376

Review 3.  Enzymatic mechanisms for catalysis of enolization: ketosteroid isomerase.

Authors:  Ralph M Pollack
Journal:  Bioorg Chem       Date:  2004-10       Impact factor: 5.275

4.  Unraveling quantum mechanical effects in water using isotopic fractionation.

Authors:  Thomas E Markland; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2012-05-07       Impact factor: 11.205

5.  Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase.

Authors:  Arieh Warshel; Pankaz K Sharma; Zhen T Chu; Johan Aqvist
Journal:  Biochemistry       Date:  2007-02-13       Impact factor: 3.162

6.  Low-barrier hydrogen bonds and enzymic catalysis.

Authors:  W W Cleland; M M Kreevoy
Journal:  Science       Date:  1994-06-24       Impact factor: 47.728

7.  NMR evidence for the participation of a low-barrier hydrogen bond in the mechanism of delta 5-3-ketosteroid isomerase.

Authors:  Q Zhao; C Abeygunawardana; P Talalay; A S Mildvan
Journal:  Proc Natl Acad Sci U S A       Date:  1996-08-06       Impact factor: 11.205

8.  Uncovering the determinants of a highly perturbed tyrosine pKa in the active site of ketosteroid isomerase.

Authors:  Jason P Schwans; Fanny Sunden; Ana Gonzalez; Yingssu Tsai; Daniel Herschlag
Journal:  Biochemistry       Date:  2013-10-23       Impact factor: 3.162

Review 9.  Specificity in transition state binding: the Pauling model revisited.

Authors:  Tina L Amyes; John P Richard
Journal:  Biochemistry       Date:  2013-02-04       Impact factor: 3.162

Review 10.  Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes.

Authors:  Daniel Herschlag; Aditya Natarajan
Journal:  Biochemistry       Date:  2013-03-14       Impact factor: 3.162

View more
  24 in total

1.  Hydration effect on proton transfer in melamine-cyanuric acid complex.

Authors:  Shihai Yan; Baotao Kang; Jin Yong Lee; Lixiang Sun
Journal:  J Mol Model       Date:  2016-06-28       Impact factor: 1.810

2.  Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory.

Authors:  J Gao
Journal:  Methods Enzymol       Date:  2016-07-22       Impact factor: 1.600

3.  Electric Fields and Fast Protein Dynamics in Enzymes.

Authors:  Ioanna Zoi; Dimitri Antoniou; Steven D Schwartz
Journal:  J Phys Chem Lett       Date:  2017-12-11       Impact factor: 6.475

Review 4.  Recent Advances in Clusteroluminescence.

Authors:  Zhaoyu Wang; Haoke Zhang; Siqi Li; Dangyuan Lei; Ben Zhong Tang; Ruquan Ye
Journal:  Top Curr Chem (Cham)       Date:  2021-03-03

5.  Dissecting Proton Delocalization in an Enzyme's Hydrogen Bond Network with Unnatural Amino Acids.

Authors:  Yufan Wu; Stephen D Fried; Steven G Boxer
Journal:  Biochemistry       Date:  2015-11-25       Impact factor: 3.162

6.  A Critical Test of the Electrostatic Contribution to Catalysis with Noncanonical Amino Acids in Ketosteroid Isomerase.

Authors:  Yufan Wu; Steven G Boxer
Journal:  J Am Chem Soc       Date:  2016-09-01       Impact factor: 15.419

7.  Origins of Enzyme Catalysis: Experimental Findings for C-H Activation, New Models, and Their Relevance to Prevailing Theoretical Constructs.

Authors:  Judith P Klinman; Adam R Offenbacher; Shenshen Hu
Journal:  J Am Chem Soc       Date:  2017-12-15       Impact factor: 15.419

8.  Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing.

Authors:  Takeshi Murakawa; Kazuo Kurihara; Mitsuo Shoji; Chie Shibazaki; Tomoko Sunami; Taro Tamada; Naomine Yano; Taro Yamada; Katsuhiro Kusaka; Mamoru Suzuki; Yasuteru Shigeta; Ryota Kuroki; Hideyuki Hayashi; Takato Yano; Katsuyuki Tanizawa; Motoyasu Adachi; Toshihide Okajima
Journal:  Proc Natl Acad Sci U S A       Date:  2020-05-05       Impact factor: 11.205

Review 9.  Protons and Hydroxide Ions in Aqueous Systems.

Authors:  Noam Agmon; Huib J Bakker; R Kramer Campen; Richard H Henchman; Peter Pohl; Sylvie Roke; Martin Thämer; Ali Hassanali
Journal:  Chem Rev       Date:  2016-06-17       Impact factor: 60.622

10.  Glutamate Mediates Proton-Coupled Electron Transfer Between Tyrosines 730 and 731 in Escherichia coli Ribonucleotide Reductase.

Authors:  Clorice R Reinhardt; Elvira R Sayfutyarova; Jiayun Zhong; Sharon Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2021-04-15       Impact factor: 15.419

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.