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Title: Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis: Distal Substitutions in Liver Alcohol Dehydrogenase

Journal Article · · Protein Science
DOI:https://doi.org/10.1002/pro.3370· OSTI ID:1511715
 [1];  [2];  [3]; ORCiD logo [4]
  1. Department of Biochemistry, The University of Iowa, Iowa City IA 52242-1109; Diagnostic Virology Laboratory, USDA, Ames IA 50010
  2. Department of Biochemistry, The University of Iowa, Iowa City IA 52242-1109; Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin 9054 New Zealand
  3. Department of Biochemistry, The University of Iowa, Iowa City IA 52242-1109; No 92, Jing Mao 1st Rd., Taichung Taiwan 406, Republic of China
  4. Department of Biochemistry, The University of Iowa, Iowa City IA 52242-1109

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
National Institutes of Health (NIH)
OSTI ID:
1511715
Journal Information:
Protein Science, Vol. 27, Issue 3; ISSN 0961-8368
Publisher:
The Protein Society
Country of Publication:
United States
Language:
ENGLISH

References (106)

Impact of Enzyme Motion on Activity journal November 2002
Flexibility, Diversity, and Cooperativity: Pillars of Enzyme Catalysis journal December 2011
Catalytic Efficiency of Enzymes: A Theoretical Analysis journal December 2012
Prediction of distal residue participation in enzyme catalysis: Distal Residue Participation in Enzyme Catalysis journal April 2015
Dynamically Achieved Active Site Precision in Enzyme Catalysis journal December 2014
Picosecond-Resolved Fluorescent Probes at Functionally Distinct Tryptophans within a Thermophilic Alcohol Dehydrogenase: Relationship of Temperature-Dependent Changes in Fluorescence to Catalysis journal June 2014
Identification of a Long-range Protein Network That Modulates Active Site Dynamics in Extremophilic Alcohol Dehydrogenases journal March 2013
Remote Mutations Alter Transition-State Structure of Human Purine Nucleoside Phosphorylase journal February 2008
Remote Mutations and Active Site Dynamics Correlate with Catalytic Properties of Purine Nucleoside Phosphorylase journal May 2008
Protein Dynamics in Enzymatic Catalysis:  Exploration of Dihydrofolate Reductase journal January 2000
Evidence for a Functional Role of the Dynamics of Glycine-121 of Escherichia coli Dihydrofolate Reductase Obtained from Kinetic Analysis of a Site-Directed Mutant journal December 1997
Network of coupled promoting motions in enzyme catalysis journal February 2002
Coupling Interactions of Distal Residues Enhance Dihydrofolate Reductase Catalysis:  Mutational Effects on Hydride Transfer Rates journal October 2002
Effect of Mutation on Enzyme Motion in Dihydrofolate Reductase journal April 2003
The role of enzyme dynamics and tunnelling in catalysing hydride transfer: studies of distal mutants of dihydrofolate reductase journal July 2006
Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase journal April 2005
A Distal Mutation Perturbs Dynamic Amino Acid Networks in Dihydrofolate Reductase journal June 2013
Catalytic Contributions from Remote Regions of Enzyme Structure journal December 2011
Connecting Protein Conformational Dynamics with Catalytic Function As Illustrated in Dihydrofolate Reductase journal January 2013
Protein Mass-Modulated Effects in the Catalytic Mechanism of Dihydrofolate Reductase: Beyond Promoting Vibrations journal May 2014
Extension and Limits of the Network of Coupled Motions Correlated to Hydride Transfer in Dihydrofolate Reductase journal January 2014
Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer journal May 2014
Network of Remote and Local Protein Dynamics in Dihydrofolate Reductase Catalysis journal March 2015
Active Site and Remote Contributions to Catalysis in Methylthioadenosine Nucleosidases journal April 2015
Automated identification of functional dynamic contact networks from X-ray crystallography journal August 2013
Energetics and Dynamics of Enzymatic Reactions journal August 2001
Temporally Overlapped but Uncoupled Motions in Dihydrofolate Reductase Catalysis journal July 2013
Update 1 of: Tunneling and Dynamics in Enzymatic Hydride Transfer journal December 2010
Role of Dynamics in Enzyme Catalysis: Substantial versus Semantic Controversies journal December 2014
Protein Dynamics and Enzymatic Chemical Barrier Passage journal December 2011
Conformational changes and catalysis by alcohol dehydrogenase journal January 2010
Unmasking of hydrogen tunneling in the horse liver alcohol dehydrogenase reaction by site-directed mutagenesis journal June 1993
A link between protein structure and enzyme catalyzed hydrogen tunneling journal November 1997
Probes of Hydrogen Tunneling with Horse Liver Alcohol Dehydrogenase at Subzero Temperatures journal February 2001
Contributions of Valine-292 in the Nicotinamide Binding Site of Liver Alcohol Dehydrogenase and Dynamics to Catalysis , journal October 2001
Barrier passage and protein dynamics in enzymatically catalyzed reactions: Barrier passage and protein dynamics journal July 2002
Identification of a Protein-Promoting Vibration in the Reaction Catalyzed by Horse Liver Alcohol Dehydrogenase journal April 2002
Rate constants for a mechanism including intermediates in the interconversion of ternary complexes by horse liver alcohol dehydrogenase journal May 1990
Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 Å resolution journal March 1981
Crystallographic investigations of nicotinamide adenine dinucleotide binding to horse liver alcohol dehydrogenase journal December 1984
Hydride Transfer in Liver Alcohol Dehydrogenase:  Quantum Dynamics, Kinetic Isotope Effects, and Role of Enzyme Motion journal November 2001
Anticorrelated motions as a driving force in enzyme catalysis: The dehydrogenase reaction journal August 2004
Low-frequency normal modes in horse liver alcohol dehydrogenase and motions of residues involved in the enzymatic reaction journal March 2007
Protein Promoting Vibrations in Enzyme CatalysisA Conserved Evolutionary Motif journal May 2003
A Computational Method to Identify Residues Important in Creating a Protein Promoting Vibration in Enzymes journal January 2003
Yeast Alcohol Dehydrogenase Structure and Catalysis journal September 2014
Another Look at the Mechanisms of Hydride Transfer Enzymes with Quantum and Classical Transition Path Sampling journal March 2015
Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations journal March 2016
Changes in Protein Architecture and Subpicosecond Protein Dynamics Impact the Reaction Catalyzed by Lactate Dehydrogenase journal March 2013
Structurally Linked Dynamics in Lactate Dehydrogenases of Evolutionarily Distinct Species journal May 2017
Substitutions of isoleucine residues at the adenine binding site activate horse liver alcohol dehydrogenase journal April 1995
Amino Acid Residues in the Nicotinamide Binding Site Contribute to Catalysis by Horse Liver Alcohol Dehydrogenase , journal March 2003
Effects of Cavities at the Nicotinamide Binding Site of Liver Alcohol Dehydrogenase on Structure, Dynamics and Catalysis journal January 2014
A 21st century revisionist's view at a turning point in enzymology journal July 2009
Elusive transition state of alcohol dehydrogenase unveiled journal May 2010
Substitutions in a Flexible Loop of Horse Liver Alcohol Dehydrogenase Hinder the Conformational Change and Unmask Hydrogen Transfer , journal October 1999
A Remote Mutation Affects the Hydride Transfer by Disrupting Concerted Protein Motions in Thymidylate Synthase journal October 2012
Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR journal January 2014
Prediction of solvent accessibility and sites of deleterious mutations from protein sequence journal June 2005
Similar Hydrophobic Replacements of Leu99 and Phe153 within the Core of T4 Lysozyme Have Different Structural and Thermodynamic Consequences journal February 1993
Repacking the Core of T4 Lysozyme by Automated Design journal September 2003
Energetics of aliphatic deletions in protein cores journal August 2006
Lessons from the lysozyme of phage T4 journal January 2010
Hydrogen-Exchange Stabilities of RNase T1 and Variants with Buried and Solvent-Exposed Ala → Gly Mutations in the Helix journal December 1999
Protein conformational stabilities can be determined from hydrogen exchange rates
  • Scholtz, J. Martin; Pace, C. Nick; Huyghues-Despointes, Beatrice M. P.
  • Nature Structural Biology, Vol. 6, Issue 10, p. 910-912 https://doi.org/10.1038/13273
journal October 1999
Clusters of isoleucine, leucine, and valine side chains define cores of stability in high-energy states of globular proteins: Sequence determinants of structure and stability: BASiC Clusters-Stability Cores of Proteins journal December 2015
Dynamic Coupling and Allosteric Behavior in a Nonallosteric Protein journal June 2006
Progressive sequence alignment and molecular evolution of the Zn-containing alcohol dehydrogenase family journal June 1992
Effects of point mutations in a hinge region on the stability, folding, and enzymic activity of Escherichia coli dihydrofolate reductase journal August 1991
Computational and Theoretical Methods to Explore the Relation between Enzyme Dynamics and Catalysis journal August 2006
Atomic-Resolution Structures of Horse Liver Alcohol Dehydrogenase with NAD + and Fluoroalcohols Define Strained Michaelis Complexes journal May 2012
Expression and Kinetic Characterization of Recombinant Human Stomach Alcohol Dehydrogenase: ACTIVE-SITE AMINO ACID SEQUENCE EXPLAINS SUBSTRATE SPECIFICITY COMPARED WITH LIVER ISOZYMES journal February 1995
Origins of the high catalytic activity of human alcohol dehydrogenase 4 studied with horse liver A317C alcohol dehydrogenase journal May 2011
Product Inhibition Studies on Yeast and Liver Alcohol Dehydrogenases * journal September 1963
The kinetics of enzyme-catalyzed reactions with two or more substrates or products journal January 1963
Deprotonation of the Horse Liver Alcohol Dehydrogenase−NAD + Complex Controls Formation of the Ternary Complexes journal September 2005
Evidence for site equivalence in the reaction mechanism of horse liver alcohol dehydrogenase with aromatic substrates at alkaline pH journal June 1977
Site-site interactions in the liver alcohol dehydrogenase catalytic mechanism journal May 1979
Probes of a Role for Remote Binding Interactions on Hydrogen Tunneling in the Horse Liver Alcohol Dehydrogenase Reaction journal February 2000
Activation of Horse Liver Alcohol Dehydrogenase upon Substitution of Tryptophan 314 at the Dimer Interface journal October 1998
Refolding and Reactivation of Liver Alcohol Dehydrogenase after Dissociation and Denaturation in 6M Guanidine Hydrochloride journal July 1978
Effect of Zinc(II) on the Refolding and Reactivation of Liver Alcohol Dehydrogenase journal July 1978
Kinetics of native and activated isozymes of horse liver alcohol dehydrogenase journal January 1977
Effects of urea and guanidine hydrochloride on the activity and the dynamical structure of equine liver alcohol dehydrogenase journal May 1986
Loop and Subdomain Movements in the Mechanism of Escherichia coli Dihydrofolate Reductase:  Crystallographic Evidence , journal January 1997
Barriers to Hydride Transfer in Wild Type and Mutant Dihydrofolate Reductase from E. c oli journal December 2003
The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase journal July 2004
Effects of a Distal Mutation on Active Site Chemistry journal February 2006
Barrier crossing in dihydrofolate reductase does not involve a rate-promoting vibration journal May 2012
A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis journal April 2011
Evidence that a ‘dynamic knockout’ in Escherichia coli dihydrofolate reductase does not affect the chemical step of catalysis journal March 2012
Active Site Modifications in a Double Mutant of Liver Alcohol Dehydrogenase:  Structural Studies of Two Enzyme−Ligand Complexes , journal June 1998
The Linear Dependence of Log(kcat/Km) for Reduction of NAD+ by PhCH2OH on the Distance between Reactants when Catalyzed by Horse Liver Alcohol Dehydrogenase and 203 Single Point Mutants journal August 1999
An integrated model for enzyme catalysis emerges from studies of hydrogen tunneling journal March 2009
Effects of the Donor–Acceptor Distance and Dynamics on Hydride Tunneling in the Dihydrofolate Reductase Catalyzed Reaction journal January 2012
Free Energy Simulations of Active-Site Mutants of Dihydrofolate Reductase journal August 2014
A Theoretical Analysis of the Proton and Hydride Transfer in Liver Alcohol Dehydrogenase (LADH) journal March 2002
Fast Protein Motions Are Coupled to Enzyme H-Transfer Reactions journal February 2013
Macromolecular TLS Refinement in REFMAC at Moderate Resolutions book January 2003
Dynamic Structures of Horse Liver Alcohol Dehydrogenase (HLADH):  Results of Molecular Dynamics Simulations of HLADH-NAD + -PhCH 2 OH, HLADH-NAD + -PhCH 2 O - , and HLADH-NADH-PhCHO journal December 2001
Structures of Horse Liver Alcohol Dehydrogenase Complexed with NAD+ and Substituted Benzyl Alcohols journal May 1994
Inhibition of restriction endonuclease Nel I cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis journal January 1986
5′–3′ Exonucleases in phosphorothioate-based oligonucleotide-directed mutagenesis journal January 1988
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures journal January 1992
Improved methods for building protein models in electron density maps and the location of errors in these models journal March 1991
Studies on liver alcohol dehydrogenase complexes journal January 1964