Mechanistic Enzymology: Bridging Structure and Function (ACS Symposium Series) PDF
Preview Mechanistic Enzymology: Bridging Structure and Function (ACS Symposium Series)
1 3 5 7 ACS SYMPOSIUM SERIES ACS SYMPOSIUM SERIES BM B MECHANISTIC RE IO IDC L VOLUME 1357 H O G INAN GIC ENZYMOLOGY GI A S L ST TI BRIDGING STRUCTURE AND FUNCTION C R THEORETICAL, COMPUTATIONAL, AND U E CN EXPERIMENTAL PERSPECTIVES TZ UY RM E O Mechanistic enzymology is the basis of many applications, from drug AL NO design to cleaning products. This work offers a timely synopsis of advanced DG understanding of enzymatic regulation and function. Chapters are authored Y F by both those in traditional protein studies and those challenging paradigms, U N bridging disconnected fields, and presenting a unified view of enzyme C mechanisms. Biochemists, structural biologists, and other researchers T I O working with enzymes will find this work useful. Each chapter is written to N maximize accessibility to students and bridge developed theory with current scientific literature. This work serves as a valuable teaching tool to introduce foundational topics to students, bridging distantly connected fields toward the presentation of a unified view of enzyme mechanism. PUBLISHED BY THE American Chemical Society MILLER M I L L E R Mechanistic Enzymology: Bridging Structure and Function 1357 ACS SYMPOSIUM SERIES Mechanistic Enzymology: Bridging Structure and Function Justin M. Miller,Editor Middle Tennessee State University - Chemistry 1301 East Main Street Murfreesboro, Tennessee, United States American Chemical Society, Washington, DC Library of Congress Cataloging-in-Publication Data Names: Miller, Justin M., editor. Title: Mechanistic enzymology : bridging structure and function / Justin M. Miller, editor, Middle Tennessee State University -- Chemistry, 1301 East Main Street Murfreesboro, Tennessee, United States. Description: Washington, DC : American Chemical Society, [2020] | Series: Acs symposium series ; 1357 | Includes bibliographical references and index. Identifiers: LCCN 2020034013 (print) | LCCN 2020034014 (ebook) | ISBN 9780841298842 (hardcover) | ISBN 9780841298835 (ebook other) Subjects: LCSH: Enzymology. Classification: LCC QP601 .M438 2020 (print) | LCC QP601 (ebook) | DDC 612/.0151--dc23 LC record available at https://lccn.loc.gov/2020034013 LC ebook record available at https://lccn.loc.gov/2020034014 ThepaperusedinthispublicationmeetstheminimumrequirementsofAmericanNationalStandardforInformation Sciences—Permanence of Paper for Printed Library Materials, ANSI Z39.48n1984. Copyright © 2020 American Chemical Society AllRightsReserved.ReprographiccopyingbeyondthatpermittedbySections107or108oftheU.S.CopyrightAct isallowedforinternaluseonly,providedthataper-chapterfeeof$40.25plus$0.75perpageispaidtotheCopyright ClearanceCenter,Inc.,222RosewoodDrive,Danvers,MA01923,USA.Republicationorreproductionforsaleofpagesin thisbookispermittedonlyunderlicensefromACS.DirecttheseandotherpermissionrequeststoACSCopyrightOffice, Publications Division, 1155 16th Street, N.W., Washington, DC 20036. Thecitationoftradenamesand/ornamesofmanufacturersinthispublicationisnottobeconstruedasanendorsementor asapprovalbyACSofthecommercialproductsorservicesreferencedherein;norshouldthemerereferencehereintoany drawing,specification,chemicalprocess,orotherdataberegardedasalicenseorasaconveyanceofanyrightorpermission totheholder,reader,oranyotherpersonorcorporation,tomanufacture,reproduce,use,orsellanypatentedinventionor copyrightedworkthatmayinanywayberelatedthereto.Registerednames,trademarks,etc.,usedinthispublication,even without specific indication thereof, are not to be considered unprotected by law. PRINTED IN THE UNITED STATES OF AMERICA Foreword TheACSSymposiumSeriesisanestablishedprogramthatpublisheshigh-qualityvolumesof thematicmanuscripts.Forover40years,theACSSymposiumSerieshasbeendeliveringessential research from world leading scientists, including 36 Chemistry Nobel Laureates, to audiences spanning disciplines and applications. BooksaredevelopedfromsuccessfulsymposiasponsoredbytheACSorotherorganizations. Topics span the entirety of chemistry, including applications, basic research, and interdisciplinary reviews. Beforeagreeingtopublishabook,prospectiveeditorssubmitaproposal,includingatableof contents. The proposal is reviewed for originality, coverage, and interest to the audience. Some manuscripts may be excluded to better focus the book; others may be added to aid comprehensiveness. All chapters are peer reviewed prior to final acceptance or rejection. Asarule,onlyoriginalresearchpapersandoriginalreviewpapersareincludedinthevolumes. Verbatim reproductions of previous published papers are not accepted. ACS Books Contents 1. Introduction: Viewing Science through Multiple Lenses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Justin M. Miller 2. Enzyme Active Site Architecture: The Whole Is Greater Than the Sum of the Parts. . . . . . 9 Justin M. Miller and Chad Brambley 3. Integrative Structural Biology: Using X-ray Crystallography, Small-Angle X-ray Scattering, and Cryogenic Electron Microscopy to Determine Protein Structures. . . . . . . 31 Jamie R. Wallen 4. Evolving Role of Conformational Dynamics in Understanding Fundamental Biomolecular Behavior. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 David Ban 5. KatG Structure and Mechanism: Using Protein-Based Oxidation to Confront the Threats of Reactive Oxygen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 Jessica R. Krewall, Laura E. Minton, and Douglas C. Goodwin 6. Understanding Enzyme Catalysis Mechanism Using QM/MM Simulation Methods. . . 121 Tao Yu and Hong Guo 7. Tunneling through the Barriers: Resolving the Origins of the Activation of C-H Bonds Catalyzed by Enzymes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139 Chris Whittington, John Latham, and Adam R. Offenbacher 8. Enzymatic Biodegradation by Exploring the Rational Protein Engineering of the Polyethylene Terephthalate Hydrolyzing Enzyme PETase fromIdeonella sakaiensis 201-F6. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 Mitch H. Weiland Editor Biography. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175 Indexes Author Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179 Subject Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181 vii Chapter1 Introduction: Viewing Science through Multiple Lenses Justin M.Miller Middle Tennessee State University, Department of Chemistry, 1301 East Main Street, Murfreesboro, Tennessee 37132, United States of America *Email:[email protected] It affirms…that the same is true for the steps from electrons to atoms, from atoms to molecules, from molecules to crystals. It holds that the properties of atoms do indeed dependonthosewhichtheelectronshavewhentheyareintheatoms;thepropertiesof moleculesonthosewhichtheatomshavewhentheyareinthemolecules.Itholdstoothat thepropertiesoflivingthingsdependonthoseoftheirphysicalconstituentswhenthelatter areinlivingthings;theactivitiesofthinkingbeingsontheactionoftheirphysiological constituents when the latter are part of a thinking being; the activities of societies on thoseoftheirunitindividualswhentheseindividualsformpartoftheirsociety…Butit contendsthattheconstituentsofeachgradeacquirenewproperties,newmodesofaction, inbecomingpartofthe“emergent”thingof“higher”grade.Itholdsthatthephysics ofatoms,ofmolecules,isnotfullyknowntillthesearestudiedinthelivingaswell as in the non-living(1,2). -Herbert Spencer Jennings, The Biological Basis of Human Nature, 1930 Noteworthy scientific advancements represent revisions to existing paradigms built from repeatedfailureandignorance.Scientistsintentionallydevotethemselvestolivinginaworldofthe unknown.Theythriveoffofthepursuitofknowledge.Thislifestyleinvolvesmuchfailuresinceno experimentaldesigncanorshouldbeassumedaprioritoautomaticallyleadtosuccess.Sciencehas beendescribedasaprocessofstumblingaroundinadarkroomuntilalightswitchisaccidentally discovered,whichshedslightonthecurrenttopicofstudy.Oncethescientisthasmarveledatthis newly lit room long enough to gain an appreciation for its décor, he or she then promptly moves ontothenextdarkroom.Scientificadvancementisoftenpresentedinpopularcultureasinvolving so-called“eureka”momentsofsingleindividuals,buttherealityisthatmajorinnovationisnearly always the result of incremental modifications to existing models involving many individuals and the tools accessible during a given era. That is not to say that major leaps in knowledge cannot happen.However,itisnotalwaysguaranteedthatsuchideaswillremaininthepublicconsciousness afterthedeathoftheinnovator.ConsidertheexampleofCharlesBabbage’sAnalyticalEngine,the mechanical general-purpose computer first proposed in 1837. Though it was technically possible tobuildusingthetechnologyofthetime,Babbage’sdesignwasneverconstructedduetothehigh © 2020 American Chemical Society
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