Frontiers in Protein Structure, Function, and Dynamics

457 Pages·2020·9.322 MB·English

by  Dev Bukhsh Singh, Timir Tripathi

Dev Bukhsh Singh
Timir Tripathi  Editors
Frontiers
in Protein
Structure,
Function, and
Dynamics
Frontiers in Protein Structure, Function,
and Dynamics
(cid:129)
Dev Bukhsh Singh Timir Tripathi
Editors
Frontiers in Protein
Structure, Function,
and Dynamics
Editors
DevBukhshSingh TimirTripathi
InstituteofBiosciencesandBiotechnology DepartmentofBiochemistry
ChhatrapatiShahuJiMaharajUniversity NorthEasternHillUniversity
Kanpur,UttarPradesh,India Shillong,Meghalaya,India
ISBN978-981-15-5529-9 ISBN978-981-15-5530-5 (eBook)
https://doi.org/10.1007/978-981-15-5530-5
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Preface
Proteins are highly complex biomolecules. They are the most diverse group of
biologically important substances and are often considered to be the central com-
pound necessary for life. They play major roles in cellular metabolism, defense,
communication,transport,storage,andrecognition;alltheprocessesarerequiredfor
thestructure,function,andregulationofthebody’stissuesandorgans.Thecollec-
tionofproteinswithinacelldeterminesitshealthandfunction.Proteinsinteractwith
otherbiomoleculestoperformbiologicalfunctions.Accordingly,proteinsciencehas
been a center of basic research as well as applied to areas such as biotechnology,
medicine,andagriculture.
The structure of a protein is defined by its amino acid sequence. The central
dogmaofstructuralbiologystatesthatafoldedthree-dimensionalproteinstructureis
essential for its biological function. However, the view of protein structures has
recentlychangedfromnativestructuresbeingconsideredtobeasingle,rigid,static
entitiesintodynamicentitieswithinternalmotionswhereconformationalensembles
coexist.Thesemotionsandtheresultingconformationaldynamicsplayanessential
role in protein functions. Therefore, full understanding of the protein structure–
function relationship requires knowledge of protein dynamics in correlation with
biological systems. Proteins typically do not function alone, but in physical or
functional interaction with other proteins, forming macromolecular complexes.
Thedynamicnatureofproteinsisoftenaltereduponthebindingofligands,proteins,
ornucleicacids.Severalcovalentandnon-covalentinteractionsplayacriticalrolein
maintainingthestructuralintegrityoftheprotein.Hence,inordertounderstandthe
natureofprotein,itisimportanttounderstandandquantifyallpossibleinteractions
thatcontrolproteinstructureanddynamicsthatregulateitsfunctions.
In the last few decades, experimental techniques such as X-ray crystallography,
nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy
have made substantial progress. Going beyond the static picture of single protein
structures has been more challenging. Nowadays, a number of techniques such as
NMRrelaxation,fluorescencespectroscopy,andsinglemoleculemethodshavebeen
developedwhichprovideinformationontheconformationalflexibilityanddynam-
ics of proteins. However, computational simulation methods such as molecular
dynamics(MD)currentlyprovidetheroutinemeanstoobtaininformationonprotein
dynamicsatanatomiclevelontimescalesofnano-tomicroseconds.
v
vi Preface
This book provides a compendium of important topics on advanced research in
thefieldofproteinscience.Eachchapteraddressesspecificaspectsofproteinswitha
definitivethemedesignedtoenhancethereader’sunderstandingofproteinisolation
tostructure,function,anddynamics.Thelatestdevelopmentsinthefieldhavebeen
discussedandkeyconceptsintroducedinasimpleyetcomprehensivewaytoensure
that readers can grasp the essentials. This book will be an invaluable resource that
wouldbeveryusefultoundergraduates,graduatestudents,postdoctoralresearchers,
andinstructorsinvolvedinbiophysics,structuralbiology,orbioinformaticscourses
orresearchonproteinstructure–functionrelationships.
Chapter 1 provides an overview of protein extraction, purification, estimation,
storage, and dynamics, which is the first step in understanding protein structure,
function, and dynamics. Chapters 2 and 3 cover the major aspects of protein
purificationtechniques,proteincharacterizationmethods,proteinstructuredetermi-
nationapproaches,andtheimportanceofmolecularinteractionsinproteinstability.
Experimental protein structure determination methods including nuclear magnetic
resonance, X-ray crystallography, and cryo-electron microscopy are discussed.
Computational strategies to predict protein structure and conformation are also
considered.Chapters4and5discusstheuseofgroup-specificreagentsusedinthe
identification ofactive-site functional groups of enzymes.The kinetics of inactiva-
tion, effects of protectants, kinetic parameters, and spectral analysis are also
elaborated.
Understanding of protein–protein interactions and complex formation allows
analysisofmolecularfunctions.Protein–proteininteractionscanbestudiedthrough
variousphysical,molecular,andgeneticmethods.ThegoalofChap.6istopresent
various methods from wet and dry labs to rationalize tools for the investigation of
protein interactions of various nature and strength. Chapter 7 describes the impor-
tance of protein–ligand binding, the thermodynamic parameters describing the
binding and the methods to measure these parameters. Chapter 8 describes the
importance of water molecules maintaining protein structural stability, folding,
competition with the ligand, and other biomolecular processes. Chapter 9 provides
comprehensive information on various approaches and packages used in MD
simulations of biomolecules. Chapter 10 provides fundamental understanding of
the single-molecule fluorescence techniques and their applications in studying
proteinfolding and aggregate formation in disease conditions. Separate sections in
thischapterdiscusstheuseofthesetechniquesonthestudyofbothfoldedaswellas
intrinsicallydisorderedproteins.
Misfolding and aggregation of proteins and their accumulation as fibrils are
hallmarks of protein misfolding disorders and several neurodegenerative diseases.
Chapter 11 discusses how protein quality control fails during various protein
misfoldingdiseases.Themechanismofproteinmisfoldingandtherolesofmolecu-
larchaperonesduringfoldingarealsodiscussed.Chapter12discussesthestrategies
that exist in protein sequences to scuffle their uncontrolled aggregation. Using the
example of insulin aggregation in diabetes, the chapter considers how intracellular
protein deposits can be modulated for therapeutic purposes. Chapter 13 provides
information on the structure and function of different types of muscarinic
Preface vii
acetylcholine receptors and their target class of antimuscarinic drugs, mechanism,
epidemiology,sideeffects,antagonisticeffect,andclinicalsignificance.
Chapter 14 outlines the current state of understanding of dopamine beta-
hydroxylase, describing its therapeutic importance involving the heart and the
brain,withstructure-basedinhibitorsexpectedtocombathypertensionandcocaine
addiction specifically. Chapter 15 focuses on the structural and molecular basis of
forcegenerationthatleadstothedirectionalmotilityinmolecularmotors,takingan
example of kinesin. Recent findings on the bidirectional movement of kinesin-5
motors and several structural determinants that regulate directional switching are
also discussed. Chapter 16 emphasizes on the structure–activity relationship of
cathepsins cysteine proteases. It attempts to enhance understanding of cathepsins
andpresentsthemasdrugtargets tocontrolthedegradationofextracellularmatrix
and other components of the disease. Chapter 17 outlines the important structural
and functional roles of the iron-binding protein ferritins in the physiology of
Mycobacteriumtuberculosis.
Kanpur,UttarPradesh,India DevBukhshSingh
Shillong,Meghalaya,India TimirTripathi
Contents
1 ProteinPurification,Estimation,Storage,andEffect
onStructure–Function–Dynamics. . . . . . . . . . . . . . . . . . . . . . . . . . 1
AwanishKumar
2 ExperimentalandComputationalMethodstoDetermineProtein
StructureandStability. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
NachiappanMutharasappan,GuruRaviRao,RichardMariadasse,
SarithaPoopandi,AmalaMathimaran,PrabhuDhamodharan,
RajamanikandanSundarraj,ChitraJeyarajPandian,
andJeyakanthanJeyaraman
3 Wet-LabApproachestoDetermineThree-DimensionalStructures
ofProteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
RajanKumarPandey,RupalOjha,andVijayKumarPrajapati
4 UseofGroup-SpecificReagentsinActiveSiteFunctionalGroup
ElucidationI:Cys,Ser,Tyr,andTrpResidues. . . . . . . . . . . . . . . . 71
PravinKumarAmbasht
5 UseofGroup-SpecificReagentsinActiveSiteFunctionalGroup
ElucidationII:Asp,Glu,Arg,Lys,andHisResidues. . . . . . . . . . . 95
PravinKumarAmbasht
6 Protein-ProteinInteractionsModeling:FromDrytoWetLab. . . . 119
EktaKhareandDevBukhshSingh
7 ThermodynamicsofProtein-LigandBinding. . . . . . . . . . . . . . . . . . 145
KomalS.Khatri,PriyaModi,ShilpaSharma,andShashankDeep
8 SynergisticEffectsofHydrationSitesinProteinStability:
ATheoreticalWaterThermodynamicsApproach. . . . . . . . . . . . . . 187
JayashreeBiswal,PrajishaJayaprakash,RaghuRangaswamy,
andJeyaramanJeyakanthan
9 MolecularDynamicsSimulation:MethodsandApplication. . . . . . 213
SakshiSinghandVinayKumarSingh
iixx
x Contents
10 ProteinFolding,DynamicsandAggregationatSingle-Molecule
Resolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
RitobritaChakrabortyandKrishnanandaChattopadhyay
11 ProteinMisfoldingandNeurodegenerativeDiseases. . . . . . . . . . . . 259
AnandNarayanSingh,NiveditaSaxena,andManishKumarVerma
12 ManagementofInsulinThroughCo-SoluteEngineering:
ATherapeuticApproach. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
SaniaBashir,NehaSami,SayemaBashir,FaizanAhmad,
Md.ImtaiyazHassan,andAsimulIslam
13 StructuralandFunctionalAspectsofMuscarinicReceptors
inCorrelationwithAnticholinergicDrugs. . . . .. . . . . . .. . . . . . .. 317
PramodKumarSingh,RajendraNath,RamNaraian,
andManishKumarGupta
14 DopamineBetaHydroxylase:AnEnzymewithTherapeutic
PotentialtoCombatNeuralandCardiovascularDiseases. . . . . . . . 339
SwatiKundu,ManishaSaini,SanjayKumarDey,andSumanKundu
15 MolecularMotors:SubdomainDynamics
andMechanochemistry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
MeenakshiSinghandSudhirKumarSingh
16 StructuralandFunctionalDynamicsofLysosomalCysteine
ProteaseswithParticularReferencetoCathepsinB
andCathepsinH. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391
SudhirK.Agarwal,ShaliniSingh,andSamirSharma
17 AnInsightintotheImportanceofFerritinsinthePhysiology
ofMycobacteriumtuberculosis:UniqueStructuralandFunctional
Properties. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 425
GarimaKhare,PrachiNangpal,andAnilKumarTyagi
About the Editors
DevBukhshSingh isanAssistantProfessorattheDepartmentofBiotechnology,
Chhatrapati Shahu Ji Maharaj University, India. He received his Ph.D. in Biotech-
nologyfromGautamBuddhaUniversity,India,aftercompletinghisB.Sc.andM.Sc.
degreesattheUniversityofAllahabad,Prayagraj,andM.Tech.inBioinformaticsat
the Indian Institute of Information Technology, Prayagraj, India. He has been
actively involved in teaching and research since 2009, particularly in the areas of
molecularmodeling,chemoinformatics,inhibitor/drugdesign,andinsilicoevalua-
tion. He has authored many research and review articles and book chapters in the
fieldsofmedicinalresearch,molecularmodeling,drugdesign,andsystemsbiology.
He is a member of various national and international academic and research
organizations,andhasservedasarefereeforseveralinternationaljournalspublished
bySpringer,BenthamScience,andTaylor&Francis.
TimirTripathi isaSeniorAssistantProfessorattheDepartmentofBiochemistry,
North-Eastern Hill University, Shillong, India. He obtained his Ph.D. degree from
theCentralDrugResearchInstitute,Lucknowin2010.Hewasavisitingfacultyat
ICGEB,NewDelhi,India(2011),andKhonKaenUniversity,Thailand(2015).His
research interests are focused on understanding the structure-function-folding-
misfolding-aggregation-flexibility-dynamics relations in proteins. He has done
pioneeringworkontheprotein-substrateinteraction&dynamics,andunderstanding
the roles of non-catalytic domains in regulating the catalytic activity of key drug
target proteins. His work has provided a platform for the development of novel
therapeuticstrategies.HehasreceivedvariousawardsincludingtheDr.D.M.Bose
Award(2008),DSTFastTrackYoungScientistProjectAward(2012),DBTOver-
seasAssociateshipAward(2012),BRSI-MalviyaMemorialAward(2017),ICMR-
ShakuntalaAmirChandPrize(2018),andISCB-YoungScientistAward(2019).In
2019, he was elected as a member of the National Academy of Sciences, India
(NASI) and the Royal Society of Biology (RSB), London. He has published more
than 70 research papers, reviews, commentaries and viewpoint articles in highly
respected international journals. He has handled ten research grants as PI from
various national and international funding agencies including the DBT, DST,
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