Proteomics in Biology, Part B

513 Pages·2017·19.557 MB· 536 \513

by  Arun K. Shukla (Eds.)

METHODS IN ENZYMOLOGY
Editors-in-Chief
ANNA MARIE PYLE
Departments of Molecular, Cellular and Developmental
Biology and Department of Chemistry
Investigator, Howard Hughes Medical Institute
Yale University
DAVID W. CHRISTIANSON
Roy and Diana Vagelos Laboratories
Department of Chemistry
University of Pennsylvania
Philadelphia, PA
Founding Editors
SIDNEY P. COLOWICK and NATHAN O. KAPLAN
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CONTRIBUTORS
C.S.Ang
Bio21MolecularScienceandBiotechnologyInstitute,UniversityofMelbourne,Parkville,
VIC,Australia
J.Armengaud
CEA,DRF,IBiTec-S,SPI,Li2D,Laboratory“InnovativeTechnologiesforDetection and
Diagnostics”,Bagnols-sur-Ce`ze,France
J.V.Arrington
PurdueUniversity;PurdueUniversityInstituteforIntegrativeNeuroscience,Purdue
University,WestLafayette,IN,UnitedStates
K.Baerenfaller
ETHZurich,Zurich,Switzerland
M.S.Baker
FacultyofMedicineandHealthSciences,MacquarieUniversity,NorthRyde,NSW,
Australia
T.Bonaldi
EuropeanInstituteofOncology,Milano,Italy
S.Brooks
UniversityofAlabama,Tuscaloosa,AL,UnitedStates
M.Bui
ChromatinStructureandEpigeneticMechanismsUnit,LaboratoryofReceptorBiology and
GeneExpression,CCR,NCI,NIH,Bethesda,MD,UnitedStates
J.H.Caufield
CenterfortheStudyofBiologicalComplexity,VirginiaCommonwealthUniversity,
Richmond,VA,UnitedStates
E.S.-W.Chen
InstituteofBiologicalChemistry,AcademiaSinica,Taipei,Taiwan
E.Chevet
InsermERL440Oncogenesis,Stress,Signaling,Universit(cid:1)edeRennes1;CentredeLutte
ContreleCancerEuge`neMarquis,Rennes,France
Y.Dalal
ChromatinStructureandEpigeneticMechanismsUnit,LaboratoryofReceptorBiology and
GeneExpression,CCR,NCI,NIH,Bethesda,MD,UnitedStates
C.Duport
SQPOV,UMR0408,AvignonUniversit(cid:1)e,INRA,Avignon,France
A.Economou
KULeuven,RegaInstituteforMedicalResearch,LaboratoryofMolecularBacteriology,
Leuven,Belgium;IMBB-FoRTH,Iraklio,Greece
xiii
xiv Contributors
B.A.Garcia
EpigeneticsProgram,PerelmanSchoolofMedicine,UniversityofPennsylvania,
Philadelphia,PA,UnitedStates
N.J.Garg
UniversityofTexasMedicalBranch;InstituteforTranslationalSciences;Institute for
HumanInfectionsandImmunity,UniversityofTexasMedicalBranch,Galveston,TX,
UnitedStates
N.Gupta
FromtheChromatinBiologyLaboratory,MolecularBiologyandGeneticsUnit,Jawaharlal
NehruCentreforAdvancedScientificResearch,Bangalore,India
A.Hashiguchi
FacultyofMedicine,UniversityofTsukuba,Tsukuba,Japan
J.Heierhorst
St.Vincent’sInstituteofMedicalResearch,TheUniversityofMelbourne,Fitzroy,VIC,
Australia
N.C.Hoch
St.Vincent’sInstituteofMedicalResearch,TheUniversityofMelbourne,Fitzroy,VIC,
Australia
C.-C.Hsu
PurdueUniversity,WestLafayette,IN,UnitedStates
Z.-C.Hua
TheStateKeyLaboratoryofPharmaceuticalBiotechnology,CollegeofLifeSciences,
NanjingUniversity,Nanjing,China
K.A.Janssen
EpigeneticsProgram,PerelmanSchoolofMedicine,UniversityofPennsylvania,
Philadelphia,PA,UnitedStates
R.Jones
MSBioworks,LLC,Annarbor,MI,UnitedStates
T.J.D.Jørgensen
UniversityofSouthernDenmark,OdenseM,Denmark
S.Komatsu
NationalInstituteofCropScience,NARO,Tsukuba,Japan
G.Lauc
GenosGlycoscienceResearchLaboratory;FacultyofPharmacyandBiochemistry,
UniversityofZagreb,Zagreb,Croatia
Y.-M.Lee
FacultyofScience,NationalUniversityofSingapore,Singapore
Q.Lin
FacultyofScience,NationalUniversityofSingapore,Singapore
Contributors xv
Y.Li
ProteomicsFacility,UniversityofIowa,IowaCity,IA,UnitedStates
J.Liu
KeyLaboratoryofMedicalMolecularVirology(MOE/MOH)andInstitutesofBiomedical
Sciences,ShanghaiMedicalCollege,FudanUniversity,Shanghai,PRChina
Y.Liu
UniversityofMichigan,AnnArbor,MI,UnitedStates
J.Mehla
CenterfortheStudyofBiologicalComplexity,VirginiaCommonwealthUniversity,
Richmond,VA,UnitedStates
A.A.Mehus
UniversityofNorthDakotaSchoolofMedicineandHealthSciences,UniversityofNorth
Dakota,GrandForks,ND,UnitedStates
L.N.Mishra
FromtheChromatinBiologyLaboratory,MolecularBiologyandGeneticsUnit,Jawaharlal
NehruCentreforAdvancedScientificResearch,Bangalore,India
M.Miyagi
CenterforProteomicsandBioinformatics,CaseWesternReserveUniversity,Cleveland,
OH,UnitedStates
W.W.Muhonen
UniversityofNorthDakotaSchoolofMedicineandHealthSciences,UniversityofNorth
Dakota,GrandForks,ND,UnitedStates
L.Negroni
InstitutdeG(cid:1)en(cid:1)etiqueetdeBiologieMol(cid:1)eculaireetCellulaire(IGBMC),INSERMU964,
CNRSUMR7104,StrasbourgUniversity,Illkirch,France
E.C.Nice
MonashUniversity,Clayton,VIC,Australia
A.Nita-Lazar
CellularNetworksProteomicsUnit,LaboratoryofSystemsBiology,NIAID,NIH,
Bethesda,MD,UnitedStates
R.Noberini
CenterforGenomicScience,IstitutoItalianodiTecnologia,Milano,Italy
A.G.Nuccio
CellularNetworksProteomicsUnit,LaboratoryofSystemsBiology,NIAID,NIH,
Bethesda,MD,UnitedStates
M.Papanastasiou
IMBB-FoRTH,Iraklio,Greece
S.Pentakota
FromtheChromatinBiologyLaboratory,MolecularBiologyandGeneticsUnit,Jawaharlal
NehruCentreforAdvancedScientificResearch,Bangalore,India
xvi Contributors
M.Pope
ProteomicsFacility,UniversityofIowa,IowaCity,IA,UnitedStates
M.R.S.Rao
FromtheChromatinBiologyLaboratory,MolecularBiologyandGeneticsUnit,Jawaharlal
NehruCentreforAdvancedScientificResearch,Bangalore,India
N.Sakhawalkar
CenterfortheStudyofBiologicalComplexity,VirginiaCommonwealthUniversity,
Richmond,VA,UnitedStates
J.B.Shabb
UniversityofNorthDakotaSchoolofMedicineandHealthSciences,UniversityofNorth
Dakota,GrandForks,ND,UnitedStates
H.-M.Shen
YongLooLinSchoolofMedicine;NUSGraduateSchoolforIntegrativeSciencesand
Engineering,NationalUniversityofSingapore,Singapore
S.Sidoli
EpigeneticsProgram,PerelmanSchoolofMedicine,UniversityofPennsylvania,
Philadelphia,PA,UnitedStates
S.J.Stafford
SealyCenterofMolecularMedicine,UniversityofTexasMedicalBranch,Galveston, TX,
UnitedStates
M.Subramanian
UniversityofIowa,IowaCity,IA,UnitedStates
R.Summers
UniversityofAlabama,Tuscaloosa,AL,UnitedStates
J.Svozil
ETHZurich,Zurich,Switzerland
W.A.Tao
PurdueUniversity;PurdueUniversityInstituteforIntegrativeNeuroscience;Purdue
UniversityCenterforCancerResearch,PurdueUniversity,WestLafayette,IN,
UnitedStates
Y.Temel
MUMC+;MHeNs,ExperimentalNeurosurgery,MaastrichtUniversity,Maastricht,
TheNetherlands
I.Trbojevi(cid:1)c-Akmacˇi(cid:1)c
GenosGlycoscienceResearchLaboratory,Zagreb,Croatia
M.B.Trelle
UniversityofSouthernDenmark,OdenseM,Denmark
M.-D.Tsai
InstituteofBiologicalChemistry,AcademiaSinica,Taipei,Taiwan
Contributors xvii
A.Tsirigotaki
KULeuven,RegaInstituteforMedicalResearch,LaboratoryofMolecularBacteriology,
Leuven,Belgium
K.C.Tsolis
KULeuven,RegaInstituteforMedicalResearch,LaboratoryofMolecularBacteriology,
Leuven,Belgium
P.Uetz
CenterfortheStudyofBiologicalComplexity,VirginiaCommonwealthUniversity,
Richmond,VA,UnitedStates
I.Ugrina
GenosGlycoscienceResearchLaboratory;FacultyofPharmacyandBiochemistry,
UniversityofZagreb,Zagreb,Croatia
J.Wang
TheStateKeyLaboratoryofPharmaceuticalBiotechnology,CollegeofLifeSciences,
NanjingUniversity,Nanjing,China;YongLooLinSchoolofMedicine;FacultyofScience,
NationalUniversityofSingapore;InterdisciplinaryResearchGroupinInfectiousDiseases,
Singapore-MITAllianceforResearch&Technology(SMART),Singapore
J.E.Wiktorowicz
SealyCenterofMolecularMedicine;InstituteforTranslationalSciences;Institutefor
HumanInfectionsandImmunity,UniversityofTexasMedicalBranch,Galveston,TX,
UnitedStates
Y.K.Wong
YongLooLinSchoolofMedicine;FacultyofScience,NationalUniversityofSingapore,
Singapore
Y.Xie
KeyLaboratoryofMedicalMolecularVirology(MOE/MOH)andInstitutesofBiomedical
Sciences,ShanghaiMedicalCollege,FudanUniversity,Shanghai,PRChina
Y.Yakkioui
MUMC+;MHeNs,ExperimentalNeurosurgery,MaastrichtUniversity,Maastricht,
TheNetherlands
C.L.Yu
ProteomicsFacility,UniversityofIowa,IowaCity,IA,UnitedStates
C.Zhang
BaylorCollegeofMedicine,Houston,TX,UnitedStates
J.Zhang
YongLooLinSchoolofMedicine,NationalUniversityofSingapore,Singapore;Clinical
ResearchInstitute,ZhejiangProvincialPeople’sHospital,Hangzhou,China
X.Zhao
KeyLaboratoryofMedicalMolecularVirology(MOE/MOH)andInstitutesofBiomedical
Sciences,ShanghaiMedicalCollege,FudanUniversity;MicrobiologyLaboratory,Shanghai
MunicipalCenterforDiseaseControlandPrevention,Shanghai,PRChina
PREFACE
Biological and cellular processes are incredibly complex and result from a
largenumberofexceptionallywellfine-tunedandinterconnectedindivid-
ualevents.Althoughinvestigationoftheseeventsatindividualisticleveland
in isolated context typically provides important functional insights, their
studyatsystemslevelandinglobalcontextisabsolutelyessentialtodecipher
theinnerworkingsofcellularandbiologicalphenomena.Thishasbeenone
ofthekeychallengesinthemoderneraofbiology;however,recentsurgeof
proteomicsstrategiesandapproacheshavemadeitpossible.Acombination
of well-established and continuously evolving proteomics methodologies
hasstartednotonlytorevealthemolecularbasisofawholerangeofbiolog-
icalphenomenaandregulation,butithasalsoemergedasamajorengineto
open new translational and therapeutic opportunities. The field of proteo-
mics has evolved exceptionally rapidly in the last decade or so, and it is a
monumental task and near impractical to cover every aspect in a couple
of book volumes. Therefore, we have made the selection of chapters to
cover a range of conventional approaches and well-established platforms,
afewrecentbreakthroughswithrespecttodiscoveryofnovelexperimental
framework,andfinally,afewchaptershighlightingtheuntappedpotentialof
proteomics approaches with a futuristic outlook.
Manyoftheproteomicsprotocolshavebeenstandardizedacrossdiffer-
ent laboratories and published in many primary research articles, and
therefore,theyaremostlyaccessibletoanyinterestedresearcherinthefield.
WehaveincludedafewchaptersinthesetwovolumesofMethodsinEnzy-
mology that briefly describe routine sample preparation strategies and then
focus more on recent modifications that have been tested and validated
experimentally. One of the key areas that has immensely benefited from
the recent applications of proteomics is the identification, quantitation,
and analysis of post-translational modifications such as glycosylation, phos-
phorylation,andacetylation.Here,wehavecollectedanumberofchapters
describingtheapplicationofproteomicsapproachesinstudyingawiderange
ofpost-translationalmodifications,eitherintheformofgenericprotocolsor
withaparticularbiologicaltargetasacaseexample.Proteomics-basedstudies
typicallygeneratelargebodyofdatawhichononehandrepresentgoldmine
forextractingnovelfunctionalinsightsbutontheotherposeamajorchallenge
in terms of unbiased, careful, and rigorous analysis. These large proteomics
xix
xx Preface
datasetsofferuniquepossibilitiesasahypothesisgenerationplatformtodesign
subsequentexperimentalstrategiestogainnovelfunctionalinsightsintobio-
logical processes. Considering that data handling and analysis represents an
absolutely critical component in proteomics pipeline, we have included a
number of chapters in these two volumes that specifically focus on recent
trends in proteomics data analysis and interpretation.
Oneofthepowersofproteomicsapproacheshasbeenthepossibilityof
studyingthebiologicalprocessesatorganellarandorganismlevels.Thishas
openedupthepossibilitiesofobtainingaglobalandholisticviewofbiolog-
ical processes in physiologically relevant context instead of in isolation.
Anumberofchaptersinthesetwovolumescoverthisaspect,forexample,
analysisofbodyfluiddegradomics,globalassessmentofproteinsynthesisin
C. elegans, comprehensive analysis of E. coli membrane proteins, and a few
others. These chapters underline the robust platform that proteomics can
provide for generating important systems-wide clues in biology. Another
importantapplicationofproteomics,inadditiontobeingadiscoveryengine
for basicbiology,isthatitcanopenupnewpossibilitiesindiseaseetiology
and therapeutics, for example, by identifying novel biomarkers or by
presenting a comparative proteome-wide view of pathological vs normal
tissues. We have incorporated a number of chapters that specifically high-
light the power of proteomics-based approaches in disease models such as
identificationofnovelbiomarkers,quantitativeproteomeprofilingoftumor
tissues, and identifying key aspects of host–pathogen interactions. These
chapters categorically underscore the emerging utility of proteomics
approaches in translational biology and highlight a frontier where a major
focus of the field is headed currently.
Itakethisopportunitytosincerelythankalltheauthorsfortheirexcel-
lent contributions which have made these two volumes possible. I also
express my gratitude to the editorial and production team of Methods in
Enzymologyforbeautifullycoordinatingthisproject.Onbehalfoftheentire
MethodsinEnzymologyteam,Ipresenttwovolumesentitled“Proteomicsin
Biology:PartA”and“ProteomicsinBiology:PartB.”Isincerelyhopethat
youfindthecontentofthesetwovolumesextremelyusefulandIwelcome
your feedback and comments.
With best compliments
ARUN K. SHUKLA
Indian Institute of Technology, Kanpur, India
CHAPTER ONE
Protein Cysteinyl-S-Nitrosylation:
Analysis and Quantification
J.E. Wiktorowicz*,{,§, S.J. Stafford*, N.J. Garg†,{,§,1
*SealyCenterofMolecularMedicine,UniversityofTexasMedicalBranch,Galveston,TX,UnitedStates
†UniversityofTexasMedicalBranch,Galveston,TX,UnitedStates
{InstituteforTranslationalSciences,UniversityofTexasMedicalBranch,Galveston,TX,UnitedStates
§InstituteforHumanInfectionsandImmunity,UniversityofTexasMedicalBranch,Galveston,TX,
UnitedStates
1Correspondingauthor:e-mailaddress:[email protected]
Contents
1. Introduction 1
2. SNOFloMethodology 3
3. Applications 10
References 13
Abstract
Thethiolmoietyofcysteineresiduescanundergoanumberofbiologicmodifications
including oxidation, sulfenylation, nitrosylation, persulfidation, metalation, and other
modifications. These modifications can control biological function, including gain as
well as loss of function. Herein, we focus attention on the proteomic analysis of
S-nitrosylationinhealthanddisease.Wedescribeanovelquantitativeapproachthat
combinesaccurate,sensitivefluorescencemodificationofcysteinyl-S-nitrosylationthat
leaveselectrophoreticmobilityunaffected(SNOFlo),andintroduceuniqueconceptsfor
measuringchangesinS-nitrosylationstatusrelativetoproteinabundance.Wepresent
several studies where suitability of this approach for investigating endogenous
S-nitrosylationisaddressed.
1. INTRODUCTION
It is currently estimated that the human genome consists of some
20,700+ genes (GENCODE 19). In contrast, with posttranscriptional
processing (e.g., alternative splicing, RNA editing) and posttranslational
modifications, there are likely to be over 1M “proteoforms” (defined in
Smith, Kelleher, Consortium for Top Down Proteomics, 2013) in the
human cell. These molecular events occur ubiquitously (pun intended)
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