Table Of ContentMETHODS IN ENZYMOLOGY
Editors-in-Chief
JOHN N. ABELSON and MELVIN I. SIMON
Division of Biology
California Institute of Technology
Pasadena, California
ANNA MARIE PYLE
Departments of Molecular, Cellular and Developmental
Biology and Department of Chemistry Investigator
Howard Hughes Medical Institute
Yale University
Founding Editors
SIDNEY P. COLOWICK and NATHAN O. KAPLAN
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CONTRIBUTORS
R.W.Adamiak
DepartmentofStructuralChemistryandBiologyofNucleicAcids,InstituteofBioorganic
ChemistryPolishAcademyofSciences,andEuropeanCenterforBioinformaticsand
Genomics,InstituteofComputingScience,PoznanUniversityofTechnology,Poznan,
Poland
KirillA.Afonin
BasicResearchLaboratory,CenterforCancerResearch,NationalCancerInstitute,
Frederick,Maryland,USA
M.Antczak
EuropeanCenterforBioinformaticsandGenomics,InstituteofComputingScience,Poznan
UniversityofTechnology,Poznan,Poland
StefanBadelt
InstituteforTheoreticalChemistry,UniversityofVienna,Vienna,Austria
EckartBindewald
BasicScienceProgram,LeidosBiomedicalResearchInc.,NationalCancerInstitute,
NationalInstitutesofHealth,Frederick,Maryland,USA
J.Blazewicz
DepartmentofStructuralChemistryandBiologyofNucleicAcids,InstituteofBioorganic
ChemistryPolishAcademyofSciences,andEuropeanCenterforBioinformaticsand
Genomics,InstituteofComputingScience,PoznanUniversityofTechnology,Poznan,
Poland
JanuszM.Bujnicki
InternationalInstituteofMolecularandCellBiology,Warsaw,andFacultyofBiology,
InstituteofMolecularBiologyandBiotechnology,AdamMickiewiczUniversity,Poznan,
Poland
GiovanniBussi
ScuolaInternazionaleSuperiorediStudiAvanzati(SISSA),Trieste,Italy
HaoyuanChen
CenterforIntegrativeProteomicsResearch,BioMaPSInstituteandDepartmentof
ChemistryandChemicalBiology,RutgersUniversity,Piscataway,NewJersey,USA
ClarenceYuCheng
DepartmentofBiochemistry,StanfordUniversity,Stanford,California,USA
Fang-ChiehChou
DepartmentofBiochemistry,StanfordUniversity,Stanford,California,USA
P.Clote
BiologyDepartment,BostonCollege,Boston,Massachusetts,USA
xi
xii Contributors
FrancescoColizzi
ScuolaInternazionaleSuperiorediStudiAvanzati(SISSA),Trieste,Italy
RhijuDas
DepartmentofBiochemistry,andDepartmentofPhysics,StanfordUniversity,Stanford,
California,USA
FrancescoDiPalma
ScuolaInternazionaleSuperiorediStudiAvanzati(SISSA),Trieste,Italy
ThakshilaDissanayake
CenterforIntegrativeProteomicsResearch,BioMaPSInstituteandDepartment
ofChemistryandChemicalBiology,RutgersUniversity,Piscataway,NewJersey,USA
NikolayV.Dokholyan
DepartmentofBiochemistryandBiophysics,SchoolofMedicine,UniversityofNorth
Carolina,ChapelHill,NorthCarolina,USA
ChristophFlamm
InstituteforTheoreticalChemistry,UniversityofVienna,Vienna,Austria
GeorgeM.Giambas¸u
CenterforIntegrativeProteomicsResearch,BioMaPSInstituteandDepartmentof
ChemistryandChemicalBiology,RutgersUniversity,Piscataway,NewJersey,USA
HolgerGohlke
Mathematisch-NaturwissenschaftlicheFakulta¨t,Institutfu€rPharmazeutischeund
MedizinischeChemie,Heinrich-Heine-Universita¨tDu€sseldorf,Du€sseldorf,Germany
StefanHammer
InstituteforTheoreticalChemistry,andResearchGroupBioinformaticsandComputational
Biology,UniversityofVienna,Vienna,Austria
ChristianA.Hanke
Mathematisch-NaturwissenschaftlicheFakulta¨t,Institutfu€rPharmazeutischeund
MedizinischeChemie,Heinrich-Heine-Universita¨tDu€sseldorf,Du€sseldorf,Germany
ScottP.Hennelly
NewMexicoConsortium,andTheoreticalBiologyandBiophysics,TheoreticalDivision,
LosAlamosNationalLaboratory,LosAlamos,NewMexico,USA
IvoL.Hofacker
InstituteforTheoreticalChemistry,andResearchGroupBioinformaticsandComputational
Biology,UniversityofVienna,Vienna,Austria
ChangbongHyeon
SchoolofComputationalSciences,KoreaInstituteforAdvancedStudy,SeoulRepublicof
Korea
NamheeKim
DepartmentofChemistryandCourantInstituteofMathematicalSciences,NewYork
University,NewYork,USA
MariaKireeva
GeneRegulationandChromosomeBiologyLaboratory,CenterforCancerResearch,NCI,
NationalCancerInstitute,Frederick,Maryland,USA
Contributors xiii
SerdalKirmizialtin
NewMexicoConsortium,andTheoreticalBiologyandBiophysics,TheoreticalDivision,
LosAlamosNationalLaboratory,LosAlamos,NewMexico,USA
AndreyKrokhotin
DepartmentofBiochemistryandBiophysics,SchoolofMedicine,UniversityofNorth
Carolina,ChapelHill,NorthCarolina,USA
ErichR.Kuechler
CenterforIntegrativeProteomicsResearch,BioMaPSInstituteandDepartmentof
ChemistryandChemicalBiology,RutgersUniversity,Piscataway,NewJersey,USA
GrzegorzŁach
InternationalInstituteofMolecularandCellBiology,Warsaw,Poland
Tai-SungLee
CenterforIntegrativeProteomicsResearch,BioMaPSInstituteandDepartmentof
ChemistryandChemicalBiology,RutgersUniversity,Piscataway,NewJersey,USA
Jong-ChinLin
InstituteforPhysicalScienceandTechnology,andDepartmentofChemistryand
Biochemistry,UniversityofMaryland,CollegePark,MD,USA
P.Lukasiak
DepartmentofStructuralChemistryandBiologyofNucleicAcids,InstituteofBioorganic
ChemistryPolishAcademyofSciences,andEuropeanCenterforBioinformaticsand
Genomics,InstituteofComputingScience,PoznanUniversityofTechnology,Poznan,
Poland
DavidH.Mathews
DepartmentofBiochemistry&Biophysics,andCenterforRNABiology,Universityof
RochesterMedicalCenter,Box712,Rochester,NewYork,USA
JoseN.Onuchic
CenterforTheoreticalBiologicalPhysics;DepartmentofPhysicsandAstronomy;
DepartmentofChemistry;DepartmentofBiosciences,andDepartmentofBiochemistryand
CellBiology,RiceUniversity,Houston,Texas,USA
MariaT.Panteva
CenterforIntegrativeProteomicsResearch,BioMaPSInstituteandDepartmentof
ChemistryandChemicalBiology,RutgersUniversity,Piscataway,NewJersey,USA
AnnaPhilips
EuropeanCenterforBioinformaticsandGenomics,InstituteofBioorganicChemistry,
PolishAcademyofScience,Poznan,Poland
M.Popenda
DepartmentofStructuralChemistryandBiologyofNucleicAcids,InstituteofBioorganic
ChemistryPolishAcademyofSciences,Poznan,Poland
K.J.Purzycka
DepartmentofStructuralChemistryandBiologyofNucleicAcids,InstituteofBioorganic
ChemistryPolishAcademyofSciences,Poznan,Poland
xiv Contributors
BrianK.Radak
CenterforIntegrativeProteomicsResearch,BioMaPSInstituteandDepartmentof
ChemistryandChemicalBiology,RutgersUniversity,Piscataway,NewJersey,USA
KarissaY.Sanbonmatsu
NewMexicoConsortium,andTheoreticalBiologyandBiophysics,TheoreticalDivision,
LosAlamosNationalLaboratory,LosAlamos,NewMexico,USA
TamarSchlick
DepartmentofChemistryandCourantInstituteofMathematicalSciences,NewYork
University,NewYork,USA
AlexanderSchug
SteinbuchCentreforComputing,KarlsruheInstituteofTechnology,Karlsruhe,Germany
BruceA.Shapiro
BasicResearchLaboratory,CenterforCancerResearch,NationalCancerInstitute,
Frederick,Maryland,USA
MichaelF.Sloma
DepartmentofBiochemistry&Biophysics,andCenterforRNABiology,Universityof
RochesterMedicalCenter,Box712,Rochester,NewYork,USA
M.Szachniuk
DepartmentofStructuralChemistryandBiologyofNucleicAcids,InstituteofBioorganic
ChemistryPolishAcademyofSciences,andEuropeanCenterforBioinformaticsand
Genomics,InstituteofComputingScience,PoznanUniversityofTechnology,Poznan,
Poland
D.Thirumalai
InstituteforPhysicalScienceandTechnology,andDepartmentofChemistryand
Biochemistry,UniversityofMaryland,CollegePark,MD,USA
JeseongYoon
SchoolofComputationalSciences,KoreaInstituteforAdvancedStudy,SeoulRepublicof
Korea
DarrinM.York
CenterforIntegrativeProteomicsResearch,BioMaPSInstituteandDepartmentof
ChemistryandChemicalBiology,RutgersUniversity,Piscataway,NewJersey,USA
MaiZahran
DepartmentofChemistryandCourantInstituteofMathematicalSciences,NewYork
University,NewYork,USA
PREFACE
ItisclearfromtheEncyclopediaofDNAElements(ENCODE)projectthat
a significant portion in the transcriptome does not translate into protein
sequences. Many of these sequences function through the formation of
specificRNAstructures.Riboswitchesrepresentanimportantclassofnon-
coding RNAs. Riboswitches perform functions as genetic “switches” that
regulate whenandwheregenesareexpressed.Tounderstandthestructure
andfunctionofriboswitchesrequirescomputationalmodelsthatcanpredict
stable and metastable structures, their folding stabilities, kinetic pathways,
transitionstates,andrateconstantsfortheconformationalswitches,inaddi-
tiontotheeffectsofmetalionsandligandbindingonRNAfolding,allfrom
the nucleotide sequence.
Thisbookrepresentsastate-of-the-artcollectionofadvancedcomputa-
tional methods for modeling RNA riboswitch structure, thermal stability,
dynamics, and kinetics. Given the fact that riboswitches have been exten-
sively studied experimentally, yet currently the accuracy of computational
predictionforriboswitchremainsgenerallyinconsistent,thisvolumeispar-
ticularlytimely.Webelievethatthisvolumewillexcitefuturemoreradical
advances in computational modeling for riboswitches and other
noncoding RNAs.
OneofthemajorscientificchallengesforRNAmodelingrelatestohow
we use the knowledge derived from limited information about known
RNAstructures.Effectivestructurepredictionmethodsofteninvolveinte-
gration of knowledge-based algorithm and physics-based or experimental
data-based models. Several chapters present methods along this line:
Purzycka et al. and Cheng et al. developed motif library-based and
fragment-based methods, respectively; Sloma and Mathews developed
methods that incorporate high-throughput structure probing data into
secondary structure prediction; Kirmizialtin et al. employed selective
0
2-hydroxyl acylation by primer extension (SHAPE) data and developed a
new force field for molecular dynamics simulation; and Krokhotin and
Dokholyan incorporated SHAPE into discrete molecular dynamics to
predict RNA structure.
Another major challenge for the computational modeling of
riboswitchescomesfromconformationalsamplingduetothelargeconfor-
mational space of the molecule and the flexibility of RNA structure.
xv
xvi Preface
Toenhancethequalityofconformationalsampling,KrokhotinandDokh-
olyan developed a three-bead coarse-grained structure model in molecular
dynamicssimulationandKimetal.developedagraph-theoreticapproachto
efficientsamplingofRNAmotifstructures.Thesemethodsofferveryinter-
esting new tools for modeling RNA folding.
Kinetics are intrinsic to RNA folding and conformational switching.
Riboswitches can fold cotranscriptionally into the conformations that cor-
respond to ON and OFF states. The kinetics of RNA folding and confor-
mational switching are critical for understanding riboswitch structure and
function. This volume contains several chapters that address the methods
to model riboswitch kinetics. Badelt et al. developed a cotranscriptional
kinetics model by integrating RNA secondary structure with the dynamic
energy landscape. Lin et al. developed a three-dimensional coarse-grained
self-organized polymer model to predict riboswitch dynamics under force.
Using a steered molecular dynamics-based method, Di Palma et al. devel-
oped an all-atom model to predict ligand-induced riboswitch stability and
structure changes at atomic resolution. Hanke and Gohlke presented a
critical analysis for the performances of the different force fields, including
the Mg2+ ion effects, in riboswitch simulations. In addition to the physical
models, informatics-based approaches have been highly successful in
predicting riboswitch structures and finding riboswitch genes. Clote pres-
ented a comprehensive introduction for the different computational
methods with particular emphasis on informatics-based approaches for
riboswitch structure and kinetics.
Conformational changes in riboswitches can be induced by ligands or
ions. It is thus important to have a reliable tool to predict the binding sites
andbindingmodes.Thisvolumecontainstwochaptersonthisissue.Using
knowledge-basedscoringfunctions,Philipsetal.developednovelmethods
(“LigandRNA” and “MetalionRNA”) for the prediction of riboswitch
binding.Pantevaetal.presentedamultiscalemethodformodelingconfor-
mational switching, metal ion binding, and enzymatic reactions. In these
chapters, the related computational methods are discussed, as well as their
limitations and pitfalls.
RNAconformational switchingcanalsobeinducedby thepresenceof
other RNA or DNA molecules. Afonin et al. presented a thermodynamic
model for predicting association and dissociation of RNA/DNA hybrids
containing a novel split functionality. The results demonstrate the great
promise of using RNA structure and conformational switches in RNA
nanotechnology.
Preface xvii
Finally,wewouldliketothankthefabulousteamofauthors,whohave
put together high-quality chapters. Without the phenomenal works of the
authors, it is simply impossible to publish such a quality volume.
SHI-JIE CHEN
DONALD H. BURKE-AGU¨ERO
CHAPTER ONE
Automated 3D RNA Structure
Prediction Using the
RNAComposer Method
1
for Riboswitches
K.J.Purzycka*,M.Popenda*,M.Szachniuk*,†,M.Antczak†,P.Lukasiak*,†,
J.Blazewicz*,†,R.W.Adamiak*,†,2
*DepartmentofStructuralChemistryandBiologyofNucleicAcids,InstituteofBioorganicChemistryPolish
AcademyofSciences,Poznan,Poland
†EuropeanCenterforBioinformaticsandGenomics,InstituteofComputingScience,PoznanUniversityof
Technology,Poznan,Poland
2Correspondingauthor:e-mailaddress:[email protected]
Contents
1. Introduction 4
2. RNAFRABASE—OpeningtheRoutetoRNAComposer 7
3. RNAComposer—FromtheRNASecondaryStructuretoRNA3DStructure 8
3.1 GeneraldescriptionoftheRNAComposermethod 8
3.2 RNAComposerinputdata 12
3.3 Outputdataandqualitycontrolofthe3Dmodels 13
3.4 RNAComposerwebserver 15
4. PredictingtheTertiaryStructureofRiboswitcheswithRNAComposer 16
4.1 RNAComposeraccuratelypredicts3Dstructureofseveralcomplex
riboswitches 16
4.2 Applicationexample1:Thec-di-GMP-IIriboswitch 21
4.3 Applicationexample2:Thec-di-GMP-IIriboswitchrelatives 23
5. ConclusionsandPerspectives 28
Acknowledgments 31
References 31
Abstract
UnderstandingthenumerousfunctionsofRNAsdependscriticallyontheknowledgeof
theirthree-dimensional(3D)structure.Incontrasttotheproteinfield,amuchsmaller
numberofRNA3DstructureshavebeenassessedusingX-raycrystallography,NMRspec-
troscopy,andcryomicroscopy.ThishasledtoagreatdemandtoobtaintheRNA3D
1This work is dedicated to Professor Colin B. Reese (FRS) on the occasion of his 85th birthday
anniversary.
MethodsinEnzymology,Volume553 #2015ElsevierInc. 3
ISSN0076-6879 Allrightsreserved.
http://dx.doi.org/10.1016/bs.mie.2014.10.050
