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DrawingBiopolymers
Biopolymersarecomplexmolecularassembliesthatadoptpreciseanddefinedshapesandstructures.Theirdefined
shapeandstructureareinfactkeystotheirrole.Biopolymersarechain-likemoleculesmadeupofrepeatingchemical
blocksandcanbeverylonginlength.Biopolymersareclassifiedinthreegroups,dependingonthenatureofthe
repeatingunittheyaremadeof:
Polysaccharidesaremadeofsugars
Proteinsofaminoacids
Nucleicacidsofnucleotides
ChemBioDrawprovidesafriendlyinterfaceallowinguserstodrawbiopolymersandcreatesequenceseasily.Using
theBiopolymereditor,userscandrawpolypeptidesandnucleotidesequencesusingpre-definedlabelsassignedto
nucleicandaminoacids.Youcanexpand,contract,orremovelabelstocompletethedrawing.
TodisplaytheBiopolymertoolbar,navigatetoView>ShowBiopolymerToolbar.TheBiopolymerstoolbarappears:
TheBiopolymerstoolbarincludesthefollowingoptions:
BiopolymerEditor:Enablesallthenucleicandaminoacids
SingleLetterAminoAcid:Enablesalltheaminoacids
BetaAminoAcids,L-AminoAcids,D-aminoAcids:EnablesadditionofBeta,L-,andD-aminoacids
DNASequence:EnablesthedeoxyribonucleotidesthatcanbeusedtocreateaDNAmolecule
RNASequence:EnablestheribonucleotidesthatcanbeusedtocreateaRNAmolecule
Todrawasequence:
1. SelectoneofthesetoolsfromtheBiopolymertoolbar:
AA1tool(Single-letteraminoacidtool).Createapolypeptidechainusingaone-letterlabeltorepresenteach
aminoacid.
YoucancreatethesequencesbytypingtheIUPACcodeforthestandardaminoacids,orbypressingtheiconsonthe
toolbar.Bydefault,Lamino-acidsarecreated.Single-lettersequencesaredrawnwithafixedseparation,sothat
residuesalignwithresiduesinadjacentrows.YoucancreateD-aminoacidsusingtheDaminoacidstereochemistry
option.
Single-letterD-aminoacidsaredisplayedinlowercase.Three-letterDaminoacidshavetheprefix"D-".
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Note:The<SHIFT>keyactsasatoggle.Hence,toenterD-aminoacids,press<SHIFT>whileenteringasingle-
lettersequencewhileinLmode.Alternatively,toenterL-aminoacidswhileinDmode,press<SHIFT>whileenter-
ingasingle-lettersequence.
Note:Youcanenterthree-letteraminoacidsusingthe"BiopolymerEditor"onpage102,andyoucanuseeither
thekeyboardortoolbartoenterresidues.
DNAtool.CreateaDNAchainusinglabelsthatrepresenteachofthenucleicacids.
RNAtool.CreateanRNAchainusingnucleicacidlabels.
2. Clickwhereyouwanttostartthesequence.Atextboxappears.
3. Inthetextbox,enterthesingle-letterlabelfortheresidue.
Note:Foralistofresiduelabels,see"IUPACCodes"onpage111.
4. Repeatstep2foreachresidue.
5. Whenyourchainiscomplete,press<ENTER>,or<Esc>.
Bydefault,whencreatingasequence,newresiduesareinsertedafterthecurrentactiveresidue.Theinsertionpointis
indicatedbyanorangechevron.Youcanoverwriteorreplaceasequenceatomusingtheresiduereplacementbutton.
Youcanalsoreplaceasequenceatombyhoveringoveraresidueandpressingahotkey,whennoactiveresidueis
present.
BiopolymerEditor
TheBiopolymerstoolbarcontainsatoolcalledBiopolymerEditor.
Usingthebiopolymereditor,youcancreateasequencebyexplicitlyspecifyingtheresiduenameinsteadofthe
IUPACcode.Whenyouenteraletter,theauto-completionfeaturesuggestsamatchwithaknownresidueinthelib-
rary.Forexample,whenyouenter'a',theresidue'Ala'issuggested.Toacceptthesuggestion,press<SPACE>or
<ENTER>key.PressTABtomovethecarettotheendoftheselectedlabel.
Toenterbaminoacids,typeanicknamesuchasbAla.The‘b’isconvertedtothebsymbol.Youcanalsocreateb
aminoacidsusingtheb-aminoacidbuttoninthebiopolymereditor.b-aminoacidsalwaysdisplayusingthree-letter
codes.Glycinedoesnothaveabetacarbon,andsothereisnobetaversion.
ToenterD-aminoacids,specify"d-"beforetheresiduename.GlycineisalsoachiralandsodoesnothaveaDver-
sion.
Note:UsetheD-aminoacidandb-aminoacidbuttonssimultaneouslytoproduceD-baminoacids.
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Youcanalsooverwriteandreplacethesequenceatomsusingtheresiduereplacementbuttoninthebiopolymer
editor.Formoreinformation,see"ReplacingResidues"onpage109.
ToggleAminoAcids
ToggleAminoAcidStyleAA1<->AA3optionletsyouchangetheaminoacidrepresentationfromsingleletterto
tripleletterandviceversa.Forexample,
1. Selectthesequence.
2. Right-clickandselectTogglefromAminoAcidStyleAA1<->AA3.
Youcanalsochangetheaminoacidrepresentationofexpanded,substituted,andprotectedaminoacids.For
example,
TheToggleAminoAcidStereoL<->DoptionletsyouchangethestereochemistryoftheaminoacidfromLtoD
andviceversa.
Totoggleaminoacids:
1. Selectthesequence.
2. Right-clickandselectToggleAminoAcidStereoL<->D.
ProtectingGroups
YoucanaddprotectinggroupssuchasTrtandFmoctoaminoacidscontainingadditionalNH
2
orOHgroups(Arg,
Aad).Protectedgroupsarespecifiedwithinbrackets’()’.
Toaddaprotectinggroup:
1. Inasequence,enter‘(‘ afteracompletedresiduenameasshownbelow:
2. Enterthenameoftheprotectinggroupandenter‘)’attheendofthename.
ThenameoftheprotectinggroupdeterminesifitwillprotecttheNH
2
orOHgroup.IfprefixedbyO,thenitprotectsthe
OHgroup.
Youcanexpandandcontractprotectedresiduesjustlikeanyotherresidue.
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Ifnoleavinggroupisfound,afteryouenter’)’,adialogpromptsyoutospecifytheattachmentpoint.
Youcanexpandandcontractprotectedresiduesjustasanyotherresidues.
PastingSequences
YoucanpastesequencesinFASTAformat.Sinceonlysingle-letterIUPACcodesarepresentintheFASTAformat,
youmustindicatewhetherthiscorrespondstoapeptide,DNA,orRNAbiopolymersequence.YoucanpasteALL
IUPACsymbolsforresidues,withtheexceptionofthosecharactersindicatingspacesoromissions.
Topasteasequence:
1. Right-clickandnavigatetothePasteSpecialsubmenu.
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2. Selectoneofthreeoptionstopaste:
FASTAPeptide
FASTARNA
FASTADNA
Whenyouhoveryourmouseovertheresidue,adescriptionoftheresidueandsequencedataappears.
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PasteTextStrings
Youcanalsopastetextstringswithvalidseparators.Space,tab,anddashareconsideredasvalidseparators.The
textstringyoucopycanbegeneratedwithinoroutsideofChemBioDraw.Thetextstringsmustcontainvalidresidue
names/nicknames,optionallyincludingtermini.Ifnoterminiareexplicitlydefined,thendefaultterminiisassigned.
Topasteatextstring:
1. Copythetextstring(forexample,“H-Ala-Gly-Pro-NH2”)andright-clickinanemptyspace.
2. Fromthecontextmenu,selectPasteSpecial>Biopolymer.Thetextstringispastedasasequence.
Note:Thelabelsinthetextstringmustcorrespondtoexplicitnicknames.
ExpandingSequences
Aftercreatingasequence,youcanexpandthewholesequence,orjustspecificlabels.
Toexpandasequence:
1. Selectoneormorelabelsinthesequenceusinglassotoolormarquetool.(Holddownthe<SHIFT>keytoselect
morethanone.)
2. NavigatetoStructure>ExpandLabel.
Whenyouexpandaresidueintoitsstructure,thelabelappearsbelowthestructure.
ContractingLabels
Tocollapsethestructurebacktoitslabel(inthesequence):
1. Double-clickthelabeltoselectthestructure.
2. Navigateto o Structure>ContractLabel.
Ifyoueditthelabelpriortocontractingthestructure,thenewlabeltextisincorporatedintothecontractedstructure.
Forexample,ifyoumodifyaresidue,andchangeitsnamefromAlatoAla',oncontraction,thesequencecontainsthe
stringAla'.
CleanUpBiopolymers
Afteryoucontractthelabels,youcanusetheCleanUpBiopolymercommandtocleanthesequence.Thiscom-
mandre-arrangesthesequencesothattheresiduesarealigned,andwrapped.Tospecifythenumberof'residuesper
line'andthenumberof'residuesperblock'inabiopolymer,selectthebiopolymerandnavigatetoObject>Object
Settings>BiopolymerDisplaytab.
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ModifyingSequenceResidues
Note:Whenyoumodifyaresiduestructureinyourdrawing,youmustdefineanewnicknametoensurethatthe
contractedlabelincludesyourchanges.
Tomodifyasequenceresidue.
1. Iftheresidueinthesequenceiscontracted,right-clicktheresidueandselectExpandLabel.
2. Modifytheresidue.
3. UsingtheTexttool,renametheresiduelabeltoreflectanewstructure.Intheexamplebelow,the"Ser"labelhas
beenrenamedas"hSer"(forhomoserine).
Figure8.1:Twoexpandedserineresidues.Theresidueonthelefthasbeenmodifiedtocreatehomoserine.
Tocontractalabel:
1. Usingaselectiontool,right-clicktheresiduelabelandselectSelectLinkedObjects,ordouble-clickonthelabel
fortheexpandedresidue,andtheassociatedstructureisselected.
2. NavigatetoStructure>ContractLabel.
Figure8.2:Thecontractedlabel.
Youmustdefineanewnicknametoensurethatthecontractedlabelincludesyourchanges.Forexample,youcan
defineanewnickname'hSer',whichincludesthehydroxylgroupintheresiduedefinitionitself.
MergingSidechainswithResidue
TheMergeSidechainsWithResiduefeatureletsyoueditanexpandedresidueandthenintegratethosechanges
intotheresiduedefinition.
Tomergeasidechain:
1. Double-clicktheresiduelabeltoselecttheresidue.
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2. Right-clickandselectBiopolymer>MergeSidechainsWithResiduefromthecontextmenu.Theentireside-
chainismergedwiththeresidue.
Theresidueisselectedandyoucanedittheresiduelabel.
RemovingResidues
Whenyouremovearesidue,thebondsareautomaticallyre-createdbetweentheadjacentlabels,andanygaps
closed.
Toremovearesidue:
1. Ifthelabelisexpanded,contractthestructurebacktoitslabel.
2. Selectthelabel,orhoveroverit.
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3. Pressthe<DELETE>key.
ReplacingResidues
TheBiopolymertoolbarhastwodistinctmodesofdataentry:InsertionmodeandReplacementmode.Insertionmode
isthedefaultmode.IntheInsertionmode,anorangechevronindicatesthepositioninwhichthenextresiduewillbe
inserted.Forexample,theorangechevroninthesequencebelowindicatesthatthenextresiduewillbeinsertedafter
the4thGlyresidue.
YoucanreplacearesidueinasequenceusingtheReplacecurrentresiduebuttoninthebiopolymertoolbar.Inthe
replacementmode,anorangerectangleindicateswhichresidueisreplaced.Forexample,theorangerectangleinthe
sequenceshownbelowindicatesthatthe3rd'G'residuewillbereplaced.
Themethodofreplacingresiduesisdemonstratedfortetraglycinesequencebelow:
1. Drawatetraglycinesequence.
2. SelectBioploymerEditorintheBiopolymertoolbar.
3. Inthetetraglycinesequence,clickonthe4th"Gly"residue.Anorangechevronindicatesthepositionwherethe
nextresiduewillbeinserted:
4. Select"Replacecurrentresidue"modeinthebiopolymertoolbar.The"Gly"textisselected.
5. Type"Ala"orclickthe"Ala"buttontoreplace"Gly".
Tochangetheformofaresidue:
1. Onthetetrapeptidesequenceabove,clickonthe2ndGlyresidue.
2. Clickandselectboththe"L-aminoacid"andthe"Beta-aminoacid".
3. Click"Cys"buttontoreplace"Gly"withbeta--Cys,asshown:
AddingResidues
Youcanaddoneormoreresiduestoanexistingsequence.
Toaddaresidue:
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1. Choosetheappropriatebiopolymertool.
2. Clickaresidueyouwantthenewresiduetobeadjacentto.Anorangechevronindicatestheinsertionpoint.
3. Typethenewresidue.Thenewlabelisaddedtotherightoftheexistingresidue.
Note:Toprepend,orinsertatthebeginningofasequence,selecttheterminusatom,selecttheaminogroup(pro-
teinsequence)or3’group(DNA/RNAsequence).
NumberingResidues
YoucandisplaytheresidueIDaboveanyresidue.
TodisplaytheresidueID:
1. Selecttheresidue.
2. Right-clickandselectShowResidueIDfromthecontextmenu.TheresidueIDappearsabovetheresidue.
NonlinearSequences(Multi-lineSequences)
Everysequencehasadefinedlinesizeandablocksize.Whenablocksizeisreached,anadditionalspaceisadded
tothesequence.Whenalinesizeisreached,subsequentresiduesareaddedonanewline.However,youcancreate
sequencewithirregularlinesbyselectinganddragging.Youcanplacearesidueonanewlinebyselectingtheresidue
inaSequencetoolmode,andpressing<ALT>+<ENTER>.Subsequentresiduesareplacedonanewline.
Toaddanewlineasyouareenteringthesequence,press<ALT>+<ENTER>onyourkeyboard.Subsequent
residuesareenteredonanewline,andthelinesizeissetforthatparticularsequence.
Tocreateamulti-linesequence:
1. Drawthesequence.
2. Usethesequencingtooltoselecttheresidueyouwantattheendofthefirstline(suchas‘His’intheexample
above).
3. Press<ALT>+<ENTER>onyourkeyboard.
HybridBiopolymers
YoucancreatemixedorhybridbiopolymersusingtheBiopolymertoolbarbycombiningthevariousBiopolymertools.
Hence,youcaninsertnucleicacidintoaminoacidsequencesandvice-versa,andRNAandDNAcanbeused
together.
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