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BranchedBiopolymers
Residuelabelstypicallyhavetwoattachmentpoints.However,youcanaddattachmentpointssothatthesequence
branches.Forexample:
Whenyouaddanattachmentpoint,youspecifytheatomintheexpandedlabeltowhichthebondwillattach.
Tobondfromasequence:
1. Drawabondstartingatthelabelfromwhichtocreateabranch.TheModifyNicknamedialogappears,displaying
thesequencestructureyouselected.
2. IntheModifyNicknamedialog,double-clicktheatominthestructureonwhichyouwanttoaddtheattachment
point.Anewattachmentpointappears.
3. ClickOK.
IUPACCodes
Usethesecodestoenternucleotidesoraminoacidsinyoursequence:
IUPACNuc-
leotideCode
Base
IUPACAmino
AcidCode
Three
LetterCode
AminoAcid
A
Adenine
A
Ala
Alanine
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C
Cytosine
C
Cys
Cysteine
G
Guanine
D
Asp
AsparticAcid
T(orU)
Thymine(orUracil)
E
Glu
GlutamicAcid
R
AorG[Either
puRine]
F
Phe
Phenylalanine
Y
CorT[Either
pYrimidine]
G
Gly
Glycine
S
GorC[Threehydro-
genbond(Strong)]
H
His
Histidine
W
AorT[Twohydro-
genbonds(Weak)]
I
Ile
Isoleucine
K
GorT[Ketogroupin
base]
K
Lys
Lysine
M
AorC[AMinegroup
inbase]
L
Leu
Leucine
B
CorGorT[NotA(B
isletterafterA)]
M
Met
Methionine
D
AorGorT[NotC]
N
Asn
Asparagine
H
AorCorT[NotG]
P
Pro
Proline
V
AorCorG[NotUin
RNAcontext;notT
inDNAcontext]
Q
Gln
Glutamine
N
anybase[A/U/G/C
inRNAcontext;
A/T/G/CinDNAcon-
text]
R
Arg
Arginine
S
Ser
Serine
T
Thr
Threonine
V
Val
Valine
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if (bmp == null) throw new Exception("fail to load the document preview"); //. Copyright © <2000-2016> by <RasterEdge.com>. All Rights Reserved.
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W
Trp
Tryptophan
Y
Tyr
Tyrosine
Thetablesbelowlistthethreelettercodesfornon-specificandnon-proteinogenicaminoacids.
IUPACAmino
AcidCode
Three
Letter
Code
Non-specificAminoAcid
B
Asx
asparagineorasparticacid
Z
Glx
glutamicacidorglutamine
J
Xle
leucineorisoleucine
X
Xaa
Anyaminoacid(nonickname)
IUPACAmino
AcidCode
Three
Letter
Code
Non-proteinogenicAmino
Acid
O
Pyl
Pyrrolysine
U
Sec
Selenocysteine
Aib
α
-Aminoisobutyricacid
Abz
2-Aminobenzoicacid
Nle
Norleucine
Cyclic,Crosslinked,andBranchedPeptides
Youcancreatecyclicpeptidesbybondingtogethertheterminalresiduesinapeptidesequence.Aloopedbondindic-
atesthepeptideiscyclic.Anexampleofcyclicpeptideisshownbelow:
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Youcancreateacrosslinkedpeptidesuchasinsulin,usingthebiopolymertoolandbondtool.
BranchedPeptides
Abranchedpeptideisformedwherearesiduehasmultiplepossibleleavinggroups.Forexample,Arghastwoamino
groupsandAsphastwocarboxylgroups.Apolymerizationreactioncouldpotentiallytakeplaceateitherofthese
groups,oratboth.Henceprotectinggroupsareoftenemployedduringthepolymerizationreactionstoselectively
allowpolymerizationatonlyasinglesite.
ConsiderthefollowingexampleinwhichthepeptideisbranchedattheAspresidue:
Inthefollowingexample,theresidueisbranchedattheArgresidue:
Youcancreateabranchedpeptideusingthesolidbondtooltoconnectthebranchingresidueinthefirstchaintothe
branchingresidueinthesecondchain.Iftheresidueshaveleavinggroupsthatcanbeautomaticallyfound,thenit
branchesatthosepoints.Otherwise,theModifynicknamedialogappearsandyouneedtomanuallydefinethethird
attachmentpoint.Considerthefollowingexampleforcreatingbranchedpeptide:
1. Drawtwobiopolymerchainsasshownbelow:
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2. Usingthesolid-bondtool,dragfromthelowerchain'sGly-3totheupperchain'sArg-3.Theterminalhydrogenon
thelowerchainisremovedandthebranchedpeptideappearsas:
Iftheresiduesdoesnothaveleavinggroupsthatcanbeautomaticallyfound,theModifynicknamedialogappearsand
youneedtomanuallydefinethethirdattachmentpoint.Considerthefollowingexample,
1. Drawtwobiopolymerchainsasshownbelow:
2. Usingthesolid-bondtool,dragfromthelowerchain'sMet-4totheupperchain'sMet-5.Sinceneitherofthese
residueshavedefinedleavinggroups,theModifyNicknamedialogappearstwice,onceforeachresidue.
3. Definenewattachmentpoints.Theresultingstructureis:
DisulfideBridges
YoucanbuilddisulfidebridgeseitherbetweenCysresidueswithinthesamestructure,orbetweenresiduesintwodif-
ferentstructures.Forexample,considertheendocrinehormoneInsulin.
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Insulinconsistsoftwochains,anAchainandaBchain,connectedbydisulfidebridges.
AChain
GIVEQCCTSICSLYQLENYCN
BChain
FVNQHLCGSHLVEALYLVCGERGFFYTPKT
YoucanbuildthesechainseitherbycopyingandpastingtheabovetextusingthePasteSpecial>FASTAPeptide
commandorbyusingtheBiopolymertoolbartobuildeachchain.
Tobuildintra-sequencedisulfidebridge:
1. Selectthesinglebondtool.
2. DrawabondbetweentheC(6)andC(11)residuesintheAchain,asshownbelow:
Tobuildinter-sequencedisulfidebridges:
1. SelectthebondtoolanddrawabondbetweentheC(7)inAchainandC(7)inB-chain.
2. DrawanotherbondbetweentheC(20)inAchainandC(19)inBchain,asshownbelow:
LactamBridges
YoucandrawlactambridgesbetweenLys-AspandLys-Gluresidues.Theresiduesconnectviaamidebonds
betweensidechains.Youcanalsomixdisulfideandlactambridges.
Todrawalactambridge:
1. DrawasequencethatcontainsLysandeitherAsporGlu.
2. Usingsolidbondtool,drawabondfromLystotheotherresidue.Anexampleisshownbelow:
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AdvancedDrawingTechniques
Theadvancedfeatureshelpyousavetimeorperformfunctionsthatcannotbeaccomplishedusingthebasictools.
Forexample,youcanviewyourdrawingas3Dmodelsorcreatestereoisomersattheclickofthemouse.Usingother
features,youcan:
Add
bonds
to
characters
in
atom
labels
Create
bonds
whose
attachment
is
not
explicitly
defined
Add
atom
numbers
Contractandexpandsectionsofstructures
View
structure
perspective
Create
mass
fragmentation,
retrosynthesis,
and
synthesis
drawings
Draw
with
templates
Createandedittemplates
Labelfunctionalgroupswithnicknames.
ColoringObjects
Youcanselectandcolorobjects,partorallofachemicalstructure,boxes,curves,arrows,orbitals,andreaction
mechanismsymbols.
Tocoloranobject:
1. Selecttheobject.
2. Dooneofthefollowing:
ClicktheColorbuttonontheStyletoolbar,andselectthecolorfromthemenuthatappears.
ChooseacolorfromtheColormenu.
Right-clickandselectthecolorfromthecontextmenu.
NavigatetoObject>ObjectSettingsandselectthecolorintheDrawingtab.ClickOKwhenfinished.
ColoringGroups
ChemBioDrawcolorsgroupsdifferentlyfromintegralgroups.Whenyoucoloranintegralgroup,itsobjectsacquirethe
newcolorbutretaintheoriginalshading.Whenyoucoloranormalgroup,thenewcolorisappliedandtheoriginalshad-
ingisignored.
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Figure9.1:
A)
Themitochondrionstructureinitsdefaultcolor;B)Thestructurecoloredblueasagroup;C)Thestruc-
turecoloredblueasanintegralgroup.
Thenewcolorappliestoallstructuresinthegroup,eveniftheoriginalcolorsoftheobjectsinthegrouparenotthe
same.Seeexamplebelow:
Figure9.2:A)Thestructurecoloredpinkasanintegralgroup;B)Thestructurecoloredpinkasagroup.
Labels
Inadditiontorepresentingatoms,labelscanrepresentregionsofastructurethatyoudefine.Forexample,youcan
assignalabeltoanunimportantregionofamoleculeandthencontractthatregiontoreducethesizeofyourdrawing.
Youcanthenexpandthelabel,toseethewholemolecule.
CreatingLabels
Tocreateacontractedlabel:
1. Selecttheareaofthestructuretocontract.
2. NavigatetoStructure>ContractLabel.TheContractLabeldialogappears.
3. Typealabelforthecontractedstructure.
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4. ClickOK.
Thelabelreplacestheselectedportionofthestructure.
Note:Iftheareaofthestructureyoucontractcontainserrors,anerrordialogappears.ClickIgnoretoviewother
errors.ClickIgnoreAlltoignoreallerrorsorStoptoendthecontractprocess.
ExpandingLabels
Ifyourstructurescontaindefinednicknames,longatomlabels,orcontractedlabels,ChemBioDrawcanrestoreyour
structurestothefully-expandedform.
Toexpandatomlabels:
1. Selectaselectiontool.
2. Selectthelabeltoexpand,ordouble-clickthestructuretoselectalllabelsinthestructure.
3. NavigatetoStructure>ExpandLabel.YoucanalsousetheExpandLabeltoolintheStructuretoolbar.Your
structureisredrawninitsexpandedform.Belowisanexampleofexpandinglabels:
Contracted:
Expanded:
Whenyouexpandalabelthatcontainsadivalentnickname,forexampleH-Ala-OH,theattachmentorderdependson
theorderinwhichthebondsarecreated.
MultipleAtoms
Labelscancompriseagroupofatoms.Whenyouexpandthelabel,itexpandstocreatethestructure.
Contracted:
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