BMB170a_2011_LECTURE3

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Unformatted text preview: !"!#!$#%&'()*+,-./0$12+ 304/5-0+67+84/+9+ •! :$1$2&+5;+<04.1=*->+*1=+?0-@*->+2/-54/5-0+ •! ".A045A*-+25-B*402+ •! ,-./0$1+2/*C$A$D$1E+B.-402+ ?&0+!P2&00/+ +F0E5A*-+204.1=*->+ 2/-54/5-02+1./+2/*C$A$D0=+ C>+&>=-.E01+C.1=2+ C0/G001+10*-C>+-02$=502+ ,HI<+J'KL'M+6(N(OK+ VW/01=0=+;.A>;0;@=0+4&*$1+J!P2/-*1=M+ •! XD$EPD*EY+*;;0*-*140+ +,Q+RST+U+ •! ,0;@=0+C.1=2+.B+*=Z*401/+-02$=502+;.$1/+$1+.;;.2$/0+=$-04@.12+ •! IA/0-1*/0+2$=04&*$12+0W/01=+.1+.;;.2$/0+2$=02+.B+2/-*1=+ I1@P;*-*AA0A++ !P2&00/+ 9SLU+ 1 +++= +++ OS) +6S9U ++++, +++ +RSTU ++++" + +'T)[ ++++# + +P'6K[ ++++$+ +\'6L[ ++:$E2S+OSL7+!-*1=01+*1=+?..D0+ ,*-*AA0A+!P2&00/+ +1 +++= +++ OS) +6S9U +++++, ++++ ++++" % +RSTU ++'T)[ % #% +P''K[ % $+ +++\''6[ ++ :$E2S+OSR7+!-*1=01+*1=+?..D0+ "$W0=+2&00/2+*-0+2/*@2@4*AA>+A022+A$_0A>+ •! B.-+R+2/-*1=0=+2&00/+ –! :$W+.1+`-2/+2/-*1=+ –! 6O+=$a0-01/+E0.^0/-$02++ •! -*1=.^+=$2/-$C5@.1+ –! 0W;04/+6L'R#6O++ –! ]'')+0W*^;A02+.B+0*4&+ J5#=+Q+5;#=.G1M+ V^C0-A>+!"#$%&#,-./0$12+JO))9M+LLNK'+ !P2&00/2+&*d0+*+ 4&*-*4/0-$2@4+/G$2/+ F$E&/+&*1=0=+*A.1E+2/-*1=2+ $1+4&*$1+=$-04@.1+ 30b+&*1=0=+&++/.+2/-*1=2+ %&./&$*+c"!+J'K(6M+(LNOKL+ e$2/.-@.1+$1+2&00/2+4*1+C0+/G$2/2+.-+ C01=2+ + I1@P;*-*AA0A+/01=+/.+C0+^.-0+ =$2/.-/0=+ + V^C0-A>+!"#$%&#,-./0$12+JO))9M+LLNK'+ 3..;+4.1104@.12+C0/G001+*=Z*401/+*1@P ;*-*AA0A+!P2/-*1=2+ O+F02$=502+;-0=.^$1*1/+ !-*1=01+f+?..D0+:$E+OST+ F0d0-20+h+/5-12+ !#$" !#$" !#%" !#&" !" ?>;0+gg+?5-1+ !#%" !" !#&" ?>;0+g+?5-1+ <$C*1=*+f+?&.-1/.1+H*/5-0+J'KTLM+6'RN'()+ <$A_+</-54/5-0+ •! <$A_+$2+;*4_0=+hP2&00/+ •! IA/0-1*@1E+20i50140+ .B+PEA>P*A*PEA>P*A*P+ •! O+20;*-*/0+2;*4$1E2+ •! H0*-A>+B5AA>+0W/01=0=7+ 1./+^54&+E$d0+ •! <0i50140+d*-$*1/2+ *A/0-+;A$*C$A$/>+ e$4_0-2.1+f+j0$27+'"()*")(!#$+,#-*./+#/0# 1(/"!2+3#J'KRKM+ !P2&00/2+*1=+*^>A.$=+`C-$A2+ !A*_0+f+<0-;0AA+</-54/5-0+J'KKRM+9NKTK+ H0A2.1+!"#$%&#H*/5-0+JO))LM+96LN((6+ Scurvy •! Jacques Cartier (1536) “Some did lose all their strength, and could not stand on their feet…. Others also had all their skins spotted with spots of blood of a purple colour: then did it ascend up to their ankles, knees, thighs, shoulders, arms, and necks. Their mouths became stinking, their gums so rotten, that all the flesh did fall off, even to the roots of the teeth, which did also almost all fall out” •! In 1865 British Sailors were given limes to help combat the disease leading to the nickname ‘limeys’ Collagen •! 25% of the protein in your body is collagen •! Used in basic cell structure –! Tendons –! Organelle structure –! Bones/teeth (forms basal matrix) •! Composed of three chains forming a triple helix –! ~1400aa –! Every third residue is Gly –! -HyP-Pro-Gly- !*20^01/+^0^C-*102+.B+^*1>+ .-E*10AA02+JgkM+ Collagen Structure (1bkv) •! Repeating unit forms stable packing •! Hydroxyproline essential for regular packing –! prolyl hydroxylase uses ascorbic acid (vitamin C) to add oxygen –! Extra hydrogen bond stabilizes from 24C to 58C jA>+ m>;+ •! ,.A>;-.A$10+gg+A0bP&*1=0=+&0A$W+ –! 1+Q+6+l+=+Q+6S'+Ul+"+Q+P'O)[+ –! J#,$M+Q+JP(L[7+'L)[M+ n-*^0-+!"#$%+H*/5-0+</-54/+!$.A+J'KKKM+RN9L9P(+ ,-.+ ,*5A$1Eo2+./&0-+$=0*2+ •! ,*5A$1Eo2+d$2$.1+.B+'P &0A$W#!P2&00/+;*4_$1E+ •! "04&*1$2^+.B+^524A0+ 4.1/-*4@.1+ –! &0A$WP2&00/+/-*12$@.1+ –! ,*5A$1E+f+%.-0>+,HI<+ J'KL'M+6(NOR'+ 'P&0A$W#+!P2&00/+</-54/5-02+ KU+ KU+Q+O+W+9SL+U+ !'!+^.@B2+$1+2/-54/5-02+4.1/*$1$1E+ ;*-*AA0A+!P2&00/2+ •! I=Z*401/+;*-*AA0A+!P2/-*1=2+ 525*AA>+4.1104/0=+C>+*1+'P &0A$W+ •! m0A$4*A+*W$2+$2+*A^.2/+ ;*-*AA0A+/.+2/-*1=2+ •! IA^.2/+*AA+4.1104@.12+*-0+ -$E&/P&*1=0=+pKLq+ F$E&/P&*1=0=+ 30bP&*1=0=+ :$ES+OS'T7+!-*1=01+*1=+?..D0+ !'!+^.@B+4*1+-025A/+$1+C*--0A2+.-+2&00/2+ IAA+-$E&/+&*1=0=+^.@B2+ </-*1=+.-=0-N++'+O+6+9++ <*^0+2$=0+.B+2&00/+pp+C*--0A+2&00/+ :$ES+9SO7+!-*1=01+*1=+?..D0+ </-*1=+.-=0-N++9+6+'+O++ O1=+*1=+6-=+.;;.2$/0+2$=0+.B+2&00/+pp+.;01+2&00/+ !'!+^.@B+4*1+-025A/+$1+C*--0A2+.-+2&00/2+ '())*+,"" -*+!.*/"01"/(2*"/!3*"04"/5)(13/" :$ES+9S'7+!-*1=01+*1=+?..D0+ 6-**5,"" -*+!.*/"01"705-"/!3*/"04"/5)(13/" '!+C*--0A+01D>^0+ •! %*1+4A.20+C*--0A+G$/&+T+2/-*1=2+++ •! H00=+*/+A0*2/+O))+-02$=502+/.+ B.-^+C*--0A+ •! I4@d0+2$/0+$2+*/+C.r.^+.B+ ;.4_0/+4-0*/0=+C>+/&0+T+A..;2+ */+%P/0-^$1*A+01=2+!P2/-*1=2+ •! 3..;+-0E$.12+*44.^^.=*/0+ =$a0-01/+-02$=502+/.+4-0*/0+ =$a0-01/+01D>^*@4+*4@d$@02+ I4@d0+2$/0+.B+F5!$2%.+J%8O+`W*@.1+$1+;A*1/2M+'-CA+ :$ES+9ST7+!-*1=01+*1=+?..D0+ ".-0+d*-$*C$A$/>+$1+.;01+/G$2/0=+'/!+ 2/-54/5-02+ •! 8;01+!+2&00/2N+s25*AA>+ 200+9+t+')+ •! ?G.+2/-*1=2+Z.$10=+C>+ 4-.22P.d0-+ •! I4@d0+2$/0++ –! />;$4*AA>+*/+%+/0-^$1*A+0=E0+ .B+!+2&00/+J*2+$1+C*--0A2M+++ –! */+4-0d$40+*/+0=E0+.B+!+ 2&00/++ –! 3.._+B.-+G&0-0+2/-*1=+ .-=0-+-0d0-20=+$1+*+ /.;.A.E>+=$*E-*^+ :$ES+9S'67+!-*1=01+*1=+?..D0+ I1@P;*-*AA0A+!P2/-54/5-02+ •! <$^;A02/+/.;.A.E>N+5;P*1=P=.G1+ C*--0A2+ •! V*4&+2544022$d0+2/-*1=+*==0=+ *=Z*401/+/.+;-0d$.52+2/-*1=+ •! ,*4_$1E+.B+/G.+/G$2/0=+!+2&00/2+ -025A/2+$1+C*--0A+ 8*910+"7!13!1:";)05*!1"<$.7/=" F0@1.A+Jd$/*^$1+IM+C$1=2+$1+ &>=-.;&.C$4+$1/0-$.-+ :$E2S+LSO+*1=+LS67+!-*1=01+*1=+?..D0+ I1@;*-*AA0A+!+2/-54/5-02N+j-00_+_0>2+ ,.22$CA0+B.A=$1E++ ;*/&G*>+ :$ES+OS'R7+!-*1=01+*1=+?..D0+ j-00_+_0>2+4*1+B.-^+Z0AA>+-.AA+C*--0A2+ :$E2S+LS'(7+LS'T7+!-*1=01+*1=+?..D0+ ,*-*AA0A+!+&0A$402+ ,04/*/0+A>*20+JO,V%M+ e.02+;-$^*->+20i50140+=0/0-^$10+204.1=*->+ 2/-54/5-0u+ •! <04.1=*->+2/-54/5-0+;-0=$4@1E+2.bG*-0+$2+d0->+E..=+ –! F0i5$-02+&.^.A.E>+ –! !*20=+.1+/&0+,e!+ –! <0i50140+*A.10+4*1+/0AA+>.5+*+A./+ •! H.+P+%&*^0A0.1+20i501402+ –! <0i501402+/&*/+*;;0*-+$1+C./&+&0A$W+*1=+2&00/+204.1=*->+ 2/-54/5-0+0A0^01/2+ –! I2+.B+O))(+Jv5+!"#$%S+,-./0$12+R(NL9TPLTM+ •! R+-02$=502+J'L'KM+ •! (+-02$=502+JLRM++ •! T+-02$=502+JOM+k3wkn3mH+f+:I3e33"V+ Chameleon sequences k3wkn3mH adopts two different 2˚ structures Fe binding Dlp-2 1JIG Baculovirus protein P35 1P35 e0`1$1E+<5-B*402+ 8*>)*/*15"(502/"(/"?@A"/>-*)*/" (13")0++"0B*)"C!5-"3*D1*3"/>-*)*" E3*19D*/"(..*//!7+*"()*(/"(13" B0!3/" F+$2+E010-*AA>+]'S9+Jkex+.B+mO8M+ %.1/*4/+J".A045A*-+25-B*40M+Q+kex+01d0A.;0+ I44022$CA0+<5-B*40+Q+I/.^+$2+*44022$CA0+J4.1d0WM+ F$4&*-=2+I11+F0d+!$.4&+!$.;&>2+J'K((MRN'L'+ ".A045A*-+25-B*40+ F;G"D:H)*/"()*"*I*.9B*+J"B(1" 3*)"A((+/")(3!!" F$C.154A0*20+<+J'-1dM+ K0+*.H+()"/H)4(.*" VA04/-.2/*@4+;./01@*A2+ ^*;;0=+.1/.+25-B*40+ ,-./0$1+;*4_$1E+ •! ,-./0$12+ –! zd.A#C5-$0=+*/.^p+Q+'LP'R+U6+ •! 2^*AA+^.A045A0+W/*A2++ –! zd.A#C5-$0=+*/.^p+]+'T+U6+ •! ,*4_$1E+ –! k0->+0{4$01/+ –! />;$4*AA>+z+Oq+$1/0-1*A+d.A5^0+$1+ 4*d$@02+ F$4&*-=2+I11+F0d+!$.4&+!$.;&>2+J'K((MRN'L'+ ,.5;.1+%5--+8;+</-54/+!$.A+JO))9M'9NO66+ y5$AA$1+f+"*r&0G2++I4/*+%->2/+JO)))M+eLRN(K'+ I44022$CA0+25-B*40+*-0*+ •! %*A45A*/0=+*+;A./+.B+2.Ad0=+ 2/-54/5-02+ " ++ –! I44022$CA0+25-B*40+*-0*+I2+$2+*+A$10*-+ B514@.1+.B+^.A045A*-+G0$E&/+ ++ As = 6.3 MW 0.73 –! Approaches the 2/3 power law of surface to volume for a set of bodies of similar shape and density" –! 57% non-polar, 39% polar, 4% charged" •! Buried surface area" –! Estimate total surface using G-X-G and A-X-A models" AT = 1.48 MW + 21 –! Fraction buried is:" %buried = 1 ! AS / AT "$AA0-7+c*1$17+302_+f+%&./&$*+c"!+J'KT(M"'KRNR9'+++ e$2/-$C5@.12+C0/G001+C5-$0=+*1=+25-B*40+ ;.2$@.12+ •! ]OLq+.B+*^$1.+*4$=2+*-0+C5-$0=+ •! + F*@.+.B+25-B*40#C5-$0= + +-02$=502+ + + + +6P') + + + + ++H7e7y7V7F7n + +;.A*-#4&*-E0=+ + + + +'P6 + + + + +++++w7?7<7,+ + + + ++++++)S(P)SK+ + ++++ ++++++++++++I7j7m+ + + ++++++++z+)S( + + + ++++++++%7g737"7:7k7x ++++++*;.A*-+ •! VW;.20=#C5-$0=+$2+1./+*1+*AAP.-P1.10+0a04/+ –! I;.A*-+-02$=502+4*1+C0+.1+/&0+25-B*40+ –! ,.A*-+-02$=502+4*1+C0+C5-$0=S+++ –! IAA+II2+4.1/*$1+2/-.1EA>+;.A*-+E-.5;2+J;0;@=0+C.1=M+*1=+&*d0+ 1.1P;.A*-+*/.^2+J4*-C.1+$1+%hM++ –! ,.A*-+*/.^2+*-0+2.^0@^02+C5-$0=+*1=+A./2+.B+1.1;.A*-+*/.^2+ *-0+.1+/&0+;-./0$1+25-B*40+ "$AA0-+!"#$%+c"!+J'KT(M"'KRNR9'+++ !-$0B+/&0-^.=>1*^$42+ •! j$CC2+B-00+010-E>+|j+ –! Va04@d0+^0*25-0+.B+A$_0A$&..=+.B+*+ -0*4@.1+&*;;01$1E+ •! V1/&*A;>+|m+ –! m0*/+4.1/01/+J520B5A+G.-_M+ –! g1/0-1*A+010-E>+G$/&+*+d.A5^0+*1=+ ;-0225-0+4.^;.101/+ •! V1/-.;>+|<+ "G = "H # T"S "G = # RT ln K eq H = U + pV –! I+^0*25-0+.B+=$2.-=0-+JG0+*AA+&0*=+$1+ /&*/+=$-04@.1+O1=+A*GM+ –! s1520B5A+G.-_+ •! <;04$`4+m0*/+|%;+ –! m0*/+010-E>+/&*/+-0i5$-0=+/.+$14-0*20+ /0^;0-*/5-0+ –! s20B5A+^0*25-0+B.-+*+^*/0-$*A+ </*C$A$D$1E+B.-402+ TK+_4*A#^.A+ 9'+_4*A#^.A+ 6+_4*A#^.A+ )SL+_4*A#^.A+ '+_4*A#^.A+ Petsko G.A., Ringe, D., Protein Structure and Function 2004, figure1-10, pg. 11.+ V*-A>+&$2/.->+.B+/&0+X&>=-.;&.C$4+0a04/Y+ •! x&.+G*2+$12/-5^01/*A+$1+4&*-*4/0-$D$1E+/&0+ $1/0-*4@.12+C0/G001+G*/0-+*1=+1.1;.A*-+ 25C2/*1402u+ * +!01Z*^$1+:-*1_A$1+'((9+ C +3.-=+F*>A0$E&+'TK)+ 4 +IE102+,.4_0A2+'TKO+ = +g-d$1E+3*1E^5$-+'K'(+ 0 +*AA+.B+/&0+*C.d0+ X!01+:-*1_A$1+<@AA0=+/&0+x*d02Y+%S+?*1B.-=7+8WB.-=+JO))9M+++ •! &r;N##$1=0^.d0-$/*2S.-E#u;*E0}$=Q9'+ :-*1_A$1+,.1=+VW;0-$^01/+ •! &r;N##$1=0^.d0-$/*2S.-E#u;*E0}$=Q9'+ •! :-*1_A$1+JB.AA.G$1E+.1+&$2+-0*=$1E+.B+,A$1>+/&0+ VA=0-M+-04.E1$D0=+/&0+4&*1E0+$1+25-B*40+/012$.1+ •! 3.-=+F*>A0$E&+JH.C0A+B.-+=$24.d0-$1E+I-E.1M+520=+ /&0+^0/&.=+/.+^0*25-0+/&0+24*A0+.B+*+^.A045A0+ •! IE102+,.4_0A2+$^;-.d0=+.1+F*>A0$E&o2+ ^0*25-0^01/2+J$1+&0-+_$/4&01~M+ •! 3*1E^5$-+4*^0+5;+G$/&+/&0+^.A045A*-+^.=0A+ JH.C0A+$1+%&0^$2/->M+ IE102+,.4_0A2+ ,.4_0A2+JF*>A0$E&M+J'TK'M+H*/5-0+96N96(+ m>=-.;&.C$4+0a04/+*1=+;-./0$12+ •! X/&0+C0&*d$.5-+.B+/&0+&>=-.;&.C0+E-.5;2+.B+/&0+;-./0$1+^52/+C0+254&+*2+/.+&.A=+$/+/.E0/&0-S+ I2+e*1$0AA$'O+*1=+3*1E^5$-'9+&*d0+;.$1/0=+.5/7+.1+/&0+C*2$2+.B+25-B*40P`A^+G.-_7+/&0+;-./0$1+ ^.A045A0+$1+2.A5@.1+^52/+&*d0+$/2+&>=-.;&.C0+E-.5;2+.5/+.B+4.1/*4/+G$/&+G*/0-7+/&*/+$27+$1+ 4.1/*4/+G$/&+0*4&+./&0-7+G&0-0*2+.1+/&0+25-B*40+/&0+^.A045A0+$2+C-._01+5;+$1/.+*+`A^+.B+')U+ /&$4_1022+$1+G&$4&+/&0+&>=-.;&.C0+E-.5;2+*-0+=-$d01+.5/+.B+4.1/*4/+G$/&+/&0+G*/0-S+g1+/&$2+ G*>+*+B.-40+.B+*22.4$*@.1+$2+;-.d$=0=+G&$4&+$2+1./+2.+^54&+/&*/+.B+*r-*4@.1+C0/G001+ &>=-.;&.C0+E-.5;27+G&$4&+$2+*AG*>2+G0*_7+C5/+/&*/+.B+-0;5A2$.1+.B+/&0+E-.5;2+.5/+.B+/&0+ G*/0-+^0=$5^S++ + +3*1E^5$-+&*2+520=+/&$2+;$4/5-0+*2+*+Z52@`4*@.1+.B+/&0+4>4A.A+4*E0+&>;./&02$27+C5/+$/+$2+2/-$4/A>+ i5$/0+$1=0;01=01/+.B+$/7+*1=+/&0+^.=0A+.5/A$10=+*C.d0+&*2+/&0+*=d*1/*E0+.B+*44.51@1E+d0->+ 2*@2B*4/.-$A>+B.-+/&0+;&01.^01.1+.B+=01*/5-*@.17+;*-@45A*-A>+.1+*+25-B*40SY+ –! !0-1*A+X?&0+</-54/5-0+.B+,-./0$12Y+H*/5-0+J'K6KM+'96NRR6+ •! "*W+,0-5/D+J'KLKM7+-020*-4&+2/5=01/+.B+!0-1*Ao2+Xg+4*11./+-0^0^C0-+G&*/+!0-1*A+2*$=+*C.5/+ &>=-.;&.C$4+E-.5;2+$1+;-./0$127+C5/+g+=.+-0^0^C0-+C0$1E+d0->+$^;-0220=+C>+n*5D^*11o2+ -0d$0GY+ –! $1+?*1B.-=+,-./+<4$+J'KK(M+RN'6LT+ •! n*5D^*11o2+X<.^0+B*4/.-2+.1+/&0+$1/0-;-0/*@.1+.B+;-./0$1+=01*/5-*@.1Y+I=d*1402+$1+,-./0$1+ %&0^$2/->+J'KLKM+'9N'+$2+/&0+`-2/+*5/&.-$/*@d0++=$24522$.1+.B+X&>=-.;&.C$4+C.1=2Y+ + n*5D^*11+I=d+,-./+%&0^+J'KLKM+'9N'+ ...
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