Biophysik der Moleküle

kl. Phys. HS Mo 14:00-15:15 u. Do 9:00-10:00

2. Vorlesung Rädler WS 2010

Tutorials: Do 10-11 od. Do 11-12 od. Do 18-19

protein-conformation- the peptide bond

21. Oct. 2010

Monomer/ Oligomere Polymer/Aggregat

Zucker Glucose, Energie, Zellmarker

PolysaccharideStrukturbausteine

Fettsäuren Lipide, FettEnergiespeicher

MembranenKompartmentisierung

Nukleinsäuren ATP, cAMPEnergie, Signalsubstanzen

RNA, DNAInformationsspeicher

Aminosäuren PeptideHormone

Proteine, Enzyme. Motoren, molekulare

Erkennung

Op#scheAk#vitätEsgibtStoffe(z.B.Weinsäure),diediePolarisa#onsebenedeseinfallendenlinearpolarisiertenLichtsbeiDurchgangdurcheineSchichtdicke,l,drehen.

αs:spezifischerDrehwinkel

c:Konzentra#onl:Probenlänge

DerDrehwinkel,α,istbes#mmtdurch:

(Pasteur,1843)

BiologischeRelevanzvonStereoisomerie

Rechts/LinksNatrium‐Ammoniumtartrat

WirkungvonThalidomid(Contergan)

Links‐undrechtsdrehendeAminosäuren

Enan1omere:MolekülediesichzueinanderwieSpiegelbilderverhalten

Optical Rotation Dispersion and Circular Dichroism

210

,lo

m

_ 0

(c)

Schhati. sp.c\a Iot ü ottaeed roronrbi. (r) Ab@rption sF.l.um.(ü) CD Golz li@) ard oRD (dasr.l ti@) sperm ror a positi!€ corlon .flcct.(c) CD and ORD sFclm for. rcgaile Co(on.frccr.

C : lEol(nl - nJ/t dogr€es

d = 2.303(,{L -,4r)180/4,t d€Crees ellipticityoptical rotation

positiveCotton effect

negativeCotton effect

CD spectrum of poly-L-alanin (in a-helix conformation)

9

primarystructure

secondarystructure

tertiarystructure

quarternarystructure

There are 20Amino Acids

• hydrophobicity• polarity• charge

• aromaticity• size and shape

Properties of Amino Acids effect on protein structure

„subnanometerbuilding blocks“sorted by:

side groups:H, methyl, methylene, phenylene

aromatic

usually located on the interior of the protein

forms disulfide bridges

polar groups which cannot ionize easily

smallest amino acid

cyclic ringcreates fixedkink

polar hydoxyl groupsform H-bonds

polar amine groupsform H-bonds

Gly and Pro of particularconformational importance

+

+

- -

-

acidic

basic

imidazolside chain(pH sensitive)

Glu & Asp carboxyl groups

all mainly located at the hydrophilic surface of proteins

Lys & Arg amino groups

21. AA: Selenocystein

22. AA: Pyrrolysine

Selenocystein wird über einen als Rekodierung bezeichneten Mechanismus während der Translation eingebaut

Es gibt mehr als 20 Aminosäuren !

Pyrrolysin kommt in Methan umsetzenden Archaea Bakterien vor

The mesomeric effect 1) forces the atoms of the peptide bond to lie in one plane 2) leads to a strong dipol moment

The petide backbone prefers the trans-conformation

19

20

Steric repulsion limits the freedom of rotation

Ramachandra Plot

green: regime of sterically allowed anglesorange: location of secondary structures

22

primarystructure

secondarystructure

tertiarystructure

quarternarystructure

we need to studythe sterical constraintsand molecular interactions

The structure of the alpha helixis determined by H-bridges

24

The beta-sheet structure

25

26

Next challenge -understanding protein folding

Minimization of G=E-TS+PV

Minimize the solvation energy.Decrease the conformational entropy.