Post on 30-Dec-2015
description
transcript
GlobularGlobularproteinsproteins
Fibrous proteinsFibrous proteins
H-bonds (NH:::OC)H-bonds (NH:::OC) & & hydrophobic forceshydrophobic forces
MembraneMembraneproteinsproteins
Secondary structures (Secondary structures (-helices-helices, , -strands-strands) ) are most conserved structural elements. are most conserved structural elements. They form a basis of protein classificationThey form a basis of protein classification
One protein - various One protein - various crystallization, NMRcrystallization, NMR
Homologous Homologous (closely related) (closely related)
proteinsproteins
PROTEIN HAS DEFINITE 3D STRUCTUREPROTEIN HAS DEFINITE 3D STRUCTURE
Globular proteinsGlobular proteins
Fibrous proteinsFibrous proteins
H-bonds (NH:::OC)H-bonds (NH:::OC) & & hydrophobic forceshydrophobic forces
MembraneMembraneproteinsproteins
SequenceSequence & & StructureStructure
PROTEIN CHAINPROTEIN CHAINCAN FORM ITS UNIQUE 3D STRUCTURE CAN FORM ITS UNIQUE 3D STRUCTURE
SPONTANEOUSLYSPONTANEOUSLYIN VITROIN VITRO
BIND BIND TRANSFORM TRANSFORM RELEASE RELEASE:: ENZYMES ENZYMES (chymotrypsin)(chymotrypsin)
Note small active siteNote small active site
POST-TRANSLATIONAL MODIFICATIONSPOST-TRANSLATIONAL MODIFICATIONSSometimes,Sometimes,
CHAIN CUT-INDUCED DEFORMATIONCHAIN CUT-INDUCED DEFORMATION MAKES ENZYME ACTIVEMAKES ENZYME ACTIVE
Chymotripsin ChymotripsinoChymotripsin Chymotripsinogengen
active active cat. sitecat. site
non-non-active active cat. sitecat. site
POST-TRANSLATIONAL MODIFICATIONS:POST-TRANSLATIONAL MODIFICATIONS:(especially in eukaryotes):(especially in eukaryotes):
PROTEIN CHAIN CUTS (proteolysis),PROTEIN CHAIN CUTS (proteolysis), - SPLICING (inteins) - SPLICING (inteins) - CYCLIZATION - CYCLIZATION - INTERNAL CHEM. TRANSFORMATION - INTERNAL CHEM. TRANSFORMATION
GLYCOSYLATION, etc. GLYCOSYLATION, etc.
MODIFICATION OF ENDS (acetylation, etc.)MODIFICATION OF ENDS (acetylation, etc.)
MODIFICATION OF SIDE CHAINS (S-S bonding,MODIFICATION OF SIDE CHAINS (S-S bonding, phosphorilation, etc.) phosphorilation, etc.)
COFACTORS …COFACTORS …
SometimesSometimes::
Different folds with the same active site: Different folds with the same active site: the same biochemical functionthe same biochemical function
SometimesSometimes::
Similar folds with different active sites: Similar folds with different active sites: different biochemical functiondifferent biochemical function
4-helix bundle
COFACTORS: HEME, 2Fe, RNA, …
Standard positions of active sites Standard positions of active sites in protein foldsin protein folds
PROTEIN PHYSICSPROTEIN PHYSICS
LECTURE 2LECTURE 2
Elementary interactions:Elementary interactions:covalentcovalent
Protein chainProtein chain::
regular backboneregular backbone&&
gene-encoded sequencegene-encoded sequenceof side chains of side chains
Protein chainProtein chain
Covalent bond Covalent bond lengths:lengths:
0.9 – 1.8 0.9 – 1.8 ÅÅ
Covalent bond Covalent bond angles:angles:
109109oo – 120 – 120oo
Atom radii:Atom radii:1 – 2 1 – 2 ÅÅ
Main-chainMain-chainpeptide group: peptide group: flat & rigidflat & rigid
Side Side chains: chains:
L-L-amino amino acidsacids
______
Protein chainProtein chain
____________ ____________
Ala Ala __LL
GlyGly
ThrThr
IleIle
TwoTwoasymmetricasymmetric side side chains:chains:
asymmetricasymmetricbackbone- backbone- side_chain:side_chain:
Peptide group: Peptide group: flat & rigidflat & rigid
sp2sp2 + + pp sp2sp2 + + pp
Covalent bondingCovalent bonding
CountingCountingangles: angles:
__________________________________________________________________________________________00oo180o
120o
Potentials: from IR spectra of vibrations Potentials: from IR spectra of vibrations
sp2 - sp2 (sp2 - sp2 () )
sp3 – sp3 (sp3 – sp3 () )
sp2 – sp3 (sp2 – sp3 () )
Pro Pro
All,All,but Probut Pro
CHCH33-CH-CH33 C-CHC-CH22-CH-CH22-C-C
__________________________________________________________________________________________classical