Introduction & overview

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Presentation transcript:

Introduction & overview PROTEIN PHYSICS LECTURE 1 Introduction & overview

Globular proteins Membrane proteins Fibrous proteins H-bonds (NH:::OC) & hydrophobic forces

Protein chain (gene-encoded sequence)

PROTEIN HAS DEFINITE 3D STRUCTURE Homologous (closely related) proteins One protein - various crystallization, NMR Secondary structures (a-helices, b-strands) are most conserved structural elements. They form a basis of protein classification

Globular proteins Sequence & Structure Membrane proteins Fibrous proteins H-bonds (NH:::OC) & hydrophobic forces

C A T H Globular domains

CAN FORM ITS UNIQUE 3D STRUCTURE PROTEIN CHAIN CAN FORM ITS UNIQUE 3D STRUCTURE SPONTANEOUSLY IN VITRO

BIND  TRANSFORM  RELEASE: ENZYMES (chymotrypsin) Note small active site

non-active cat. site active cat. site POST-TRANSLATIONAL MODIFICATIONS Sometimes, CHAIN CUT-INDUCED DEFORMATION MAKES ENZYME ACTIVE non-active cat. site active cat. site Chymotripsin Chymotripsinogen

POST-TRANSLATIONAL MODIFICATIONS: (especially in eukaryotes): PROTEIN CHAIN CUTS (proteolysis), - SPLICING (inteins) - CYCLIZATION - INTERNAL CHEM. TRANSFORMATION GLYCOSYLATION, etc. MODIFICATION OF ENDS (acetylation, etc.) MODIFICATION OF SIDE CHAINS (S-S bonding, phosphorilation, etc.) COFACTORS …

Different folds with the same active site: Sometimes: Different folds with the same active site: the same biochemical function

COFACTORS: HEME, 2Fe, RNA, … 4-helix bundle COFACTORS: HEME, 2Fe, RNA, … Sometimes: Similar folds with different active sites: different biochemical function

Standard positions of active sites in protein folds

Elementary interactions: PROTEIN PHYSICS LECTURE 2 Elementary interactions: covalent

gene-encoded sequence Protein chain: regular backbone & gene-encoded sequence of side chains

Covalent bond lengths: Protein chain Covalent bond lengths: 0.9 – 1.8 Å Covalent bond angles: 109o – 120o Atom radii: 1 – 2 Å

Side chains

Side chains: L-amino acids Protein chain Side chains: L-amino acids ___ ______ ______ Main-chain peptide group: flat & rigid

backbone- side_chain: Gly asymmetric backbone- side_chain: Ala _L Thr Two asymmetric side chains: Ile

Peptide group: flat & rigid sp2 + p sp2 + p Covalent bonding

Main-chain: f (N-Ca) , y (Ca-C’), w (C’=N) Side-chain: c1, c2, ...

_____________________________________________ Counting angles: 120o 180o 0o _____________________________________________

sp2 - sp2 (w) w = 180o w = 0o

Potentials: from IR spectra of vibrations _____________________________________________ classical Pro sp2 - sp2 (w) All, but Pro sp3 – sp3 (c) C-CH2-CH2-C CH3-CH3 sp2 – sp3 (f, y)