Protein Structure September 7, 12 2006.

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Presentation transcript:

Protein Structure September 7, 12 2006

Basics of Protein Structure Primary structure: sequence Secondary structure: α-helix, -sheet, -strand, loop Supersecondary structure, motifs Tertiary structure: folding into functional domains with ordered structure composed of secondary structure elements Quaternary structure Complexes of monomers to form active structures

Amino acid

20 amino acids - the building blocks

Amino acid categories Aliphatic Valine, Alanine, Leucine and Isoleucine Aromatic Phenylalanine, Tyrosine and Tryptophan Charged Aspartic, Glutamic, Histidine, Lysine, Arginine Polar Serine, Threonine, Cysteine, Methionine, Asparagine, Glutamine Odd couple Glycine, Proline

Aliphatic residues

Aromatic Residues

Charged Residues Side-chains are charged under physiological conditions Acid are negatively charged Basic are positively charged

Polar Residues

The Odd Couple

Peptide-bond formation

Backbone torsion angles w f phi y psi omega 180° trans 0° cis

Ramachandran Plot

Other chemical bonds Disulfide bonds or bridges Formed by oxidation of thiol groups of two cysteines Form a bond about 2Å in length. Predominant feature in many small proteins H-bonds not truly covalent Dipolar attraction between O and H Complex geometry wrt distances and angles

Side Chain Conformation

Side Chain Torsion Angles The side chain torsion angles are named c1(chi1), c2(chi2), c3 (chi3), etc., as shown below for lysine.

Hydrophilic or hydrophobic…? Virtually all soluble proteins feature a hydrophobic core surrounded by a hydrophilic surface Peptide backbone is inherently polar Neutralize potential H-donors & acceptors using ordered secondary structure

Alpha helix H-bonds between N-H and C=O groups in polypeptide backbone Compact structure 3.6 residues Pitch: 5.6Å/turn Rise: 1.5Å/residue Polar/hydrophilic residues on 1 face with nonpolar or hydrophobic residues on other face

Secondary Structure: -helix 3.6 residues / turn Axial dipole moment Not Proline & Glycine Protein surfaces

Beta-sheet Extended structure Side-chains project alternately up or down Amphipathic is solvent exposed polar residues on one side and non-polar on other side

Secondary Structure: -sheets

Secondary Structure: -sheets Parallel or antiparallel Alternating side-chains No mixing Loops often have polar amino acids

Parallel -sheets:

Antiparallel -sheets:

Silk fibroin

Supersecondary structures Also called motifs Simple combinations of secondary structures

-hairpins

Two-residue -hairpins

Three-residue -hairpins

-meander

corners are observed to have a right-handed twist when viewed from the concave side

Helix hairpins

The  corner

EF hand

 motifs

Greek Key Motif

Tertiary Structure Combinations of motifs to form domains Three main classes All alpha Alpha/beta All beta

Alpha Domain Structures Four helix bundle Globin fold

Myohemeyrthrin

Cytochrome b452

Ferritin

Globins

Packing of helices

Alpha/beta TIM barrel Rossmann fold Horseshoe fold

TIM Barrel

Horseshoe Fold

Rossmann Fold

All Beta Up and down barrels Greek key barrels Jelly roll barrels

Up and down barrel retinol binding protein

Greek Key Barrel

Jellyroll barrel

Beta helix

Protein Structure Databases CATH - Protein Structure Classification hierarchical classification of protein domain structures UCL, Janet Thornton & Christine Orengo clusters proteins at four major levels: Class(C) Architecture(A) Topology(T) Homologous superfamily (H) [ http://www.biochem.ucl.ac.uk/bsm/cath_new/ ]

Class(C) derived from secondary structure content is assigned automatically Architecture(A) describes the gross orientation of secondary structures, independent of connectivity. Topology(T) clusters structures according to their topological connections and numbers of secondary structures [ http://www.biochem.ucl.ac.uk/bsm/cath_new/ ]

Quaternary Structure

Quaternary Structure

Quaternary Structure

References "Crystallization, X-ray studies, and site-directed cysteine mutagenesis of the DNA-binding domain of OmpR", E. Martínez-Hackert, S. Harlocker, M. Inouye, H. M. Berman and A. M. Stock, Journal/Protein Sci., 5:1429-1433, 1996. http://www.cryst.bbk.ac.uk/ (School of Crystallography, Birkbeck, University of London) http://www.ebi.ac.uk/msd/roadshow.html (MSD-EBI Roadshow) "Introduction to protein structure", Brandon and Tooze, 3, 21, 1999.