Protein-a chemical view A chain of amino acids folded in 3D Picture from on-line biology bookon-line biology book Peptide Protein backbone N / C terminal.

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Presentation transcript:

Protein-a chemical view A chain of amino acids folded in 3D Picture from on-line biology bookon-line biology book Peptide Protein backbone N / C terminal

Amino Acids 20 types in nature Different properties – side chain Positively charged – Arg, His, Lys A good reference site good reference site Negatively charged – Asp, Glu Polar but uncharged – Ser, Thr (OH), Asn, Gln(CO) Special – Cys, Gly, Pro Hydrophobic – Ala, IIe, Leu, Met, Phe, Trp, Tyr, Val, Generally:

Protein – a 3D view Bond length, bond angle – fairly restricted Torsion angles on backbone –  (phi),  (psi),  (omega) Picture from , mostly plane(180°, rare case 10°in cis) , , free but with an average characteristic distribution- Ramachandran plot

Torsion Angles Dihedral angles  (phi),  (psi),  (omega) N C N C 

Secondary structures Helix - hydrogen bond (CO) i -(NH) i+4  -helix ( ) 1.5 Å / residue  -sheet is composed of multiple  -strands Picture from site Zig-zag backbone, side-chains opposite directions, ~30°/residue twist, mostly antiparallel Hydrogen bond between two  -strands Turn, loop/coil

Protein tertiary and quaternary structure Tertiary – 3D folding of a polypeptide chain involves non-local interaction Quaternary – multiple chains/multi subunits PDB: SCOP database – protein classification

Super Secondary Structures  -hairpin 1, 2, 3, 4 residue hairpin,  -meander  -corner ext/chapter2.htm helix-hairpin Helix-loop-helix

Super Secondary Structures  -hairpin 1, 2, 3, 4 residue hairpin,  -meander  -corner ext/chapter2.htm helix-hairpin Helix-loop-helix

Classification of Structures Different classification methods Class, architecture, topology and homology CATH – hierarchy

Protein Folding Problem A protein folds into a unique 3D structure in physiological condition 3D structure is a key to understand function mechanism Rational drug design 3D structure prediction What is the protein folding problem?

Sequence  ?  Structure Globin fold 9 structures, 59 critical positions (31+28) 99% to 16% sequence homology No pattern in the critical residues Hydrophobicity of residue