Proteina chemical view

1
Protein-a chemical view

• A chain of amino acids folded in 3D

• Peptide
• Protein backbone
• N / C terminal

• Picture from on-line biology book

2
Amino Acids

• 20 types in nature

• Different properties side chain

Generally

• Positively charged Arg, His, Lys

• 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,

• A good reference site http//www.emc.maricopa.edu/
  faculty/farabee/BIOBK/BioBookCELL2.html

3
Protein a 3D view

• Bond length, bond angle fairly restricted

• Torsion angles on backbone
• ?(phi), ?(psi), ?(omega)

• ?, mostly plane(180, rare case 10in cis)
• ?, ?, free but with an average characteristic
  distribution- Ramachandran plot

• Picture from http//www.expasy.org/swissmod/course
  /text/chapter1.htm

4
Torsion Angles

• Dihedral angles

?(phi), ?(psi), ?(omega)
N
C
?
C
N
5
Secondary structures

• Helix - hydrogen bond (CO)i-(NH)i4
• ?-helix (3.613) 1.5Å / residue

• ?-sheet is composed of multiple ?-strands

• Hydrogen bond between two ?-strands

• Zig-zag backbone, side-chains opposite directions
  , 30/residue twist, mostly antiparallel

Picture from www.expasy.org site http//www.expasy
.org/swissmod/course/text/chapter1.htm

• Turn, loop/coil

6
Protein tertiary and quaternary structure

• Tertiary 3D folding of a polypeptide chain
• involves non-local interaction

• Quaternary multiple chains/multi subunits

PDB http//www.pdb.org
SCOP database protein classification
7
Super Secondary Structures

• ?-hairpin
• 1, 2, 3, 4 residue hairpin, ?-meander

• ?-corner

• helix-hairpin

• Helix-loop-helix

http//swissmodel.expasy.org/course/text/chapter2.
htm
8
Super Secondary Structures

• ?-hairpin
• 1, 2, 3, 4 residue hairpin, ?-meander

• ?-corner

• helix-hairpin

• Helix-loop-helix

http//swissmodel.expasy.org/course/text/chapter2.
htm
9
Classification of Structures

• Different classification methods

• CATH hierarchy

• Class, architecture, topology and homology

• http//www.cathdb.info/latest/index.html

10
Protein Folding Problem

• A protein folds into a unique 3D structure in
  physiological condition

• What is the protein folding problem?

• 3D structure is a key to understand function
  mechanism

• Rational drug design

• 3D structure prediction

11
Sequence? ? ?Structure

• Globin fold

• 99 to 16 sequence homology

• 9 structures, 59 critical positions (3128)

• No pattern in the critical residues
• Hydrophobicity of residue