Sequence analysis courseSequence analysis course

Lecture 8

Sequence databank searching 1

Protein main-chain and side-chain

‘R’ designates the side-chain

charge

(cystein bridge)

VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

PRIMARY STRUCTURE (amino acid sequence)

QUATERNARY STRUCTURE (oligomers)

SECONDARY STRUCTURE (helices, strands)

TERTIARY STRUCTURE (fold)

Protein structure hierarchical levelsProtein structure hierarchical levels

Compared to preceding plot, RMSD is better able to pin-point relationships between more divergent sequences (RMSD stays relatively small for a longer time as compared to PAM distance). Note that the spread around RMSD is larger