Structural Alignment with SPRITE and Chimera

Overview

Teaching: 30 min
Exercises: 120 min

Questions

• How can structural alignment be used to study protein function?

Objectives

• Students will describe typical characteristics of an enzyme active site. Students will understand and be able to explain the term motif and apply it to enzyme active sites.

• Students will be able to query structures of unknown function against a library of enzyme active site motif templates.

• Students will distinguish between good alignments and poor alignments.

• Students will propose a function for proteins of unknown function and develop plans for testing their hypothesis in silico and in vitro.

SPRITE is a software package that can search the structure of a protein to determine if it has an active site with a motif of known catalytic function. The active site of an enzyme is the region of the protein where the substrate binds and the chemical reaction takes place. This is often a groove or pocket on the surface of the enzyme that allows the substrate to bind. This region also contains the amino acids necessary for catalysis to occur. The arrangement of those amino acids in space is called a motif.

Module Resources

Access student module here

Key Points

• Your students will use a computer alignment algorithm that includes quantitative measures and visual inspection to measure quality of alignments.

• These results can be compared and contrasted with sequence alignment (BLAST, Pfam) and and full backbone alignment (Dali) results in other BASIL modules.