Protein Secondary Structure,Bioinformatics Tools, and

Multiple Sequence Alignments

Finding Similar SequencesPredicting Secondary Structures

Predicting Protein Folds (Tertiary Structures)

Tools for Identifying Protein Domains based only on Primary Sequence: PROSITE

What is the local sequence preference: a-helix or b-strand or random?

Tools for finding Similar Proteins: FASTA

Also identifies reported crystal structures

Alternative Site: BLAST identifies Similar Proteins

Sequence Alignment Matrix

V A T T P D K S W L T VA 0 5 0 0 1 0 0 1 -2 -1 0 0S -1 1 2 2 0 0 0 5 0 -1 2 -1T 0 0 5 5 0 0 0 2 -1 0 5 0P -1 1 0 0 8 0 0 0 -3 -2 0 -1E -2 1 1 1 1 2 1 1 -2 -2 1 -2R -1 -1 0 0 0 -2 2 1 0 -1 0 -1A 0 5 0 0 1 0 0 1 -2 -1 0 0S -1 1 2 2 0 0 0 5 0 -1 2 -1W -1 -2 -1 -1 -3 -3 -2 0 6 0 -1 -1L 2 -1 0 0 -2 -2 -1 -1 0 5 0 2G -1 0 -1 -1 0 0 0 0 -2 -2 -1 -1T 0 0 5 5 0 0 0 2 -1 0 5 0A 0 5 0 0 1 0 0 1 -2 -1 0 0

Sequence A:VATTPDKSWLTV

Sequence B:ASTPERASWLGTA

VATTPDK-SWLTV- |*||** |||-ASTPERASWLGTAscore 39

VATTPDK-SWL-TV |*||** ||| |*-ASTPERASWLGTAscore 45

Multiple Sequence Alignment

Sequence A:LTLTLTLT

Sequence B:HAHAHAHAH

Sequence C:THTHTHTHT

LTLTLTLT-HAHAHAHAHscore -4

-LTLTLTLTHAHAHAHAHscore 0

-LTLTLTLT- | | | |THTHTHTHT- | | | |-HAHAHAHAH

The third sequence from a homologous protein allows alignment It’s a very good idea to have more than one template!

Multiple Sequence Alignment

Can also display helices, beta-sheets; buried vs exposed; Look for a consensus of different methods, etc

Conclusions

Bioinformatics Tools: Can be based on Statistical Analysis, or Scoring, or Physics

Sequence matching is the realm of computer science more than chemistry/biochemistry

Biochemistry/Chemistry is fundamental to 3D structure prediction