Protein Secondary Structure, Bioinformatics Tools, and Multiple Sequence Alignments Finding Similar...

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