AndMotioninBiology

CS273:AlgorithmsforStructure Handout#5
andMotioninBiology
StanfordUniversity Tuesday,13April2004
Lecture#5: 13April2004
Topics: Sequencemotifidentification
Scribe: SamanthaChui

1. 1.Introduction

Aprotein’sfunctionisdeterminedbyit’s3-Dstructure,whichinturnisdeterminedby the specific amino acid sequence. It is this sequence which directs the folding of theprotein into its major configuration.The goal then is to predict the 3-D folding of aprotein given its amino acid sequence. This is done by looking for structural motifs andpositions of specific secondary structures. Several programs have written to predict thesestructures,includingNewCoils,PairCoil,BetaWrap,PSIPRED,andTRILOGY.

2. 2.ProteinHierarchy

Theprimarystructureofaproteinisitsaminoacidsequence.Thesecondarystructureis the initial folding of the sequence into alpha helices and beta sheets.The tertiarystructure is a more complex folding of the protein upon itself. The quarternary structureis the combination of two or more of the same protein. And finally, the supramolecularstructure is the combination of several different protein subunits. It is this 3-D structurethat determines the function of the protein,either for signaling,transport,catalysis,movement,structure,orregulation.

1. 2.1.PrimaryStructure

Aproteinistypeapolymerwhichismadeupofaseriesofmonomers,aminoacids.Thereare twenty different kinds of amino acids. They can be categorized into three groups: 1)hydrophilic,2)hydrophobic,and3)special(Figure1).
The hydrophilic amino acids can be further categorized as either basic or acidic. Basichydrophilicaminoacidsarepositivelychargedwhereasacidichydrophilicaminoacidsarenegativelycharged,accordingtothepolarityoftheRgroup.
Thesetwentyaminoacidshavedistinctshapesandproperties.Theyarejoinedinasequenceviapeptidebonds.Peptidebondsareformedthroughhydrolysisbetweenthecarboxyl group of oneamino acid andthe amino groupof another.

Figure1:Categoriesofaminoacids

2.