14 - Lecture 14 Protein structure and design Sunday October...

Info iconThis preview shows pages 1–7. Sign up to view the full content.

View Full Document Right Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: Lecture 14: Protein structure and design Sunday, October 3, 2010 Despite significant advances in understanding protein structure and folding, our ability to predict the secondary or tertiary structure from the primary structure or design a protein from scratch is severely limited. However, there are a few tools we can use to address this problem. Sunday, October 3, 2010 Secondary structure prediction : the Chou-Fasman method . Using a set of well-determined protein structures, they first tabulated the frequency (F) that a given amino acid occurs in a secondary structure motif (helix, sheet or turn/random coil): F(helix) = # occurrences in helix/total # occurrences Then the PROPENSITY (P) for that amino acid to be part of a helix is then calculated by: (Ala, for example) P (helix,Ala) = F(helix,Ala)/ave. F(helix, all amino acids) Sunday, October 3, 2010 When tabulated, this generates the following table: (which we saw in a slightly different form in the last lecture, same idea) Sunday, October 3, 2010 This can then be used to analyze a sequence of amino acids for the potential to form elements of secondary structure Sunday, October 3, 2010 What we are looking for are four amino acid stretches that have high helix-forming propensities or three amino acid stretches that have high sheet-forming propensities. that have high sheet-forming propensities....
View Full Document

This note was uploaded on 11/12/2010 for the course CHEN 3320 at Colorado.

Page1 / 16

14 - Lecture 14 Protein structure and design Sunday October...

This preview shows document pages 1 - 7. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online