Lecture4

Lecture4 - #1 Concepts: secondary structure prediction...

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Unformatted text preview: #1 Concepts: secondary structure prediction sequence comparison domains linkers Quaternary structure- Homo vs. hetero oligomers Subunits Allostery Architectures types- globular proteins filamentous, structural proteins membrane proteins supermolecular assemblies Examples #2 Predicting folds: alpha-helix propensity KRVKNYRKRVEDELAKVCNDILSVIDHHDL-algorithm to look at each aa in a protein sequence and neighboring (~7 on each side) and add up their helical propensity to score that aa-do this down the protein => if regions where score is high for consecutive aa, then predict helix-similar scoring for beta-sheets and turns-based on counting how many times a given aa shows up in an alpha helix in known protein structures #3 #4 Eight proteins with the same fold- Sequences should be at least: A. 100% identical B. 90% identical C. 50% identical D. 20% identical #5 Which amino acid pairs are most chemically similar? Least? A. valine and alanine B. phenylalanine and isoleucine C. asparagine and lysine D. tryptophan and aspartate #6 Sequence comparison: conservation=> identity => similarity => gaps => #7 Highly conserved identical residues => Residues with conserved similarity => Highly variable residues => #8 Scoring similarity based on conservation: How often is an aa different between related structures? If it is different, what aa takes its place? #9 BLOSSUM scores correlate with chemical similarity #10 Back to sequence alignment: finding proteins or regions of proteins with sequence similarity => -use BLOSSUM matrix to score potential matches. BLAST: commonly used alignment algorithm #11 Multi-domain proteins: linkers go to PyMol src #43 Oligomers: Dimers, Trimers, Tetramers, etc. homo-oligomer hetero-oligomer buried surface area Go to Pymol exosome, PK #44 Filamentous proteins #45 Collagen go to PyMol proline #46 Membrane proteins Would it be favorable for an alpha-helix to sit sideways in the membrane?...
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This note was uploaded on 01/17/2011 for the course BIOC 100A taught by Professor Harrynoller during the Fall '10 term at UCSC.

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Lecture4 - #1 Concepts: secondary structure prediction...

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