Instructor: Glenn L. Millhauser, Department of Chemistry & Biochemistry  (chemistry.ucsc.edu/~glennm)
glennm-AT-chemistry.ucsc.edu
Office: 256 PSB  x92176
Office Hours: Mon 3:00-4:00

Important Note -- Guest Lectures by Prof. Scott Lokey on Wed and Fri, Feb 7th and 9th

download syllabus

Text: Protein Structure and Function by Petsko and Ringe, paperback at the bookstore and web version at www.new-science-press.com or www.sinauer.com

Optional Text: Bioinformatics for Dummies by Claverie and Notredame, available at the bookstore or at www.dummies.com

Calendar: first lecture, Friday Jan 5;  last lecture Wednesday Mar 14;  final Tuesday Mar 20, 8:00 AM
                   holidays, Mon Jan 15 and Mon Feb 19  (ucsc academic calendar)

Chemistry 200B is focused on many different aspects of protein structure and function including:
    • amino acids
    • polypeptide chains
    • Ramachandran space
    • secondary structure
    • helix folding
    • protein motifs
    • energetics of protein stability
    • protein representation
    • protein molecular dynamics
    • folding pathways
    • structure prediction
    • membrane proteins
    • protein preparation (synthesis, expression)
    • techniques in bioinformatics
    • diseases related to protein misfolding (Alzheimer’s, prions, ...)


Course assignments will consist of several problem sets and presentation of papers, with a possible final project or other activities related to the material.


There are several texts on reserve in the Science Library:
    Introduction to protein structure by Branden and Tooze
    Introduction to protein architecture : the structural biology of proteins by Arthur M. Lesk
    Biophysical chemistry, volumes 1,2 & 3 by Charles R. Cantor and Paul R. Schimmel
    Proteins : structures and molecular properties by Thomas E. Creighton


Weekly Papers

Problem Set #1 -- due Friday Jan 26

Problem Set #2 -- Due Wednesday Feb 21

Problem Set #3 -- due Tuesday March 20 by 5:00 pm
       (sequence for problem 1)


Handouts
formamide pi orbital
membrane proteins
conformational disease  (great review by Fabrizio & Dobson)
       March 10, 2007 article from SJ Mercury News on Parkinson's Disease (html, pdf)


Protein Viewers
       pymol -- elegant rendering capabilities, runs on numerous platforms
       molmol -- excellent for intermediate MW proteins and for showing both 2˚ structure and side chains, mainly for unix
       chimera -- Highly Recommended -- from uscf, easy to install and use, excellent graphics and available for lots of platforms
       Swiss-pdb viewer -- easy to use and available for lots of platforms
       cn3d -- the program of choice for pubmed, easy to install and use, more modern than rasmol, uses a non-pdb file format
       rasmol -- an old favorite, easy to use and available for lots of platforms but a bit out of date
       iMol -- very basic and easy to use, runs on macs

Databases
       the protein data bank -- where you can easily search and find all the structures
       pubmed -- protein sequences, as well as easy links to biomedical publications


Web Tools
    Helical Wheel Applet  -- note that you can slide through sequences longer than 18 residues with the arrow buttons

    Getting Protein Sequences from Pubmed
       enter protein name, an author, keyword, whatever
       select the protein you want
       set Display option to FASTA

    Getting Protein Sequences from Swiss-Prot (more specific than Pubmed)
       enter protein name, species and other key words
       click Go
       select your desired hit
       if you want FASTA format, scroll to bottom and clisk FASTA format

    Predicting Secondary Structure using PSIPRED
       paste in your desired sequence
       enter your email address
       server will email you the results

    Predicting Transmembrane Segments using hydropathy plots in ProtScale
       paste in your desired sequence
       select hydrophobicity scale and window size
       click submit

    Predict Transmembrane Segments using HMM using TMHMM
       paste in your sequence
       click submit -- wait a bit

    Finding Homologous Proteins using BLAST
       select protein-protein BLAST (blastp)
       paste in your sequence
       click BLAST!
       click Format!

    Multiple Sequence Alignment with T-COFFEE
       prepare a properly formatted sequence file (example with agouti sequences)
       either paste or upload your sequences
       click Run and wait a bit until alignment is complete
       for really nice output, click Start Jalview

    Multiple Sequence Alignment with ClustalW
       works pretty much the same way as T-COFFEE but offers more input/output options

last updated 03-13-07