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

NOTE:  With the end of the quarter, some links below have been disabled.

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, Wednesday Jan 9;  last lecture Monday Mar 17;  final Thursday Mar 20, 8:00 AM
                   holidays, Mon Jan 21 and Mon Feb 18  (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


Problem Set #1 -- due Feb 11 in class

Problem Set #2 -- due March 5 in class 

Problem Set #3 -- due March 21 in Glenn's dept mailbox



Weekly Papers


Handouts
formamide pi orbital    see the pi bond electron density for a peptide bond

membrane proteins

serpin video from Huntington  Trends in Biochemical Sciences  2006  vol. 31, 427-435


Neurodegenerative disease links
    handout from class

    great review by Chiti and Dobson

    life with Parkinson's -- wonderful article from the Merc about living with the disease and the hope for a cure



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

    Structural Classification of Proteins (SCOP) database
       click on "top of hierarchy" and start browsing your favorite structure classes
       have Chimera open side-by-side with SCOP to examine various structures

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

    Predicting Structure using HMM  SAM-T06 (developed by K. Karplus and colleagues, UCSC)
        enter your email address
        select "Email the secondary structure predictions" and any other desired options
        paste in your desired sequence -- FASTA format required
        takes a bit of computational time -- Logo output for secondary structure is elegant (key to code)

    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 blast
       paste in your sequence
       click BLAST

    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 03-27-08