Under Construction

Biol 6312
Proteins
Spring 2005

This page will provide links to exercises designed for this course and to sites of general interest to students in this course.

Exam on April 4. Chapters in the book Section 1 (0,1,3-7,9,10,12-22) Section 2 (0-16) Section 5 (1-3) All lecture notes. Does not cover RasMol/Jmol/HTML.

Test pages for HW#4

• Urmi
• Oleg
• Andrea
• Genying
• Anima
• Indu
• Sandesh
• Manjunath

Structure Predictions (#6)

• Urmi
• Oleg
• Andrea
• Genying
• Anima
• Indu
• Sandesh
• Manjunath

Final projects

• Genying

• HW#1 Epsilon Subunit
• Alpha-Helix
• Disulfide
• Metal-Cysteine
• FAD
• PQQ
• Helix Bundle packing
• Variable Loops packing
• Leucine Zipper
• Proline Kinked Helix
• Knot
• Water in Protein Structure
• Glycine-glycine contacts in helix
• Beta-strands
• Type I turn
• Multiple domains of lac repressor
• 2 domains-back and forth
• gamma-crystallin-gene duplication
• Same fold-different functions
• Different folds-similar functions
• Convergent evolution-catalytic triads
• ROP-4 helix bundle
• Myohemerythrin-4 helix bundle
• Cytochrome b562-4 helix bundle
• Leptin&Growth hormone-4 helix bundles
• Myoglobin-globin fold
• Neuroglobin&cytoglobin-globin fold
• Phycocyanin-globin fold
• GCN4-Coiled coil
• Hetero-trimeric coiled-coil
• CRBP-Up&down β-barrel
• Immunoglobulin-β-sandwich
• Greek key: Gamma-crystallin or Immunoglobulin
• Allantoicase-Jelly roll fold
• Haemopexin-4-bladed beta-propeller
• G-protein beta subunit-7-bladed beta propeller
• Neuraminidase-6-bladed beta propeller
• TIM-alpha/beta barrel
• Flavodoxin-open twisted sheet
• Ribonuclease inhibitor-horseshoe fold
• TATA binding protein-alpha+beta fold
• Scorpion toxin-irregular fold
• Zinc finger-irregular fold
• Lactate Dehydrogenase-
• Motifs
• Coiled-Coils
• Hemagglutinin
• Prions
• Preparing a Chime Tutorial
• Temperature-sensitive Mutants of EcoR I
• Thermal Stability: Citrate Synthase
• Alpha-helical Membrane Protein: Bacteriorhodopsin
• Beta-sheet Membrane Protein: Porin/Hemolysin
• Serine Proteases

Nucleic Acids Research Database Issue 2005

Journals:

• To obtain full text, in some cases you must be on the university network. If not you must log in at the library on-line resources page: OR)
• Protein Science
• PNAS (Full text prior to 6 months ago.)
• Biochemistry
• Science (Full text prior to 6 months ago)
• Nature (Full text prior to one year ago.)
  • Nature Structural Biology
• Proteins (Full text)
• Annual Reviews of Biochemistry (Full text to 1997)
• Annual Review of Biophysics & (Full text to 1997)
• Journal of Biological Chemistry (Full text to 1980)
• Biophysical Journal (Full text prior to one year ago)

J. Molecular Biology
• Biochimica et Biophysica Acta (Full text to about 1995)
• Structure with Folding and Design (Full text to 1999)
• Cell
• Molecular Cell
• Trends in Biochemical Sciences (Full text to 1997)
• Current Opinion in Structural Biology (Full text to 1999)
• Biochemical and Biophysical Research Communications (Full text to 1997)
• Archives of Biochemistry and Biophysics (Full text to 1997)
• Structure with Folding and Design (Full text to 1999)
• Advances in Biophysics (Full text to 1995)

• EMBO Journal (Full text to 1997)

Other Links:

• Protein Data Bank
• RasMol Home Page
  • Latest RasMol
• HIC-Up
• Entrez Browser
• EXPASY (Swiss-Prot and more)
• CATH
• SCOP
• The Institute for Genomic Research
• EMBL
• PredictProtein
• Klotho
• Science's Functional Genomics
• 2005 Nucleic Acids Research Database Issue
• CE-MC:Multiple Protein Structure Alignment Server