Protein Structure and Function

Biology 5325 / Medical School M15

Fall Term 2006

Coursemaster: Jay Ponder

General Information

Syllabus & Schedule [TEXT] [PDF]

Lecture Summaries

Lecture 1 (Aug 31): Taxonomy I: Primary & Secondary Structure [PDF]

Lecture 2 (Sep 5): Taxonomy II: Motifs & Supersecondary Structure [PDF]

Lecture 3 (Sep 7): Taxonomy III: Tertiary Structure & Fold Types [PDF]

Lecture 4 (Sep 12): Folding I: Forces that Determine Protein Structure [PDF]

Lecture 5 (Sep 14): Folding II: Mechanisms of Protein Folding [PDF]

Lecture 6 (Sep 19): Folding III: Characterization of Folding Pathways [PDF]

Lecture 7 (Sep 21): Folding IV: Mutagenesis Studies [PDF]

Lecture 8 (Sep 26): Special Topics I: Electrostatics and Solvation [PDF]

Lecture 9 (Sep 28): Spectroscopy I: Background and Basic Principles [PDF]

Lecture 10 (Oct 3): Spectroscopy II: Absorption and Fluorescence [PDF]

Lecture 11 (Oct 5): Spectroscopy III: Circular Dichroism and Optical Rotation [PDF]

Lecture 12 (Oct 10): Spectroscopy IV: Fluctuation Spectroscopy [PDF]

Lecture 13 (Oct 12): Spectroscopy V: Mass Spectrometry [PDF]

Lecture 14 (Oct 17): Protein Design I: Structural Scaffolds [PDF]

Lecture 15 (Oct 19): Protein Design II: Enzymatic Function [PDF]

Lecture 16 (Oct 26): NMR I: Basic NMR Principles and Parameters [PDF]

Lecture 17 (Oct 31): NMR II: Vector & Product Operator Formalisms [PDF]

Lecture 18 (Nov 2): NMR III: Heteronuclear Correlation Experiments [PDF]

Lecture 19 (Nov 7): NMR IV: Resonance Assignment Strategies [PDF]

Lecture 20 (Nov 9): NMR V: Protein Structure Determination [PDF]

Lecture 21 (Nov 14): Special Topics II: 19F NMR Studies of Protein Folding [PDF]

Lecture 22 (Nov 16): Special Topics III: GPCR Signal Transduction [PDF]

Lecture 23 (Nov 21): NMR VI: Further Applications of NMR [PDF]

Lecture 24 (Nov 28): X-Ray I: Biological Imaging by X-Ray Diffraction [PDF]

Lecture 25 (Nov 30): X-Ray II: Crystals - Growth & Physical Properties [PDF]

Lecture 26 (Dec 5): X-Ray III: X-Ray Data Collection [PDF]

Lecture 27 (Dec 7): X-Ray IV: Phasing by Isomorphous Replacement [PDF]

Lecture 28 (Dec 12): X-Ray V: Phasing by Molecular Replacement [PDF]

Problem Sets and Exams

Problem Set 1 [PDF] Answers [PDF]

Problem Set 2 [PDF] Answers [PDF]

Problem Set 3 [PDF] Answers [PDF]

Exam 1 Questions from 2005 [PDF]

Exam 2 Questions from 2005 [PDF]

Exam 1 Answer Key from 2006

Exam 2 Answer Key from 2006 [PDF]

Handouts & Reading - Structure & Folding

Useful Web Sites for Protein Sequence and Structure Analysis [PDF]

Measuring the Conformational Stability of a Protein,
C. N. Pace, B. A. Shirley and J. A. Thomson,
from Protein Structure: A Practical Approach,
edited by T. Creighton, pg 311-330, Oxford University Press, 1987 [PDF]

Mutant Sequences as Probes of Protein Folding Mechanisms,
C. R. Matthews and M. R. Hurle, Bioessays, 6, 254-257 (1987) [PDF]

The Protein Folding "Speed Limit", J. Kubelka, J. Hofrichter and W. A. Eaton,
Current Opinion in Structural Biology, 14, 76-88 (2004) [PDF]

Handouts & Reading - Optical Spectroscopy

The Interactions of Matter with Light I: The Classical Electron Theory of Optics,
from Quantum Chemistry, by W. Kauzmann, pg 546-585, Academic Press, 1957 [PDF]

Handouts & Reading - Nuclear Magnetic Resonance

Overview and Study Guide for Protein NMR Lectures [PDF]

Introduction to NMR, from Biomolecular NMR Spectroscopy,
by J. N. S. Evans, Ch 1, pg 3-54, Oxford University Press, 1995 [PDF]

Product Operator Formalism & Vector Model,
from A Handbook of Nuclear Magnetic Resonance, 2nd Edition,
by R. Freeman, pg 185-194 & 328-333, Addison-Wesley Longman, 1997 [PDF]

Polarization Transfer,
from A Handbook of Nuclear Magnetic Resonance, 2nd Edition,
by R. Freeman, pg 178-184, Addison-Wesley Longman, 1997 [PDF]

Two-Dimensional Spectroscopy,
from A Handbook of Nuclear Magnetic Resonance, 2nd Edition,
by R. Freeman, pg 318-326, Addison-Wesley Longman, 1997 [PDF]

Correlation Spectroscopy,
from A Handbook of Nuclear Magnetic Resonance, 2nd Edition,
by R. Freeman, pg 76-83, Addison-Wesley Longman, 1997 [PDF]

Handouts & Reading - X-Ray Crystallography

X-Ray Diffraction, from Principles of Physical Biochemistry,
by K. E. van Holde, W. C. Johnson and P. S. Ho, pg 242-311, Prentice-Hall, Inc., 1998 [PDF]

The hkl Manual, by D. Gewirth [PDF]

Modeling Software

Software Information [TEXT]

KineMage [DIR]

RasMol [DIR]