Syllabus & Schedule [TEXT] [PDF]
Lecture 1 (Aug 27): Protein Taxonomy I: Primary & Secondary Structure [PDF]
Lecture 2 (Sep 1): Protein Taxonomy II: Motifs & Supersecondary Structure [PDF]
Lecture 3 (Sep 3): Protein Taxonomy III: Tertiary Structure & Fold Types [PDF]
Lecture 4 (Sep 8): Protein Folding I: Forces that Determine Structure [PDF]
Lecture 5 (Sep 10): Protein Folding II: Mechanisms of Protein Folding [PDF]
Special Topics (Sep 11): GPCRs: Transmembrane Signal Transduction [PDF]
Lecture 6 (Sep 16): Protein Folding III: Characterization of Folding Pathways [PDF]
Lecture 7 (Sep 17): Protein Folding IV: Mutagenesis Studies [PDF]
Lecture 8 (Sep 22): Protein Folding V: Structure Prediction & Design [PDF]
Lecture 9 (Sep 24): X-Ray I: Crystals, Symmetry, Diffraction, Bragg's Law [PDF]
Lecture 10 (Sep 29): X-Ray II: Structure Factors, Density & Patterson Maps [PDF]
Lecture 11 (Oct 2): X-Ray III: Phase Determination Methods & Refinement [PDF]
Lecture 12 (Oct 6-15): NMR: Folded and Disordered Proteins via NMR [PDF]
Lecture 13 (Oct 22-29): RNA I: Introduction to Ribonucleic Acids [PDF]
Lecture 14 (Nov 3-10): RNA II: Group I Introns and Folding [PDF]
Lecture 15 (Nov 12): RNA III: Ligand Binding by RNA [PDF]
Special Topics (Dec 4): Perturbation of Membrane Structures by Oxysterols [PDF]
Problem Set 1 [PDF] Answers [PDF]
Problem Set 2 [PDF] Answers [PDF]
Problem Set 3 [PDF] Answers [PDF]
Problem Set 4 [PDF]
Problem Set 5 [PDF] Answers [PDF]
Exam 1 from Fall 2007 [PDF] Answers [PDF]
Exam 1 from Fall 2009 [PDF] Answers [PDF]
The Anatomy and Taxonomy of Protein Structure, J. S. Richardson,
[Updated by D. C. Richardson and J. S. Richardson, 2000-2007]
Advances in Protein Chemistry, 34, 167-339 (1981)
[PDF]
Looking at Proteins: Representations, Folding, Packing, and Design,
J. S. Richardson, D. C. Richardson, N. B. Tweedy, K. M. Gernert,
T. P. Quinn,
M. H. Hecht, B. W. Erickson, Y. Yan, R. D. McClain, M. E. Donlan
and M. C. Surles,
Biophysical Journal, 63, 1186-1209 (1992)
[PDF]
Rules for Alpha Helix Termination by Glycine, R. Aurora, R. Srinivasan
and G. D. Rose, Science, 264, 1126-1130 (1994)
[PDF]
Semianalytical Treatment of Solvation for Molecular Mechanics and
Dynamics,
W. C. Still, A. Tempczyk, R. C. Hawley and T. Hendrickson,
Journal of the American Chemical Society, 112, 6127-6129 (1990)
[PDF]
Measuring the Conformational Stability of a Protein,
C. N. Pace and J. M. Scholtz,
from Protein Structure: A Practical Approach, 2nd Edition,
edited by T. Creighton, pg 299-321, Oxford University Press, 1997
[PDF]
Mutant Sequences as Probes of Protein Folding Mechanisms,
C. R. Matthews and M. R. Hurle, Bioessays, 6, 254-257 (1987)
[PDF]
Protein Stability Curves, W. J. Becktel and J. A. Schellman,
Biopolymers, 26, 1859-1877 (1987)
[PDF]
Understanding Protein Folding via Free-Energy Surfaces
from Theory and Experiment,
A. R. Dinner, A. Sali, L. J. Smith, C. M. Dobson and M. Karplus,
Trends in Biochemical Sciences, 25, 331-339 (2000)
[PDF]
The Protein Folding "Speed Limit", J. Kubelka, J. Hofrichter and
W. A. Eaton,
Current Opinion in Structural Biology, 14, 76-88 (2004)
[PDF]
The Protein Folding Problem, K. A. Dill, S. B. Ozkan, M. S. Shell and
T. R. Weikl, Annual Reviews of Biophysics, 37, 289-316 (2008)
[PDF]
X-Ray Diffraction and the Determination of Molecular Structure,
from Physical Chemistry with Applications to the Life Sciences,
D. Eisenberg and D. Crothers, pg 798-846, Benjamin/Cummings, Inc., 1979
[PDF]
X-Ray Diffraction, from Principles of Physical Biochemistry,
K. E. van Holde, W. C. Johnson and P. S. Ho,
Chapter 6, Pages 242-311, Prentice-Hall, Inc., 1998
[PDF]
Insights into the Sirtuin Mechanism from Ternary Complexes Containing
NAD+ and Acetylated Peptide, K. G. Hoff, J. L. Avalos, K. Sens and
C. Wolberger, Structure, 14, 1231-1240 (2006)
[PDF]
Questions:
1. How were the crystals prepared of the enzyme in complex with the peptide
and NAD+ substrates?
2. What are the specific types of data supporting the model for the bound
substrates (Fig. 1)?
3. How do the authors' results support the reaction mechanism proposed
in Fig. 6?
Interconversion Between Two Unrelated Protein Folds in the
Lymphotactin Native State,
R. L. Tuinstra, F. C. Peterson, S. Kutlesa, E. S. Elgin, M. A. Kron
and B. F. Volkman,
Proceedings of the National Academy of Sciences USA, 105,
5057-5062 (2008)
[PDF]
Software Information [TEXT]
KineMage [DIR]
RasMol [DIR]
PyMOL [DIR]
VMD [DIR]