Chemistry & Physics of Biological Molecules

Biology 5357 / Medical School M15

Fall Term 2011

Coursemaster: Jay Ponder


General Information

Syllabus & Schedule [TEXT] [PDF]


Lecture Summaries

Lecture 1 (Aug 30): Protein Taxonomy I: Primary & Secondary Structure [PDF]

Lecture 2 (Sep 1): Protein Taxonomy II: Motifs & Supersecondary Structure [PDF]

Lecture 3 (Sep 6): Protein Taxonomy III: Tertiary Structure & Fold Types [PDF]

Lecture 4 (Sep 8): Protein Folding I: Forces that Determine Structure [PDF]

Lecture 5 (Sep 13): Protein Folding II: Mechanisms of Protein Folding [PDF]

Lecture 6 (Sep 15): Protein Folding III: Characterization of Folding Pathways [PDF]

Lecture 7 (Sep 20): Protein Folding IV: Mutagenesis Studies [PDF]

Lecture 8 (Sep 22): Protein Folding V: Structure Prediction & Design [PDF]

Lecture 9 (Sep 27): X-Ray I: Crystals, Symmetry, Diffraction, Bragg's Law [PDF]

Lecture 10 (Sep 29): X-Ray II: Structure Factors, Density & Patterson Maps [PDF]

Special Topics (Sep 30): Protein Crystallography in Practice [PDF]

Lecture 11 (Oct 4): X-Ray III: Phase Determination Methods & Refinement [PDF]

Lecture 12 (Oct 6): NMR I: Introduction of NMR [PDF]

Lecture 13 (Oct 7): NMR II: J-Coupling, H-Bonds & Chemical Shift Mapping [PDF]

Lecture 14 (Oct 11): NMR III: Structure Determination by NMR [PDF]

Lecture 15 (Oct 13): NMR IV: Protein Dynamics by NMR [PDF]

Lecture 16 (Oct 18): NMR V: Disordered & Unfolded Proteins [PDF]

Lecture 17 (Oct 25): Nucleic Acids I: Revisiting the Central Dogma [PDF]

Lecture 18 (Oct 27): Nucleic Acids II: Introduction to Structure [PDF]

Lecture 19 (Nov 1): Nucleic Acids III: Structure of RNA [PDF]

Lecture 20 (Nov 3): Nucleic Acids IV: RNA Tertiary Interactions [PDF]

Lecture 21 (Nov 4): Nucleic Acids V: Fluorescence Experiments [PDF]

Lecture 22 (Nov 8): Nucleic Acids VI: RNA-Ligand Binding [PDF]

Lecture 23 (Nov 10): Nucleic Acids VII: RNA Folding- Principles & Practice [PDF]

Lecture 24 (Nov 15): Nucleic Acids VIII: Tetrahymena Group I Intron [PDF]

Lecture 25 (Nov 17): Nucleic Acids IX: Small Ribozymes [PDF]

Lecture 26 (Nov 22): Introduction to Membranes [PDF]

Lecture 27 (Dec 1): What Makes a Membrane? [PDF]

Special Topics (Dec 2): Membrane Protein Structure & Function [PDF]

Lecture 28 (Dec 8): Stability, Environment and Interaction [PDF]

Special Topics (Dec 9): Ion Channels & Electrical Signaling [PDF]


Problem Sets and Exams

Problem Set 1 [PDF] Answers [PDF]

Problem Set 2 [PDF] Answers [PDF]

Problem Set 3 [PDF] Answers [PDF]

Problem Set 4 [PDF] Answers [PDF]

Problem Set 5 [PDF] Answers [PDF]

Problem Set 6 [PDF] Answers [PDF]

Problem Set 7 [PDF]

Exam 1 from Fall 2009 [PDF] Answers [PDF]

Exam 1 from Fall 2011 [PDF] Answers [PDF]

Exam 2 from Fall 2010 [PDF]

Exam 2 from Fall 2011 [PDF]


Handouts & Reading

Protein Structure & Taxonomy

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]

Interesting Web Sites for Protein Structural Analysis [PDF]

Protein Folding and Stability

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 Crystallography

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]

The Structural Immunology of Antibody Protection against West Nile Virus,
M. S. Diamond, T. C. Pierson and D. H. Fremont,
Immunological Reviews, 225, 212-225 (2008) [PDF]

NMR Spectroscopy

Mechanism of Coupled Folding and Binding of an Intrinsically Disordered Protein,
K. Sugase, H. J. Dyson and P. E. Wright,
Nature, 447, 1021-1025 (2007) [PDF]

Nucleic Acids

The Antiquity of RNA-Based Evolution, G.F. Joyce,
Nature, 418, 214-221 (2002) [PDF]

Folding and Finding RNA Secondary Structure,
D. H. Matthews, W. N. Moss and D. H. Turner,
Cold Spring Harbor Perspectives in Biology, August 4, 2010 [PDF]

The Molecular Interactions That Stabilize RNA Tertiary Structure:
RNA Motifs, Patterns, and Networks, S. E. Butcher and A. M. Pyle,
Accounts of Chemical Research, 44, xxx-xxx (2011) [PDF]

Membranes

Ion Channels and Electrical Signaling,
Jim Huettner, (lecture handout for 9 Dec 2012) [PDF]


Molecular Modeling Software

Software Information [TEXT]

KiNG [DIR]

RasMol [DIR]

PyMOL [DIR]

VMD [DIR]