Chemistry & Physics of Biomolecules

Biology 5357

Fall Term 2019

Coursemaster: Jay Ponder


General Information

Syllabus & Schedule [PDF]


Lecture Summaries

Lecture 1 (Aug 26): Taxonomy I: Primary & Secondary Structure [PDF]

Lecture 2 (Aug 28): Taxonomy II: Motifs & Supersecondary Structure [PDF]

Lecture 3 (Aug 30): Taxonomy III: Tertiary Structure & Fold Types [PDF]

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

Lecture 5 (Sep 6): Folding II: Mechanisms of Protein Folding [PDF]

Lecture 6 (Sep 9): Folding III: Characterization of Folding Pathways [PDF]

Lecture 7 (Sep 11): Protein Mutagenesis Experiments [PDF]

Lecture 8 (Sep 13): Molecular Dynamics Basics [PDF]

Lecture 9 (Sep 16): Protein Dynamics [PDF]

Lecture 10-12 (Sep 18-23): Protein Simulations & Markov State Modeling [PDF]

Lecture 13 (Sep 25): Protein Engineering: Structure Prediction & Design [PDF]

Lecture 14 (Sep 30): Polymer Statistics I: Basic Theory [PDF]

Lecture 15 (Oct 2): Polymer Statistics II: Real Chains & Applications [PDF]

Lecture 16 (Oct 4): Polymer Statistics III: Mixtures of Polymers [PDF]

Lecture 17 (Oct 7): Structure & Properties of Nucleic Acid Components [PDF]

Lecture 18 (Oct 9): Helix Assembly, A vs B vs Z DNA, Triplexes and Quadruplexes [PDF]

Lecture 19 (Oct 11): Nucleic Acid Folds [PDF]


Problem Sets and Answers

Proteins: Problem Set 1 [PDF] Answers [PDF]

Proteins: Problem Set 2 [PDF] Answers [PDF]

Proteins Module Exam (2017) [PDF] Answers [PDF]

Proteins Module Exam (2018) [PDF] Answers [PDF]


Discussion Section Articles

[For Section on Sep 5]
De Novo Design of Potent and Selective Mimics of IL-2 and IL-15,
D.-A. Silva, S. Yu, U. Y. Ulge, J. B. Spangler, K. M. Jude,
C. Labao-Almeida, L. R. Ali, A. Quijano-Rubio, M. Ruterbusch, I. Leung,
T. Biary, S. J. Crowley, E. Marcos, C. D. Walkey, B. D. Weitzner,
F. Pardo-Avila, J. Castellanos, L. Carter, L. Stewart, S. R. Riddell,
M. Pepper, G. J. L. Bernardes, M. Dougan, K. C. Garcia and D. Baker,
Nature, 565, 186-191 (2019) [PDF]

[For Section on Sep 12]
Partially Native Intermediates Mediate Misfolding of SOD1 in
Single-Molecule Folding Trajectories, S. S. Mojumdar, Z. N. Scholl,
D. R. Dee, L. Rouleau, U. Anand, C. Garen and M. T. Woodside,
Nature Communications, 8, 1881 (2017) [PDF]

[For Section on Sep 19]
Hidden Alternative Structures of Proline Isomerase Essential for Catalysis,
J. S. Fraser, M. W. Clarkson, S. C. Degnan, R. Erion, D. Kern & T. Alber,
Nature, 462, 669-674 (2009) [PDF]

[For Section on Sep 26]
Protein-Peptide Association Kinetics Beyond the Seconds Timescale from
Atomistic Simulations, F. Paul, C. Wehmeyer, E. T. Abualrous, H. Wu,
M. D. Crabtree, J. Schoneberg, J. Clarke, C. Freund, T. R. Weikl and F. Noe,
Nature Communications, 8, 1095 (2017) [PDF]

[For Section on Oct 10]
Innovative Scattering Analysis Shows that Hydrophobic Disordered
Proteins are Expanded in Water, J. A. Riback, M. A. Bowman,
A. M. Zmyslowski, C. R. Knoverek, J. M. Jumper, J. R. Hinshaw,
E. B. Kaye, K. F. Freed, P. L. Clark and T. R. Sosnick,
Science, 358, 238-241 (2017) [PDF]


Reading Materials & References

Protein Structure & Taxonomy

Proteins Are Polymers that Fold into Specific Structures, Chapter 1, Protein Actions,
I. Behar, R. L. Jernigan and K. A. Dill, pg. 1-28, Garland Science (2017) [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]

Interesting Web Sites for Protein Structural Analysis [PDF]

Protein Folding & Stability

Proteins Have Stable Equilibrium Conformations, Chapter 3, Protein Actions,
I. Behar, R. L. Jernigan and K. A. Dill, pg. 53-80, Garland Science (2017) [PDF]

Folding and Aggregration Are Cooperative Transitions, Chapter 5, Protein Actions,
I. Behar, R. L. Jernigan and K. A. Dill, pg. 107-128, Garland Science (2017) [PDF]

The Principles of Protein Folding Kinetics, Chapter 6, Protein Actions,
I. Behar, R. L. Jernigan and K. A. Dill, pg. 129-160, Garland Science (2017) [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]

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]

Polymer Physics

Polymer Physics, M. Rubinstein and R. H. Colby,
Oxford University Press, 2003, Chapter 2, Ideal Chains [PDF]

Polymer Physics, M. Rubinstein and R. H. Colby,
Oxford University Press, 2003, Chapter 3, Ideal Chains [PDF]

Polymer Physics, M. Rubinstein and R. H. Colby,
Oxford University Press, 2003, Chapter 4, Ideal Chains [PDF]

Nucleic Acid Structure & Folding

The Thermodynamics of DNA Structural Motifs, J. SantaLucia, Jr. and D. Hicks,
Annual Reviews of Biophys & Biomol Structure, 33, 415-440 (2004) [PDF]

Conformation Changes of Non-B DNA, J. Choi and T. Majima,
Chemical Society Reviews, 40, 5893-5909 (2011) [PDF]

The Free Energy Landscape of Pseudorotation in 3'-5' and
2'-5' Linked Nucleic Acids, L. Li and J. W. Szostak,
Journal of the American Chemical Society, 136, 2858-2865 (2014) [PDF]

Kinetics and Structures on the Molecular Path to the Quadruplex
Form of the Human Telomere, W. D. Wilson and A. Paul,
Journal of Molecular Biology, 426, 1625-1628 (2014) [PDF]

G-Quadruplexes: Prediction, Characterization, and
Biological Application, C. K. Kwok and C. J. Merrick,
Trends in Biotechnology, 35, 997-1013 (2017) [PDF]


Molecular Modeling Software

Software Information [TEXT]

VMD [DIR]

Chimera [DIR]

PyMOL [DIR]

KiNG [DIR]