Chemistry & Physics of Biomolecules

Biology 5357

Fall Term 2018

Coursemaster: Jay Ponder


General Information

Syllabus & Schedule [PDF]


Lecture Summaries

Lecture 1 (Aug 27): Taxonomy I: Primary & Secondary Structure [PDF]

Lecture 2 (Aug 29): Taxonomy II: Motifs & Supersecondary Structure [PDF]

Lecture 3 (Aug 31): Taxonomy III: Tertiary Structure & Fold Types [PDF]

Lecture 4 (Sep 5): Folding I: Forces that Determine Structure [PDF]

Lecture 5 (Sep 7): Folding II: Mechanisms of Protein Folding [PDF]

Lecture 6 (Sep 10): Folding III: Characterization of Folding Pathways [PDF]

Lecture 7 (Sep 12): Mutagenesis Experiments; Molecular Dynamics Basics [PDF]

Lecture 8 (Sep 14): Protein Dynamics [PDF]

Lecture 13 (Sep 26): Electron Microscopy & Protein Assemblies [PDF]

Lecture 14 (Oct 1): Structure & Properties of Nucleic Acid Components [PDF]

Lecture 15 (Oct 3): A vs B vs Z DNA, Triplexes and Quadruplexes [PDF]

Lecture 16 (Oct 5): Nucleic Acid Folds [PDF]

Lecture 17 (Oct 8): Single Molecule Methods: Optical Trapping [PDF]

Lecture 18 (Oct 10): Single Molecule Methods: Magnetic Trapping [PDF]

Lecture 19 (Oct 12): Polymer Statistics I: Basic Theory [PDF]

Lecture 20 (Oct 17): Polymer Statistics II: Real Chains & Applications [PDF]

Lecture 21 (Oct 19): Polymer Statistics III: Mixtures of Polymers [PDF]


Problem Sets and Answers

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

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

Proteins: Problem Set 3 [PDF] Answers [PDF]

Proteins: Problem Set 4 [PDF] Answers [PDF]

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

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

Nucleic Acids Module Exam (2017) [PDF] Answers [PDF]


Discussion Section Articles

[For Section on Sep 6]
Principles for Designing Proteins with Cavities Formed by Curved Beta-Sheets,
E. Marcos, B. Basanta, T. M. Chidyausiku, Y. Tang, G. Oberdorfer, G. Liu,
G. V. T. Swapna, R. Guan, D.-A. Silva, J. Dou, J. H. Pereira, R. Xiao,
B. Sankaran, P. H. Zwart, G. Montelione and D. Baker,
Science, 355, 201-206 (2017) [PDF]

[For Section on Sep 13]
The Kinetics of Folding of Frataxin,
D. Bonetti, A. Toto, R. Giri, A. Morrone, D. Sanfelice,
A. Pastore, P. Temussi, S. Gianni and M. Brunori,
Physical Chemistry Chemical Physics, 16, 6391-6397 (2014) [PDF]

[Below is a secondary paper, from many of the same authors,
in which the folding of frataxin is studied via other methods]

Understanding the Frustration Arising from the Competition Between
Function, Misfolding, and Aggregration in a Globular Protein,
S. Gianni, C. Camilloni, R. Giri, A. Toto, D. Bonetti,
A. Morrone, P. Sormanni, M. Brunori and M. Vendruscolo,
Proc. Natl. Acad. Sci. USA, 111, 14141-14146 (2014) [PDF]

[For Section on Sep 20]
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 Oct 4]
RNA G-Quadruplexes are Globally Unfolded in Eukaryotic Cells
and Depleted in Bacteria, J. U. Gao and D. P. Bartel,
Science, 353, aaf5371 (2016) [PDF]

[For Section on Oct 11]
Ultrahigh-Resolution Optical Trap with Single-Fluorophore
Sensitivity, M. J. Comstock, T. Ha and Y. R. Chemla,
Nature Methods, 8, 335-340 (2011) [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]

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]

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]

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]


Molecular Modeling Software

Software Information [TEXT]

VMD [DIR]

Chimera [DIR]

PyMOL [DIR]

KiNG [DIR]