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 9-12 (Sep 17-24): Protein Dynamics & Markov State Modeling

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]

Lecture 22 (Oct 22): Introduction of RNA Biology [PDF]

Lecture 23 (Oct 24): Tertiary Interactions in RNA Molecules I [PDF]

Lecture 24 (Oct 26): Tertiary Interactions in RNA Molecules II

Lecture 25 (Oct 29): Group I Intron Folding [PDF]

Lecture 26 (Oct 31): Protein-Nucleic Acid Interactions [PDF]

Lecture 27 (Nov 5): Structure & Composition of the Cell Membrane [PDF] [PDF & Notes]

Lecture 28 (Nov 7): Assembly & Dynamics of Membranes [PDF]

Lecture 29 (Nov 9): Bilayer Structure & Simulations [PDF]

Lecture 30 (Nov 12): Membrane Permeation [PDF]

Lecture 31 (Nov 14): Active & Facilitated Transport [PDF]

Lecture 32 (Nov 19): Self-Assembly in Membranes [PDF]

Lecture 33 (Nov 26): Introduction to Glycobiology [PDF]

Lecture 34 (Nov 28): Glycan Structure & Analysis Methods [PDF]

Lecture 35 (Nov 30): N-Linked & O-Linked Glycans [PDF]

Lecture 36 (Dec 3): Glycolipids & Glycoprotein Stability [PDF]

Lecture 37 (Dec 5): Glycan-Related Disease States [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]

Membranes: Problem Set 5 [PDF] Answers [PDF]

Carbohydrates: Problem Set 6 [PDF] Answers

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

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

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

Nucleic Acids Module Exam (2018) [PDF] Answers


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]

[For Section on Oct 18]
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]

[For Section on Oct 25]
Ligand Recognition and Helical Stacking Formation are Intimately
Linked in the SAM-1 Riboswitch Regulatory Mechanism, A.-M. Dussault,
A. Dube, F. Jacques, J. P. Grondin and D. A. Lafontaine,
RNA, 23, 1539-1551 (2017) [PDF]

[For Section on Nov 8]
Converting Escherichia coli into an Archaebacterium with a Hybrid
Heterochiral Membrane, A. Caforia, M. F. Sillakus, M. Exterkate,
S. Jain, V. R. Jumde, R. L. H. Aandringa, S. W. M. Kengen,
A. J. Minnnaard, A. J. M. Driessen and J. van der Oost,
Proc. Natl. Acad. Sci. USA, 115, 3704-3709 (2018) [PDF]

[For Section on Nov 15]
Transport Domain Unlocking Sets the Iptake Rate of an Aspartate
Transporter, N. Akyuz, E. R. Georgieva, Z. Zhou, S. Stolzenberg,
M. A. Cuendet, G. Khelashvilli, R. B. Altman, D. S. Terry,
H. Weinstein, O. Boudker and S. C. Blanchard,
Nature, 518, 68-73 (2015) [PDF]

[For Section on Nov 29]
An Intrinsic Mechansim of Secreted Protein Aging and Turnover,
W. H. Yang, P. V. Aziz, D. M. Heithoff, M. J. Mahan, J. W. Smith and J. D. Marth,
Proc. Natl. Acad. Sci. USA, 112, 13657-13662 (2015) [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]

RNA Structural Biology

Geometric Nomenclature and Classification of RNA Base Pairs,
N. B. Leontis and E. Westhof, RNA, 7, 499-512 (2001) [PDF]

RNA Structural Motifs: Building Blocks of a Modular Biomolecule,
D. K. Hendrix, S. E. Brenner and S. R. Holbrook,
Quarterly Reviews of Biophysics, 38, 221-243 (2005) [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, 1302-1311 (2011) [PDF]

The Essential Role of Stacking Adenines in a Two-Base-Pair RNA
Kissing Complex, W. Stephenson, R. N. Asare-Okai, A. A. Chen, S. Keller,
R. Santiago, S. A. Tenenbaum, A. E. Garcia, D. Fabris and P. T. X. Li,
Journal of the American Chemical Society, 135, 5602-5611 (2013) [PDF]

Membrane Proteins

The Photosynthetic Reaction Centre from the Purple Bacterium
Rhodopseudomonas viridis, J. Deisenhofer and H. Michel,
Nobel Prize Lecture, Chemistry, Stockholm (1988) [PDF]

The Identification of the Sodium-Potassium Pump, J. C. Skou,
Nobel Prize Lecture, Chemistry, Stockholm (1997) [PDF]

Glycobiology

Biological Roles of Glycans, Glycobiology, 27, 3-49 (2017) [PDF]

Essentials of Glycobiology, 3rd Edition,
edited by A. Varki, et al., CHS Press, 2017 [EBook]


Molecular Modeling Software

Software Information [TEXT]

VMD [DIR]

Chimera [DIR]

PyMOL [DIR]

KiNG [DIR]