Chemistry & Physics of Biomolecules

Biology 5357

Fall Term 2017

Coursemaster: Jay Ponder


General Information

Syllabus & Schedule [PDF]


Lecture Summaries

Lecture 1 (Aug 28): Taxonomy I: Primary & Secondary Structure [PDF]

Lecture 2 (Aug 30): Taxonomy II: Motifs & Supersecondary Structure [PDF]

Lecture 3 (Sep 1): Taxonomy III: Tertiary Structure & Fold Types [PDF]

Lecture 4 (Sep 6): Folding I: Forces that Determine Structure [PDF]

Lecture 5 (Sep 8): Folding II: Mechanisms of Protein Folding [PDF]

Lecture 6 (Sep 11): Folding III: Characterization of Folding Pathways [PDF]

Lecture 7 (Sep 13): Mutagenesis Experiments; Molecular Dynamics Basics [PDF]

Lecture 8 (Sep 15): Protein Dynamics [PDF]

Lecture 13 (Sep 27): Electron Microscopy & Protein Assemblies [PDF]

Lecture 14 (Oct 2): Structure & Properties of Nucleic Acid Components [PDF]

Lecture 15 (Oct 4): A vs B vs Z DNA, Triplexes and Quadruplexes [PDF]

Lecture 16 (Oct 6): Nucleic Acid Folds [PDF]

Lecture 17 (Oct 9): Single Molecule Methods: Optical Trapping [PDF]

Lecture 18 (Oct 11): Single Molecule Methods: Magnetic Trapping [PDF]

Lecture 19 (Oct 13): Polymer Statistics I: Basic Theory [PDF]

Lecture 20 (Oct 18): Polymer Statistics II: Real Chains & Applications [PDF]

Lecture 21 (Oct 23): Polymer Statistics III: Mixtures of Polymers [PDF]

Lecture 22 (Oct 25): Introduction of RNA Biology [PDF]

Lecture 23 (Oct 27): Tertiary Interactions in RNA Molecules [PDF]

Lecture 24 (Oct 30): Small Ribozymes [PDF]

Lecture 25 (Nov 1): Riboswitches [PDF]

Lecture 26 (Nov 6): Introduction to Membranes [PDF]

Lecture 27 (Nov 8): Molecular Composition & Structure [PDF]

Lecture 28 (Nov 10): Lipid Definition & Types [PDF]

Lecture 29 (Nov 13): Cholesterol & Other Sterols [PDF]

Lecture 30 (Nov 15): Lipid Crystallography [PDF]

Lecture 31 (Nov 17): Assembly & Thermodynamics [PDF]

Lecture 32 (Nov 20): Thermal Behavior of Membranes [PDF]

Lecture 33 (Nov 27): Phase Transitions & Forces [PDF]

Lecture 34 (Nov 29): Membrane Curvature [PDF] Notes [PDF]

Lecture 35 (Dec 1): Membrane Dynamics [PDF] Notes [PDF]

Lecture 36 (Dec 4): Ion Channels & Electrical Signaling [PDF]

Lecture 37 (Dec 6): Membrane Transport [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]

Nucleic Acids: Problem Set 5 [PDF] Answers [PDF]

Membranes: Problem Set 6 [PDF]

Membranes: Problem Set 7 [PDF]


Examinations and Answer Keys

Proteins Exam [PDF] Answer Key [PDF]

Nucleic Acids Exam [PDF] Answer Key [PDF]

Membranes Exam [PDF] Answer Key [PDF]


Discussion Section Articles

[For Section on Sep 7]
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 14]
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 21]
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 28]
Transition Networks for Modeling the Kinetics of Conformational
Change in Macromolecules, F. Noe and S. Fischer,
Current Opinion in Structural Biology, 18, 154-162 (2008) [PDF]

[For Section on Oct 5]
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 12]
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 26]
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 9]
Direct Visualization of Despersed Lipid Bicontinuous Cubic
Phases by Cryoelectron Tomography, D. Demurtas, P. Guichard,
I. Martiel, R. Mezzenga, C. Herbert and L. Sagalowicz,
Nature Communications, 6, 8915 (2015) [PDF]

[For Section on Nov 16]
Chemical Properties of Lipids Strongly Affect the Kinetics of the
Membrane-Induced Aggregation of alpha-Synuclein, C. Galvagnion,
J. W. Brown, M. M. Ouberai, P. Flagmeier, M. Vendruscolo,
A. K. Buell, E. Sparr and C. M. Dobson,
Proc. Nat. Acad. Sci. USA, 113, 7065-7070 (2016) [PDF]

[For Section on Nov 30]
Mechanism of Reversible Peptide-Bilayer Attachment:
Combined Simulation and Experimental Single-Molecular Study,
N. Schwierz, S. Krysiak, T. Hugel and M. Zacharias,
Langmuir, 32, 810-821 (2016) [PDF]


Reading Materials & References

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 & 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]

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]

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]

A Fast-Acting Reagent for Accurate Analysis of RNA Secondary and
Tertiary Structure by SHAPE Chemistry, S. A. Mortimer and K. W. Weeks,
Journal of the American Chemical Society, 129, 4144-4145 (2007) [PDF]

Polymer Physics

Polymer Physics, M. Rubinstein and R. H. Colby, Oxford University Press,
2003, Chapters 2-4 (Ideal Chains, Real Chains & Thermodynamics of Mixing) [PDF]

RNA Structural Biology

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]

Ion Channels

Ion Channels & Electrical Signaling, J. Huettner [PDF]


Molecular Modeling Software

Software Information [TEXT]

VMD [DIR]

Chimera [DIR]

PyMOL [DIR]

KiNG [DIR]