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]

Lecture 20 (Oct 16): Single Molecule Methods I: Optical Trapping [PDF]

Lecture 21 (Oct 21): Single Molecule Methods II: Magnetic Tweezers [PDF]

Lecture 22 (Oct 23): Introduction to RNA Biology I [PDF]

Lecture 23 (Oct 25): Introduction to RNA Biology II

Lecture 24 (Oct 28): Tetrahymena Group I Intron [PDF]

Lecture 25 (Oct 30): Folding of the Group I Intron [PDF]

Lecture 26 (Nov 1): Binding of Nucleic Acids by Proteins [PDF]

Lecture 27 (Nov 6): Introduction to Glycobiology [PDF]

Lecture 28 (Nov 8): Glycan Structure & Analysis Methods [PDF]

Lecture 29 (Nov 11): Classes of Glycoproteins & Glycolipids [PDF]

Lecture 30 (Nov 13): Carbohydrate-Related Biology & Disease States [PDF]

Lecture 31 (Nov 15): Glycan Recognition in Cell Adhesion & Signaling [PDF]

Lecture 32 (Nov 18): Structure & Composition of the Cell Membrane [PDF] Notes [PDF]

Lecture 33 (Nov 20): Assembly & Membrane Structure [PDF]

Lecture 34 (Nov 25): Membrane Dynamics & Simulations [PDF]

Lecture 35 (Dec 2): Self-Assembly in Membranes [PDF]

Lecture 36 (Dec 4): Membrane Permeation [PDF]

Lecture 37 (Dec 6): Active & Facilitated Transport [PDF]

Exams, 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]

Proteins Module Exam (2019) [PDF] Answers [PDF]

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

Nucleic Acids Module Exam (2018) [PDF] Answers [PDF]

Nucleic Acids Module Exam (2019) [PDF] Answers [PDF]

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

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

Carbohydrates & Membrane Proteins Module Exam (2018) [PDF] Answers [PDF]

Carbohydrates & Membrane Proteins Module Exam (2019) [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, 1881-1892 (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, 1095-1104 (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]

[For Section on Oct 24]
A Guanine-Flipping and Sequestration Mechanism for G-Quadruplex Unwinding
by Rec Helicases, A. F. Voter, Y. Qiu, R. Tippana, S. Myong and J. L. Keck,
Nature Communications, 9, 4201-4208 (2018) [PDF]

[For Section on Oct 31]
Probing the Mechanisms of DEAD-Box Proteins as General RNA Chaperones:
The C-Terminal Domain of CYT-19 Mediates General Recognition of RNA,
J. K. Grohman, M. Del Campo, H. Bhaskaran, P. Tijerina, A. M. Lambowitz
and R. Russell, Biochemistry, 46, 3013-3022 (2007) [PDF]

[For Section on Nov 7]
Induced Fit in RNA-Protein Recognition, J. R. Williamson,
Nature Structural Biology, 7, 834-837 (2000) [PDF]

[For Section on Nov 14]
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]

[For Section on Nov 21]
Force Induced Conformational Changes in PIEZO1,
Y-C. Lin, Y. R. Guo, A. Miyagi, J. Levring, R. MacKinnon and S. Scheuring,
Nature, 573, 230-234 (2019) [PDF]

[For Section on Dec 5]
Side-Chain Hydrophobicity Scale Derived from Transmembrane Protein,
Folding into Lipid Bilayers, C. P. Moon and K. G. Fleming,
Proc. Natl. Acad. Sci. USA, 108, 10174-10177 (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]

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]

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]


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

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

Glycobiology Simplified: Diverse Roles of Glycan Recognition in
Inflammation, R. L. Schnaar, Journal of Leukocyte Biology, 99, 1-14 (2016) [PDF]

UniLectin3D: Curated Database with Lectin 3D Structural Information [WEB]

LfDB: Lectin Frontier DataBase with Glycan-Lectin Affinity Data [WEB]

Membranes & Membrane Proteins

The Lipid Bilayer Membrane and its Protein Constituents,
J. L. Robertson, Journal of General Physiology, 150, 1472-1483 (2019) [PDF]

Physical Principles of Membrane Organization, J. N. Israelachvili,
S. Marcelja and R. G. Horn, Quarterly Reviews of Biophysics, 13, 121-200 (1980) [PDF]

Structural Significance of Lipid Diversity as Studied
by Small Angle Neutron and X-ray Scattering, J. N. Kucerka,
F. A. Heberle, J. Pan and J. Katsaras, Membranes, 5, 454-472 (2015) [PDF]

Membrane Protein Folding and Stability: Physical Principles,
S. H. White and W. C. Wimley, Annual Reviews of Biophysics
and Biomolecular Structure, 28, 319-365 (1999) [PDF]

Hydrophobicity Scales: A Thermodynamic Looking Glass Into
Lipid-Protein Interactions, J. L. McCallum and D. P. Tielmann,
Trends in Biochemical Sciences, 38, 653-662 (2011) [PDF]

Determinants of Cation Transport Selectivity: Equilibrium
Binding and Transport Kinetics, S. W. Lockless,
Journal of General Physiology, 146, 3-13 (2015) [PDF]

Molecular Modeling Software

Software Information [TEXT]


Chimera [DIR]