Schedule | Canvas | AA flash cards | Molecular Interactions | Williams | Structures | Pymol ATP_synthase |

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Course Description: This course covers principles of protein, nucleic acid, carbohydrate and lipid structure, assembly, and function. Topics include detailed descriptions of three-dimensional structures and mechanisms, in the context of molecular interactions. Students learn to understand, visualize and analyze large biological assemblies in three dimensions. The course is tuned to meet the needs of graduate students who require background and tools for analyzing large biological structures in their research.

Class structure: This class will be conducted in-person, in the classroom. However, because some students are more comfortable maintaining social distance, all class activities will be available in real time online, and will be recorded and posted. Therefore, it is not necessary for students to attend class. Many classes will be inverted, although there will also be more conventional lectures. The inverted lectures are intended for the professor to assist students with their assignments.

Bluejeans, Canvas and the course homepage (here) will be used for exchanging information and for broadcasting the lectures online.

Subsets of the class will meet weekly for in-person discussion coffee hours (coffee provided by the professor) to be conducted in an outdoor venue (locations TBD). These meetings would be optional. For specific Georgia Tech policies related to COVID-19, please refer to this site and this site.

Students are expected to attend each lecture, either in-person or online, unless there is a compelling reason to miss. Students are expected to check their email, monitor the course syllabus, email and the course Canvas page on a daily basis.

Grades: This course is intended to be safe, informative, helpful, and fun. There are no exams. Grades are determined by assignments, presentations and a final course project. To receive credit for an assignment, it must be complete, on-time, and organized. Assignments are posted in the schedule and are due at midnight of their due date. Assignment due dates are fixed and are not negotiable under any circumstances. A project is due on the last day of the semester.

To receive a letter grade of A, a student must appropriately complete all the assignments, the course project, and the presentation. Due dates for assignments are listed on the course schedule. There are over 30 assignments - nearly one for every lecture. Each student will present important aspects of their protein/RNA to the class, using PyMol. Powerpoint will not be used for presentations.

Project: Each student will identify a protein or RNA that is especially relevant to their research. Each student will independently perform a variety of functional and structural analysis on their protein or RNA. Students should identify and communicate to the professor the name, pdb entry code, and resolution of their protein/RNA by lecture 6.

Textbook: There is no official textbook. Students must have access to a book that is roughly equivalent to Lehninger Principles of Biochemistry, Seventh Edition. The sections assigned from Lehninger can be found in any standard biochemistry text.

Required Software: PyMol and Endnote- available from OIT

Instructor: Professor Loren Williams

Office: Room 1309 IBB

Lectures: Some class sessions will be conventional lectures but most sessions will be inverted, so that students can work together and with the instructor to complete assignments.

Email: loren.williams@chemistry.gatech.edu

When sending an e-mail message, please put the following information in the subject line:
CHEM 6572, firstname lastname, subject

Example: CHEM 6572, Marie Curie, request for radiation badge.

TA None

Time and Place: 11 AM - 11:50 AM MWF, Cherry Emerson 204, or Bluejeans.

Office hours: I will remain on Bluejeans after every class for as long as anyone wants to talk with me. For less public interactions, specific Bluejeans meetings can be set up. I can meet with students upon request.

Accomodation: If you require special accommodation we will work with you. Please contact the ADAPTS office and the professor.

Honor Code: In this class we will adhere to the Georgia Tech Honor Code.

Schedule

TOP | Molecular Interactions | Williams

Supplementary Materials:

• Branden and Tooze, Introduction to Protein Structure, Second Edition, Garland Publishing, 1999.
• R.D. Blake, Informational Biopolymers of Genes and Gene Expression, University Science Books, 2005
• Voet and Voet, Biochemistry, John Wiley & Sons, Inc.
• Jane Richardson's Anatomy of Protein Structure
• Library of Pymol Scripts, List of Pymol Commands.

Background Protein Literature

TOP | Molecular Interactions | Williams

1. Williams, L. "Molecular Interactions", [web site] [short range repulsion PyMol script; water PyMol script; CG base pairing PyMol script; ATP-Mg²⁺ PyMol script]
2. Runnels, C., Lanier, K.A., Williams, J.K., Bowman, J.C., and Williams, L.D. "The Essential Nature of Biopolymers", J. Mol. Evolution, 86, pgs 598–610(2018) [paper] [DNA PyMol script, RNA PyMol script peptide PyMol script cellulose PyMol script].
3. Ramachandran, G.N., Ramakrishnan, C., and Sasisekharan, V. "Stereochemistry of Polypeptide Chain Configurations", J. Mol. Biol. 7, 95-99 (1963) [paper] [peptide bond PyMol script; φ/ψ PyMol script] [biography of Ramachandran]
4. Pauling, L., Corey, R.B., and Branson, H.R. "The Structure of Proteins - 2 Hydrogen-Bonded Helical Configurations of the Polypeptide Chain", Proc. Natl. Acad. Sci. U.S.A. 37, 205-211 (1951) [Pauling 1951 α-helix paper] [α-helix PyMol script] [Pauling 1951 β-sheet paper paper] [antiparallel β-sheet PyMol script; parallel β-sheet PyMol script] [biography of Pauling, biography of Corey] [background papers by Dunitz 2001, Eisenberg 2003]
5. Kyte, J., and Doolittle, R.F. "A Simple Method for Displaying the Hydropathic Character of a Protein", J. Mol. Biol. 157, pgs 105-132 (1982) [paper] [hydropathy Web Server].
6. Vojtěchovský, J., Chu, K., Berendzen, J., Sweet, R.M. and Schlichting, I., "Crystal structures of myoglobin-ligand complexes at near-atomic resolution", Biophysical Journal, 77 pgs 2153-2174 (1999) [paper] [myoglobin PyMol script] [Kendrew's paper; biography of Kendrew; biography of Dorothy Crowfoot Hodgkins]
7. Anfinsen, C.B., Haber, E., Sela, M., and White, F.H., Jr. "The Kinetics of Formation of Native Ribonuclease During Oxidation of the Reduced Polypeptide Chain", Proc. Natl. Acad. Sci. U.S.A. 47, pgs 1309-1314 (1961) [paper] [ribonuclease A PyMol script] [info on ribonuclease] [biography of Anfinsen] [background paper by Levinthal] [background papers by Onuchic & Wolynes 2004, Karplus 1997, Honig 1999, Williams, 2018, Eisenberg on Lisa Steiner]
8. Kovacs, N.A., Petrov, A.S., Lanier, K.A., and Williams, L.D. "Frozen in Time: The History of Proteins", Mol. Biol. Evol. 34, pgs 1252–1260 (2017) [paper] [PyMol script] [background papers by Dill and Lupas].
9. Levitt, M., and Chothia, C. "Structural Patterns in Globular Proteins", Nature 261, 552-558 (1976) [paper] [protein domain PyMol script] [background papers by Shultz & Schirmer 1974 and Levitt]
10. Knowles, T.P., Vendruscolo, M., and Dobson, C.M. "The Amyloid State and Its Association with Protein Misfolding Diseases", Nature reviews. Molecular cell biology 15, pgs 384 (2014) [paper] [Nowick paper] [PyMol script for Dobson paper] [PyMol script for Nowick paper] [PyMol script for Nowick paper] [Eisenberg 2007] [Prusiner 1998, Eisenberg 2005]
11. Buller, A.R., and Townsend, C.A. "Intrinsic Evolutionary Constraints on Protease Structure, Enzyme Acylation, and the Identity of the Catalytic Triad", Proc. Natl. Acad. Sci. U.S.A. 110, E653-E661 (2013) [paper] [PyMol script] [serine_protease_mechanism.ppt]
12. Saibil, H.R., Fenton, W.A., Clare, D.K., and Horwich, A.L. "Structure and Allostery of the Chaperonin Groel", J. Mol. Biol. 425, 1476-1487 (2013) [paper] [PyMol script] [Videos 1A, 1B, 2, 3 4]
13. Tompa, P. "Intrinsically Disordered Proteins: A 10-Year Recap", Trends Biochem. Sci. 37, 509-516 (2012) [paper] [Dunker Slides].

    Background Nucleic Acids Literature

    TOP | Molecular Interactions | Williams

14. Watson, J.D., and Crick, F.H. "Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid.", Nature 171, 737-738 (1953) [paper] [PyMol script] [Franklin Paper, 1953; background on Franklin] [How to draw base pairs] [Race for the Double Helix pt 1 / Race for the Double Helix pt 2] ]
15. Hoogsteen, K. "Crystal and Molecular Structure of a Hydrogen-Bonded Complex between 1-Methylthymine and 9-Methyladenine", Acta Crystallographica 16, 907-916 (1963) [paper] [PyMol script] [background paper by Leontis and Westhof]
16. Davis, J.T. "G‐Quartets 40 Years Later: From 5′‐GMP to Molecular Biology and Supramolecular Chemistry", Angewandte Chemie International Edition 43, pgs 668-698 (2004) [paper] [background paper by Davies] [PyMol script]
17. Kim, S.H., Suddath, F.L., Quigley, G.J., McPherson, A., Sussman, J.L., Wang, A.H., Seeman, N.C., and Rich, A. "Three-Dimensional Tertiary Structure of Yeast Phenylalanine Transfer RNA", Science 185, 435-440 (1974) [paper] [PyMol script] [tRNA video] [1974 New Scientist, 1974 letters; Rich to Crick, Aug 9 | Crick to Rich, Sept 4 | Rich to Crick, Oct 11 | Crick to Rich, Oct 22]
18. Mohan, S., Hsiao, C., Bowman, J.C., Wartell, R., and Williams, L.D. "RNA Tetraloop Folding Reveals Tension between Backbone Restraints and Molecular Interactions", J. Am. Chem. Soc. 132, pgs 12679-12689 (2010) [paper] [GNRA tetraloop Pymol Script] [20 Superimposed GNRA Tetraloops]
    18a. Yakovchuk, P., Protozanova, E., and Frank-Kamenetskii, M.D. "Base-Stacking and Base-Pairing Contributions into Thermal Stability of the DNA Double Helix", Nucleic Acids Res. 34, pgs 564-574 (2006) [paper] [Background paper by Privalov] [PyMol script]
19. Jain, A., and Vale, R.D. "RNA Phase Transitions in Repeat Expansion Disorders", Nature (2017) [paper].
20. Simonovic, M., and Steitz, T.A. "A Structural View on the Mechanism of the Ribosome-Catalyzed Peptide Bond Formation", Biochim. Biophys. Acta 1789, 612–623 (2009) [paper] [PyMol script / codon chart / video 1 / video 2 3:40]
21. Liu, X., Bushnell, D.A., and Kornberg, R.D. "RNA Polymerase II Transcription: Structure and Mechanism", Biochimica et Biophysica Acta-Gene Regulatory Mechanisms 1829, 2-8 (2013) [paper] [PyMol script ][ppt]
22. Jiang F, Zhou K, Ma L, Gressel S, and Doudna J.A. "Structural Biology. A Cas9-guide RNA complex preorganized for target DNA recognition", Science 348, 1477-1481 (2015) [paper] [Lander Paper] [PyMol script]
23. Yan, C., Hang, J., Wan, R., Huang, M., Wong, C.C., and Shi, Y. "Structure of a Yeast Spliceosome at 3.6-Angstrom Resolution", Science 349, pgs 1182-1191 (2015) [paper].