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CHEM 6572/4803
Macromolecular Structure
Fall 2018
revised 9/16/2018

| Syllabus | Protein Literature | Nucleic Acid Literature | Schedule | Assignments | amino acid flash cards | Google Drive | alignment | Crisper John Oliver |


Course Description: This course covers principles of protein and nucleic acid structure, folding, assembly, stability, dynamics and function. Topics include detailed descriptions of three-dimensional structures, in the context of molecular interactions, polymer conformations and thermodynamics. Students will learn to visualize and analyze large molecules in three dimensions. The class will learn to make clear, aesthetic and informative illustrations of complex systems as shown here and here.

Instructor: Professor Loren Williams

Office: Room 1309 IBB

Email: loren.williams@chemistry.gatech.edu (best mode of communication)

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.

E-mail can only be accepted from Georgia Tech accounts.

TA: no (budget cuts)

Time and Place: 10:10 am - 11:00 am MWF, 1222 Molecular Sciences & Engr.

Office hours: Mon and Fri 11 AM, or by appointment. To make an appointment, please contact my administrator, Keisha Harville (keisha.harville@chemistry.gatech.edu). It is best to check with her before you plan to visit my office.


Course Structure:. During this course you will be required (i) to read and understand all of the course literature (links below), (ii) to present various aspects of the course literature to the class, and (iii) to complete a variety of assignments.

Literature: This course will be taught using peer-reviewed literature as source material, rather than a textbook. The papers here and here will form the basis of the class. All of these materials are required reading.

Presentations: Each student will make a series of presentations of papers to the class. Presenting students must have complete mastery of the technical material of their assigned papers. All students are expected to read and understand all of the papers. Periodic quizes will be administered over the reading assignments.

Supplementary Materials:

Software: Each student must download and install Pymol on their computer. Download it using the link at the bottom of this page.

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.

Grades: will be based on assignments and quizzes (50%), and class participation, including presentations and class discussions (50%). All students are expected to participate in class discussions and to not be passive observers. Quizzes will cover assigned reading and class discussions. Quizzes will sometimes be announced in advance but not always.


Assignments

The class is going to start very quickly. We have a lot of important material to cover.

On Friday of the week one, run this Pymol Script on Hydrogen Bonding, to write out a figure png from it, and email it to Professor Williams. The figure must be ray traced with resolution 1000x1000 (type "ray 1000,1000, then "save beautifulfigure.png"). The subject line of the email should be: CHEM 6572 (or 4803), first-name last-name, Hydrogen bonding image.

On Wednesday of week two there will be a quiz on molecular interactions. I will give you a solution [like 1M NaCl (aq)], or part of the structure of a biopolymer, for which you will have to describe all of the molecular interactions.

By Monday of week three, please send me an an email with the name and pdb entry code for your project protein, along with the sequence, in FASTA format. The subject line of the email should be: CHEM 6572 (or 4803), first-name last-name, project protein information. Download this zipped directory and follow the instructions on the top level to set up a Pymol script for your protein.

On Wednesday of week three we will have a quiz on amino acids and nucleotides. You will be required to draw the chemical structures all 20 amino acids and all five nucleotides. For amino acids You have to know (i) the one letter code, (ii) the three letter code, (iii) the correct chemical structure, (iv) with correct stereochemistry (at the Cα only), (v) the predominant sidechain protonation states at pH 5, 6, 7 and 8. For nucleotides you have correctly draw bases, canonical base pairs, and (deoxy)riboses, 5', 3' and 2' phosphates and cyclic phosphates. We are not going to go over the amino acid or nucleotide structures in too much detail in class. Please learn them on your own if you don't already know them. You have to know them cold.

By friday of the third week, please pull up an alpha helix with this script and email me an beautiful 1000x1000 ray traced image showing the number of atoms you see in the smallest hydrogen bonded ring. The subject line of the email should be: CHEM 6572 (or 4803), first-name last-name, alpha helix HB ring.

On Wednesday of week five you will have a quiz in which you will have to draw a peptide of any sequence with correct stereochemistry. You will have to label some phi and psi, mark out coplaner atoms, draw the hydrogen bonds for an alpha helix, and maybe draw a beta sheet of either orientation. You will have to draw Newman projections of phi and psi, for any angle or secondary structure.

On Friday of week five you should be ready to present your protein to the class. You will have to optimize your script to do that, so please get that together.


Syllabus

TOP | Molecular Interactions | Williams


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", (2017) [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. Springer, B.A., Sligar, S.G., Olson, J.S., and Phillips, G.N.J. "Mechanisms of Ligand Recognition in Myoglobin", Chem. Rev. 94, pgs 699-714 (1994) [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, 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].
  14. Nucleic Acids Literature

    TOP | Molecular Interactions | Williams

  15. 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] ]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. Jain, A., and Vale, R.D. "RNA Phase Transitions in Repeat Expansion Disorders", Nature (2017) [paper].
  21. 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]
  22. 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]
  23. 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]
  24. 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].

Schedule & Assignments

TOP | Molecular Interactions | Williams

This schedule will be finalized at the end of the first week when we have a reasonably accurate list of students enrolled in the class.

Presentor Topic Date
Professor Course Intro & Paper 1: Molecular Interactions week 1: m, 8-20
Professor Paper 1: Molecular Interactions week 1: w, 8-22
Professor Paper 1: Molecular Interactions week 1: f, 8-24
------------ ------------ ------------
Professor Paper 1: Water and the Hydrophobic Effect week 2: m, 8-27
Professor Quiz 1 on Paper 1 & Introduction to the PBD week 2: w, 8-29
Professor Paper 2: The Essential Nature of Biopolymers week 2: f, 8-31
------------ ------------ ------------
**Holiday** Labor Day week 3: m, 9-03
Professor Quiz 2 week 3: w, 9-05
Professor Paper 2 week 3: f, 9-07
------------ ------------ ------------
Professor Paper 3 week 4: m, 9-10
Professor Paper 4 week 4: w, 9-12
Professor background week 4: f, 9-14
------------ ------------ ------------
Professor background week 5: m, 9-17
Professor background week 5: w, 9-19
Professor background week 5: f, 9-21
------------ ------------ ------------
Students 1, 2 & 3 Paper 5 week 6: m, 9-24
Students 4, 5 & 6 paper 6 week 6: w, 9-26
Students 7, 8 & 9 paper 7 week 6: f, 9-28
------------ ------------ ------------
Professor background week 7: m, 10-01
Students 10, 11 & 12 paper 8 week 7: w, 10-03
Students 13, 14 & 15 paper 9 week 7: f, 10-05
------------ ------------ ------------
No Class Fall Break week 8: m, 10-08
Students 19, 17 & 18 paper 10 week 8: w, 10-10
Students 16, 20 & 21 paper 11 week 8: f, 10-12
------------ ------------ ------------
Professor background week 9: m, 10-15
Professor background week 9: w, 10-17
Students 2, 4 & 6 paper 12 week 9: f, 10-19
------------ ------------ ------------
Professor background week 10: m, 10-22
Students 1, 3 & 5 paper 13 week 10: w, 10-24
Professor Background week 10: f, 10-26
------------ ------------ ------------
Students 8, 10 & 12 paper 14 week 11: m, 10-29
Professor background week 11: w, 10-31
Students 7, 9 & 11 paper 15 week 11: f, 11-02
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Professor background week 16: m, 11-05
Students 14, 16 & 18 paper 17 week 12: w, 11-07
Students 17, 15 & 21 paper 18 week 12: f, 11-09
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Students 13, 19 & 20 paper 19 week 13: m, 11-12
Professor paper 20 week 13: w, 11-14
Professor paper 21 week 13: f, 11-16
------------ ------------ ------------
Professor paper 22 week 14: m, 11-19
no class Thanksgiving week 14: w, 11-21
no class Thanksgiving week 14: f, 11-23
------------ ------------ ------------
Professor background week 15: m, 11-26
Professor paper 23 week 15: w, 11-28
Professor paper 24 week 15: f, 11-30
------------ ------------ ------------
Professor background week 16: m, 12-03
------------ --the end--- ------------

TOP | Molecular Interactions | Williams


List of Students:

  1. Bentata Benezry, Jonathan
  2. Brightbill, Eleanor
  3. Chivukula, Vasanta
  4. Dautel, Dylan
  5. Davis, Ontavious
  6. Flores, Jonathan
  7. Griffitts, Fletcher
  8. Guth, Rebecca
  9. Hudadoff, Sarah
  10. Jin, Decarle
  11. Johnson, Abigail
  12. Lane, Weldon
  13. Ma, Minh Thu
  14. Mcavoy, Andrew
  15. Nguyen, Nguyet
  16. Rothschild-Mancinelli, Brooke
  17. Saccuzzo, Emily
  18. Sui, Xuelin
  19. Sun, Yi
  20. Wu, Yuqi
  21. Yi, Dongqi