Schedule | Assignments | Protein Literature | Nucleic Acid Literature | small molecule flash cards | Alignment |
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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. Students will learn to visualize and analyze large molecules in three dimensions and to make clear and informative illustrations of complex assemblies.
Special COVID-19 Notes. For specific Georgia Tech policies related to COVID-19, please refer to this site and this site. This graduate level class is offered in the fall of 2020 in a hybrid format. This course will be informal and flexible, and will be tuned to meet the needs of the specific students in the class. Lectures by the professor and student presentations will be conducted on bluejeans. Some pre-recorded videos can be watched at students' convenience. Course reading and background material is posted online. Subsets of the class might 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 optional.
Email, Bluejeans chat, and Teams will be used for exchanging information. Grades will be determined by course projects, assignments, presentations and participation in online discussions. There will be no exams. All relevant information is provided in the course syllabus (here) which will be finalized before the first scheduled class period.
You are expected to attend class (online) every session unless you have a compelling reason not to. You are expected to check your email and monitor the course syllabus on a daily basis. This course is intended to be safe, informative, helpful, and fun.
Instructor: Professor Loren Williams
Office: Room 1309 IBB
Lectures: The first three weeks the course will be conducted exclusively online. During the fourth week the presentation mode will be reassessed by the class.
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.
TA: none
Time and Place: 11:00 am - 11:50 am MWF, Bluejeans. Klaus 1447 (we probably will not use this space for this course).
Office hours: By appointment. To make an appointment, please contact my administrator, Keisha Harville (keisha.harville@chemistry.gatech.edu). Meetings will be by appointment on Bluejeans.
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.
Supplementary Materials:
Software: Each student must download and install Pymol on their computer.
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: (not applicable during Fall 2020) 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.
TOP | Molecular Interactions | Williams
Images: On the dates indicated on the schedule, open the appropriate Pymol script and create several png images (ray 2000x2000) illustrating the specified structure. Email the images to Loren. The subject line of the email should be: CHEM 6572 (or 4803), first-name last-name, Torsion Image (or α-Helix Image, β-Sheet Image, etc).
Pymol Exercises: On the dates indicated on the schedule, email the completed Pymol Exercises to Loren. The subject line of the email should be: CHEM 6572 (or 4803), first-name last-name, Pymol Exercise Number. Useful Pymol commands.
Bioinformatics Toolkit: As outlined in the lecture (video 18 above) and in Claudia's tutorial tutorial, search for sequences in the PDB that are homologous to your protein using HHpred in the MPI bioinformatics toolkit. Select the 10 best, make sure to select unique hits (select only hits with different identifiers). Forward the selected hits to AlignmentViewer (click on View Alignment). The logo plot will show the most conserved positions in the alignment. Copy the input sequences from the input tab and go to PhyML (in the Classification tab). Compute the maximum-likelihood tree of your sequences. The names of the nodes in the final tree correspond to PDB entries (PDBcode_chain) Use the fetch command (or load) to view these in pymol. Inspect the protein structures related to your query. From your inspection, what are the functions of the highly conserved sequences? Where are the insertions?
name="PrLit" Protein Literature
TOP | Molecular Interactions | Williams
TOP | Molecular Interactions | Williams
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, Introduction to Pymol |
week 1: m, 8-17 |
| Professor | Molecular Interactions Molecular Interactions Powerpoint Videos A, B, C Paper 1, Sections A, B, C Short Range Repulsion Image due |
week 1: w, 8-19 |
| Professor | Molecular Interactions Videos D, E, F Paper 1, Sections D, E, F Hydrogen Bonding Image due |
week 1: f, 8-21 |
| ------------ | ------------ | ------------ |
| Professor | Molecular Interactions Videos G Paper 1, Sections G, H Base Pairing Image due Pymol Exercise 1 due |
week 2: m, 8-24 |
| Professor | Coordinate files and the PBD How to Use the PDB PDF |
week 2: w, 8-26 |
| Professor | The Peptide Bond Protein Structure Powerpoint How to draw a peptide Peptide Bond Image due |
week 2: f, 8-28 |
| ------------ | ------------ | ------------ |
| Professor | Amino Acids AA Powerpoint AA Flash Cards AA Venn Diagram Project Topic Due |
week 3: m, 8-31 |
| Professor | Essential Nature of Biopolymers (Paper 2) Evolution and Tinkering Polymers Powerpoint |
week 3: w, 9-02 |
| Professor | Ramachandran (Paper 3) φ / ψ φψ map Torsion Image due Pymol Exercise 2 due | week 3: f, 9-04 |
| ------------ | ------------ | ------------ |
| **Holiday** | Labor Day | week 4: m, 9-07 |
| Professor | Pauling (Paper 4) Jane Richardson's Molprobity Make a φψ map with Molprobity α-Helix Image due |
week 4: w, 9-09 |
| Professor |
β-Sheet Proteins Protein Folds Powerpoint β-Sheet Image due |
week 4: f, 9-11 |
| ------------ | ------------ | ------------ |
| Professor | α-Helix Proteins Albumin Image due Myoglobin Sequence Searching Pymol Exercise 3 due |
week 5: m, 9-14 |
| Professor | b-sheet proteins Porin Image due |
week 5: w, 9-16 |
| Professor | complex folds Project sequence due Project hydropathy plot due |
week 5: f, 9-18 |
| ------------ | ------------ | ------------ |
| Students 1, 2 & 3 | Paper 5 Pymol Exercise 4 due |
week 6: m, 9-21 |
| Students 4, 5 & 6 | paper 6 Myoglobin Image due |
week 6: w, 9-23 |
| Students 7, 8 & 9 | paper 7
Ribonuclease A Image due |
week 6: f, 9-25 |
| ------------ | ------------ | ------------ |
| Dr. Claudia Alvarez Carreno | MSAs Multiple Sequence Alignment Tutorial Pymol Exercise 5 due (word doc) |
week 7: m, 9-28 |
| Students 10, 11 & 12 | paper 8 Ribosome Image due |
week 7: w, 9-30 |
| Students 13, 14 & 15 | paper 9 Protein Folds Images due SCOP database CASP database Pfam database |
week 7: f, 10-02 |
| ------------ | ------------ | ------------ |
| Professor | Background | week 8: m, 10-05 |
| Students 16, 17 & 18 | paper 10 Pymol Exercise 6 due |
week 8: w, 10-07 |
| Students 19, 20 & 21 | paper 11 Bioinformatics Toolkit Assignment Due |
week 8: f, 10-09 |
| ------------ | ------------ | ------------ |
| Professor | Enzymes Serine Protease Powerpoint Serine Protease Image due |
week 9: m, 10-12 |
| Professor | Enzymes | week 9: w, 10-14 |
| Students 22, 23 & 24 | paper 12 | week 9: f, 10-16 |
| ------------ | ------------ | ------------ |
| Professor | background Pymol Exercise 7 due |
week 10: m, 10-19 |
| Students 1, 4 & 7 | paper 13 | week 10: w, 10-21 |
| Professor | Background | week 10: f, 10-23 |
| ------------ | ------------ | ------------ |
| Students 2, 5 & 8 | paper 14 Pymol Exercise 8 due DNA Image due Draw Base Pairs Powerpoint |
week 11: m, 10-26 |
| Professor | DNA Nucleic Acid Powerpoint |
week 11: w, 10-28 |
| Students 3, 6 & 9 | paper 15 Hoogsteen Image due |
week 11: f, 10-30 |
| ------------ | ------------ | ------------ |
| Professor | RNA RNA Image due |
week 12: m, 11-02 |
| Students 10, 14 & 17 | paper 17 tRNA Image due |
week 12: w, 11-04 |
| Professor | paper 18 GNRA Tetraloop Image due Pymol Exercise 8 due |
week 12: f, 11-06 |
| ------------ | ------------ | ------------ |
| Students 12, 16 & 19 | paper 19 | week 13: m, 11-09 |
| Students 13, 17 & 20 | paper 20 | week 13: w, 11-11 |
| Professor | The Ribosome | week 13: f, 11-13 |
| ------------ | ------------ | ------------ |
| Professor | Conclusion | week 14: m, 11-16 |
| ------------ | --the end--- | ------------ |
TOP | Molecular Interactions | Williams
List of Students:
