Antibody Structure: The Immunoglobulin Fold and Antibody-Antigen Interactions Molecular Memory 2022-01-26 | Dr. KP gives an overview of antibody structure, and takes a look at a human antibody bound to the SARS-CoV-2 spike protein. PDB IDsAvailable at rcsb.org: 1igt, 7k90REFERENCES• Akkaya, M., Kwak, K. & Pierce, S.K. B cell memory: building two walls of protection against pathogens. Nat Rev Immunol 20, 229–238 (2020). doi.org/10.1038/s41577-019-0244-2• Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002.• Barnes, C.O., Jette, C.A., Abernathy, M.E. et al. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature 588, 682–687 (2020). doi.org/10.1038/s41586-020-2852-1• Chiu ML, Goulet DR, Teplyakov A, Gilliland GL. Antibody Structure and Function: The Basis for Engineering Therapeutics. Antibodies (Basel). 2019;8(4):55. Published 2019 Dec 3. doi:10.3390/antib8040055• Lambert, J. M., & Berkenblit, A. (2018). Antibody–drug conjugates for cancer treatment. Annual review of medicine, 69, 191-207.• Nose M, Wigzell H. Biological significance of carbohydrate chains on monoclonal antibodies. Proc Natl Acad Sci U S A. 1983;80(21):6632-6636. doi:10.1073/pnas.80.21.6632• Pan S, Manabe N, Yamaguchi Y. 3D Structures of IgA, IgM, and Components. Int J Mol Sci. 2021;22(23):12776. Published 2021 Nov 26. doi:10.3390/ijms222312776• Vollmers, H. Peter, and Stephanie Brändlein. Natural antibodies and cancer. New biotechnology 25.5 (2009): 294-298.
The Mechanisms of Glycolysis (Part 2) Molecular Memory 2021-11-08 | Dr. KP takes you through the arrow pushing for the final 5 steps of glycolysis. These reactions are part of the energy-yielding payoff phase of the pathway! 00:00 Intro00:24 Glyceraldehyde-3-phosphate dehydrogenase04:47 Phosphoglycerate kinase05:46 Phosphoglycerate mutase07:14 Enolase08:45 Pyruvate kinaseREFERENCES: • Appling, D. R., Anthony-Cahill, S. J., & Mathews, C. K. (2016). Biochemistry: Concepts and connections. Pearson Education.• McMurry, J., Begley, T. P., & Begley, T. (2005). The organic chemistry of biological pathways. Roberts and Company Publishers.
The Mechanisms of Glycolysis (Part 1) Molecular Memory 2021-10-25 | Dr. KP takes you through the arrow pushing for the first 5 steps of glycolysis.00:00 Introduction00:12 Hexokinase03:43 Glucose-6-phosphate isomerase08:10 Phosphofructokinase10:15 Aldolase14:50 Triose phosphate isomeraseREFERENCES: • Appling, D. R., Anthony-Cahill, S. J., & Mathews, C. K. (2016). Biochemistry: Concepts and connections. Pearson Education.• McMurry, J., Begley, T. P., & Begley, T. (2005). The organic chemistry of biological pathways. Roberts and Company Publishers.
Wheres My Dimer? Symmetry Mates in PyMOL Molecular Memory 2021-04-12 | If you've ever modeled a protein in PyMOL and it looks like you're missing a subunit of your dimer, you may need to generate a symmetry mate to visualize the whole structure. This tutorial will help!
Understanding PHI and PSI Angles, Ramachandran Plots, & Newman Projections Molecular Memory 2021-01-25 | This video was created using models, images, and inspiration from the Proteopedia page: The Ramachandran Principle Phi (φ) and Psi (ψ) Angles in Proteinsproteopedia.org/wiki/index.php/Tutorial:Ramachandran_principle_and_phi_psi_anglesREFERENCES: • Ramachandran, G.N.; Ramakrishnan, C.; Sasisekharan, V. (1963). "Stereochemistry of polypeptide chain configurations". Journal of Molecular Biology. 7: 95–9. • Prilusky J, Hodis E, Canner D, Decatur W, Oberholser K, Martz E, Berchanski A, Harel M, Sussman JL. Proteopedia: A status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules. J Struct Biol. 2011 Apr 23. PMID:21536137 doi:10.1016/j.jsb.2011.04.011
PyMOL Tutorial: Modeling the SARS-CoV-2 RBD Interactions with ACE (COVID-19 Coronavirus Proteins) Molecular Memory 2020-04-22 | A follow up PyMOL tutorial for my SARS-CoV-2 Structure. How I modeled the polar interactions between the spike protein RBD and ACE before the paper was published (and a follow up interaction now that the paper is published!)PDB ID: 6VW1Reference: Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., ... & Li, F. (2020). Structural basis of receptor recognition by SARS-CoV-2. Nature, 1-8.
SARS-CoV-2 Structure (COVID-19 Coronavirus) Molecular Memory 2020-04-03 | A structural exploration of the proteins produced by SARS-CoV-2. PDB FILES: 6VSB - Spike protein6VW1 - RBD of the spike protein in complex with ACE26SGC - Rabbit ribosome stalled on a poly-A tail6Y2E - SARS CoV-2 main protease 6Y2F - SARS CoV-2 main protease bound to an inhibitorREFERENCES:• Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C. L., Abiona, O., ... & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science, 367(6483), 1260-1263.• White, J. M., Delos, S. E., Brecher, M., & Schornberg, K. (2008). Structures and mechanisms of viral membrane fusion proteins: multiple variations on a common theme. Critical reviews in biochemistry and molecular biology, 43(3), 189-219.• Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., ... & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science.• Fehr, A. R., & Perlman, S. (2015). Coronaviruses: an overview of their replication and pathogenesis. In Coronaviruses (pp. 1-23). Humana Press, New York, NY.
PyMOL: Superimpose (& Amazing NMR Structures!) Molecular Memory 2020-03-28 | How to superimpose proteins to examine structural changes, and a look at how we can explore protein dynamics with NMR solution structures.
Teaching Online 5: Content Creation Molecular Memory 2020-03-20 | How I create content. Other resources and ready-made content: Online Course Guide (with ASBMB): asbmb.org/education/online-teachingWeCreateEdu Videos: drive.google.com/open?id=1K-4RkOpGH3sBhSuqebeSe-PCsV3LmwQzLqBGDveJEWMDigital Course Creation with Mary Poffenroth: marypoffenroth.com/digital
Teaching Online 4: Course Design Molecular Memory 2020-03-19 | What I've learned about setting up an LMS for a successful course.
Teaching Online 3: Synchronous STEM Molecular Memory 2020-03-18 | Synchronous sessions can be done thought meeting software or your LMS. Here's ideas to make these active learning sessions, particularly for STEM courses. EffSynchronous
Teaching Online 2: Successful Discussions Molecular Memory 2020-03-17 | Using asynchronous discussion boards for collaborative learning in your courses, particularly in STEM courses.Link to part of my note to students: docs.google.com/document/d/1XHvTVgWvPTyoFnwMeXAGvQQjeZzgJrcOaJ3J2OsrBi0/edit?usp=sharing
Teaching Online 1: Assessments Molecular Memory 2020-03-16 | How to create exam-style and quiz questions. Options for hand graded or self-graded work. Focused on STEM, but I hope this will be useful to all!
PyMOL: Build Your Own Sequences (for Learners & Instructors) Molecular Memory 2020-02-10 | How to build an amino acid sequence in PyMOL from scratch. Cap it off with a carboxy terminus, and reorient side chains using the mutagenesis wizard.
How to Sketch Molecular Orbitals for π Systems Molecular Memory 2020-02-03 | Learn how to sketch the molecular orbitals (MOs) for ethylene, butadiene, and the allyl cation and anion, and understand why they matter.
Acetoacetic & Malonic Esters (& Dianions) Molecular Memory 2019-12-16 | The acetoacetic ester synthesis and the malonic ester synthesis. Formation of dianions from the acetoacetic ester, and their unique reactivity.
The Claisen Condensation Molecular Memory 2019-11-25 | Learn the mechanism of the Claisen condensation reaction, along with some important points about the reaction.
Aldol Reaction: Mechanism and Retrosynthesis Molecular Memory 2019-11-18 | A look at the base- and acid-catalyzed mechanisms of the aldol reaction, with an introduction to retrosynthetic analysis of aldol products.
Weinreb Amides and More (Forming Ketones Using Organometallic Reagents) Molecular Memory 2019-11-12 | Esters add Grignards and alkyllithium reagents twice—but what if we want to form a ketone? Dr. KP takes you through a few methods to form ketones from carboxylic acids and derivatives.
Alkyllithium and Grignard Reagents Molecular Memory 2019-11-04 | An introduction to organometallic reagents and some of the key reactions they undergo.
SN1/SN2/E1/E2 Practice Problems Molecular Memory 2019-10-28 | Here, I walk you through six practice problems on substitution and elimination, showing you my four-step method for determining reaction mechanisms.
Allylic and Benzylic Substrates: SN1/SN2/E1 or E2? Molecular Memory 2019-10-21 | Allylic and benzylic substrates in substitution and elimination.
10 min SN1/SN2/E1/E2 Summary! Molecular Memory 2019-10-14 | Dr. KP makes you table of structures to help you generalize how the substrate and nucleophile promote SN1/SN2/E1/E2.
Elimination reactions: E1, E2, and E1CB Molecular Memory 2019-10-07 | The mechanisms of three elimination reactions, a deep look at the transition states and two E2 practice problems using Newman projections and chair conformations.
SN1 vs. SN2: The Nucleophile and Leaving Group Molecular Memory 2019-09-30 | How does the nucleophile influence the reaction mechanism? What makes a good leaving group? Dr. KP goes over these topics in our continued exploration of the SN1 and SN2 mechanism.
SN1 vs. SN2: Reaction Mechanisms & Solvent Molecular Memory 2019-09-28 | This video introduces the SN1 and SN2 mechanisms, and reviews how substrate structure and solvent influence the mechanism. Part 2 on the way!
Reactions of Carboxylic Acids & Carboxylic Acid Derivatives Molecular Memory 2019-09-23 | Reactions of carboxylic acids and carboxylic acid derivatives (acid chlorides, anhydrides, esters, and amides). An overview of the addition-elimination mechanism and review of the major reactions.
Addition to Carbonyl (C=O) by Nucleophiles Molecular Memory 2019-09-16 | The addition of cyanide, aceylide anion, and Grignard reagents to the carbonyl group.
PyMOL: Lets make a MOVIE! Molecular Memory 2019-07-29 | Impress your colleagues with great protein videos embedded in your talks. Here, we'll expand on our work with scenes to create a movie in PyMOL. It's easier than you think! :)
PyMOL: Labels (That actually look good!) Molecular Memory 2019-07-15 | The default setting for PyMOL labels isn't great. Learn to resize and reposition labels with Dr. KP in this easy tutorial, and be on your way to making publication-quality images!
PyMOL: Working with Scenes (will save your butt!) Molecular Memory 2019-07-08 | Building on my previous PyMOL tutorial with multiple ligands, improved commands, scenes, and basic measurement.
Coenzyme A Chemistry Molecular Memory 2019-02-25 | Why are coenzyme A esters important? A look at the chemistry they enable, and examples of their use in the citric acid cycle and fatty acid synthesis.
Aldolase Mechanism Molecular Memory 2019-02-18 | The mechanism of the reaction catalyzed by fructose bisphosphate aldolase.
Biotin Carboxylation Mechanism Molecular Memory 2019-02-05 | Walk through the arrow pushing mechanism of enzymatic carboxylation reactions with Dr. KP.
PyMOL: Active Sites in Minutes (Using only Sequence Info!) Molecular Memory 2019-01-29 | How do you model an active site, when all you have is a PDB file? Dr. KP shows you time-saving techniques and commands for AS modeling in PyMOL. Download PyMOL for free: pymol.org/edu/?q=educationalCommands used in this video: docs.google.com/document/d/1y9-NepfpCSoRztepZzd4KzmIVvcWHCN2ILG7dg0SZ30/edit?usp=sharingPDB ID: 2aceRaves, M. L., Harel, M., Pang, Y. P., Silman, I., Kozikowski, A. P., & Sussman, J. L. (1997). Structure of acetylcholinesterase complexed with the nootropic alkaloid,(–)-huperzine A. Nature structural biology, 4(1), 57-63.
Phosphoglucoisomerase: A VR Experience Molecular Memory 2018-12-31 | Experience the PGI enzyme in a unique way. Dive into the active site, examine the reaction mechanism, and explore the interactions that stabilize an protein dimer. Link to a 2D version of this video: youtu.be/ait8vbj4s8oModel your own proteins! pymol.org/edu/?q=educationalhttp://jmol.sourceforge.net/downloadFind PGI in the PDB: http://www.rcsb.orgPDB files used in this video: 1dqr, 1hox, 1g98, 1jihPrimary References: •Jeffery, C. J., Bahnson, B. J., Chien, W., Ringe, D., & Petsko, G. A. Biochemistry, 2000, 39(5), 955-964.• Lee, J. H., Chang, K. Z., Patel, V., & Jeffery, C. J. Biochemistry, 2001, 40(26), 7799-7805.
Phosphoglucoisomerase: A VR Experience (2D Version) Molecular Memory 2018-12-31 | Experience the PGI enzyme in a unique way. Dive into the active site, examine the reaction mechanism, and explore the interactions that stabilize an protein dimer. Link to a 3D version of this video: youtu.be/SqwrDMYarGgModel your own proteins! pymol.org/edu/?q=educationalhttp://jmol.sourceforge.net/downloadFind PGI in the PDB: http://www.rcsb.orgPDB files used in this video: 1dqr, 1hox, 1g98, 1jihPrimary References: •Jeffery, C. J., Bahnson, B. J., Chien, W., Ringe, D., & Petsko, G. A. Biochemistry, 2000, 39(5), 955-964.• Lee, J. H., Chang, K. Z., Patel, V., & Jeffery, C. J. Biochemistry, 2001, 40(26), 7799-7805.
What does DNA REALLY look like? (In 3D!) Molecular Memory 2018-12-10 | Explore DNA structure with Dr. KP! Learn how to label 5’ and 3’ ends of DNA strands, and journey through some amazing DNA protein complexes! All in 3D! (Google cardboard or VR headset required for the best experience). Link to a 2D version of this video: youtu.be/DYfimg69dZwModel your own proteins! pymol.org/edu/?q=educationalhttp://jmol.sourceforge.net/downloadFind DNA in the PDB: http://www.rcsb.orgPDB files used in this video: 1eqz, 1n14, 5u8s
What does DNA REALLY look like? (2D Version) Molecular Memory 2018-12-10 | Explore DNA structure with Dr. KP! Learn how to label 5’ and 3’ ends of DNA strands, and journey through some amazing DNA protein complexes! All in 3D! Link to a 3D version of this video: youtu.be/11pS0pNT-Rw (Google cardboard or VR headset required for the best experience). Model your own proteins! pymol.org/edu/?q=educationalhttp://jmol.sourceforge.net/downloadFind DNA in the PDB: http://www.rcsb.orgPDB files used in this video: 1eqz, 1n14, 5u8s
Retrosynthesis Part 4: Two Group 1,4 Disconnections Molecular Memory 2018-11-05 | A more advanced look at how we can achieve the 1,4 substitution pattern in synthetic targets via retrosynthetic disconnections.
Nitroenolates Molecular Memory 2018-11-01 | A look at alkylation of nitroenolates and the nitroaldol reaction. Please excuse my voice! I was a little sick when I made this one!
Alkene Reactions 1: Markovnikov Addition & Rearrangement Molecular Memory 2018-10-29 | Introducing alkene reactions resulting in Markovinkov addition, including oxymercuration. How to spot a carbocation rearrangement.
The Wittig Reaction: Structure, Mechanism, and Stereochemistry Molecular Memory 2018-10-22 | An overview of the Wittig reaction, used to produce alkenes from phosphonium ylids and carbonyl compounds.
Conjugate Addition Molecular Memory 2018-10-15 | How do we determine if a nucleophile will add to a conjugated system in a 1,2- or 1,4-mechanism? Here, we'll look at the 3 main factors to help us figure this out!
Whats so special about CUPRATES? Molecular Memory 2018-10-12 | Cuprates are amazing organometallic reagents. They have less ionic character than Grignard or alkyllithiums reagents, so they promote some cool, unique chemistry. Come have a look with me!
EWG or EDG Trick Follow Up! Molecular Memory 2018-10-02 | The EDG/EWG trick works great for some groups, but what about the halogens? And what about the nitroso group that my awesome viewers pointed out? Dr. KP follows up to explain the EWG/EDG trends in a few more groups!
Acidity, Basicity, and Equilibrium in Organic Chemistry Molecular Memory 2018-09-17 | What are the common trends in acidity for organic compounds? What effects should I look for? Dr. KP explores the effects that make an organic compound acidic or basic, and does a couple equilibrium practice problems.
Protecting Groups in Organic Synthesis Molecular Memory 2018-09-10 | What is a protecting group, and how do you use it? Dr. KP reviews protecting groups for the carbonyl group, alcohols, and amines.
Retrosynthesis (Part 3): Pharmaceutical Synthesis Practice Problems Molecular Memory 2018-09-03 | Explore the synthesis of four pharmaceutical drugs through retrosynthesis practice problems that involve one- and two-group disconnections. Learn about the Mannich reaction and how to apply it retrosynthetically.
EAS Synthesis Practice Problems Molecular Memory 2018-08-27 | Electrophilic aromatic substitution synthesis practice problems. Includes an introduction to blocking groups, regioselectivity, activation/deactivation, and the Gattermann-Koch reaction.
