1 / 11

Lab assignment

Lab assignment. Make sure you save frequently, and when you are finished, upload your presentation into the appropriate lab check section for your lab day

tyra
Download Presentation

Lab assignment

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Lab assignment • Make sure you save frequently, and when you are finished, upload your presentation into the appropriate lab check section for your lab day • Grading will be based on positive attitude and perseverance in exploring a new tool, willingness to come up with your own ideas about what is relevant and interesting about your structures, and following the instructions. • For the exam, you are responsible for understanding protein-nucleic acid interactions as covered in your textbook, in class, and in problem set 11. While you will not be asked to reproduce aspects of specific structures from these presentations, by making the effort to apply the general concepts and look in detail at specific interactions this afternoon, you will be helping yourself master the material.   • HINTS: • • Use control F to search for commands on the page if you don’t immediately see where they are! • • If you don’t remember how you got to one of the linked resource sites, just use google and remember to type your pdb code in! • • Don’t forget to be changing the slide titles and information to reflect your structures instead of the sample template • * asterisks are next to views that you may want to return to as you’re putting together your “stories” about your structures • *for your structural stories, you can also include classic themes, like highlighting a certain motif, demonstrating what kind of residues are often found in certain places (ie ends of helices), etc.

  2. Androgen Receptor: 1GS4 • Sample protein • Pdbcode of structure-1GS4 • Source of information about function and structure (review, lecture notes from date xxx, book or paper citation, website, etc.) • Functionally relevant residues and features of the structure you will explore (at least two of the following) • catalytic residues • locations of disease-related mutations • nucleotide or other cofactor binding sites • sites of protein-protein or protein-nucleic acid interactions.

  3. Knobby surface view Charged surface

  4. Hydrophobic/polar

  5. Salt bridges+ Cation Pi interactions + core residue distance • 6.2 A between C-alpha ser O and Leu C • Salt bridges • Glu706, Arg710 • Glu772,Arg788 • Arg744, Asp695 • Arg786,Glu872 • Glu681, Lys808 • Cation pi: • Arg831-Phe916 • Tyr857, Lys861 • Trp718, Lys 808, Phe 804

  6. Ser740contacts Hydrophobic Hbonds

  7. 1GS4structural information • Humans, E. Coli, 1.95A • related by homologous chain: 1T74, 1XQ2

  8. Leu 744contacts in CSU Hydrogen bonds

  9. Conservation

  10. Residue conservation

  11. 1gs4Ramachandran plot

More Related