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.

Androgen Receptor: 1GS4• Sample protein• Pdb code 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.

Knobby surface view

Charged surface

Hydrophobic/polar

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

Ser740 contacts

Hbonds Hydrophobic

1GS4 structural information

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

Leu 744 contacts in CSU

Hydrogen bonds

Conservation

Residue conservation

1gs4 Ramachandran plot