Midterm-Exam

Make a web page which gives the answers to the following problems. E-mail its WWW address to J. K. Hwang

Problem 1:

Here is protein X (header). Download and open it with RASMOL, and answer the following questions:
  1. How many chains are there?  4What are the chain designatores (.i.e., the names of the chain)a,b,c,d,?

  2. It is known that almost all helices are buried inside the membrane, while the sides are exposed in extracellular and intracellular parts. Use this information to estimate the thickness of the membrane.about 35 A

  3. There are three metal ions, what are they ?K

  4. What are the residues, excluding water and metal ions, that are within 4.5 Å of the first metal ion ?

    5.  gly77,tyr 78, gly79
(All the above answer should come with rasmol gif figures)
 
 

Problem 2:

Find the paper where the authors published the structure of protein X mentioned in problem 1. Give the name of the Journal and the abstract.
       D.A.Doyle, et al.,  The structure of the potassium channel: molecular basis of K+ conduction and selectivity.
       Science. 1998 Apr 3;280(5360):69-77.

       PMID: 9525859; UI: 98192802.[abstract]
 

Probelm 3:

The human serum response factor is a transcription factor belonging to the MADS domain protein family with members characterized from the plant and animal kingdoms. The X-ray crystal structure of the serum response factor core in a specific-recognition DNA complex shows that the functions of DNA binding, dimerization and accessory-factor interaction are compactly integrated into a novel protein unit. Please find the its PDB file in Protein Data Bank.
  1. What is its PDB ID #?1SRS
  2. How many helices and beta-sheets in one protein chain?2 helices, 2 beta-sheets
  3. Please define the starting and ending residue of the helix. (ex. Ala25 -> Gly34)Asn 153-Thr179; Glu209-Leu219
  4. Find the model of molecular surface colored by electrostatic potential from Graphical Representation and Analysis of Structure Server at Columbia university. Put this picture in your webpage.

(Note:. If I cannot access your page, you will be treated as absent from test. So double check the address that you mail to me!)

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