HOMEWORK 4

Problem 1:

Here is protein X (header). Download and open it with RASMOL, and answer the following questions:

1. How many chains are there? What are the chain designatores (.i.e., the names of the chain)?

ANS:four chains
           chainA,chainB,chainC,chainD

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.

ANS:34

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

ANS:K

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

ANS:tyr78 ,gly79, gly77

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.

ANS:

Science 1998 Apr 3;280(5360):69-77
The structure of the potassium channel: molecular basis of K+ conduction and selectivity.

The potassium channel from Streptomyces lividans is an integral membrane protein with sequence similarity to all known K+ channels, particularly in the pore region. X-ray analysis with data to 3.2 angstroms reveals that four identical subunits create an inverted teepee, or cone, cradling the selectivity filter of the pore in its outer end. The narrow selectivity filter is only 12 angstroms long, whereas the remainder of the pore is wider and lined with hydrophobic amino acids. A large water-filled cavity and helix dipoles are positioned so as to overcome electrostatic destabilization of an ion in the pore at the center of the bilayer. Main chain carbonyl oxygen atoms from the K+ channel signature sequence line the selectivity filter, which is held open by structural constraints to coordinate K+ ions but not smaller Na+ ions. The selectivity filter contains two K+ ions about 7.5 angstroms apart. This configuration promotes ion conduction by exploiting electrostatic repulsive forces to overcome attractive forces between K+ ions and the selectivity filter. The architecture of the pore establishes the physical principles underlying selective K+ conduction.

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 #?

ANS:1SRS

2. How many helices and beta-sheets in one protein chain?

ANS:four helices and four beta-sheet

3. Please define the starting and ending residue of the helix. (ex. Ala25 -> Gly34)

ANS:

HELIX 1   ASN 153 ->THR 179
HELIX 2   GLU 209 ->LEU 219
HELIX 3   ASN 153 ->THR 179
HELIX 4   GLU 209-> LEU  219

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.