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)?
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.
3.There are three metal ions, what are they?
4.What are the residues, excluding water and metal ions, that are within 4.5 ?of the first metal ion?
(All the above answer should come with rasmol gif figures)

Ans:
1.There are four chains.Blue is chain A; red is chain B ; green is chain C ;and yellow is chain D

2.The thickness of the membrane is about 34.19 nm.

3.

4.There are 12 residues that are within 4.5 ?of the first metal ion(2829).

Chain A:Gly 77,TYR 78, GLY 79
Chain B:Gly 77,TYR 78, GLY 79
Chain C:Gly 77,TYR 78, GLY 79
Chain D:Gly 77,TYR 78, GLY 79

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:
The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity
Declan A. Doyle, Jo?o Morais Cabral, Richard A. Pfuetzner, Anling Kuo, Jacqueline M. Gulbis, Steven
L. Cohen, Brian T. Chait, and Roderick MacKinnon
Science 1998 April 3; 280: 69-77.
Abstrate:
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 #?
2.How many helices and beta-sheets in one protein chain?
3.Please define the starting and ending residue of the helix. (ex. Ala25 -> Gly34)
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.

 
Ans:
1.1SRS
2.There are four helies and four sheets.

3.
HELIX    1   Chian A ASN 153 to THR 179  
HELIX    2   Chain A GLU 209 to LEU 219                                   
HELIX    3   Chain B ASN 153 to THR 179                                    
HELIX    4   Chain B GLU 209 to LEU 219  
4.