Correction of Mid-Term Exam of Bioinformatics

Problem 1:

  1. There are 4 chains, they are A, B, C and D.

  2. The thickness of memebrance is about 30 angstom

  3. They are Potassium.

  4. They are Gly 77, tyr 78 and Gly 79 on chain A, Gly 77, Tyr 78 and Gly 79 on chain B, Gly 77, Tyr 78 and Gly 79 on chain C, Gly 77, Tyr 78 and Gly 79 on chain D.

Problem 2:

The Journal is Science. The Abstract is here:

Science 1998 Apr 3;280(5360):69-77

The structure of the potassium channel: molecular basis of K+ conduction and selectivity.

Doyle DA, Morais Cabral J, Pfuetzner RA, Kuo A, Gulbis JM, Cohen SL, Chait BT, MacKinnon R

Laboratory of Molecular Neurobiology and Biophysics and the Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

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.

Problem 3:

  1. Its PDB ID# is 1SRS
  2. There are two helices and two beta-sheet in one protein chain.
  3. Helix 1 (ASN A 153 -> THR A 179), Helix 2 (GLU A 209 -> LEU A 219), Helix 3 (ASN B 153 -> THR B 179), Helix 4 (GLU B 209 -> LEU B 219)
  4. The picture is here:

    the model of molecular surface colored by electrostatic potential from Graphical Representation and Analysis of Structure Server at Columbia university

    Have a good day!