I need help with E-H pleasseeeeeee 7. Protein structure. Examine the three-dimen

Question

I need help with E-H pleasseeeeeee

7. Protein structure. Examine the three-dimensional atomic structure of the protein EF-G-2 from the bacterium Thermus thermophilus. Find the atomic coordinates of the crystal structure of this protein at http://www.rcsb.org/pdb/home/home.do. Look for the file name called 2DY1. Visualize the structure using Jmol software (http://bioinformatics.org/firstglance/fgij/ ). Answer the following questions A) How many amino acid residues are in EF-G-2 B) What is the resolution of the crystal structure? C) What ligand is bound to EF-G-2? D) Describe the topology of domain 3 of EF-G-2. How many a-helices and ß-strands? Are the B-strands parallel or anti-parallel? What neighboring domains interact non-covalently with domain 3? E) Find the amino acid residue Glu187. This residue makes electrostatic interactions with residue F Find Lys469. In what type of sccondary structure is this residue? This residue makes hydrogen bonds with residue G) Which residues are part of ß-tums? [Circle the numbers corresponding to these residues.] 415 417 419 421 H Which residues are part of the hydrophobic core of EF-G-2? [Circle the numbers corresponding to these resides 402 403 406 407

Explanation / Answer

A) There are 665 amino acid residues, present in EF-G-2.

B) The resolution of the crystal structure is 1.6 A.

C) Two ligands are bound with this molecule. They are GTP and Mg.

D) Topology of a protein is the mutual orientation of secondary structures, such as alpha-helices and beta sheets in a protein. Domain 3 contains 4 standard beta sheets and 2 helices on one side of the sheet, called alpha-beta sandwich. Domain 3 has residues 405-482, but the structure is not yet known properly due to the poor electron density and mapping. Domain IV and V are the neighboring domains, interact non covalently with domain 3. Two strands are present to connect domain III and V to domain IV. This structure as well as C-terminal tail, makes a mixed 5 stranded beta sheet with one helix at the C-terminal end.

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