Question

Bioinformatics #3

1. According to the PDB page for 1GBT and the PubChem database, the substrate used in this study to yield the acyl–enzyme intermediate was ___________, which has a monoisotopic molecular weight of ________.

4-nitrophenyl-4-guanidinobenzoate; 300.26948 g/mole

1-nitrophenyl-1-guanidinobenzoate; 300.26948 g/mole

4-nitrophenyl-4-guanidinobenzoate; 300.085855 g/mole

1-nitrophenyl-1-guanidinobenzoate; 300.085855 g/mole

2. As observed in Protein Workshop, the guanidinobenzoyl group of the substrate is bound to the domain of the protein that ___________ contain the L1 and L2 regions.

does not

does

3. Which of the following pairs of residues forms a cystine group that helps define the shape of the binding site for the guanidinobenzoyl group of the covalently bound intermediate?

Cys 42 and Cys 58

Cys 191 and Cys 220

Cys 128 and Cys 232

Cys 22 and Cys 157

4. Based on a surface rendering for 1GBT and a hydrophobicity color scale (in either Protein Workshop or Ligand Explorer), which of the following statements best describes the binding site for the guanidinobenzoyl group?

The edges of the binding site are slightly nonpolar, and the guanidino group points to a polar residue at the bottom of binding site.

The edges of the binding site are highly nonpolar, and the guanidino group points to a polar residue at the bottom of binding site.

The edges of the binding site are slightly nonpolar, and the guanidino group points to a nonpolar residue at the bottom of binding site.

The edges of the binding site are highly nonpolar, and the guanidino group points to a nonpolar residue at the bottom of binding site.

5. As shown using Ligand Workshop (using the “Neighbor Residues” option), the side chain of which polar amino acid is likely present at the bottom of the binding site for the guanidinobenzoyl group?

Ser 217

Gly 226

Asp 189

Ser 190

6. As shown using the CPK rendering style in Protein Workshop, the orbitals of the Asp 189 side chain overlap with ________ to form __________.

atom NE of the substrate; an ion pair and/or hydrogen bonds

atoms NH1 and NH2 of the substrate; an ion pair and/or hydrogen bonds

atom NE of the substrate; only hydrogen bonds

atoms NH1 and NH2 of the substrate; only hydrogen bonds

7. According to Ligand Explorer, which of the following amino acids are involved in hydrogen bonds with the intermediate, and which pair of atoms has the shortest bond length?

Asp 189, Ser 190, and Gly 219; NH2 of GBS and O of Gly 219

Asp 189, Ser 190, and Gly 219; NH2 of GBS and OD2 of Asp 189

Ser 190 and Gly 219; NH2 of GBS and O of Gly 219

Asp 189, Ser 190, and Gly 219; NH2 of GBS and OD1 of Asp 189

8. Which of the following statements is consistent with the interaction between Ser 195 and the intermediate?

Atom OG of Ser 195 is covalently bound to atom CB of GBS, which is an sp3 hybridized carbon.

Atom OG of Ser 195 is covalently bound to atom CB of GBS, which is an sp2 hybridized carbon.

Atom OG of Ser 195 is covalently bound to atom CD of GBS, which is an sp3 hybridized carbon.

Atom OG of Ser 195 is covalently bound to atom CD of GBS, which is an sp2 hybridized carbon.

9. According to Ligand Explorer, the substrate is involved in hydrophobic interactions with carbons (or C-H groups) from both polar and nonpolar amino acids.

True

False

Answer 1

1)

4-nitrophenyl-4-guanidinobenzoate (or p-nitrophenyl-p-guanidinobenzoate); 300.26948 g/mole is correct.

The substrate 4-nitrophenyl-4-guanidinobenzoate (or p-nitrophenyl-p-guanidinobenzoate) is used in this study during the crystallization under condition in which the acyl-enzyme intermediate, (guanidinobenzoyl)tripsin, was stable. The molecular weight of 4-nitrophenyl-4-guanidinobenzoate is 300.26948 g/mole having exact mass 30.085855 g/mole.

2) does not

3) Ser 195 nucleophilicaly attacks the substrate to form covalent bond. The Cystine group is formed by Cys 42 and Cys 58 that helps define the shape of the binding site for the guanidinobenzoyl group of covalently bound intermediate.