BITS Pilani, K K Birla Goa Campus

Second Semester, 2017-2018

MIDTERM KEY Biomolecular Modeling BIO F417
09.03.2018 Max. Marks 30 Duration: 90 minutes

Q1. Refer to class notes.

Q2. Thermodynamic data suggest that the protein-DNA interaction at high salt concentration is
accompanied by the removal of large numbers of water molecules from the buried hydrophobic surface
area. In addition, the involvement of ions appears to influence the binding which can be explained by
binding of cations in the interface between the electrostatically negative lateral lobes on the protein and
the negatively charged DNA.

Q3. Please refer to the DNA-protein interaction slides in the lecture

Q4. Please refer to the Force fields lecture notes / slides

Q5. (i) antiparallel, (ii) parallel, (iii) left, (iv) right

Q6. Phi (Ci-1-Ni-CAi-Ci) -> not possible; here i=1 (Gly) & i=2 (Ala).

Q7. “Query coverage” low & “E-value” high -> not possible to select template(s) from BLASTp result;
need to explore “Fold recognition” methods; if not successful then try “ab initio” methods.

Q8.

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