BITS Pilani, K K Birla Goa Campus

Second Semester, 2017-2018

MIDTERM Test Biomolecular Modeling BIO F417
09.03.2018 Max. Marks 30 Duration: 90 minutes
Instructions: Read the instructions for each question carefully. There are a total of eight questions in
this exam. Your answers should be short and to the point. If your answer is not legible, it will
automatically be marked incorrect. Do not spend too much time on any one question.

Q1. Briefly summarize what the hydrophobic effect is and give the four pieces of evidence that it is
important in protein folding. [8]

Q2. It is usually observed that low salt concentrations favor protein binding to DNA. But in case of TATA
binding protein, from Pyrococcus woesei (a hyperthermophilic archeal organism), with an
oligonucleotide containing a specific binding site, O’Brien et al., (JMB, 1998) have observed that at high
salt concentrations the equilibrium binding constant increases with increasing salt concentration. Please
explain the possible reasons behind their observation. [4]

Q3. Given below is the Watson-Crick A-T base pair. Some of the transcription factors are highly
sophisticated in terms of differentiating A-T vs T-A base pairs. Design a protein that will specifically
recognize A-T but not T-A base pair. You have to show the possible amino acids of the protein involved
in interactions with the DNA that can differentiate these two base pairs. (Hint: Draw the A-T and T-A
base pairs and identify the unique differences that will help in placing the appropriate amino acids in the
binding site of the protein). [4]

Q4. Given the force field equation below, briefly explain each of the terms? [5]

(PTO)
Q5. Fill the following boxes in the Ramachandran plot: [2]

Q6. Schematically represent the Gly-Ala dipeptide and highlight the required atoms for calculation of Phi
angle of Gly? [2]
Q7. The sequence of type-2 restriction enzyme KpnI from Klebsiella pneumonia upon template search
using NCBI BLASTp against protein database (pdb) gave the following results: [2]
Query
Accession Description E value Identity
coverage
Crystal Structure Of A Putative Mandelate
pdb|3T9P|A RacemaseMUCONATE Lactonizing Enzyme Family 10% 2.3 48%
Protein [Roseovarius sp. TM1035]
Nmr Structure Of Plasmid Copy Control Protein Orf56
pdb|2K9I|A 16% 2.9 38%
[Sulfolobus islandicus]
Crystal Structure Of Probable Transcriptional Regulator
pdb|2NNN|A 24% 5.5 32%
[Pseudomonas aeruginosa]
The Structure Of Dna-Binding Domain Of Response
pdb|3ZQ7|A 29% 6.4 23%
Regulator [Escherichia coli K-12]
Crystal Structure Of The Class Ib Ribonucleotide
pdb|1UZR|A 37% 9.4 25%
Reductase R2f-2 Subunit [Mycobacterium tuberculosis]
What is the next line of action for protein 3D modeling?

Q8. The aim of the ProFunc server is to help identify the likely biochemical function of a protein from its
three-dimensional structure. Draw schematic diagram showing the different methods that are applied to
a given structure when it is submitted to the ProFunc server. [3]

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