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Protein Biomolecular Interactions Online Exam Quiz

Important questions about Protein Biomolecular Interactions. Protein Biomolecular Interactions MCQ questions with answers. Protein Biomolecular Interactions exam questions and answers for students and interviews.

Which of the following is untrue about Amino acid conservation?

Options

A : a. It has been known for some time that conservation of residues at the surface of a protein family is often related to function

B : b. Conservation of residues at the core of a protein family is often related to function

C : c. This may be an enzyme active-site or binding site

D : d. Unlike hydrophobicity or electrostatic potential, displaying residue conservation on the molecular surface has no physical or chemical basis

Which of the following is untrue about Shape Complementarity?

Options

A : a. The complementarity between two proteins or a protein and ligand can be described by surface contact or overlap

B : b. The complementarity between two proteins or a protein and ligand can be described by the overall buried surface area of two molecules in contact

C : c. The complementarity between two proteins or a protein and ligand can be described by the number of adjacent surface points (atoms or residues)

D : d. The hydrophobic effect barely has impact on protein folding

The burial of surface area (or the maximization of surface contact) is an approximation of the effect of shape complementarity.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Which of the following is untrue about Grid Representation?

Options

A : a. To speed up the matching process the topology of the protein can be simplified from atomic level detail to a series of cubic elements

B : b. To speed up the matching process discretizing the 3-dimensional space using a grid is done

C : c. Discretizing allows very fast computer matching using search methods such as Fourier transform

D : d. Fourier transform is hardly used in computer matching

In Grid representation, in a translational scan the mobile molecule B moves through the grid representing the static molecule A and a signal describing shape complementarity, fc, is generated for each mapping. Mathematically the correlation function, fc, of fA and fB is given by ______ where N is the number of grid points along the cubic axes i, j, and k and ?, ?, and ? are the translational vectors of the mobile molecule B relative to the static one A.

Options

A : a. fc = \(\sum_{i=1,j=1,k=1}^N\) (fA,i,j,k * fBi+?j+?k+?)

B : b. fc = \(\sum_{i=0,j=0,k=0}^N\) (fA,i,j,k * fBi+?j+?k+?)

C : c. fc = \(\sum_{i=1,j=1,k=1}^N\) (fA,0,0,0 * fBi+?j+?k+?)

D : d. fc = \(\sum_{i=0,j=0,k=0}^N\) (f0,i,j,k * fBi+?j+?k+?)

In Grid representation, the lowest score represents the best surface complementarity for a given translational scan.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

In Property-based measures, displaying physical properties on the molecular surface of molecules can help to guide molecular docking.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Which of the following is untrue about Hydrophobicity?

Options

A : a. The hydrophobic effect plays a dominant role in the folding of proteins

B : b. Hydrophobic residues aggregate away from contact with water

C : c. Hydrophobic residues aggregate to form hydrophobic cores with more polar residues

D : d. Hydrophobic residues form the solvent accessible surface but restrict the solubility of the protein

Oligomers are often obligate complexes meaning that the free-energy cost of dissociation is high and they exist as oligomers under physiological conditions.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Which of the following is untrue about Electrostatic Complementarity?

Options

A : a. The electrostatic properties of biomolecules play an important role in determining interactions

B : b. The burial of charged residues at protein-protein/DNA interfaces is thought to be generally net destabilizing with the hydrophobic effect being the primary driving force

C : c. Charged groups involved in the biomolecular interface are often stabilized by other polar or oppositely charged groups on the interacting molecule

D : d. Charged groups involved in the biomolecular interface are often stabilized by similar polar or same charged groups on the interacting molecule

Proteins are dynamic entities that undergo _______

Options

A : a. only fluctuation of flexible loop regions about equilibrium positions when in solution

B : b. only limited conformational change of amino acid side-chains when in solution

C : c. both limited conformational change of amino acid side-chains and fluctuation of flexible loop regions about equilibrium positions when in solution

D : d. illimitable or total conformational change of amino acid side-chains when in solution

Typical motions of proteins will be primarily treated by a rigid body model for docking.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

In case of Protein-ligand docking, ______ ligands are often _____ in adapting their shape to fit the receptor binding pocket.

Options

A : a. small molecule, highly flexible

B : b. large molecule, highly flexible

C : c. large molecule, more flexible

D : d. small molecule, less flexible

In Multiple conformation rigid-body method, a ligand is assumed to be able to adopt a number (N) of different _______ that are computed _____ the ligand being docked into the receptor.

Options

A : a. low-energy conformations, after

B : b. low-energy conformations, prior to

C : c. high-energy conformations, prior to

D : d. high-energy conformations, after

The disadvantage of Multiple conformation rigid-body method is that the active conformation may be missed as the result of a minor structural difference not considered in the ______ ligand conformations. Where, the N is the number of low-energy conformations.

Options

A : a. N +1

B : b. N

C : c. N²

D : d. N/2

In Stochastic search methods, they include methods such as Monte Carlo simulation, simulated annealing, Tabu search, genetic algorithms and evolutionary programming.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

In a Monte Carlo simulation the score (or energy) is calculated at each step and compared to the previous step. The probability of accepting the step is given by _________ where ?E is the difference in energy; kB is Boltzmann’s constant and T the temperature.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Genetic methods (genetic algorithms and evolutionary programming) store multiple solutions. These solutions form a population of members.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Stochastic methods can guarantee reaching a global optimal solution and the methods are computationally costly in comparison to the other methods.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Which of the following is true regarding Protein flexibility?

Options

A : a. Methods have been described for the introduction of side-chain flexibility to both protein-ligand and protein-protein docking

B : b. Methods have been described for the introduction of side-chain flexibility to protein-ligand docking only

C : c. The Mean Field principle is rarely used in this

D : d. Methods have been described for the introduction of side-chain flexibility to protein-protein docking only

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