# Bioinformatics Questions and Answers – Molecular Complementarity

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This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Molecular Complementarity”.

1. Which of the following is untrue about Amino acid conservation?
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) Conservation of residues at the core of a protein family is often related to function
c) This may be an enzyme active-site or binding site
d) Unlike hydrophobicity or electrostatic potential, displaying residue conservation on the molecular surface has no physical or chemical basis

Explanation: However, the evolutionary information can sometimes delineate a functional epitope allowing residues to be identified that are important for binding. In order to infer structure-function relationships, the proteins must be structurally related, preferably a large family of proteins with related function.

2. Which of the following is untrue about Shape Complementarity?
a) The complementarity between two proteins or a protein and ligand can be described by surface contact or overlap
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) The complementarity between two proteins or a protein and ligand can be described by the number of adjacent surface points (atoms or residues)
d) The hydrophobic effect barely has impact on protein folding

Explanation: For example simple atom neighbor counting and the simple surface contact scores are of this type. Whilst these measures are easily calculated they also have some physical basis for being effective scoring functions. The principal driving force for protein folding and binding is the hydrophobic effect, which involves the free energy gain of removing non-polar surface area from water.

3. The burial of surface area (or the maximization of surface contact) is an approximation of the effect of shape complementarity.
a) True
b) False

Explanation: However, since no distinction is generally made between polar and non-polar surface area this is an approximation. As burial of the former is unfavorable or neutral the sentence is held true.

4. Which of the following is untrue about Grid Representation?
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) To speed up the matching process discretizing the 3-dimensional space using a grid is done
c) Discretizing allows very fast computer matching using search methods such as Fourier transform
d) Fourier transform is hardly used in computer matching

Explanation: The shape of a molecule is described by mapping it to a 3-D grid of uniformly spaced points. Clearly the level of detail is controlled by the grid spacing. The larger the grid spacing the cruder the representation with respect to the atomic level.

5. 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 α, β, and γ are the translational vectors of the mobile molecule B relative to the static one A.
a) fc = $$\sum_{i=1,j=1,k=1}^N$$ (fA,i,j,k * fBi+αj+βk+ɣ)
b) fc = $$\sum_{i=0,j=0,k=0}^N$$ (fA,i,j,k * fBi+αj+βk+ɣ)
c) fc = $$\sum_{i=1,j=1,k=1}^N$$ (fA,0,0,0 * fBi+αj+βk+ɣ)
d) fc = $$\sum_{i=0,j=0,k=0}^N$$ (f0,i,j,k * fBi+αj+βk+ɣ)

Explanation: The overlap between points representing the surface of the molecules is scored favorably, however, overlap with points representing the core of the static molecule are scored unfavorably. Zero correlation score is given to two molecules not in contact. Negative scores represent surface overlap with the core region of molecule A.

6. In Grid representation, the lowest score represents the best surface complementarity for a given translational scan.
a) True
b) False

Explanation: The highest score represents the best surface complementarity for a given translational scan. Note that the mobile molecule must be mapped differently to the grid for each rotational change applied to the molecule.

7. In Property-based measures, displaying physical properties on the molecular surface of molecules can help to guide molecular docking.
a) True
b) False

Explanation: Indeed in many cases, displaying physical properties on the molecular surface of molecules can help to guide molecular docking. Alternatively sequence conservation might also help, particularly where a homologous family of proteins maintain a specific binding partner.

8. Which of the following is untrue about Hydrophobicity?
a) The hydrophobic effect plays a dominant role in the folding of proteins
b) Hydrophobic residues aggregate away from contact with water
c) Hydrophobic residues aggregate to form hydrophobic cores with more polar residues
d) Hydrophobic residues form the solvent accessible surface but restrict the solubility of the protein

Explanation: Clearly a hydrophobic interface will drive the formation of protein-protein or protein-ligand interactions. It has been noted that hydrophobicity is fairly common at protein-protein interfaces particularly in homodimers (two identical protein monomers that associate) and oligomeric proteins.

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

Explanation: In some cases biological function is dependent on this. However, many protein interactions are non-obligatory being made/broken according to their environment. These proteins must be independently stable in solution. These are commonly heterodimeric complexes including enzyme inhibitor and antibody-antigen complexes as well as a host of other casual interacting proteins. The hydrophobic effect is often much less dominant and interfaces are more polar in nature partly because of issues relating to protein stability and aggregation. Therefore, hydrophobicity is useful as a guide to molecular complementarity in selective protein-protein interactions.

10. Which of the following is untrue about Electrostatic Complementarity?
a) The electrostatic properties of biomolecules play an important role in determining interactions
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) Charged groups involved in the biomolecular interface are often stabilized by other polar or oppositely charged groups on the interacting molecule
d) Charged groups involved in the biomolecular interface are often stabilized by similar polar or same charged groups on the interacting molecule