This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Structural Analyses of Domain Interactions”.
1. Which of the following is untrue?
a) Many entries in the Protein DataBank (PDB) are three-dimensional structures of multiple domains
b) The structures in PDB provide experimental information about interactions between domains at atomic detail
c) There are comparatively few three-dimensional structures compared to the amount of data available from the lower resolution large-scale experiments
d) Many entries in the Protein DataBank (PDB) are two-dimensional structures of multiple domains
View Answer
Explanation: Analysis of structures consisting of multiple domains has uncovered some of the principles of domain interactions in three dimensions. This information can therefore be complementary to the experimental data on protein interactions and to the predicted interactions.
2. In protein domain family interaction map, the physical contacts of the domains in different families are represented by the lines between the nodes.
a) True
b) False
View Answer
Explanation: Each node in this graph represents a protein domain family. There are a few families that are hubs in the network: these are large families that are functionally versatile, such as Rossmann domains indicated by an ‘R’ here. Most families engage in only one or two types of interactions.
3. In the Interaction map of domain families, the interactions of one family represent the sum of all the interactions of domains in that family.
a) True
b) False
View Answer
Explanation: To study the large-scale patterns and evolution of interactions between protein domains, the interactions in terms of the domain families can be summarized. Thus the interactions of one family represent the sum of all the interactions of domains in that family. Precise information about contacts between individual domains can be extracted by analysis of PDB entries.
4. Most domain families only interact with one or two other families, while a few families are extremely versatile in their interactions and are connected to many families.
a) True
b) False
View Answer
Explanation: The result of the known interactions between members of structural protein families is a graph of connections between families, where the nodes are protein families and the edges represent an interaction between at least one of the domains from each of the two families. This pattern is observed at the level of individual proteins as well, as similar networks can be constructed for the individual proteins in the yeast proteome, for instance.
5. Almost ______ engage in interactions with domains from their own family when one includes oligomeric proteins.
a) one fifith of all known families
b) one fourth of all known families
c) all of all known families
d) half of all known families
View Answer
Explanation: In this case, half of all known families engage in interactions with domains from their own family. Such symmetrical interactions appear to be particularly favorable.
6. In order to understand the geometry of domain combinations, different structures of homologous pairs of domains must be studied.
a) True
b) False
View Answer
Explanation: This is important because though the methods for structure prediction of individual domains are well established, much less is known about assemblies of domains. The network of domain family interactions is a purely two-dimensional map: it lays out the connections between families but does not provide information on the three-dimensional geometry of interactions.
7. The investigation (Aloy and Russel) of domain combinations in multidomain proteins by Bashton and Chothia focuses on two-domain proteins belonging to the Rossmann domain family.
a) True
b) False
View Answer
Explanation: These proteins generally consist of one Rossmann domain and one catalytic domain. As for the analysis of transient interactions, all the proteins belonging to one family of catalytic domains form the same type of interface to the Rossmann domains.
8. The linkers between the catalytic domain and the Rossmann domain were conserved in each family.
a) True
b) False
View Answer
Explanation: This means that interface conservation within one catalytic family is a result of the direct evolutionary relationship between the proteins that have a particular pair of domains. In other words, each set of Rossmann domain proteins with a particular catalytic domain has descended from one common ancestral recombination event.
9. Across the different types of catalytic families, the position of the two domains with respect to one another varied, but only within a range of about ______
a) 20°
b) 10°
c) 90°
d) 80°
View Answer
Explanation: This is the result of a functional constraint in these enzymes: the catalytic domain can only take up a variety of positions, as the substrate needs to be held sufficiently close to the NAD(P) cofactor of the Rossmann domain. In other multidomain proteins where there is no such strict functional constraint, the domain interfaces of one domain family to other families may well be more variable.
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