This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Coiled Coil Prediction”.
1. Coiled coils are super helical structures involving two to more interacting α-helices from the same or different proteins.
a) True
b) False
View Answer
Explanation: The individual α-helices twist and wind around each other to form a coiled bundle structure. The coiled coil conformation is important in facilitating inter- or intra protein interactions. Proteins possessing these structural domains are often involved in transcription regulation or in the maintenance of cytoskeletal integrity.
2. Which of the following is true regarding Coiled coil?
a) They have an integral repeat of twenty residues
b) They have an integral repeat of seven residues
c) They have an integral repeat of thirty residues
d) The sequence periodicity doesn’t contribute in designing algorithms to predict the structural domain.
View Answer
Explanation: Coiled coils have an integral repeat of seven residues (heptads) which assume a side-chain packing geometry at facing residues. For every seven residues, the first and fourth are hydrophobic, facing the helical interface; the others are hydrophilic and exposed to the solvent. The sequence periodicity forms the basis for designing algorithms to predict this important structural domain.
3. Which of the following is untrue regarding Coils?
a) It is a web-based program that detects coiled coil regions in proteins
b) It scans a window of fourteen, twenty-one, or twenty-eight residues
c) It scans a window of fourteen or twenty-one residues only
d) It compares the sequence to a probability matrix compiled from known parallel two-stranded coiled coils
View Answer
Explanation: By comparing the similarity scores, the program calculates the probability of the sequence to adopt a coiled coil conformation. The program is accurate for solvent-exposed, left-handed coiled coils, but less sensitive for other types of coiled coil structures, such as buried or right-handed coiled coils.
4. In Multicoil, The scoring matrix is constructed based on a database of known three-stranded coiled coils only.
a) True
b) False
View Answer
Explanation: Multicoil is a web-based program for predicting coiled coils. The scoring matrix is constructed based on a database of known two-stranded and three-stranded coiled coils. The program is more conservative than Coils. It has been recently used in several genome-wide studies to screen for protein–protein interactions mediated by coiled coil domains.
5. Leucine zipper domains are a special type of coiled coils found in transcription regulatory proteins which contain two anti parallel α-helices held together by hydrophobic interactions of leucine residues.
a) True
b) False
View Answer
Explanation: The heptad repeat pattern is L-X(6)-L-X(6)-L–X(6)-L. This repeat pattern alone can sometimes allow the domain detection, albeit with high rates of false positives. The reason for the high false-positive rates is that the condition of the sequence region being a coiled coil conformation is not satisfied. To address this problem, algorithms have been developed that take into account both leucine repeats and coiled coil conformation to give accurate prediction.
6. Which of the following is untrue regarding PSIPRED?
a) It is a web-based program that predicts protein secondary structures
b) It uses a combination of evolutionary information and neural networks
c) It uses a combination of evolutionary information only
d) The multiple sequence alignment is derived from a PSI-BLAST database search
View Answer
Explanation: A profile is extracted from the multiple sequence alignment generated from three rounds of automated PSI-BLAST. The profile is then used as input for a neural network prediction similar to that in PHD, but without the jury layer. To achieve higher accuracy, a unique filtering algorithm is implemented to filter out unrelated PSI-BLAST hits during profile construction.
7. Prof is not similar to PHD.
a) True
b) False
View Answer
Explanation: Prof stands for Protein forecasting. It is an algorithm that combines PSI-BLAST profiles and a multistaged neural network, similar to that in PHD. In addition, it uses a linear discriminant function to discriminate between the three states.
8. Jpred combines the analysis results from six prediction algorithms, including PHD, PREDATOR, DSC, NNSSP, Jnet, and ZPred.
a) True
b) False
View Answer
Explanation: The query sequence is first used to search databases with PSI-BLAST for three iterations. Redundant sequence hits are removed. The resulting sequence homologs are used to build a multiple alignment from which a profile is extracted. The profile information is submitted to the six prediction programs. If there is sufficient agreement among the prediction programs, the majority of the prediction is taken as the structure.
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