This set of Bioinformatics Question Bank focuses on “Secondary Structure Prediction for Transmembrane Proteins”.
1. Which of the following is untrue regarding the transmembrane proteins?
a) Constitute up to 30% of all cellular proteins
b) They are responsible for performing a wide variety of important functions in a cell, such as signal transduction, cross-membrane transport, and energy conversion
c) The membrane proteins are also of tremendous biomedical importance
d) They are not drug targets or receptors
Explanation: The membrane proteins are also of tremendous biomedical importance, as they often serve as drug targets for pharmaceutical development. There are two types of integral membrane proteins: α-helical type and β-barrel type. Most transmembrane proteins contain solely α-helices, which are found in the cytoplasmic membrane. A few membrane proteins consist of β-strands forming a β- barrel topology, a cylindrical structure composed of antiparallel β-sheets.
2. The structures of this group of proteins, however, are comparatively a lot difficult to resolve either by x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy.
Explanation: For this group of proteins, prediction of the transmembrane secondary structural elements and their organization is particularly important. Fortunately, the prediction process is somewhat easier because of the hydrophobic environment of the lipid bilayers, which restricts the transmembrane segments to be hydrophobic as well.
3. Which of the following is untrue regarding Prediction of Helical Membrane Proteins?
a) For membrane proteins consisting of transmembrane α–helices, these transmembrane helices are predominantly hydrophobic with a specific distribution of positively charged residues
b) The α-helices generally run perpendicular to the membrane plane
c) The α-helices generally run parallel to the membrane plane
d) The α-helices have an average length between seventeen and twenty-five residues
Explanation: The hydrophobic helices are normally separated by hydrophilic loops with average lengths of fewer than sixty residues. The residues bordering the transmembrane spans are more positively charged. Another feature indicative of the presence of transmembrane segments is that residues at the cytosolic side near the hydrophobic anchor are more positively charged than those at the lumenal or periplasmic side. This is known as the positive-inside rule.
4. The early algorithms based their prediction on hydrophobicity scales.
Explanation: A number of algorithms for identifying transmembrane helices have been developed where the early algorithms based their prediction on hydrophobicity scales. They typically scan a window of seventeen to twenty-five residues and assign membrane spans based on hydrophobicity scores. Some are also able to determine the orientation of the membrane helices based on the positive-inside rule.
5. Predictions solely based on hydrophobicity profiles have lowest error rates.
Explanation: Predictions solely based on hydrophobicity profiles have high error rates. As with the third-generation predictions for globular proteins, applying evolutionary information with the help of neural networks or HMMs can improve the prediction accuracy significantly.
6. The presence of ______ signal peptides can significantly compromise the prediction _______ because the programs tend to confuse hydrophobic signal peptides with membrane helices.
a) hydrophobic, accuracy
b) hydrophobic, error
c) hydrophilic, accuracy
d) hydrophilic, error
Explanation: Predicting transmembrane helices is relatively easy. The accuracy of Some of the best predicting programs, such as TMHMM or HMMTOP, can exceed 70%. To minimize errors, the presence of signal peptides can be detected using a number of specialized programs and then manually excluded.
7. Which of the following is untrue regarding TMHMM?
a) It is a web-based program based on an HMM algorithm
b) It is trained to recognize transmembrane helical patterns
c) It is not trained to recognize transmembrane helical patterns
d) When a query sequence is scanned, the probability of having an α-helical domain is given
Explanation: It is trained to recognize transmembrane helical patterns based on a training set of 160 well-characterized helical membrane proteins. The orientation of the α-helices is predicted based on the positive-inside rule. The prediction output returns the number of transmembrane helices, the boundaries of the helices, and a graphical representation of the helices. This program can also be used to simply distinguish between globular proteins and membrane proteins.
8. Which of the following is untrue regarding Phobius ?
a) It is a web-based program designed to overcome false positives caused by the presence of signal peptides
b) The program incorporates distinct HMM models for signal peptides only
c) The program incorporates distinct HMM models for signal peptides as well as transmembrane helices
d) After distinguishing the putative signal peptides from the rest of the query sequence, prediction is made on the remainder of the sequence
Explanation: In addition to the given data, it has been shown that the prediction accuracy can be significantly improved compared to TMHMM (94% by Phobius compared to 70% by TMHMM). In addition to the normal prediction mode, the user can also define certain sequence regions as signal peptides or other nonmembrane sequences based on external knowledge.
9. Which of the following is true regarding Prediction of β-Barrel Membrane Proteins?
a) For membrane proteins with β-strands only, the β-strands forming the transmembrane segment are amphipathic in nature
b) For membrane proteins with β-strands only, the β-strands forming the transmembrane segment are only hydrophilic in nature
c) For membrane proteins with β-strands only, the β-strands forming the transmembrane segment are only hydrophobic in nature
d) They contain six to nine residues
Explanation: As stated, for membrane proteins with β-strands only, the β-strands forming the transmembrane segment are amphipathic in nature. They contain ten to twenty-two residues with every second residue being hydrophobic and facing the lipid bilayers whereas the other residues facing the pore of the β-barrel are more hydrophilic.
10. Scanning a sequence by hydrophobicity does not reveal transmembrane β-strands.
Explanation: These programs for predicting transmembrane α-helices are not applicable for this unique type of membrane proteins. To predict the β-barrel type of membrane proteins, a small number of algorithms have been made available based on neural networks and related techniques.
Sanfoundry Global Education & Learning Series – Bioinformatics.
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