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Multiple choice question for engineering

Set 1

1. Which of the following is an incorrect statement about the terminologies related to protein sorting?
a) Subcellular localization is an integral part of protein functionality
b) Many proteins exhibit functions only after being transported to certain compartments of the cell
c) All the proteins exhibit functions after being transported to certain compartments of the cell
d) Protein sorting is also known as protein targeting

View Answer

Answer: c [Reason:] The study of the mechanism of protein trafficking and subcellular localization is the field of protein sorting, which has become one of the central themes in modern cell biology. Identifying protein subcellular localization is an important aspect of functional annotation, because knowing the cellular localization of a protein often helps to narrow down its putative functions.

2. For many eukaryotic proteins, newly synthesized protein precursors have to be transported to specific membrane-bound compartments and be proteolytically processed to become functional
a) True
b) False

View Answer

Answer: a [Reason:] These compartments include chloroplasts, mitochondria, the nucleus, and peroxisomes. To carry out protein translocation, unique peptide signals have to be present in the nascent proteins, which function as “zip codes” that direct the proteins to each of these compartments.

3. Once the proteins are translocated within the organelles, protease cleavage takes place to remove the signal sequences and generate mature proteins
a) True
b) False

View Answer

Answer: a [Reason:] it is an example of posttranslational modification. Even in prokaryotes, proteins can be targeted to the inner or outer membranes, the periplasmic space between these membranes, or the extracellular space. The sorting of these proteins is similar to that in eukaryotes and relies on the presence of signal peptides.

4. The signal sequences have a ___consensus but contain some specific features. They all have a ______ core region preceded by one or more positively charged residues.
a) weak, hydrophilic
b) weak, hydrophobic
c) strong, hydrophilic
d) strong, hydrophilic

View Answer

Answer: b [Reason:] However, the length and sequence of the signal sequences vary tremendously. Peptides targeting mitochondria, for example, are located in the N-terminal region.

5. The signal sequences are typically _______ residues long, rich in _____ charged residues such as arginines as well as hydroxyl residues such as serines and threonines, but devoid of ______ charged residues.
a) 28 to 80, positively, negatively
b) 300 to 800, negatively, positively
c) 28 to 80, negatively, positively
d) 300 to 500, positively, negatively

View Answer

Answer: a [Reason:] they have the tendency to form amphiphilic α-helices. These targeting sequences are cleaved once the precursor proteins are inside the mitochondria.

6. Chloroplast localization signals are also located in the ___-terminus and are about 25 to 100 residues in length, containing very few _______ charged residues but many hydroxylated residues such as serine.
a) N, negatively
b) C, negatively
c) C, positively
d) N, positively

View Answer

Answer: a [Reason:] Chloroplast localization signals are also called transit Peptides. An interesting feature of the proteins targeted for the chloroplasts is that the transit signals are bipartite.

7. Chloroplast localization signals consist of two adjacent signal peptides, one for targeting the proteins to the stromaportion of the chloroplast before being cleaved and the other for targeting the remaining portion of the proteins to the thylakoids.
a) True
b) False

View Answer

Answer: a [Reason:] Localization signals targeting to the nucleus are variable in length (seven to forty-one residues) and are found in the internal region of the proteins. They typically consist of one or two stretches of basic residues with a consensus motif K(K/R)X(K/R). Nuclear signal sequences are not cleaved after protein transport.

8. Which of the following is an incorrect statement about SignalP
a) It only uses neural networks
b) It only uses HMMs
c) It is a web-based program that predicts subcellular localization signals
d) It uses both neural networks and HMMs

View Answer

Answer: b [Reason:] The neural network algorithm combines two different scores, one for recognizing signal peptides and the other for protease cleavage sites. The HMM-based analysis discriminates between signal peptides and the N-terminal transmembrane anchor segments required for insertion of the protein into the membrane.

9. Which of the following is not one of the training sets in SignalP?
a) Prokaryotes
b) Eukaryotes
c) Gram-positive bacteria
d) Gram-negative bacteria

View Answer

Answer: a [Reason:] This distinction is necessary because there are significant differences in the characteristics of the signal peptides from these organisms. Therefore, appropriate datasets need to be selected before analyzing the sequence. The program predicts both the signal peptides and the protease cleavage sites of the query sequence.

10. TargetP is a neural network-based program, similar to SignalP.
a) True
b) False

View Answer

Answer: a [Reason:] It predicts the subcellular locations of eukaryotic proteins based on their N-terminal amino acid sequence only. It uses analysis output from SignalP and feeds it into a decision neural network, which makes a final choice regarding the target compartment.

Set 2

1. The main feature of computer visualization programs is interactivity, which allows users to visually manipulate the structural images through a graphical user interface.
a) True
b) False

View Answer

Answer: a [Reason:] At the touch of a mouse button, a user can move, rotate, and zoom an atomic model on a computer screen in real time, or examine any portion of the structure in great detail, as well as draw it in various forms in different colors. Further manipulations can include changing the conformation of a structure by protein modeling or matching a ligand to an enzyme active site through docking exercises.

2. A Protein Data Bank (PDB) data file for a protein structure contains only x, and z coordinates of atoms.
a) True
b) False

View Answer

Answer: b [Reason:] Because a Protein Data Bank (PDB) data file for a protein structure contains only x, y, and z coordinates of atoms, the most basic requirement for a visualization program is to build connectivity between atoms to make a view of a molecule. The visualization program should also be able to produce molecular structures in different styles, which include wire frames, balls and sticks, space-filling spheres, and ribbons.

3. A wire-frame diagram is a line drawing representing bonds between atoms.
a) True
b) False

View Answer

Answer: a [Reason:] The wire frame is the simplest form of model representation. It is useful for localizing positions of specific residues in a protein structure, or for displaying a skeletal form of a structure when Cα atoms of each residue are connected.

4. Balls and sticks are solid spheres and rods, representing atoms and bonds, respectively.
a) True
b) False

View Answer

Answer: a [Reason:] These diagrams can also be used to represent the backbone of a structure. In a space-filling representation, each atom is described using large solid spheres with radii corresponding to the van der Waals radii of the atoms.

5. Ribbon diagrams use cylinders or spiral ribbons to represent α-helices and broad, flat arrows to represent β-strands.
a) True
b) False

View Answer

Answer: a [Reason:] This type of representation is very attractive in that it allows easy identification of secondary structure elements and gives a clear view of the overall topology of the structure. The resulting images are also visually appealing.

6. Different representation styles can be used in combination to highlight a certain feature of a structure while deemphasizing the structures surrounding it.
a) True
b) False

View Answer

Answer: a [Reason:] For example, a cofactor of an enzyme can be shown as space-filling spheres while the rest of the protein structure is shown as wire frames or ribbons. Some widely used and freely available software programs are there for molecular graphics.

7. Which of the following is wrong about Swiss-PDB Viewer?
a) It is a structure viewer for multiple platforms
b) It is a structure viewer for single platforms
c) It is essentially a Swiss-Army knife for structure visualization and modeling
d) It is capable of structure visualization, analysis, and homology modeling

View Answer

Answer: b [Reason:] It is essentially a Swiss-Army knife for structure visualization and modeling because it incorporates so many functions in a small shareware program. It allows display of multiple structures at the same time in different styles, by charge distribution, or by surface accessibility. It can measure distances, angles, and even mutate residues. In addition, it can calculate molecular surface, electrostatic potential, Ramachandran plot, and so on. The homology modeling part includes energy minimization and loop modeling.

8. Which of the following is an incorrect statement?
a) WebMol is a web-based program built based on a modified RasMol code and thus shares many similarities with RasMol
b) WebMol is a web-based program that is totally different from RasMol
c) Chime is a plug-in for web browsers
d) Chime is not a standalone program and has to be invoked in a web browser

View Answer

Answer: b [Reason:] Chime is also derived from RasMol and allows interactive display of graphics of protein structures inside a web browser. RasMol runs directly on a browser of any type as an applet and is able to display simple line drawing models of protein structures. It also has a feature of interactively displaying Ramachandran plots for structure model evaluation.

9. Which of the following is an incorrect statement?
a) Molscript is a UNIX program capable of generating wire-frame
b) Molscript is capable of generating space-filling
c) Molscript is not capable of generating ball-and-stick styles
d) In particular, secondary structure elements can be drawn with solid spirals and arrows representing α-helices and β-strands, respectively

View Answer

Answer: c [Reason:] Visually appealing images can be generated that are of publication quality. The drawback is that the program is command-line–based and not very user friendly. A modified UNIX program called Bobscript is available with enhanced features.

10. Ribbons another UNIX program similar to Molscript, generates ribbon diagrams depicting protein secondary structures
a) True
b) False

View Answer

Answer: a [Reason:] Aesthetically appealing images can be produced that are of publication quality. However, the program, which is also command-line-based, is extremely difficult to use.

Set 3

1. The building blocks of proteins are ______ naturally occurring amino acids, small molecules that contain a free amino group (NH2) and a free carboxyl group (COOH).
a) ten
b) twenty
c) nine
d) nineteen

View Answer

Answer: b [Reason:] Both of these groups are linked to a central carbon (Cα), which is attached to hydrogen and a side chain group (R). Amino acids differ only by the side chain R group. The chemical reactivities of the R groups determine the specific properties of the amino acids. Amino acids can be grouped into several categories based on the chemical and physical properties of the side chains, such as size and affinity for water.

2. Within the hydrophobic set of amino acids, they can be further divided into aliphatic and aromatic.
a) True
b) False

View Answer

Answer: a [Reason:] Aliphatic side chains are linear hydrocarbon chains and aromatic side chains are cyclic rings. Within the hydrophilic set, amino acids can be subdivided into polar and charged. Charged amino acids can be either positively charged (basic) or negatively charged (acidic).

3. ______ the smallest amino acid, has a hydrogen atom as the R group.
a) valine
b) proline
c) Glycine
d) threonine

View Answer

Answer: c [Reason:] Of particular interest within the twenty amino acids are glycine and proline. It can therefore adopt more flexible conformations that are not possible for other amino acids. Proline is on the other extreme of flexibility. Its side chain forms a bond with its own backbone amino group, causing it to be cyclic. The cyclic conformation makes it very rigid, unable to occupy many of the main chain conformations adopted by other amino acids.

4. The peptide formation involves two amino acids covalently joined together between the carboxyl group of one amino acid and the amino group of another.
a) True
b) False

View Answer

Answer: a [Reason:] this reaction is a condensation reaction involving removal of elements of water from the two molecules. The resulting product is called a dipeptide. The newly formed covalent bond connecting the two amino acids is called a peptide bond. Once an amino acid is incorporated into a peptide, it becomes an amino acid residue. Multiple amino acids can be joined together to form a longer chain of amino acid polymer.

5. A linear polymer of more than fifty amino acid residues is referred to as a ________
a) dipeptide
b) oligopeptide
c) peptide
d) polypeptide

View Answer

Answer: d [Reason:] A polypeptide, also called a protein, has a well-defined three-dimensional arrangement. On the other hand, a polymer with fewer than fifty residues is usually called a peptide without a well-defined three-dimensional structure. The residues a peptide or polypeptide are numbered beginning with the residue containing the amino group, referred to as the N-terminus, and ending with the residue containing the carboxyl group, known as the C-terminus.

6. Which of the following is not correct?
a) The rigid double bond structure forces atoms associated with the peptide bond to lie in the same plane, called the dipeptide plane
b) A peptide bond is actually a partial double bond owing to shared electrons between
O=C–N atoms
c) Because of the planar nature of the peptide bond and the size of the R groups, there are considerable restrictions on the rotational freedom by the two bonded pairs of atoms around the peptide bond
d) The angle of rotation about the bond is referred to as the dihedral angle (also called the tortional angle)

View Answer

Answer: a [Reason:] The rigid double bond structure forces atoms associated with the peptide bond to lie in the same plane, called the peptide plane. For a peptide unit, the atoms linked to the peptide bond can be moved to a certain extent by the rotation of two bonds flanking the peptide bond.

7. Which of the following is not correct about the stabilizing Forces?
a) Protein structures from secondary to quaternary are maintained by noncovalent forces
b) They include electrostatic interactions but not van der Waals forces, and hydrogen bonding
c) Electrostatic interactions are a significant stabilizing force in a protein structure
d) Electrostatic interactions occur when excess negative charges in one region are neutralized by positive charges in another region

View Answer

Answer: b [Reason:] include electrostatic interactions, van der Waals forces, and hydrogen bonding. The result is the formation of salt bridges between oppositely charged residues. The electrostatic interactions can function within a relatively long range (15 Å). Hydrogen bonds are a particular type of electrostatic interactions similar to dipole–dipole interactions involving hydrogen from one residue and oxygen from another. Hydrogen bonds can occur between main chain atoms as well as side chain atoms.

8. Which of the following is not correct about the α-Helices?
a) An α-helix has a main chain backbone conformation that resembles a corkscrew
b) Nearly all known α-helices are right handed, exhibiting a leftward spiral form
c) Nearly all known α-helices are right handed, exhibiting a rightward spiral form
d) In right handed helix, there are 3.6 amino acids per helical turn

View Answer

Answer: b [Reason:] The structure is stabilized by hydrogen bonds formed between the main chain atoms of residues i and i + 4. The hydrogen bonds are nearly parallel with the helical axis. The average φ and ψ angles are 60◦ and 45◦, respectively, and are distributed in a narrowly defined region in the lower left region of a Ramachandran plot.

9. Which of the following is not correct about the β-sheet?
a) A β-sheet is a fully extended configuration built up from several spatially adjacent regions of a polypeptide chain
b) Each region involved in forming the β-sheet is a β-strand
c) The β-strand conformation is pleated with main chain backbone zigzagging and side chains positioned on same sides of the sheet
d) β-Strands are stabilized by hydrogen bonds between residues of adjacent strands

View Answer

Answer: c [Reason:] The β-strand conformation is pleated with main chain backbone zigzagging and side chains positioned alternately on opposite sides of the sheet. β-strands near the surface of the protein tend to show an alternating pattern of hydrophobic and hydrophilic regions, whereas strands buried at the core of a protein are nearly all hydrophobic. The β-strands can run in the same direction to form a parallel sheet or can run every other chain in reverse orientation to form an antiparallel sheet, or a mixture of both.

10. Which of the following is not correct about the Coils and Loops?
a) They are regular structures
b) They are irregular structures
c) The loops are often characterized by sharp turns or hairpin-like structures
d) If the connecting regions are completely irregular, they belong to random coils

View Answer

Answer: a [Reason:] Residues in the loop or coil regions tend to be charged and polar and located on the surface of the protein structure. They are often the evolutionarily variable regions where mutations, deletions, and insertions frequently occur. They can be functionally significant because these locations are often the active sites of proteins.

11. Globular proteins are usually insoluble.
a) True
b) False

View Answer

Answer: b [Reason:] Globular proteins are usually soluble and surrounded by water molecules. They tend to have an overall compact structure of spherical shape with polar or hydrophilic residues on the surface and hydrophobic residues in the core. Such an arrangement is energetically favorable because it minimizes contacts with water by hydrophobic residues in the core and maximizes interactions with water by surface polar and charged residues. Common examples of globular proteins are enzymes, myoglobins, cytokines, and protein hormones.

12. Which of the following is not correct about the Integral Membrane Proteins?
a) Membrane proteins exist in lipid bilayers of cell membranes
b) The exterior of the proteins spanning the membrane must be very hydrophobic to be stable
c) The exterior of the proteins spanning the membrane must be very hydrophilic to be stable
d) Most typical transmembrane segments are α-helices

View Answer

Answer: c [Reason:] Because they are surrounded by lipids, the exterior of the proteins spanning the membrane must be very hydrophobic to be stable. Occasionally, for some bacterial periplasmic membrane proteins, they are composed of β-strands. The loops connecting these segments sometimes lie in the aqueous phase, in which they can be entirely hydrophilic.

13. Which of the following is not correct about the X-ray Crystallography?
a) In x-ray protein crystallography, proteins need to be grown into large crystals in which their positions are fixed in a repeated, ordered fashion
b) The protein crystals are illuminated with an intense x-ray beam
c) The x-rays are deflected by the electron clouds surrounding the atoms in the crystal producing a regular pattern of diffraction
d) The protein crystals are illuminated with an intense infrared beam

View Answer

Answer: d [Reason:] The diffraction pattern is composed of thousands of tiny spots recorded on a x-ray film. The diffraction pattern can be converted into an electron density map using a mathematical procedure known as Fourier transform. To interpret a three-dimensional structure from two-dimensional electron density maps requires solving the phases in the diffraction data.

14. Which of the following is not correct about the NMR?
a) It stands for Nuclear Magnetic Resonance
b) NMR spectroscopy detects spinning patterns of atomic nuclei in a electric field
c) NMR spectroscopy detects spinning patterns of atomic nuclei in a magnetic field
d) Protein samples are labeled with radioisotopes such as 13C and 15N

View Answer

Answer: b [Reason:] radiofrequency radiation is used to induce transitions between nuclear spin states in a magnetic field. Interactions between spinning isotope pairs produce radio signal peaks that correlate with the distances between them. By interpreting the signals observed using NMR, proximity between atoms can be determined.

15. One can search a structure in PDB using the four-letter code or keywords related to its annotation.
a) True
b) False

View Answer

Answer: a [Reason:] Each entry is given a unique code, PDB id, consisting of four characters of either letters A to Z or digits 0 to 9 such as 1LYZ and 4RCR. The identified structure can be viewed directly online or downloaded to a local computer for analysis.

Set 4

1. The classification results from both systems, SCOP and CATH are quite dissimilar.
a) True
b) False

View Answer

Answer: b [Reason:] Due to the differences in classification criteria, one might expect that there would be huge differences in classification results. In fact, the classification results from both systems are quite similar. Exhaustive analysis has shown that the results from the two systems converge at about 80% of the time. In other words, only about 20% of the structure fold assignments are different.

2. The first step in structure classification is to remove redundancy from databases.
a) True
b) False

View Answer

Answer: a [Reason:] Among the tens of thousands of entries in PDB, the majority of the structures are redundant as they correspond to structures solved at different resolutions, or associated with different ligands or with single-residue mutations. The redundancy can be removed by selecting representatives through a sequence alignment–based approach.

3. The second step in structure classification is to separate structurally distinct domains within a structure.
a) True
b) False

View Answer

Answer: a [Reason:] Because some proteins are composed of multiple domains, they must be subdivided before a sensible structural comparison can be carried out. This domain identification and separation can be done either manually or based on special algorithms for domain recognition.

4. The last step in structure classification involves grouping proteins/domains of similar structures.
a) True
b) False

View Answer

Answer: a [Reason:] Once multidomain proteins are split into separate domains, structure comparison can be conducted at the domain level, either through manual inspection, or automated structural alignment, or a combination of both. This step involves grouping proteins/domains of similar structures and clustering them based on different levels of resemblance in secondary structure composition and arrangement of the secondary structures in space.

5. Which of the following is untrue about SCOP?
a) It is a database for comparing and classifying protein structures
b) It is constructed almost entirely based on manual examination of protein structures
c) The proteins are grouped into hierarchies of classes, folds, superfamilies, and families
d) The SCOP families consist of proteins having low sequence identity (>30%)

View Answer

Answer: d [Reason:] The SCOP families consist of proteins having high sequence identity (>30%). Thus, the proteins within a family clearly share close evolutionary relationships and normally have the same functionality. The protein structures at this level are also extremely similar.

6. Members within the ____ fold ______ have evolutionary relationships.
a) same, always
b) same, do not always
c) one, always
d) different, do not

View Answer

Answer: b [Reason:] Folds consist of superfamilies with a common core structure, which is determined manually. This level describes similar overall secondary structures with similar orientation and connectivity between them. Members within the same fold do not always have evolutionary relationships. Some of the shared core structure may be a result of analogy. Classes consist of folds with similar core structures.

7. In CATH, Structural domain separation is carried by
a) manual comparison only
b) computer programs only
c) human expertise only
d) a combined effort of a human expert and computer programs

View Answer

Answer: d [Reason:] CATH classifies proteins based on the automatic structural alignment program SSAP as well as manual comparison. Structural domain separation is carried out also as a combined effort of a human expert and computer programs. Individual domain structures are classified at five major levels: class, architecture, fold/topology, homologous superfamily, and homologous family.

8. Which of the following is untrue about SCOP and CATH?
a) The definition for class in CATH is quite dissimilar to that in SCOP
b) The definition for class in CATH is based on secondary structure content
c) Architecture is a unique level in CATH, intermediate between fold and class
d) The definition for class in CATH is similar to that in SCOP

View Answer

Answer: d [Reason:] The topology level is equivalent to the fold level in SCOP, which describes overall orientation of secondary structures and takes into account the sequence connectivity between the secondary structure elements. The homologous superfamily and homologous family levels are equivalent to the superfamily and family levels in SCOP with similar evolutionary definitions, respectively.

9. SCOP is _______ based on manual comparison of structures by human experts with no quantitative criteria to group proteins.
a) entirely
b) almost entirely
c) not
d) partially

View Answer

Answer: b [Reason:] It is argued that this approach offers some flexibility in recognizing distant structural relatives, because human brains may be more adept at recognizing slightly dissimilar structures that essentially have the same architecture. However, this reliance on human expertise also renders the method subjective. The exact boundaries between levels and groups are sometimes arbitrary.

10. CATH is a combination of manual curation and automated procedure, which makes the process less subjective
a) True
b) False

View Answer

Answer: a [Reason:] For example, in defining domains, CATH first relies on the consensus of three different algorithms to recognize domains. When the computer programs disagree, human intervention will take place. In addition, the extra Architecture level in CATH makes the structure classification more continuous. The drawback of the systems is that the fixed thresholds in structural comparison may make assignment less accurate.

Set 5

1. Which of the following is incorrect about protein structure comparison?
a) The comparative approach is important in finding remote protein homologs
b) Protein structures have a much higher degree of conservation than the sequences
c) Protein structures have a much lesser degree of conservation than the sequences
d) Proteins can share common structures even without sequence similarity

View Answer

Answer: c [Reason:] structure comparison is one of the fundamental techniques in protein structure analysis. Structure comparison can often reveal distant evolutionary relationships between proteins, which is not feasible using the sequence-based alignment approach alone. In addition, protein structure comparison is a prerequisite for protein structural classification into different fold classes.

2. The intermolecular approach is normally applied to relatively _____ structures.
a) distinctive
b) dissimilar
c) similar
d) different

View Answer

Answer: c [Reason:] The algorithmic approaches to comparing protein geometric properties can be divided into three categories: the first superposes protein structures by minimizing intermolecular distances; the second relies on measuring intramolecular distances of a structure; and the third includes algorithms that combine both intermolecular and intramolecular approaches.

3. Which of the following is incorrect about intermolecular approach?
a) This procedure starts with identifying equivalent residues or atoms
b) After residue–residue correspondence is established, one of the structures is moved laterally and vertically toward the other structure to allow the two structures to be in the same location
c) The structures are rotated relative to each other around the three-dimensional axes
d) The rotation doesn’t depend on the intermolecular distance

View Answer

Answer: d [Reason:] The rotation continues until the shortest intermolecular distance is reached. At this point, an optimal superimposition of the two structures is reached. After superimposition, equivalent residue pairs can be identified, which helps to quantitate the fitting between the two structures.

4. The root mean square deviation (RMSD), without the size dependency correction is ____
bioinformatics-questions-answers-protein-structure-comparison-q4

View Answer

Answer: a [Reason:] An important measurement of the structure fit during superposition is the distance between equivalent positions on the protein structures. This requires using a least square-fitting function called root mean square deviation (RMSD), which is the square root of the averaged sum of the squared differences of the atomic distances. Here D is the distance between coordinate data points and N is the total number of corresponding residue pairs.

5. The root mean square deviation (RMSD), with the size dependency correction is ____
bioinformatics-questions-answers-protein-structure-comparison-q5

View Answer

Answer: d [Reason:] In practice, only the distances between Cα carbons of corresponding residues are measured. The goal of structural comparison is to achieve a minimum RMSD. However, the problem with RMSD is that it depends on the size of the proteins being compared. For the same degree of sequence identity, large proteins tend to have higher RMSD values than small proteins when an optimal alignment is reached. Recently, a logarithmic factor has been proposed to correct this size-dependency problem. This new measure is called RMSD100.

6. The intramolecular approach does not depend on sequence similarity between the proteins to be compared.
a) True
b) False

View Answer

Answer: a [Reason:] The intramolecular approach relies on structural internal statistics and therefore does not depend on sequence similarity between the proteins to be compared. In addition, this method does not generate a physical superposition of structures, but instead provides a quantitative evaluation of the structural similarity between corresponding residue pairs.

7. Which of the following is incorrect about the intramolecular approach?
a) The method works by generating a distance matrix between residues of the same protein
b) It generates a string between residues of the same protein
c) In comparing two protein structures, the distance matrices from the two structures are moved relative to each other to achieve maximum overlaps
d) By overlaying two distance matrices, similar intramolecular distance patterns representing similar structure folding regions can be identified

View Answer

Answer: b [Reason:] For the ease of comparison, each matrix is decomposed into smaller submatrices consisting of hexapeptide fragments. To maximize the similarity regions between two structures, a Monte Carlo procedure is used. By reducing three-dimensional information into two-dimensional information, this strategy identifies overall structural resemblances and common structure cores.

8. Which of the following is incorrect about Multiple Structure Alignment?
a) The alignment strategy is different than the Clustal sequence alignment using a progressive approach
b) All structures are first compared in a pairwise fashion
c) A distance matrix is developed based on structure similarity scores such as RMSD
d) The aligned structures create a median structure that allows other structures to be progressively added for comparison based on the hierarchy described in the guide tree

View Answer

Answer: a [Reason:] In addition to pairwise alignment, a number of algorithms can also perform multiple structure alignment. The alignment strategy is similar to the Clustal sequence alignment using a progressive approach. When all the structures in the set are added, this eventually creates a multiple structure alignment.

9. Which of the following is incorrect about SSAP?
a) It is a web server that uses an intramolecular distance–based method
b) Matrices are built based on the Cβ distances of all residue pairs
c) Dynamic programming approach is not used here
d) Dynamic programming approach is used

View Answer

Answer: c [Reason:] When comparing two different matrices, a dynamic programming approach is used to find the path of residue positions with optimal scores. The dynamic programming is applied at two levels, one at a lower level in which all residue pairs between the proteins are compared and another at an upper level in which subsequently identified equivalent residue pairs are processed to refine the matching positions. An SSAP score is reported for structural similarity. A score above 70 indicates a good structural similarity.

10. VAST is a web server that performs alignment using intramolecular approaches only
a) True
b) False

View Answer

Answer: b [Reason:] VAST (Vector Alignment Search Tool) is a web server that performs alignment using both the inter- and intramolecular approaches. The superposition is based on information of directionality of secondary structural elements (represented as vectors). Optimal alignment between two structures is defined by the highest degree of vector matches.