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Correct answer is (a) \(\sum_{i=1}^N \frac{D_i^2}{N}\)

For explanation: 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.

Correct answer is (c) Molscript is not capable of generating ball-and-stick styles

The BEST explanation: 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.

The correct choice is (a) True

The best explanation: 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.

Right option is (b) False

The explanation is: 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 alignmentbetween two STRUCTURES is defined by the highest degree of vector MATCHES.

Correct answer is (a) True

To explain I WOULD say: 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.

Right answer is (c) similar

Easy explanation: 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.

Right option is (b) False

Explanation: 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.

The CORRECT choice is (a) True

Best explanation: 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.

Correct option is (d) The rotation doesn’t DEPEND on the intermolecular distance

Easy explanation: 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.

Right CHOICE is (b) It is a structure viewer for single platforms

The best I can explain: 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.

Correct choice is (d) a combined effort of a human expert and computer programs

Explanation: 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.

Correct option is (c) DYNAMIC programming approach is not used here

Easy explanation: 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.

Correct answer is (a) True

The explanation: 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.

Correct answer is (a) True

Explanation: 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.

Correct option is (d) polypeptide

Explanation: 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.

The correct answer is (d) \(\frac{RMSD}{-1.3 + 0.5 ln⁡(N)}\)

For explanation: 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.

Correct OPTION is (a) True

Explanation: 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.

Correct choice is (a) True

Easy explanation: 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.

The correct choice is (c) Protein structures have a much lesser degree of conservation than the sequences

To EXPLAIN I would say: 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.

The correct option is (d) The protein crystals are illuminated with an intense infrared beam

The explanation: 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.

Right choice is (b) same, do not ALWAYS

Easy explanation: 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.

Right ANSWER is (a) The alignment strategy is DIFFERENT than the Clustal sequence alignment USING a progressive approach

Explanation: 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.

Correct option is (a) True

Best explanation: 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.

Correct choice is (b) NEARLY all known α-helices are right handed, exhibiting a leftward spiral form

Easiest explanation: 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.

Right option is (b) twenty

The BEST explanation: 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.

Right CHOICE is (b) WEBMOL is a web-based program that is totally different from RasMol

Easy explanation: 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.

Correct choice is (a) True

The explanation: 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.

The correct answer is (d) The SCOP FAMILIES consist of proteins having low sequence identity (>30%)

To explain I would SAY: 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.

Right choice is (b) False

To EXPLAIN: 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.

The correct option is (c) The β-strand conformation is pleated with main CHAIN backbone zigzagging and side chains positioned on same sides of the sheet

Easy explanation: 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.

Correct option is (d) The definition for class in CATH is similar to that in SCOP

Easiest explanation: 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.

Correct answer is (b) NMR SPECTROSCOPY detects spinning patterns of atomic nuclei in a electric field

Easiest explanation: 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.

The correct choice is (a) They are regular structures

To EXPLAIN I would say: 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.

The CORRECT choice is (b) It generates a string between residues of the same protein

For explanation I would say: 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.

The correct ANSWER is (a) True

Easy EXPLANATION: 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).