Threading techniques MCQs With Answer

Threading techniques MCQs With Answer — Introduction

Threading, or fold recognition, is a computational approach that maps a query protein sequence onto known three-dimensional structures to infer its fold when clear homologs are absent. For M. Pharm students, understanding threading is essential for tasks such as predicting protein targets, modeling drug–protein interactions, and interpreting structural impacts of mutations. This quiz-focused blog presents targeted multiple-choice questions covering core concepts: scoring functions, profile and profile–profile alignments, environmental and contact potentials, fold libraries, significance metrics (Z‑score, TM‑score), common software, and limitations of threading. The questions emphasize practical interpretation and decision-making relevant to pharmaceutical research and structural bioinformatics workflows.

Q1. What best describes the primary goal of protein threading (fold recognition)?

• Predicting the 3D structure by aligning a sequence to a library of known folds to identify the best structural template
• Generating ab initio models from physics-based molecular dynamics without templates
• Finding nucleotide binding sites using sequence motifs
• Designing new protein sequences using directed evolution data

Correct Answer: Predicting the 3D structure by aligning a sequence to a library of known folds to identify the best structural template

Q2. Which statement distinguishes threading from classical homology modeling?

• Threading relies exclusively on high sequence identity (>70%) between query and template
• Threading attempts to recognize compatible folds even when sequence identity is low, using structure‑aware scoring
• Homology modeling does not use alignments
• Threading always produces atomic‑level loop conformations without refinement

Correct Answer: Threading attempts to recognize compatible folds even when sequence identity is low, using structure‑aware scoring

Q3. Which components are typically integrated into a threading scoring function?

• Sequence–profile scores, secondary structure agreement, solvent accessibility, and residue–residue contact potentials
• Only raw pairwise sequence identity values
• Chromatographic retention times and mass spectra
• Phylogenetic tree topology without structural terms

Correct Answer: Sequence–profile scores, secondary structure agreement, solvent accessibility, and residue–residue contact potentials

Q4. In threading, what does a high Z‑score typically indicate?

• The query sequence is likely to be intrinsically disordered
• The alignment score is significantly better than expected by random chance, suggesting a reliable template match
• That the template structure is of low resolution
• That the sequence has many low complexity regions

Correct Answer: The alignment score is significantly better than expected by random chance, suggesting a reliable template match

Q5. What are environment‑specific substitution matrices used for in threading?

• They adjust residue substitution scores based on local structural environment such as secondary structure and solvent exposure
• They provide codon‑usage corrections for expression optimization
• They estimate pKa shifts of ionizable residues
• They encode fragment assembly rules for ab initio folding

Correct Answer: They adjust residue substitution scores based on local structural environment such as secondary structure and solvent exposure

Q6. Which optimization method is commonly adapted in threading to find the best sequence‑to‑structure alignment?

• Dynamic programming with modified gap penalties and structure‑dependent scores
• Standard k‑means clustering without alignment
• Fourier transform based image matching
• Simple random sampling without scoring

Correct Answer: Dynamic programming with modified gap penalties and structure‑dependent scores

Q7. What is meant by a “fold library” in the context of threading?

• A curated set of representative protein 3D structures used as templates for aligning query sequences
• A database of ligand binding affinities
• A collection of mRNA expression profiles for different tissues
• A list of laboratory protocols for protein purification

Correct Answer: A curated set of representative protein 3D structures used as templates for aligning query sequences

Q8. Which is a major limitation of threading methods?

• They cannot model proteins when no similar fold exists in the template library
• They always outperform experimental structure determination
• They require X‑ray diffraction data as input
• They are unsuitable for any protein longer than 50 residues

Correct Answer: They cannot model proteins when no similar fold exists in the template library

Q9. What does “meta‑threading” refer to?

• Combining results from multiple threading methods to improve template selection and confidence estimation
• Using threading exclusively for membrane proteins
• Applying threading to nucleotide sequences instead of proteins
• Threading that does not use any scoring functions

Correct Answer: Combining results from multiple threading methods to improve template selection and confidence estimation

Q10. How are knowledge‑based contact potentials for threading usually derived?

• From statistical analysis of residue–residue contact frequencies observed across known protein structures
• By measuring binding constants experimentally for every residue pair
• From ab initio quantum mechanical calculations for entire proteins
• By sequencing genomes of related organisms

Correct Answer: From statistical analysis of residue–residue contact frequencies observed across known protein structures

Q11. What advantage does profile–profile alignment provide in threading over sequence–profile alignment?

• It compares two position‑specific scoring matrices, capturing more evolutionary information and improving sensitivity for remote homologs
• It ignores evolutionary information entirely to speed up computation
• It guarantees a correct tertiary structure without refinement
• It only works for small peptides under 30 residues

Correct Answer: It compares two position‑specific scoring matrices, capturing more evolutionary information and improving sensitivity for remote homologs

Q12. Why does incorporating predicted secondary structure into threading improve alignment accuracy?

• Predicted secondary structure constrains residue placements to helix, sheet or coil, helping to match sequence regions to compatible template structural segments
• Secondary structure prediction replaces the need for any template search
• Secondary structure predictions always have 100% accuracy
• Because secondary structure prediction reduces sequence length

Correct Answer: Predicted secondary structure constrains residue placements to helix, sheet or coil, helping to match sequence regions to compatible template structural segments

Q13. Which statistical approach is commonly used to assess significance of a threading hit?

• Calculating Z‑scores by comparing the alignment score to a distribution of scores from randomized sequences or unrelated templates
• Using chromatogram peak areas
• Applying the Hardy–Weinberg equilibrium test
• Counting the number of glycosylation sites only

Correct Answer: Calculating Z‑scores by comparing the alignment score to a distribution of scores from randomized sequences or unrelated templates

Q14. Which of the following is a known fold recognition/threading program?

• FUGUE
• BLASTN
• ClustalW
• MassLynx

Correct Answer: FUGUE

Q15. Which structural metric is considered size‑independent and useful to evaluate model fold correctness after threading?

• TM‑score
• Raw sequence identity percentage
• Melting temperature
• Retention factor (Rf) in TLC

Correct Answer: TM‑score

Q16. What is the core idea behind fragment‑based threading approaches?

• Matching short sequence fragments to compatible structural fragments from known proteins and assembling them into a model
• Using only single amino acid substitutions for modeling
• Modeling proteins exclusively by molecular dynamics without templates
• Ignoring structural context and using sequence length alone

Correct Answer: Matching short sequence fragments to compatible structural fragments from known proteins and assembling them into a model

Q17. Which type of potential accounts explicitly for residue–residue interaction distances in threading scoring?

• Distance‑dependent contact potentials
• Simple identity substitution matrices
• Chromatography retention potentials
• Codon usage potentials

Correct Answer: Distance‑dependent contact potentials

Q18. After obtaining a threading alignment and template, which modeling step is typically required to improve local geometry, especially loops?

• Loop modeling and local structural refinement
• Whole‑genome sequencing
• Peptide mass fingerprinting
• IPTG induction optimization

Correct Answer: Loop modeling and local structural refinement

Q19. Threading is particularly preferred over simple homology modeling when sequence identity between query and template falls into which range?

• Below ~30% (the “twilight zone”) where direct homology inference becomes unreliable
• Above 90% where templates are identical
• Exactly 50% only
• When identity is 100% only

Correct Answer: Below ~30% (the “twilight zone”) where direct homology inference becomes unreliable

Q20. What does the CASP experiment evaluate that is directly relevant to threading methods?

• Blind assessment of protein structure prediction methods, including fold recognition and threading performance
• Clinical trial outcomes for new drugs
• Protein expression yields in bacterial systems
• Peptide synthesis efficiency in solid‑phase methods

Correct Answer: Blind assessment of protein structure prediction methods, including fold recognition and threading performance

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