Questions and Answers
What is the general term for the range of energies of electromagnetic radiation?
Electromagnetic spectrum
What is the primary function of a magnetic field in Nuclear Magnetic Resonance Spectroscopy?
To align the nuclear spins of atoms
What is the term for the display of the intensity of electromagnetic radiation vs. energy or wavelength?
Spectrum
What is the phenomenon where atomic nuclei absorb and emit electromagnetic radiation at specific frequencies?
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What is the term for the study of the interaction between matter and electromagnetic radiation?
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Which of the following is NOT a standard reference used in the PDB's validation process?
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What is the primary focus of the validation process in the Protein Data Bank?
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What is the purpose of stereochemical validation in the PDB?
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What is the name of the system used by the PDB to validate deposited structures?
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What is the primary function of the depositor in the PDB's workflow?
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What is the name of the paper that describes the PDB's validation process?
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Which step in the PDB's workflow involves the depositor's approval?
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What is the name of the database that stores deposited structures in the PDB's workflow?
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What is the purpose of the archival data in the PDB's workflow?
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What is the purpose of the corrections step in the PDB's workflow?
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Study Notes
Homology Modelling
- Importance of homology modelling: random sampling of protein conformations is not feasible due to the immense number of possibilities (Levinthal's paradox)
- Structure is conserved longer than sequence in evolution
- Structure > Function >> Sequence
Template Identification
- Search for templates using sequence similarity (Blast, Psi-Blast) or fold recognition methods
- Use biological information and functional annotation in databases
- Identify active site/motifs
Alignment
- Initial alignment of target and template sequences
- Improvement of alignment through iterative refinement
- Use of biological information to improve alignment
Improving the Alignment
- Methods to improve alignment quality
- Importance of selecting the best template
Template Quality
- Crucial step in homology modelling
- 3D structure determination relies on template quality
Protein Structure Prediction
- Ab initio protein structure prediction: threading and true ab initio methods
- Homology modelling as an alternative to ab initio methods
X-ray Diffraction
- History of X-ray diffraction: discovery of X-rays, first diffraction pattern, and theory development
- Principle of X-ray diffraction: Bragg's law
X-ray Crystallography
- X-ray crystallography as a method to determine atomic structures
- Use in medical applications and protein structure determination
Side Chains
- Importance of side chain modelling
- Prediction accuracy: high for buried residues, lower for surface residues
- Methods for side chain modelling: SCWRL
Refinement and Error Recovery
- Refinement: energy minimization and molecular dynamics
- Error recovery: difficulty in recovering from errors introduced during modelling
Validation
- Importance of validation in protein structure prediction
- Methods for validation: ProQ server, Ramachandran plot, and biological/biochemical data
- Validation report: assessment of model quality using various metrics
Protein Data Bank (PDB)
- Repository of 3D protein structures
- Validation of deposited structures using community standards
- Various validation checks, including covalent bond distances and angles, stereochemistry, and atom nomenclature.
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