| what are protein functions determined by? what are the folds determined by? | • Protein functions are determined by their structures.
• Essential elements in bioinformatics.
• Conformation (folding) of protein is determined by dihedral angle (phi and psi). |
| what are amino acids linked by | Amino acids are linked by peptide bond. |
| how are the ψ (psi) against φ (phi) angles visualized? | Ramachandran plot visualizes backbone dihedral angles ψ (psi) against φ (phi) of amino acid residues in protein structure. |
| what's the difference between protein Structure Analysis and Prediction ? | -protein structure analysis - usually refers to the determination of the protein structure by physical or chemical methods.
-Protein structure prediction - refers to the inference of the protein structure using computer algorithms |
| what are the four different protein structures? | 1-Primary Structure – Sequence of amino acids
2-Secondary Structure – Local Structure such as a-helices and b-sheet.
3-tertiary Structure –Arrangement of the secondary structural elements to give 3- dimensional structure of a protein.
4- Quaternary Structure– Arrangement of the subunits to give a protein complex its 3- dimensional structure. |
| how are protein structures determined ? | • X-ray crystallography
• NMR spectroscopy
• Cryo-electron microscopy • Neutron diffraction
• Atomic force microscopy |
| what is used to measure protein structure? | X-ray diffraction analysis – must first be able to crystallize the protein and then calculate its structure by the way it disperses X-rays. determining the protein structure directly is difficult. |
| how does X-ray crystallography work ? what is used to determine quality? | – Protein need to be grown into large crystal
– The X-ray are reflected by electron cloud surrounding the atoms, diffraction patterns are converted into electron density map.
The quality is determined by
-R factor is used to determined the quality of the model, ranging from 0.0 – 0.59 |
| what are the two methods used in X-ray crystallography to resolve the structures? | • Molecular replacement
• Multiple isomorphous replacement |
| what are the steps going from x-ray got atomic model? | N |
| how does NMR (Nuclear Magnetic Resonance) work ? | – Detect spinning pattern of atomic nuclei in magnetic field
– Protein are in solution, so it is mobile and vibrating, thus a number of different models will be constructed.
– Limit to <200 amino acid residues, use radioisotope |
| what are the limitations of both X-rayDiffraction and NMRDistanceMeasurement? | • X-rayDiffraction
✓ Only a small number of proteins can be made to form crystals
✓ A crystal is not the protein’s native environment ✓ Very time consuming
• NMRDistanceMeasurement
✓ Not all proteins are found in solution
✓ This method generally looks at isolated proteins rather than protein complexes
✓ Very time consuming |
| how are structures verified and validated? | •MolProbity
•NQ-Flipper
•Procheck
•CheckMyMetal
•Prosa-web
•Uppsala Electron Density
Server
•Verify3D Structure Evaluation Server
•WHAT_CHECK
•WHAT IF |
| how does a Ramachandran Plot look like? | N |
| what's Cryo-electron microscopy? | • Transmission EM at very low temperatures (liquid nitrogen)
• Veryhighresolution(3-4Å) |
| what's Atomic force microscopy? | • Type of Scanning Probe Microscopy (SPM)
• Invented in 1985 by IBM
• Provides resolution of a fraction of a nanometer |
| what's Structure-structure alignment and comparison? | its done by placing them side by side and comparing them. |
| how are conformational changes analyzed ? | there are two forms open form and closed form .
Citrate synthase, ligand induced conformational changes
Domain motion and small structural distortions. |
| why do we Defining Domains? | Link between domain structure and function
-Different structural domains can be associated with
different functions.
-Enzyme active sites are often at domain interfaces;
domain movements play a functional role. |
| what are the Methods for Identifying Domains? | Domain limits are defined by identifying groups of residues such that the number of contacts between groups is minimized. |
