Categories
Biomedical Engineering

Learning Goal: I’m working on a biomedical engineering question and need guidanc

Learning Goal: I’m working on a biomedical engineering question and need guidance to help me learn.
using your structure, write a PyMol script to display a) protein secondary structure
hydrogen bonding and 2) polar contacts between the protein and DNA. You will need to use the “select”
and “distance” commands. What types of secondary structure does your protein exhibit? Are there any
protein side chains that may be in an incorrect rotamer (i.e. would an alternative rotamer further stabilize the protein-RNA interaction)? Does the experimental model include sodium (NA), potassium (K),
magnesium (MG), or chloride (CL) counter-ions (hint – use Pymol to select atoms with the names NA, K,
MG or CL)? Determine the total charge of your complex and explain your reasoning (hint – use can Pymol
to select charged amino acids, select charged nucleic acid bases, and/or counter-ions). Include your PyMol
script and a ray-traced image of the complex in your answer. ***my PDB structure is 5Z1G***

Categories
Biomedical Engineering

Learning Goal: I’m working on a biomedical engineering question and need guidanc

Learning Goal: I’m working on a biomedical engineering question and need guidance to help me learn.
Examine the structure using MolProbity and discuss its quality in terms of atom clashes, bond & angle geometry, side-chain
rotamers, backbone Ramachandran values, RNA sugar pucker and RNA backbone conformation. Is the
MolProbity score “good” compared the resolution of the experiment?
Attached is the MolProbity output
Answer with a few paragraphs 🙂