Myoglobin Oxygen Uptake:

How does Oxygen get inside the Myoglobin?

In an Experiment, an amino acid residue (VAL68) was mutated to (FHE 68), which resulted in reduction of oxygen uptake by a factor of 10. If VAL68 is mutated to a smaller residue such as ALA, the oxygen uptake increases by 1.5. Is this experiment consistent with the theory of channels? In the standard model, oxygen comes in from various locations, i.e. 10 different channels, uniformly. In this experiment, one channel was blocked and therefore caused in decrease in oxygen uptake. A consistent assumption is that there must be a major channel and some tiny ones.

Molecular Hinges in Protein Folding:

Why does proteins fold so fast?

Hinges are rigid areas in the structure of the protein. There are hydrophobic residues which want to stay together and form the shape of the protein.

Water Effects:

What is the force between atoms (hydrophobic effect)?

DNA Packing in the Nucleosome:

Run molecular dynamics simulation on the folded structure; then strip the DNA of protein, and run the simulation again. By comparing relative energies of the packed and unpacked conformations we can learn someting about how DNA packing takes place.

Protein completion I:

Choose a protein without hydrogen from the PDB; and build the missing part by placing the hydrogen in the best possible spot.

Protein completion II:

How to find which states have the minimum energy and therefore are the best solution?

The sites interact with each other; we can break it down to clusters that don’t interact amongst themselves and look at each cluster separately which is smaller version and can be solved faster.

Biological Graphs detangelment:

Given total number of protein and number of interactions among them, we can build an N×N matrix. We might expect that the number of interactions is N², but the total number of interactions is proportional to the number of proteins, N.

In this project, we will redraw the map such that all interactions are short; meaning, each protein interacts with those in a close range. If this is possible, then the algorithm is also helpful to prove that the number of the interactions is in fact proportional to the number of proteins.