Proteins are amino acid hetero-polymers which are connected by a peptide bond. Amino acids have an amine group and an acid group connected by an alpha carbon which has twenty possible functional groups of various chemical properties and sub-nanometers. All proteins are a combination of linearly polymerized amino acids that are folded and re-folded to form three dimensional surfaces and cavities to host various biochemical reactions and biophysical processes.
Today, after having spend five and a half years of studying proteins and doing a PhD on computational protein design, I am asking questions which I think would be very important discoveries.
Question 1: Why do all proteins show linear polymerization and no branch polymerization? Obviously I know that the existing amino acids do not permit branch polymerization as there is only one possible polymerization site. But what if I can engineer one of the linear side chains and do a CHARMM minimization? What if I run a reactive force field simulation of each of such branch polymers in a sea of polypeptides, and when phase separation happens where do they lie? Can we say something about them?
Question 2: Let us say I take my substrate and convert everything to hydrogens and make an appropriate force field and then compare the interaction energies, and use that as a blank correction? What would that mean?
Tomorrow I shall run these simulations..
Proteins Unmasked 