On further heating, the additional molecules of liquid water are more distant from the polymer chains and thus they are changing the vibrational states of CH3 groups in smaller and smaller degree.
As a negative control we selected an amino acid, Lys65, that is distant from the TCRβ chain, such that cross-linking is not expected to occur.
This may arise from the combination of Gly 335′s small volume and Asp 503′s short side chain, keeping Arg 272 and Asp 503 side chains distant from one another.
This criterion recognises that significant protein conformational change and associated energetic penalties are incurred for repositioning side chains distant from the ligand.
Fourthly, residues which have their side chain pointing away from the ligand were deselected, again recognising that significant protein conformational changes and associated energetic penalties are incurred for repositioning of side chains distant from the ligand.
This suggests that the PS chains are distant from the silica surface and entangled with the PEO chains.
A parallel is drawn between isolated molecules of DPK in solution and DPK units that are distant from each other in a polymer chain, and between aggregated molecules of DPK in solution and DPK units that are close together in entangled chains.
Importantly, the detected perturbations transmit through the protein chain to sites distant from the mutation position.
R119 is distant from those residues on the polypeptide chain, yet it still can affect the catalytic site and apparently is involved in the recognition of the first G in GCAGTG; however, there is no crystal structure currently available, and there are no other restriction enzymes that recognize HCAGTG (H = A or C or T) to offer insight as to how R119 recognizes the first G.
What about competition from chains?
At site 2545, three exclusively hydrophobic amino acids were present, methionine, isoleucine or leucine, whose side chains were > 7 Å distant from the closest copper binding histidine (His2543) (distances calculated from the haemocyanin FU g model, [PDB: 1JS8]).
