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Rhodopsin is an average sized protein of 40 kD.
For an average sized protein consisting 300 amino acids, the total number of codon paths can be as many as 10.
Hundreds of tetrahedra are typically generated by the tessellation of an average sized protein, each objectively identifying at its four vertices a quadruplet of structurally nearest neighbor residues.
In these experiments, SHMC achieves an order magnitude speedup in sampling efficiency for medium sized proteins.
Biochemical analysis of the nuclear BR1/BR2 mRNPs suggests that each of these long mRNAs is associated with approximately 500 average-sized proteins (Wurtz et al. 1990).
Together, these results establish that general intracellular- or organelle-macromolecular crowding exerts small effects on the diffusion properties of average-sized proteins at physiological concentrations, irrespective of whether they are ordered or intrinsically disordered.
An average-sized protein macromolecule contains a string of about 400 amino acid molecules.
Small to average-sized protein domains can now be designed automatically, and side-chain placement calculations can be solved for nearly all sizes of proteins and protein complexes in the growing field of structural genomics.
2) The Gibbs energy of unfolding for a small to average-sized protein is about two or three orders of magnitude smaller than the standard molal Gibbs energy for the unfolded protein itself.
These data are also consistent with the results from our recent analysis of the mobility and access of single streptavidin proteins to heterochromatin, where these interphase chromatin domains exhibited quite some permeability to this neutral average-sized protein (15).
Our results indicated that all nuclear subcompartments were easily and similarly accessible for such an average-sized protein, and even condensed heterochromatin neither excluded single molecules nor impeded their passage.
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