empirical free energies
statistical mechanical probabilities
Springer Online Journal Archives 1860-2000
Chemistry and Pharmacology
Abstract The relative importance of short- and long-range interactions is examined using a Monte Carlo simulation of protein folding on bovine pancreatic trypsin inhibitor. The model of the protein and the interaction energies were parametrized using X-ray structures of 30 native proteins. A nearest neighbor Ising model is used to determine the conformational state at each stage of the Monte Carlo procedure. Long-range interactions are simulated by contact free energies which become effective as two residues, separated by four or more residues along the chain, approach each other, and by disulfide-bond energies. Short-range interactions for residues separated by one, two, or three residues along the chain are also modeled by contact free energies and by α-helical hydrogen bonds. A hard-sphere model is used to represent repulsive interactions. The ratios of short- to long-range interactions studied are 1:1, 2:1, 1:2, 0:1, and 1:0; e.g., for the 2:1 ratio, short-range interactions are weighted twice as much as long-range interactions, and for the 1:0 ratio, long-range interactions are omitted. For each ratio of short- to long-range interactions, a “native” conformation is found by a Monte Carlo procedure, a segment of 11 residues (residue numbers 1–11) is then rotated away from the rest of the molecule [breaking the 5–55 native disulfide bond, and moving this segment so that the distance between the sulfur atoms of the 5 and 55 cystine side chains (averaged for all “native” conformations) increases from 3.9 to 7.3 Å], and the Monte Carlo simulation is carried out (allowing the conformation of the whole molecule to change) until equilibrium is attained. For each ratio, the refolded conformation is compared to the “native” one using triangular distance maps and differential geometry distance criteria. With ratios of short- to long-range interaction energies of 1:1 and 0:1, the native disulfide bond could be re-formed; with ratios of 2:1 and 1:2 it did not; and with the 1:0 ratio, even a stable “native” conformation was not achieved. Therefore, long-range interactions (in addition to short-range ones) are required to bring remote parts of the protein together and to stabilize its native conformation.
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