Paired-residue potential

A more detailed model can be constructed for the nucleons in terms of a central potential that holds all the nucleons together plus a residual potential or residual interaction that lumps together all of the other nucleon-nucleon interactions. Other such important one-on-one interactions align the spins of unlike nucleons (p-n) and cause the pairing of like nucleons (p-p, n-n). The nucleons are then allowed to move independently in these potentials, that is, the Schrodinger equation is solved for the... 

Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 1996 256 623-644. 

When pairs of electrodes, such as would be used in an impedance bridge measuring cell, are platinized, the electrodes, after preparation, should be shorted together in a saline solution and left for several days so that the residual potential difference produced by plating can be equalized. 

Here again, the ejection of a residue critically requires the assistance of two antiperiplanar lone-pair orbitals on the remaining heteroatoms of the incipient amide. In the event that only one pair is potentially available, facile decomposition will be observed only after bond reorientation (117). 

To find appropriate empirical pair potentials from the known protein structures in the Brookhaven Protein Data Bank, it is necessary to calculate densities for the distance distribution of Ga-atoms at given bond distance d and given residue assignments ai,a2- Up to a constant factor that is immaterial for subsequent structure determination by global optimization, the potentials then ciiiergo as the negative logarithm of the densities. Since... 

An ideal empirical potential function on the residue level is a function V that assigns to each sequence-coordinates pair s,x) an energy V s,x) such that... 

The polynomials Wa q) q = qik) and Wy q) (q = qi) needed to specify the pair and surface potentials are constructed from the set of such q realized in a data base of 266 proteins with a total of 46100 residues by means of density estimation techniques. 

For the robust estimation of the pair potentials, some obstacles had to be overcome. There are a huge number of different triples (si, Sk,i — k), and to find densities, we needed a way to group them in a natural way together into suitable classes. A look at the cumulative distribution functions (cdf s) of the half squared distances Cjfc at residue distance d = i — k (w.l.o.g. >0), displayed in Figure 1, shows that the residue distances 8 and higher behave very similarly so in a first step we truncated all residue distances larger than 8 to 8. 

Fig. 36. The tetrahedral and residual components of the OO pair correlation function as predicted by molecular dynamics simulation of liquid water (from Ref. 3>). Note that T >Ti. For the unsealed BNS potential T = 265 K, T3 = 588 K.

The inhibition of HFC by a series of phosphinate and phosphonate substrate analogues is summarized in Table 8.9. Since phosphinate inhibitors require synthesis of the Pi residue, they are usually prepared as diastereo-meric pairs. If the diastereomers were separated and assigned stereochemistry, this information is included in Table 8.9. A potentially significant finding in this series is that a very large aromatic group in subsite P2 enhances... 

After a proton hop, the leading rotor residue is neutralized [16, 20] and the electrostatic potential, V, between the two pairs of oppositely charged point charges in the resulting charge configuration can be written as ... 

The X-ray crystal structure of the inorganic phosphate (an inhibitor) complex of alkaline phosphatase from E. coli (9) showed that the active center consists of a Zn2Mg(or Zn) assembly, where the two zinc(II) atoms are 3.94 A apart and bridged by the bidentate phosphate (which suggests a phosphomonoester substrate potentially interacting with two zinc(II), as depicted in Fig. 2), and the Mg (or the third Zn) is linked to one atom of the zinc pair by an aspartate residue at a distance... 

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