An algorithm for packing regular multistrand polypeptide structures by energy minimization

An algorithm has been developed for packing polypeptide chains by energy minimization subject to regularity conditions, in which regularity is maintained without the addition of pseudoenergy terms by defining the energy as a function of appropriately chosen independent variables. The gradient of the energy with respect to the independent variables is calculated analytically. The speed and efficiency of convergence of the algorithm to a local energy minimum are comparable to those of existing algorithms for minimizing the energy of a single polypeptide chain. The algorithm has been used to reinvestigate the minimum-energy regular structures of three-stranded (L -Ala)₈, three-stranded (L -Val)₆, five-stranded (L -Ile)₆, and the regular and truncated three-stranded (Gly-L -Pro-L -Pro)₄ triple helices. Local minima with improved packing energies, but with essentially unchanged geometrical properties, were obtained in all cases. The algorithm was also used to reinvestigate the structures proposed previously for the I and II forms of crystalline silk fibroin. The silk II structure was reproduced with slightly improved packing and little other change. The orthorhombic silk I structure showed more change and considerably improved packing energy, but the new regular monoclinic silk I structure had considerably higher energy. The results support the structure proposed previously for silk II and the orthorhombic structure, but not the monoclinic structure proposed for silk I. © 1994 by John Wiley & Sons, Inc.     

Pharmacokinetics of the nitroxide PCA measured by in vivo EPR

PCA (2,2,5,5-tetramethylpiperidine-1-oxyl-3-carboxylic acid) is a relatively stable free radical which has been shown to be useful as a contrast agent for nuclear magnetic resonance imaging and as an imaging/spectroscopy agent for EPR. In an effort to determine the role of the liver and kidney in the pharmacokinetics of PCA, using low frequency in vivo EPR spectroscopy, we followed the clearance of PCA after intravenous injection in mice: under normal conditions, with a restricted blood supply to the kidneys, after exposure to an acute hepatotoxin CCl₄, and after exposure to lipopolysaccharide (endotoxin). The observed pharmacokinetics fit a two-component model. The fast component was dramatically affected when the renal vessels were restricted, while CCl₄ and endotoxin had a smaller but significant effect. The half times of the slow components were not significantly different (p>0.05) in the groups treated by renal blood flow occlusion, CCl₄, or LPS, compared with the control group. In conclusion, we find that the pharmacokinetics of PCA need to be completely described in term of a two component model: the fast component of the decay is mainly due to the elimination by the kidneys and also is affected by the time for the initial distribution; the slow component is related to the bioreduction of the nitroxide. In addition to the liver other tissues can also effectively metabolize PCA. The effect of oxygen on the rate of metabolism is modest at most.     

Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods

A united-residue model of polypeptide chains developed in our laboratories with united side-chains and united peptide groups as interaction sites is presented. The model is designed to work in continuous space; hence efficient global-optimization methods can be applied. In this work, we adopted the distance-scaling method that is based on continuous deformation of the original rugged energy hypersurface to obtain a smoothed surface. The method has been applied successfully to predict the structures of simple motifs, such as the three-helix bundle structure of the 10-58 fragment of staphylococcal protein A in de novo folding simulations and more complicated motifs in inverse-folding simulations. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Models having the thermodynamic properties of aqueous alkaline earth halides and NaCl-MgCl2 mixtures

A model studied earlier in relation to aqueous 1–1 electrolytes has been applied to the interpretation of the excess free energies of aqueous solutions of the alkaline earth halides up to 1 M ionic strength. Several variations on the model could be fitted to the data. In the one which seems most consistent with the other observations, the cospheres (hydration layers) on the M⁺⁺ ions were two water molecules thick rather than one as for the alkali metal, tetraalkylammonium, and halide ions. The overlap of cospheres of an M⁺⁺, M⁺⁺ pair was found to make a small attractive contribution to the interionic force, while the overlap of cospheres of an M⁺⁺, X^– pair makes a small positive contribution which is almost the same for X^–=Cl^–, Br^–, or I^–. Thus, ionic hydration shells which are not penetrated by other ions are not required to account for the observed excess free energies. The model is also fitted to NaCl-MgCl₂ mixtures to see whether the new cosphereoverlap parameter which must be determined is consistent with the others. The calculation also shows how the thermodynamic behavior of the mixtures is consistent with the mixture limiting law for unsymmetrical mixtures. The singularities in the mixing coefficients g₀ and w₀ at infinite dilution dominate their concentration dependence only up to ionic strengths of about 0.01 M in models which fit the data.Most of this report is abstracted from a thesis presented by A. Smitherman to the Graduate School of the State University of New York at Stony Brook in partial fulfillment of the requirements for the M.S. degree, August 1972.     

The coulometric titration of bromate with cuprous copper

A coulometric procedure has been developed by which 18 to 240 μg quantities of bromate may be determined to within 0.3 μg. The bromate is allowed to react with bromide in an acid solution and electrolytically generated cuprous copper is used for the titration. A dual platinum electrode indicator system is used in an amperometric end-point procedure     

Semiclassical approach to collision-induced emission in the presence of intense laser radiation: An aspect in the study of cooperative chemical and optical pumping

Collion-induced emission in molecular systems in an intense laser field is studied using the semiclassical approach, with a view towards cooperative chemical and optical pumping in laser production. The formalism is developed with the electronic-field representation, which treats collision and radiative interaction on the same footing. Electronic-field surfaces can be regarded as forming spectra for spontaneous emission; and particular emission events can be accounted for by propagating classical trajectories on emission electronic-field surfaces. Pre-emission loss from the excited state is dealt with by propagating classical trajectories on a loss surface along a complex contour of emission branch points. This loss surface is derived on the basis of localized radiative couplings between electronic-field states and provides a framework to treat the general problem of discrete state-continuum interactions. The formalism is applied to a two-state, collinear exponential model to compute S-matrix elements and transition probabilities between asymptotic states.