Cavity search: An algorithm for the isolation and display of cavity-like binding regions

Summary A set of algorithms designed to enhance the display of protein binding cavities is presented. These algorithms, collectively entitled CAVITY SEARCH, allow the user to isolate and fully define the extent of a particular cavity. Solid modeling techniques are employed to produce a detailed cast of the active site region, which can then be color-coded to show electrostatic and steric interactions between the protein cavity and a bound ligand.     

Engineering cytochrome P-450s

Cytochrome P-450 isozymes represent a critical component of nature’s spectrum of detoxification catalysts that could be exploited for bioremediation. The ethanol-inducible human cytochrome P-450 2E1 serves as a model eukaryotic P-450 that complements the bacterial P-450 cam in dehalogenation and detoxification of environmental pollutants. We explored the construction of novel chimeric P-450s using cytochrome P-450 camC and 2E1 genes. For construction of chimera 1 (478 amino acids, 55.14 kDa), 145 amino acids from the N-terminus of P-450 2E1 protein (493 amino acids, 56.84 kDa) were replaced with 130 amino acids from the N-terminus of P-450 camC protein (415 amino acids, 46.66 kDa). In chimera 2 (525 amino acids, 60.24 kDa) the strategy involves replacement of 28 amino acids in the C-terminus of chimera 1 with 75 amino acids from the C-terminus of P-450 camC gene. Homology models of both the chimeric proteins were developed using SWISS-MODEL based on the known crystal structure of cytochrome P-450 camC, BM-3, 1DT6A, and 2C17A. The models indicated that the proposed heme-binding site was intact, which is inevitable for catalytic activity of cytochrome P-450s. The expression of chimera 1 and 2 genes in Escherichia coli DH5α was evident from light-pink cell pellets, protein band in sodium dodecyl sulfate polyacrylamide gel electrophoresis, and diagnostic carbon monoxide-difference spectra. Our studies show that strategies can be developed to exploit the natural diversity of the P-450 superfamily to generate chimeric biocatalysts that would provide new templates amenable to directed evolution.     

Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields

An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol.     

Plasma Thermal Conversion of Methane to Acetylene

This paper describes a re-examination of a known process for the direct plasma thermal conversion of methane to acetylene. Conversion efficiencies (% methane converted) approached 100% and acetylene yields in the 90–95% range with 2–4% solid carbon production were demonstrated. Specificity for acetylene was higher than in prior work. Improvements in conversion efficiency, yield, and specificity were due primarily to improved injector design and reactant mixing, and minimization of temperature gradients and cold boundary layers. At the 60-kilowatt scale cooling by wall heat transfer appears to be sufficient to quench the product stream and prevent further reaction of acetylene resulting in the formation of heavier hydrocarbon products or solid carbon. Significantly increasing the quenching rate by aerodynamic expansion of the products through a converging–diverging nozzle led to a reduction in the yield of ethylene but had little effect on the yield of other hydrocarbon products. While greater product selectivity for acetylene has been demonstrated, the specific energy consumption per unit mass of acetylene produced was not improved upon. A kinetic model that includes the reaction mechanisms resulting in the formation of acetylene and heavier hydrocarbons, through benzene, is described.     

Computer simulation of conformational movement based on interconversion phenomena

A computer method has been developed which is an alternative to molecular dynamics in the sense that it pictures conformational motion. It simulates propagation in conformational movement based on conformational interconversion phenomena. The method starts with the knowledge of the topology of the conformational potential energy hyper-surface, which is described by the minima and the transition states. The topology is obtained by the recently described software . The simulation of conformational motion is based on the Boltzmann statistics of movement between the minima and the transition states at a given temperature. The method is illustrated for methyl--glucopyranoside and - -galNAc(1-3)[- -Fuc(1-2)]Gal-O-Me molecules. Conformational transitions of hydroxyl groups as well as glycosidic linkages are discussed.     

Performance of SuSi: a method for generating atomistic models of amorphous polymers based on a random search of energy minima

The performance of a recently developed method to generate representative atomistic models of amorphous polymers has been investigated. This method, which is denoted SuSi, can be defined as a random generator of energy minima. The effects produced by different parameters used to define the size of the system and the characteristics of the generation algorithm have been examined. Calculations have been performed on poly(L,D-lactic) acid (rho = 1.25 g/cm3) and nylon 6 (rho = 1.084 g/cm(3)), which are important commercial polymers.     

A model for the etching of silicon in SF6/O2 plasmas

A model has been developed to describe the chemistry which occurs in SF₆/O₂ plasmas and the etching of silicon in these plasmas. Emphasis is placed nn the gas-phase free radical reactions, and the predictions n( the model are compared with experimental results. Forty-seven reactions are included, although a subset of 18 reactions describes the chemistry equally well. Agreement between the calculated and measured concentrations of stable products downstream of the plasma is better than a factor of 2. The need for additional kinetic data and fàr well-characterized diagnostic studies of SF₆/O₂ plasmas is discussed.     

Formal Mathematical Analysis of the Existence of the Common Intersection Point in Relation to Determining the Parameters Describing Ion Adsorption at the Oxide/Electrolyte Interface: Comparison of the Triple and Four-Layer Models

For most oxide/electrolyte systems potentiometric titration curves measured for different ionic strengths have a Common Intersection Point (CIP) which corresponds to the Point of Zero Charge (PZC). However, there are systems where a CIP exists but the surface charge at this point does not equal zero (PZC CIP). In this paper theoretical analysis of the systems in which the PZC and CIP do not coincide is presented. It is based on the well-known 2-pK surface charging approach and Triple Layer Model (TLM) as well as the Four Layer Model (FLM) of the electric double layer. The appropriate mathematical criterion for CIP existence was applied with detailed derivations, both for TLM and FLM. Having determined in this manner the parameter values, one can draw proper conclusions about the features of oxide/electrolyte adsorption systems, in which PZC and CIP do not coincide. The values of adsorption parameters are found by fitting simultaneously the obtained theoretical expressions to both of the experimental titration isotherms, and to the individual isotherms of electrolyte cation adsorption measured using radiometric methods.     

Cure kinetics of epoxy-amine resins used in the restoration of works of art from glass or ceramic

The cure kinetics of two epoxy/amine resins, Araldite 2020 and AY103-HY956 widely used as adhesives in the restoration of works of art from glass or ceramic was investigated using FTIR spectroscopy. These resins are two-part adhesives, consisting of a resin - A, based on a diglycidyl ether of bisphenol A, and a hardener - B which is either a cycloaliphatic amine (isophorone diamine) for Araldite 2020, or a mixture of three aliphatic amines in HY956. The study was based on the collection of IR spectra, in the middle range (4000-600 cm⁻¹), of mixtures of resin and hardener at different proportions and isothermal temperatures (22-70 °C) as a function of curing time. A kinetic model was employed to simulate the experimental data using two kinetic rate constants. Diffusion control was incorporated to describe the cure behaviour at high degrees of conversion. From fitting to experimental data the kinetic and diffusional parameters were estimated, together with the activation energies of the kinetic and autocatalytic rate constants. It was found that higher degrees of curing are obtained at higher temperatures and increased amounts of hardener. Differences in the performance of the two adhesives are explained based on the type of the amines used as hardener.