Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations

Continuing advances in computer hardware and software are permitting atomic-resolution molecular simulations for longer time scales and on larger systems. Despite these advances, routinely performing atomistic simulations with explicit water for even small proteins, which reach the folding time of such proteins, remains intractable for the foreseeable future. An implicit approximation of the solvent environment using a solvent accessible surface area (SASA) term in a molecular mechanics potential function allows exclusion of the explicit water molecules in protein simulations. This reduces the number of particles by approximately an order of magnitude. We present a fast and acceptably accurate approximate all-atom SASA method parameterized using a set of folded and heat-denatured conformations of globular proteins. The parameters are shown to be transferable to folded and heat-denatured conformations for another set of proteins. Calculation of the approximate SASA and the associated derivatives with respect to atomic positions for a 4644 atom protein requires only 1/11th the CPU time required for calculation of the nonbonded interactions for this system. On a per atom basis, this algorithm is three times faster than the fastest previously published approximate SASA method and achieves the same level of accuracy.     

Additive empirical force field for hexopyranose monosaccharides

We present an all-atom additive empirical force field for the hexopyranose monosaccharide form of glucose and its diastereomers allose, altrose, galactose, gulose, idose, mannose, and talose. The model is developed to be consistent with the CHARMM all-atom biomolecular force fields, and the same parameters are used for all diastereomers, including both the alpha- and beta-anomers of each monosaccharide. The force field is developed in a hierarchical manner and reproduces the gas-phase and condensed-phase properties of small-molecule model compounds corresponding to fragments of pyranose monosaccharides. The resultant parameters are transferred to the full pyranose monosaccharides, and additional parameter development is done to achieve a complete hexopyranose monosaccharide force field. Parametrization target data include vibrational frequencies, crystal geometries, solute-water interaction energies, molecular volumes, heats of vaporization, and conformational energies, including those for over 1800 monosaccharide conformations at the MP2/cc-pVTZ//MP2/6-31G(d) level of theory. Although not targeted during parametrization, free energies of aqueous solvation for the model compounds compare favorably with experimental values. Also well-reproduced are monosaccharide crystal unit cell dimensions and ring pucker, densities of concentrated aqueous glucose systems, and the thermodynamic and dynamic properties of the exocyclic torsion in dilute aqueous systems. The new parameter set expands the CHARMM additive force field to allow for simulation of heterogeneous systems that include hexopyranose monosaccharides in addition to proteins, nucleic acids, and lipids.     

Thermodynamics of adsorption of uranyl ions onto amidoximated poly(acrylonitrile)/poly(N‐vinyl 2‐pyrrolidone) interpenetrating polymer networks

The interaction of uranyl ions (UO) with interpenetrating polymer networks (IPNs) based on amidoximated poly(acrylonitrile)/poly(N‐vinyl 2‐pyrrolidone) was examined. The adsorption capacity of IPN hydrogels as well as the adsorption kinetics and the effect of temperature on UO ion adsorption were investigated. Thermodynamic quantities and kinetic parameters were calculated with adsorption isotherm data. The initial adsorption‐rate values for each temperature were calculated, and the corresponding rate constants decreased with increasing temperature. The adsorption enthalpy, entropy, and free energy of the UO ion with amidoximated IPN hydrogels were calculated from basic thermodynamic relations. It was assessed that adsorption occurred by strong electrostatic interactions with an adsorption enthalpy of ?31.5 kJ/mol. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 986–993, 2004     

Functionalization of cellulose with epoxy groups via γ-initiated RAFT-mediated grafting of glycidyl methacrylate

Glycidyl methacrylate (GMA), was grafted from cellulose by the combination of radiation-induced initiation and the reversible addition-fragmentation chain transfer (RAFT) polymerization technique, leading to epoxy functionalized surfaces that enable further modifications. Cumyl dithiobenzoate and 2-cyanoprop-2-yl dithiobenzoate were employed as the RAFT agents. The effects of absorbed dose, monomer and RAFT agent concentrations and solvent choice on grafting yield were investigated. Characterization of the synthesized copolymers by ATR-FTIR spectroscopy, X-ray photoelectron spectroscopy, scanning electron microscopy, thermal analysis and contact angle measurements revealed the grafting of poly(glycidyl methacrylate) (PGMA) from cellulose. Size-exclusion chromatography analysis indicated the difficulty of controlling the polymerization of GMA due to branching and/or crosslinking reactions that might occur in PGMA structure under γ-radiation.     

Adsorption of bovine serum albumin to acrylamide–itaconic acid hydrogels

In this study, acrylamide–itaconic acid hydrogels containing different amounts of itaconic acid prepared by irradiating with γ radiation are discussed. They have been used in experiments of swelling, diffusion and bovine serum albumin (BSA) adsorption. Maximum and minimum swellings were observed with water (1520%) and BSA (890%), respectively. Diffusion of water, NaCl and BSA within hydrogels were found to be non-Fickian in character. In the experiments of BSA adsorption, type III adsorption was found. The hydrogel prepared with 60 mg itaconic acid and irradiated at 2.00 kGy was found to be the best adsorption system for BSA. The adsorption capacity of acrylamide–itaconic acid hydrogel was found to exceed that of acrylamide hydrogel by more than 80–100%.     

Re-Emerging Field of Lignocellulosic Fiber – Polymer Composites and Ionizing Radiation Technology in their Formulation

Natural cellulose-based fibers offer low cost, low density composite reinforcement with good strength and stiffness. Because of their annual renewability and biodegradability, natural fibers have materialized as environmentally-friendly alternatives to synthetic fibers in the last two decades. They are replacing synthetic materials in some traditional composites in industrial manufacturing sectors such as automotive, construction, furniture, and other consumer goods. In this work, the use of lignocellulosic fibers in green materials engineering, particularly their application as polymeric composite reinforcement and surface treatment via ionizing radiation are reviewed. Because these cellulose-based materials are intrinsically hydrophilic, they require surface modification to improve their affinity for hydrophobic polymeric matrices, which enhances the strength, durability, and service lifetime of the resulting lignocellulosic fiber-polymer composites. In spite of a long history of using chemical methods in the modification of material surfaces, including the surface of lignocellulosic fibers, recent research leans instead towards application of ionizing radiation. Ionizing radiation methods are considered superior to chemical methods, as they are viewed as clean, energy saving, and environmentally friendly. Recent applications of controlled ionizing radiation doses in the formulation of natural fiber –reinforced polymeric composites resulted in products with enhanced fiber-polymer interfacial bonding without affecting the inner structure of lignocellulosic fibers. These applications are critically reviewed in this contribution.     

Metal ion promoted hydrogels for bovine serum albumin adsorption: Cu(II) and Co(II) chelated poly[(N-vinylimidazole)-maleic acid

Poly[(N-vinylimidazole)-maleic acid] (poly(VIm-MA)), copolymeric hydrogels were prepared by gamma-irradiating ternary mixtures of N-vinylimidazole-maleic acid-water in a (60)Co-gamma source. Cu(II) and Co(II) ions were chelated within the gels at pH=5.0. The maximum adsorption capacity of the gels were 3.71 mmol/g dry gel for Cu(II) and 1.25 mmol/g dry gel for Co(II) at pH=5.0. The swelling ratios of the gels were 1200% for poly(VIm-MA), 60 and 45% for Cu(II) and Co(II)-chelated poly(VIm-MA) gels at pH=5.0 in acetate buffer solution. These affinity gels with different swelling ratios for plain poly(VIm-MA), Cu(II)-, and Co(II)-chelated poly(VIm-MA), in acetate and phosphate buffers were used in the bovine serum albumin (BSA) adsorption/desorption studies in batch reactor. The maximum BSA adsorption capacities of the gels were 0.38 g/g dry gel for plain, 0.88 g/g dry gel for Cu(II)-chelated poly(VIm-MA) and 1.05 g/g dry gel for Co(II)-chelated poly(VIm-MA) gels. Adsorption capacity of BSA by the gels was reduced dramatically by increasing the ionic strength adjusted with NaCl. More than 95% of BSA were desorbed in 10 h in desorption medium containing 0.1M of EDTA for metal ion-chelated gels at pH=4.7.     

A class of linear positive operators in weighted spaces

In this paper, we introduce a class of linear positive operators based on q-integers. For these operators we give some convergence properties in weighted spaces of continuous functions and present an application to differential equation related to q-derivatives. Furthermore, we give a Stancu-type remainder.     

On the Riesz basis property of the root functions of a discontinuous boundary problem

In this paper, we consider the nonself‐adjoint discontinuous Sturm Liouville operator with periodic (antiperiodic) boundary condition and compatibility conditions. Asymptotic formulas of eigenvalues and eigenfunctions of the operator are obtained. Using these accurate asymptotic formulas for eigenvalues and eigenfunctions, we prove the basisness of the root functions of the boundary value problem.     

The copolymerization of allyl glycidyl ether with acrylonitrile initiated by gamma-rays

Copolymers of allyl glycidyl ether (AGE) with acrylonitrile (AN) have been prepared by bulk polymerization of their monomers with gamma rays. Copolymers thus obtained were characterized by Fourier transform infrared (FTIR), and ultraviolet (UV) spectroscopic techniques. The composition of the copolymers is determined indirectly by FTIR, UV, and directly by elemental analysis. The results obtained by different methods are compared. The reactivity ratios of monomer pairs (AGE + AN) which copolymerized heterogeneously were calculated by using different methods of determination. Among the three experimental methods used for the analysis of compositions and two theoretical methods of computations, the elemental analysis technique and the application of nonlinear least-squares method gave the most reliable reactivity ratios. These are found to be 1.86 and 0.21 for acrylonitrile and allyl glycidyl ether, respectively. © 1996 John Wiley & Sons, Inc.