Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed.

Bacterial biofilms are complex surface attached communities of bacteria held together by self-produced polymer matrixs mainly composed of polysaccharides, secreted proteins, and extracellular DNAs. Bacterial biofilm formation is a complex process and can be described in five main phases: (i) reversible attachment phase, where bacteria non-specifically attach to surfaces; (ii) irreversible attachment phase, which involves interaction between bacterial cells and a surface using bacterial adhesins such as fimbriae and lipopolysaccharide (LPS); (iii) production of extracellular polymeric substances (EPS) by the resident bacterial cells; (iv) biofilm maturation phase, in which bacterial cells synthesize and release signaling molecules to sense the presence of each other, conducing to the formation of microcolony and maturation of biofilms; and (v) dispersal/detachment phase, where the bacterial cells depart biofilms and comeback to independent planktonic lifestyle. Biofilm formation is detrimental in healthcare, drinking water distribution systems, food, and marine industries, etc. As a result, current studies have been focused toward control and prevention of biofilms. In an effort to get rid of harmful biofilms, various techniques and approaches have been employed that interfere with bacterial attachment, bacterial communication systems (quorum sensing, QS), and biofilm matrixs. Biofilms, however, also offer beneficial roles in a variety of fields including applications in plant protection, bioremediation, wastewater treatment, and corrosion inhibition amongst others. Development of beneficial biofilms can be promoted through manipulation of adhesion surfaces, QS and environmental conditions. This review describes the events involved in bacterial biofilm formation, lists the negative and positive aspects associated with bacterial biofilms, elaborates the main strategies currently used to regulate establishment of harmful bacterial biofilms as well as certain strategies employed to encourage formation of beneficial bacterial biofilms, and highlights the future perspectives of bacterial biofilms.

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Here we reported the antibacterial effect and related mechanism of three nano-Mg(OH)(2) slurries using Escherichia coli as model bacteria. X-ray diffraction (XRD), scanning electron microscopy (SEM) and laser particle size analysis revealed that the as-synthesized Mg(OH)(2)_(MgCl2), Mg(OH)(2)_(MgSO4) and Mg(OH)(2)_(MgO) are all composed by nanoflakes with different sizes, and their aggregates in water are 5.5, 4.5, and 1.2 μm, respectively. Bactericidal tests showed that the antibacterial efficiency is conversely correlated with the size of Mg(OH)(2) aggregates. Transmission electron microscopy (TEM) observation have not provided evidence of cellular internalization, however, the antibacterial effect is positive correlation to the loss of integrity of cell walls. SEM and zeta potential analysis revealed that the adhering ability of Mg(OH)(2) on the bacterial surface is Mg(OH)(2)_(MgCl2) > Mg(OH)(2)_(MgSO4) > Mg(OH)(2)_(MgO), indicating the toxicity of Mg(OH)(2) may be caused by the electrostatic interaction-induced external adsorption. Confocal laser scanning microscopy (CLSM) further revealed that the adhering of Mg(OH)(2) on the bacterial surface could increase the permeability of cell membranes. Taken together, the antibacterial mechanism of nano-Mg(OH)(2) could be as follows: nano-Mg(OH)(2) adsorbed on the bacterial surface by charge attraction first, and then destroyed the integrity of cell walls, which resulting in the final death of bacteria.

The formation mechanism of an alanine-based peptide has been studied by all-atom molecular dynamics simulations with a recently developed all-atom point-charge force field and the Generalize Born continuum solvent model at an effective salt concentration of 0.2M. Thirty-two simulations were conducted. Each simulation was performed for 100 ns. A surprisingly complex folding process was observed. The development of the helical content can be divided into three phases with time constants of 0.06-0.08, 1.4-2.3, and 12-13 ns, respectively. Helices initiate extreme rapidly in the first phase similar to that estimated from explicit solvent simulations. Hydrophobic collapse also takes place in this phase. A folding intermediate state develops in the second phase and is unfolded to allow the peptide to reach the transition state in the third phase. The folding intermediate states are characterized by the two-turn short helices and the transition states are helix-turn-helix motifs-both of which are stabilized by hydrophobic clusters. The equilibrium helical content, calculated by both the main-chain Phi-Psi torsion angles and the main-chain hydrogen bonds, is 64-66%, which is in remarkable agreement with experiments. After corrected for the solvent viscosity effect, an extrapolated folding time of 16-20 ns is obtained that is in qualitative agreement with experiments. Contrary to the prevailing opinion, neither initiation nor growth of the helix is the rate-limiting step. Instead, the rate-limiting step for this peptide is breaking the non-native hydrophobic clusters in order to reach the transition state. The implication to the folding mechanisms of proteins is also discussed.

Wheat straw (WS) is a potential biomass for production of monomeric sugars. However, the enzymatic hydrolysis ratio of cellulose in WS is relatively low due to the presence of lignin and hemicellulose. To enhance the enzymatic conversion of WS, we tested the impact of three different pretreatments, e.g. sulfuric acid (H2SO4), sodium hydroxide (NaOH), and hot water pretreatments to the enzymatic digestions. Among the three pretreatments, the highest cellulose conversion rate was obtained with the 4% NaOH pretreatment at 121 °C (87.2%). In addition, NaOH pretreatment was mainly effective in removing lignin, whereas the H2SO4 pretreatment efficiently removed hemicellulose. To investigate results of pretreated process for enhancement of enzyme-hydolysis to the WS, we used scanning electron microscopy, X-ray diffraction, and Fourier transform infrared spectroscopy to analyze structural changes of raw and treated materials. The structural analysis indicated that after H2SO4 and NaOH pretreatments, most of the amorphous cellulose and partial crystalline cellulose were hydrolyzed during enzymatic hydrolysis. The findings of the present study indicate that WS could be ideal materials for production of monomeric sugars with proper pretreatments and effective enzymatic base hydrolysis.

The relationship between the photon beam quality specifier %dd(10)x and the Spencer-Attix water water to air restricted mass collision stopping-power ratio, (L/rho))air(water), is studied using Monte Carlo simulation with realistic beams in contrast to the previously used realistic but uniform spectra from an isotropic point source. The differences between accelerators with and without flattening filters are investigated since flattening filter free accelerators appear to be useful for IMRT. Our results show that the standard relationship between %dd(10)x and (L/rho)air(water), which is used in the TG-51 protocol to calculate the quality conversion factor kQ, is acceptable for beams with or without a flattening filter with a maximum error of 0.4%, although a fit to the new data would reduce the maximum error to 0.2%. Reasons for differences between the individual values of %dd(10)x and (L/ rho)air(water) with and without a flattening filter are studied. Specifically the differences due to the softening of the beam, the change in shape of the profile, and the inclusion of radial variations in the photon energy spectra, are investigated. It is shown that if TPR10(20) is used as a beam quality specifier, there are two different relationships between TPR10(20) and (L/rho)air(water) which differ by 0.4%-1%. When using TPR10(20) as a beam quality specifier in a beam without a flattening filter, one should subtract 0.5% from the value of kQ for a given value of TPR10(20).

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