Adam A. Skelton

Interplay of sequence, conformation, and binding at the Peptide-titania interface as mediated by water.

The initial stages of the adsorption of a hexapeptide at the aqueous titania interface are modeled using atomistic molecular dynamics simulations. This hexapeptide has been identified by experiment [Sano, K. I.; Shiba, K. J. Am. Chem. Soc. 2003, 125, 14234] to bind to Ti particles. We explore the current hypothesis presented by these authors that binding at this peptide-titania interface is the result of electrostatic interactions and find that contact with the surface appears to take place via a pair of oppositely charged groups in the peptide. Our data indicate that the peptide may initially recognize the water layers at the interface, not the titania surface itself, via these charged groups. We also report results of simulations for hexapeptide sequences with selected single-point mutations for alanine and compare these behaviors with those suggested from observed binding affinities from existing alanine scan experiments. Our results indicate that factors in addition to electrostatics also contribute, with the structural rigidity conferred by proline suggested to play a significant role. Finally, our findings suggest that intrapeptide interaction may provide mechanisms for surface detachment that could be detrimental to binding at the interface.

Investigating the Quartz (101̅0)/Water Interface using Classical and Ab Initio Molecular Dynamics

Two different terminations of the (1010) surface of quartz (α and β) interacting with water are simulated by classical (CMD) (using two different force fields) and ab initio molecular dynamics (AIMD) and compared with previously published X-ray reflectivity (XR) experiments. Radial distribution functions between hydroxyl and water show good agreement between AIMD and CMD using the ClayFF force field for both terminations. The Lopes et al. (Lopes, P. E. M.; Murashov, V.; Tazi, M.; Demchuk, E.; MacKerell, A. D. J. Phys. Chem. B2006, 110, 2782-2792) force field (LFF), however, underestimates the extent of hydroxyl-water hydrogen bonding. The β termination is found to contain hydroxyl-hydroxyl hydrogen bonds; the quartz surface hydroxyl hydrogens and oxygens that hydrogen bond with each other exhibit greatly reduced hydrogen bonding to water. Conversely, the hydroxyl hydrogen and oxygens that are not hydrogen bonded to other surface hydroxyls but are connected to those that are show a considerable amount of hydrogen bonding to water. The electron density distribution of an annealed surface of quartz (1010) obtained by XR is in qualitative agreement with electron densities calculated by CMD and AIMD. In all simulation methods, the interfacial water peak appears farther from the surface than observed by XR. Agreement among AIMD, LFF, and XR is observed for the relaxation of the near-surface atoms; however, ClayFF shows a larger discrepancy. Overall, results show that for both terminations of (1010), LFF treats the near-surface structure more accurately whereas ClayFF treats the interfacial water structure more accurately. It is shown that the number of hydroxyl and water hydrogen bonds to the bridging Si-O-Si oxygens connecting the surface silica groups to the rest of the crystal is much greater for the α than the β termination. It is suggested that this may play a role in the greater resistance to dissolution of the β termination than that of the α termination.

Ion pairing with linoleic acid simultaneously enhances encapsulation efficiency and antibacterial activity of vancomycin in solid lipid nanoparticles

Ion pairing of a fatty acid with an antibiotic may be an effective strategy for formulation optimization of a nanoantibiotic system. The aim of this study was therefore to explore the potential of linoleic acid (LA) as an ion pairing agent to simultaneously enhance encapsulation efficiency and antibacterial activity of triethylamine neutralized vancomycin (VCM) in solid lipid nanoparticles (SLNs). The prepared VCM-LA2 conjugate was characterized by Fourier transform-infrared (FT-IR) spectroscopy, logP and binding energy calculations. The shifts in the FT-IR frequencies of COOH, NH2 and CO functionalities, an increase in logP value (1.37) and a lower interaction energy between LA and VCM (-125.54 kcal/mol) confirmed the formation of the conjugate. SLNs were prepared by a hot homogenization and ultrasonication method, and characterized for size, polydispersity index (PI), zeta potential (ZP), entrapment efficiency (%EE), surface morphology and physical stability. In vitro antibacterial activity studies against Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) were conducted. Size, PI and ZP for VCM-LA2_SLNs were 102.7±1.01, 0.225±0.02 and -38.8±2.1 (mV) respectively. SLNs were also stable at 4 °C for 3 months. %EE for VCM-HCl_SLNs and VCM-LA2_SLNs were 16.81±3.64 and 70.73±5.96 respectively, indicating a significant improvement in encapsulation of the drug through ion pairing with LA. Transmission electron microscopy images showed spherical nanoparticles with sizes in the range of 95-100 nm. After 36 h, VCM-HCl showed no activity against MRSA. However, the minimum inhibitory concentration for VCM-HCl_SLNs and VCM-LA2_SLNs were 250 and 31.25 μg/ml respectively against S. aureus, while against MRSA it was 500 and 15.62 μg/ml respectively. This confirms the enhanced antibacterial activity of VCM-LA2_SLNs over VCM-HCl_SLNs. These findings therefore suggest that VCM-LA2_SLNs is a promising nanoantibiotic system for effective treatment against both sensitive and resistant S. aureus infections.

Interaction of liquid water with the rutile TiO2 (110) surface

A force-field which describes the interaction between the TiO2 (110) rutile surface and a modified TIP3P water [P. Mark and L. Nilsson, J. Phys. Chem. A, 105, 9954, (2001)] is tested against periodic density functional theory (PDFT). Optimizations of water on the non-hydroxylated and hydroxylated surfaces are performed using PDFT and the geometries are compared with optimizations of modified TIP3P water on the TiO2 surface using the force-field. The surface hydroxyl torsional profile is also compared using PDFT and force-field calculations as well as molecular dynamics (MD) simulations of the surface. MD simulations of liquid TIP3P water, containing dissolved Na+ and Cl− ions, on six TiO2 (110) surfaces at 298 K and 1 atm are performed for neutral surfaces and negatively-charged surfaces. Axial density and angular distributions show good agreement with results of Predota et al. [J. Phys. Chem. B, 108, 12049 (2004)] and X-ray crystal truncation rod experiments [Z. Zhang et al., Langmuir, 20, 4954 (2004)].

A critical survey of average distances between catalytic carboxyl groups in glycoside hydrolases

Published X‐ray crystallographic structures for glycoside hydrolases (GHs) from 39 different families are surveyed according to some rigorous selection criteria, and the distances separating 208 pairs of catalytic carboxyl groups (20 α‐retaining, 87 β‐retaining, 38 α‐inverting, and 63 β‐inverting) are analyzed. First, the average of all four inter‐carboxyl O…O distances for each pair is determined; second, the mean of all the pair‐averages within each GH family is determined; third, means are determined for groups of GH families. No significant differences are found for free structures compared with those complexed with a ligand in the active site of the enzyme, nor for α‐GHs as compared with β‐GHs. The mean and standard deviation (1σ) of the unimodal distribution of average O…O distances for all families of inverting GHs is 8 ± 2Å, with a very wide range from 5Å (GH82) to nearly 13Å (GH46). The distribution of average O…O distances for all families of retaining GHs appears to be bimodal: the means and standard deviations of the two groups are 4.8 ± 0.3Å and 6.4 ± 0.6Å. These average values are more representative, and more likely to be meaningful, than the often‐quoted literature values, which are based on a very small sample of structures. The newly‐updated average values proposed here may alter perceptions about what separations between catalytic residues are “normal” or “abnormal” for GHs. Proteins 2014; 82:1747–1755.

Synthesis, antimicrobial activity and molecular docking studies of pyrano[2,3-d]pyrimidine formimidate derivatives

Abstract A new series of ten poly-functionalized pyrano[2,3-d]pyrimidine formimidate derivatives were successfully synthesized. All the synthesized compounds were characterized by 1H NMR, 13C NMR, HRMS, and FT-IR spectral analysis. All the synthesized compounds were evaluated for their antimicrobial activity by using the well plate method and MIC by the broth micro dilution method against the strains of bacteria as well as fungus. Four compounds exhibited good to excellent antimicrobial activity. The theoretical binding mode of the target molecules was evaluated by docking studies, which revealed a new molecular scaffold for enhancing the antimicrobial activity of compounds.Graphical AbstractStudies on synthesis, characterization, antimicrobial activity, and molecular docking of novel pyrano[2,3-d]pyrimidine formimidate derivatives (10) are reported. Four of the compounds exhibited excellent activity.

Quantum mechanical calculations of the interactions between diazacrowns and the sodium cation: an insight into Na + complexation in diazacrown-based synthetic ion channels†

Quantum mechanical calculations were performed to study the conformational behavior and complexation between a sodium cation and a diazacrown (diaza-18-crown-6) using density functional theory (DFT), Moller–Plesset (MP2) and molecular mechanics methods. A goal of this work is to gain a fundamental understanding of the interplay between water molecules, the sodium cation and a diazacrown. Diazacrowns have a significant importance as the functional units of a synthetic sodium channel, called a hydraphile, which functions within a lipid bilayer. This study follows on from our previous classical molecular dynamics study, which investigated the free energy of transport of Na+ as it passes through a lipid bilayer. In the present study we focus on the complexation of Na+, the conformation of the diazacrown and electronic structure that cannot be accessed by classical force fields. Furthermore, we benchmark the force field used in the previous study and make a modification of the dihedral parameters to improve its description. A whole range of configurations are scanned to gain an understanding of the energy landscape and find the minimum energies for configurations involving the diazacrown, diazacrown–Na+, diazacrown–water and diazacrown–Na+–water configurations. Our results show that there is an attractive interaction between Na+ and the oxygen and nitrogen atoms of the diazacrown for which the interaction between Na+ and the oxygen atoms are the stronger of the two. Natural bond orbital (NBO) analysis shows charge-transfer between the diazacrown and Na+ resulting in a reduced positive charge for this cation. This charge transfer occurs directly and via a water-mediated mechanism and could be crucial to the action of the hydraphile sodium channel. Since, in our previous classical molecular dynamics work, it was shown that water molecules accompany Na+ cations as they are transported through a lipid bilayer, while the cations are complexed to the diazacrown moiety of the hydraphile, we aim to better understand the structural, electronic structural and energetic implications of this complexation. Calculations of a water molecule interacting with the diazacrown show that the strongest interaction involves a bridging water molecule that forms hydrogen bonds with two diazacrown oxygen atoms or an oxygen and nitrogen atom on opposite sides of the diazacrown. These interactions may be important in the ordering of water to form a water channel that allows the Na+ to pass through the lipid bilayer.

The water-channel forming ability of heptapeptide-based anion channels: insights from molecular dynamics simulations

Molecular dynamics simulations were performed to gain insight into the channel-forming capabilities of the SCMTR class of anion channels. These results support pore formation by the experimentally predicted single-surface dimeric SCMTR configuration. Simulated currents of 11.1 pA and 3.7 pA were reported for simulations involving a charge imbalance on either side of the bilayer and simulations where an electric field is applied, respectively. Stable water-channels were formed; these began from the SCMTR and extended to the opposing face. Removal of the driving force within the charge separation simulation was found to close the pore within a 10 ns simulation. As predicted, opposing face lipid head-group rearrangement was found to assist in the stabilization of the water-channel. Furthermore, these results suggest that the SCMTR molecules may help thin the bilayer by moving deeper into its surface and, thereby, helping to stabilize the water-channel. These results confirm that the proposed dimeric insertion model is sufficient to stabilize a channel, while providing atomistic insight into the channels function.

The interaction of NOTA as a bifunctional chelator with competitive alkali metal ions: a DFT study

1,4,7-Triazacyclononane-1,4,7-triacetic acid (NOTA) is a key chelator for radiolabelling pharmaceuticals. The ability of alkali metals in the human body to complex with NOTA and compete with radiometals can influence the radiolabelling process. The focus of the present work is to evaluate the NOTA–alkali metal complexation with density functional theory (B3LYP functional) using the 6-311+G(2d,2p) basis set for Li+, Na+ and K+ and Def2-TZVPD for Rb+. Two NOTA–ion conformations are reported in the study: ‘A’ where six NOTA hetero atoms (N, O) are in close proximity to the cation, and ‘B’, where four NOTA hetero-atoms interact with the cation. Interaction and relaxation energies, Gibbs free energies and entropies show that the stability of NOTA–ion complexes decreases down the group of the periodic table. Implicit water solvation affects the NOTA–ion complexation, causing a decrease in the stability of the system. NBO analysis performed through the natural atomic charges (NAC) and second order perturbation analysis reveals charge transfer between NOTA and alkali metals. The theoretical 1H NMR chemical shifts of NOTA, in vacuum and water media, are in good agreement with experiments, these values being influenced by the presence of the ions, which have a deshielding effect on the protons of NOTA. Global scalar properties, such as HOMO/LUMO energies, ΔELUMO–HOMO gap, and chemical hardness and softness, show that the chemical stability of NOTA–alkali metal complexes decreases down the periodic table. This study sheds light on the impact of competing alkali metal ions to the radiolabelling efficiency of NOTA.

Dynamics of the thumb-finger regions in a GH11 xylanase Bacillus circulans : comparison between the Michaelis and covalent intermediate

The structure and dynamics of B. circulans β-1,4-xylanase (BCX) were comparatively studied utilizing molecular dynamics. Simulations of the free enzyme, non-covalently bound, and covalently bound xylobiose intermediate were conducted and post-dynamically studied to comprehend structural changes adopted during a reaction. Results showed that (a) covalent association of the substrate with the receptor induces a change in the structural conformation of the receptor; (b) the thumb region is highly flexible in the non-covalent complex compared to the covalent complex, drawing a conformational distinction between the two systems, a characteristic brought about by a more compact covalent complex structure in contrast to the non-covalent complex. This is most likely the result of a rigid covalent bond in addition to the hydrogen bond interactions between the substrate and receptor in the latter, (c) the distance between the thumb-finger residues Asp11-Pro116 is shortened upon substrate binding indicating that the flaps are drawn towards each other resulting in partial closing of the flaps. This study provides an invaluable contribution to the understanding of the dynamics of glycosidase enzymes which could largely contribute to the design of potent inhibitors targeting GH enzymes implicated in the orchestration of disease and disorders.