Variation in the apolipoprotein E gene (APOE) has been reported to be associated with longevity in humans. The authors assessed the allelic distribution of APOE isoforms ε2, ε3, and ε4 among 10,623 participants from 15 case-control and cohort studies of age-related macular degeneration (AMD) in populations of European ancestry (study dates ranged from 1990 to 2009). The authors included only the 10,623 control subjects from these studies who were classified as having no evidence of AMD, since variation within the APOE gene has previously been associated with AMD. In an analysis stratified by study center, gender, and smoking status, there was a decreasing frequency of the APOE ε4 isoform with increasing age (χ2 for trend = 14.9 (1 df); P = 0.0001), with a concomitant increase in the ε3 isoform (χ2 for trend = 11.3 (1 df); P = 0.001). The association with age was strongest in ε4 homozygotes; the frequency of ε4 homozygosity decreased from 2.7% for participants aged 60 years or less to 0.8% for those over age 85 years, while the proportion of participants with the ε3/ε4 genotype decreased from 26.8% to 17.5% across the same age range. Gender had no significant effect on the isoform frequencies. This study provides strong support for an association of the APOE gene with human longevity.
aged; apolipoprotein E2; apolipoprotein E3; apolipoprotein E4; apolipoproteins E; longevity; meta-analysis; multicenter study
Modified DNA bases are widespread in biology. 5-Methylcytosine (mC) is a predominant epigenetic marker in higher eukaryotes involved in gene regulation, development, aging, cancer, and disease. Recently, 5-hydroxymethylcytosine (hmC) was identified in mammalian brain tissue and stem cells. However, most of the currently available assays cannot distinguish mC from hmC in DNA fragments. We investigate here the physical properties of DNA with modified cytosines, in efforts to develop a physical tool that distinguishes mC from hmC in DNA fragments. Molecular dynamics simulations reveal that polar cytosine modifications affect internal base pair dynamics, while experimental evidence suggest a correlation between the modified cytosine’s polarity, DNA flexibility, and duplex stability. Based on these physical differences, solid-state nanopores can rapidly discriminate among DNA fragments with mC or hmC modification by sampling a few hundred molecules in the solution. Further, the relative proportion of hmC in the sample can be determined from the electronic signature of the intact DNA fragment.
Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly in the developed world. We conducted a genome-wide association study in a series of families enriched for AMD and completed a meta-analysis of this new data with results from reanalysis of an existing study of a late-stage case/control cohort. We tested the top findings for replication in 1 896 cases and 1 866 controls and identified two novel genetic protective factors for AMD. In addition to the CFH (p=2.3×10−64) and ARMS2 (p=1.2×10−60) loci, we observed a protective effect at rs429608, an intronic SNP in SKIV2L (p=5.3×10−15), a gene near the C2/BF locus, that indicates the protective effect may be mediated by variants other than the C2/BF variants previously studied. Haplotype analysis at this locus identified three protective haplotypes defined by the rs429608 protective allele. We also identified a new potentially protective effect at rs2679798 in MYRIP (p=2.9×10−4), a gene involved in retinal pigment epithelium melanosome trafficking. Interestingly, MYRIP was initially identified in the family-based scan and was confirmed in the case-control set. From these efforts, we report the identification of two novel protective factors for AMD and confirm the previously known associations at CFH, ARMS2 and C3.
macular degeneration; association testing; melanosome trafficking
Although general anesthetics are known to modulate the activity of ligand-gated ion channels in the Cys-loop superfamily, there is at present neither consensus on the underlying mechanisms, nor predictive models of this modulation. Viable models need to offer quantitative assessment of the relative importance of several identified anesthetic binding sites. However, to date, precise affinity data for individual sites has been challenging to obtain by biophysical means. Here, the likely role of pore block inhibition by the general anesthetics isoflurane and propofol of the prokaryotic pentameric channel GLIC is investigated by molecular simulations. Microscopic affinities are calculated for both single and double occupancy binding of isoflurane and propofol to the GLIC pore. Computations are carried out for an open-pore conformation in which the pore is restrained to crystallographic radius, and a closed-pore conformation that results from unrestrained molecular dynamics equilibration of the structure. The GLIC pore is predicted to be blocked at the micromolar concentrations for which inhibition by isofluorane and propofol is observed experimentally. Calculated affinities suggest that pore block by propofol occurs at signifcantly lower concentrations than those for which inhibition is observed: we argue that this discrepancy may result from binding of propofol to an allosteric site recently identified by X-ray crystallography, which may cause a competing gain-of-function effect. Affinities of isoflurane and propofol to the allosteric site are also calculated, and shown to be 3 mM for isoflurane and for propofol; both anesthetics have a lower affinity for the allosteric site than for the unoccupied pore.
Although general anesthesia is performed every day on thousands of people, its detailed microscopic mechanisms are not known. What is known is that general anesthetic drugs modulate the activity of ion channels in the central nervous system. These channels are proteins that open in response to binding of neurotransmitter molecules, creating an electric current through the cell membrane and thus propagating nerve impulses between cells. One possible mechanism for ion channel inhibition by anesthetics is that the drugs bind inside the pore of the channels, blocking ion current. Here we investigate such a pore block mechanism by computing the strength of the drugs' interaction with the pore – and hence the likelihood of binding, in the case of GLIC, a bacterial channel protein. The results, obtained from numerical simulations of atomic models of GLIC, indicate that the anesthetics isoflurane and propofol have a tendency to bind in the pore that is strong enough to explain blocking of the channel, even at low concentration of the drugs.
Since their discovery in the 1950s, the structure and function of voltage-gated cation channels (VGCC) has been largely understood thanks to results stemming from electrophysiology, pharmacology, spectroscopy, and structural biology. Over the past decade, computational methods such as molecular dynamics (MD) simulations have also contributed, providing molecular level information that can be tested against experimental results, thereby allowing the validation of the models and protocols. Importantly, MD can shed light on elements of VGCC function that cannot be easily accessed through “classical” experiments. Here, we review the results of recent MD simulations addressing key questions that pertain to the function and modulation of the VGCC’s voltage-sensor domain (VSD) highlighting: (1) the movement of the S4-helix basic residues during channel activation, articulating how the electrical driving force acts upon them; (2) the nature of the VSD intermediate states on transitioning between open and closed states of the VGCC; and (3) the molecular level effects on the VSD arising from mutations of specific S4 positively charged residues involved in certain genetic diseases.
Kv1.2; gating charges; VSD intermediate states; molecular models; channelopathies; mutations; omega currents
Influenza A virus M2 (A/M2) forms a homotetrameric proton selective channel in the viral membrane. It has been the drug targets of antiviral drugs such as amantadine and rimantadine. However, most of the current virulent influenza A viruses carry drug resistant mutations alongside the drug binding site, such as S31N, V27A, and L26F etc., each of which might be dominant in a given flu season. Among these mutations, the V27A mutation was prevalent among transmissible viruses under drug selection pressure. Until now, V27A has not been successfully targeted by small molecule inhibitors, despite years of extensive medicinal chemistry research efforts and high throughput screening. Guided by molecular dynamics (MD) simulation of drug binding and the influence of drug binding on the dynamics of A/M2 from earlier experimental studies, we designed a series of potent spirane amine inhibitors targeting not only WT, but also both A/M2-27A and L26F mutants with IC50s similar to that seen for amantadine's inhibition of the WT channel. The potencies of these inhibitors were further demonstrated in experimental binding and plaque reduction assays. These results demonstrate the power of MD simulations to probe the mechanism of drug binding as well as the ability to guide design of inhibitors of targets that had previously appeared to be undruggable.
We present the results of coarse grained molecular dynamics simulation using a charge free model that is able to capture different regions of the morphological phase diagram of charged diblock copolymers. Specifically, we were able to reproduce many phases of the poly(acrylic acid)-(1,4)-poly-butadiene (PAA-PBA) diblock copolymer, Ca+2 and water systems as a function of pH and calcium concentration with short range LJ type potentials. The morphologies observed range from bilayers to cylinders to spherical micelles. Such polyanionic/cationic amphiphiles in water typically present multiple challenges for molecular simulations, particularly due to the many charge interactions which are long ranged and computationally costly. Further, it is precisely these interactions that are thought to modulate large amphiphile assemblies of interest such as lipid rafts. However, our model is able to reproduce different morphologies due to pH and with or without the addition of Ca2+ as well as the lateral phase segregation and the domain registration observed in neutral and charged diblock copolymer mixtures. The results suggest that the overall effect of charges is a local structural rearrangement that renormalizes the steric repulsion between the headgroups. This simple model which is devoid of charges is able to reproduce the complex phase diagram and can be used to investigate collective phenomena in these charged systems such as domain formation and registration or co-localization of lipid rafts across bilayer leaflets.
The M2 protein of influenza A virus performs the crucial function of transporting protons to the interior of virions enclosed in the endosome. Adamantane drugs, amantadine (AMN) and rimantidine (RMN), block the proton conduction in some strains, and have been used for the treatment and prophylaxis of influenza A infections. The structures of the transmembrane (TM) region of M2 that have been solved in micelles using NMR (residues 23-60) [Schnell and Chou (2008)] and by X-ray crystallography (residues 22-46) [Stouffer et al. (2008)] suggest different drug binding sites: external and internal for RMN and AMN, respectively. We have used molecular dynamics (MD) simulations to investigate the nature of the binding site and binding mode of adamantane drugs on the membrane-bound tetrameric M2-TM peptide bundles using as initial conformations the low-pH AMN-bound crystal structure, a high-pH model derived from the drug-free crystal structure, and the high-pH NMR structure. The MD simulations indicate that under both low-and high-pH conditions, AMN is stable inside the tetrameric bundle, spanning the region between residues Val27 to Gly34. At low pH the polar group of AMN is oriented toward the His37 gate while under high-pH conditions its orientation exhibits large fluctuations. The present MD simulations also suggest that AMN and RMN molecules do not show strong affinity to the external binding sites.
molecular dynamics; simulations; amantadine; adamantine; transmembrane; ion channel
The tetrameric M2 protein bundle of the influenza A virus is the proton channel responsible for the acidification of the viral interior, a key step in the infection cycle. Selective proton transport is achieved by successive protonation of the conserved histidine amino acids at position 37. A recent X-ray structure of the tetrameric transmembrane (TM) domain of the protein (residues 22–46) resolved several water clusters in the channel lumen, which suggest possible proton pathways to the His37 residues. To explore this hypothesis, we have carried out molecular dynamics (MD) simulations of a proton traveling towards the His37 side chains using MD with classical and quantum force fields. Diffusion through the first half of the channel to the “entry” water cluster near His37 may be hampered by significant kinetic barriers due to electrostatic repulsion. However, once in the entry cluster, a proton can move to one of the acceptor His37 in a nearly barrierless fashion, as evidenced both by MD simulations and a scan of the potential energy surface (PES). Water molecules of the entry cluster, although confined in the M2 pore and restricted in their motions, can conduct protons with a rate very similar to that of bulk water.
Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and hydrolyzes the phosphodiester linkage on the RNA strand of a DNA/RNA hybrid duplex. Due to its activity in HIV reverse transcription, it represents a promising target for anti-HIV drug design. While crystallographic data have located two ions in the catalytic site, there is ongoing debate concerning just how many metal ions bound at the active site are optimal for catalysis. Indeed, experiments have shown a dependency of the catalytic activity on the Mg2+ concentration. Moreover, in RNase H the glutamate residue E188 has been shown to be essential for full enzymatic activation regardless of the Mg2+ concentration. The catalytic center is known to contain two Mg2+ ions (Nowotny et al.) and E188 is not one of the primary metal ligands. Herein, classical molecular dynamics (MD) simulations are employed to study the metal-ligand coordination in RNase H at different concentration of Mg2+. Importantly, the presence of a third Mg2+ ion, bound to the second-shell ligand E188, is persistent feature of the MD simulations. Free energy calculations have identified two distinct conformations depending on the concentration of Mg2+. At standard concentration, a third Mg2+ is found in the catalytic pocket but it does not perturb the optimal RNase H active conformation. However, at higher concentration, the third Mg2+ ion heavily perturbs the nucleophilic water and thereby influences the catalytic efficiency of RNase H. In addition, the E188A mutant shows no ability to engage additional Mg2+ ions nearby the catalytic pocket. This finding likely explains the decrease in catalytic activity of E188A, and also supports the key role of E188 in localizing the third Mg2+ ion at the active site. Glutamate residues are commonly found surrounding the metal center in the endonuclease family, which suggests that this structural motif may be an important feature to enhance catalytic activity. The present MD calculations support the hypothesis that the RNase H can accommodate three divalent metal ions in its catalytic pocket, and provide an in-depth understanding of their dynamic role for catalysis.
Age-related macular degeneration (AMD), akin to other common age-related diseases, has a complex pathogenesis and arises from the interplay of genes, environmental factors, and personal characteristics. The past decade has seen very significant strides towards identification of those precise genetic variants associated with disease. That genes encoding proteins of the (alternative) complement pathway (CFH, C2, CFB, C3, CFI) are major players in etiology came as a surprise to many but has already lead to the development of therapies entering human clinical trials. Other genes replicated in many populations ARMS2, APOE, variants near TIMP3, and genes involved in lipid metabolism have also been implicated in disease pathogenesis. The genes discovered to date can be estimated to account for approximately 50% of the genetic variance of AMD and have been discovered by candidate gene approaches, pathway analysis, and latterly genome-wide association studies. Next generation sequencing modalities and meta-analysis techniques are being employed with the aim of identifying the remaining rarer but, perhaps, individually more significant sequence variations, linked to disease status. Complementary studies have also begun to utilize this genetic information to develop clinically useful algorithms to predict AMD risk and evaluate pharmacogenetics. In this article, contemporary commentary is provided on rapidly progressing efforts to elucidate the genetic pathogenesis of AMD as the field stands at the end of the first decade of the 21st century.
genes; complex disease; susceptibility; AMD
Molecular Dynamics simulations with the CHARMM atomistic force field have been used to study monolayers of a series of linear alkylbenzene sulfonates (LAS) at the water/air interface. Both the numbers of carbon atoms in the LAS alkyl tail (1 to 11), and the position of attachment of the benzene ring on the alkyl chain have been varied. Totally 36 LAS homologues and isomers have been investigated. The surface tensions of the systems and the average tilt angles of the LAS molecules are found to be related to both the length and the degree of branching of the alkyl tails, whereas the solubility and mobility are mostly determined by the tail length.
Computer simulation; surfactant; molecular dynamics; liquid-vacuum interface; LABS
To determine if genotype is associated with rate of growth of geographic atrophy (GA) in eyes with age-related macular degeneration (AMD).
Prospective analysis of participants in a randomized controlled clinical trial.
114 eyes of 114 participants in the Age-Related Eye Disease Study (AREDS).
Fundus photographs from AREDS participants with GA from whom a DNA specimen had been obtained and serial photographs had been taken over a minimum of 2 years were evaluated for progression as determined by change in cumulative area of GA. All fundus photographs were scanned, digitized, and centrally graded longitudinally for area of GA. The relationship of GA progression with previously identified genetic variants associated with AMD was assessed.
Main Outcome Measures
Genotype frequencies and change in cumulative area of GA.
The mean growth rate of geographic atrophy for the 114 eyes was 1.79 mm2/year (range= 0.17–4.76 mm2/year). No association between growth rate and genotype was present for variants in the CFH, C2, C3, APOE, and TLR3genes. For the single nucleotide polymorphism (SNP) rs10490924 in LOC387715/ARMS2, there was a significant association of GA growth rate, both adjusted and unadjusted for initial lesion size, with the homozygous risk genotype as compared to the homozygous non-risk genotype (unadjusted p-value = 0.002; Bonferroni corrected p-value = 0.014) and for allelic association(Bonferroni corrected p-value = 0.011). Analyses of other measures of geographic atrophy progression (progression to central GA from extrafoveal GA and development of bilateral GA in those initially with unilateral GA) showed no statistically significant association between progression and the LOC387715/ARMS2/HTRA1 genotype.
GA growth rates calculated from digitized serial fundus photographs showed no association with variants in the CFH, C2, C3, APOE, and TLR3 genes. There was a nominally statistically significant association with the LOC387715/ARMS2/HTRA1 genotype, although this finding was not supported by analyses of secondary measures of GA progression. Replication in other populations would be needed to establish the existence of an association.
A new coarse-grained (CG) intermolecular force field is presented for a series of zwitterionic lipids. The model is an extension of our previous work on nonionic surfactants and is designed to reproduce experimental surface/interfacial properties as well as distribution functions from all-atom molecular dynamics (MD) simulations. Using simple functional forms, the force field parameters are optimized for multiple lipid molecules, simultaneously. The resulting CG lipid bilayers have reasonable molecular areas, chain order parameters, and elastic properties. The computed surface pressure vs. area (π-A) curve for a DPPC monolayer demonstrates a significant improvement over the previous CG models. The DPPC monolayer has a longer persistence length than a PEG lipid monolayer, exhibiting a long-lived curved monolayer surface under negative tension. The bud ejected from an oversaturated DPPC monolayer has a large bicelle-like structure, which is different from the micellar bud formed from an oversaturated PEG lipid monolayer. We have successfully observed vesicle formation during CG-MD simulations, starting from an aggregate of DMPC molecules. Depending on the aggregate size, the lipid assembly spontaneously transforms into a closed vesicle or a bicelle. None of the various intermediate structures between these extremes seem to be stable. An attempt to observe fusion of two vesicles through the application of an external adhesion force was not successful. The present CG force field also supports stable multi-lamellar DMPC vesicles.
Coarse grain force field; lipid; vesicle; surface tension; monolayer; surface pressure
To describe the natural history of eyes with drusenoid pigment epithelial detachments (DPED) associated with age-related macular degeneration (AMD).
Multi-center clinic-based prospective cohort study.
Among 4757 participants enrolled in the Age-Related Eye Disease Study (AREDS), 255 were identified as having DPED in at least one eye and having 5 or more years of follow-up after the initial detection of the DPED.
Baseline and annual fundus photographs were evaluated for the evolution of the fundus features and the development of advanced AMD in the forms of central geographic atrophy (CGA) or neovascular (NV) AMD. Kaplan-Meier analyses of progression to advanced AMD and of moderate vision loss (≥15 letters compared with baseline) were performed.
Main Outcome Measures
Rate of progression to advanced AMD and change in visual acuity from baseline (in terms of mean letters lost and proportion losing ≥15 letters).
A total of 311 eyes (from 255 participants) with DPED were followed for a median follow-up time of 8 years subsequent to the initial detection of a DPED. Of the 282 eyes that did not have advanced AMD at baseline, advanced AMD developed within 5 years in 119 eyes (42%) (19% progressing to CGA and 23% to NV-AMD). In the remaining eyes that did not develop advanced AMD (n = 163), progressive fundus changes, typified by the development of calcified drusen and pigmentary changes, were detected. Visual decline was prominent among study eyes, with approximately 40% of all eyes decreasing in visual acuity by 15 or more letters at 5 years follow-up. Mean visual acuity decreased from 76 letters (~20/30) at baseline to 61 letters (~20/60) at 5 years. Five-year decreases in mean visual acuity averaged 26 letters for eyes progressing to advanced AMD and 8 letters for non-progressing eyes.
The natural history of eyes containing DPED is characterized by a high rate of progression to both CGA and NV-AMD. Among eyes not progressing advanced AMD, progressive development of pigmentary changes and calcified drusen were observed. Decline of visual acuity is a common outcome, with or without progression to advanced forms of AMD.
Antimicrobial peptides (AMPs) provide protection against a variety of pathogenic bacteria and are, therefore, an important part of the innate immune system. Over the last decade, there has been considerable interest in developing AMPs as intravenously administered antibiotics. However, despite extensive efforts in the pharmaceutical and biotechnology industry, it has proven difficult to achieve this goal. While researchers have solved some relatively simple problems such as susceptibility to proteolysis, more severe problems have included the expense of the materials, toxicity, limited efficacy, and limited tissue distribution.
In this Account, we describe our efforts to design and synthesize “foldamers”-- short sequence-specific oligomers based on arylamide and β-amino acid backbones, which fold into well-defined secondary structures-- that could act as antimicrobial agents. We reasoned that small “foldamers” would be less expensive to produce than peptides, and might have better tissue distribution. It should be easier to fine-tune the structures and activities of these molecules to minimize toxicity.
Because the activities of many AMPs depends primarily on their overall physicochemical properties rather than the fine details of their precise amino acid sequences, we have designed and synthesized very small “coarse-grained” molecules, which are far simpler than naturally produced AMPs. The molecular design of these foldamers epitomizes the positively charged amphiphilic structures believed to be responsible for the activity of AMPs. The designed oligomers show greater activity than the parent peptides. They have also provided leads for novel small molecule therapeutics that show excellent potency in animal models for multi-drug resistant bacterial infections. In addition, such molecules can serve as relatively simple experimental systems for investigations aimed at understanding the mechanism of action for this class of antimicrobial agents. The foldamers’ specificity for bacterial membranes relative to mammalian membranes appears to arise from differences in membrane composition and physical properties between these cell types.
Furthermore, because experimental coarse-graining provided such outstanding results, we developed computational coarse-grained models to enable molecular dynamic simulations of these molecules with phospholipid membranes. These simulations allow investigation of larger systems for longer times than conventional molecular dynamics simulations, allowing us to investigate how physiologically relevant surface concentrations of AMP mimics affect the bilayer structure and properties. Finally, we apply the principles discovered through this work to the design of inexpensive antimicrobial polymers and materials.
de novo design; antimicrobial peptide; foldamer; antibiotic; membrane-peptide interactions; antimicrobial polymers
The large quantity of protein sequences being generated from genomic data has greatly outpaced the throughput of experimental protein structure determining methods and consequently brought urgency to the need for accurate protein structure prediction tools. Reduced resolution, or coarse grained (CG) models, have become a mainstay in computational protein structure prediction perfoming among the best tools available. The quest for high quality generalized CG models presents an extremely challenging yet popular endeavor. To this point, a CG based interaction potential is presented here for the naturally occurring amino acids. In the present approach, three to four heavy atoms and associated hydrogens are condensed into a single CG site. The parameterization of the site-site interaction potential relies on experimental data thus providing a novel approach that is neither based on all-atom (AA) simulations nor experimental protein structural data. Specifically, intermolecular potentials, which are based on Lennard-Jones (LJ) style functional forms, are parameterized using thermodynamic data including surface tension and density. Using this approach, an amino acid potential dataset has been developed for use in modeling peptides and proteins. The potential is evaluated here by comparing the solvent accessible surface area (SASA) to AA representations and ranking of protein decoy data sets provided by Decoys ’R’ Us. The model is shown to perform very well compared to other existing prediction models for these properties.
coarse grain; molecular dynamics; amino acids; proteins; peptides; surface tension; decoys; solvent accessible surface area
Amphiphilic block copolymers of suitable proportions can self-assemble into surprisingly long and stable worm-like micelles, but the intrinsic polydispersity of polymers as well as polymer blending efforts and the increasing use of degradable chains all raise basic questions of curvature-composition coupling and morphological stability of these high curvature assemblies. Molecular simulations here of polyethylene glycol (PEG) based systems show that a systematic increase in the hydrated PEG fraction, in both monodisperse and binary blends, induces budding and breakup into spherical and novel ‘dumbbell’ micelles – as seen in electron microscopy images of degradable worm-like micelles. Core dimension, d, in our large-scale, long-time dissipative particle dynamics (DPD) simulations is shown to scale with chain length, N, as predicted theoretically by the Strong Segregation Limit (d ~ N2/3), but morphological transitions of binary mixtures are only crudely predicted by simple mixture rules. Here we show that for weakly demixing diblock copolymers, the coupling between local interfacial concentration and mean curvature can be described with a simple linear relationship. The computational methods developed here for PEG-based assemblies should be useful for many high curvature nanosystems.
Hole transfer processes between base pairs in natural DNA and size-expanded DNA (xDNA) are studied and compared, by means of an accurate first principles evaluation of the effective electronic couplings (also known as transfer integrals), in order to assess the effect of the base augmentation on the efficiency of charge transport through double-stranded DNA. According to our results, the size expansion increases the average electronic coupling, and thus the CT rate, with potential implications in molecular biology and in the implementation of molecular nanoelectronics. Our analysis shows that the effect of the nucleobase expansion on the charge-transfer (CT) rate is sensitive to the sequence of base pairs. Furthermore, we find that conformational variability is an important factor for the modulation of the CT rate. From a theoretical point of view, this work offers a contribution to the CT chemistry in π-stacked arrays. Indeed, we compare our methodology against other standard computational frameworks that have been adopted to tackle the problem of CT in DNA, and unravel basic principles that should be accounted for in selecting an appropriate theoretical level.
Three atomistic, empirical models for phosphatidylglycerol (PG) lipids are tested against structural data in the crystal and liquid crystal states. Simulations of the anhydrous crystal of dimyristoyl-phosphatidylglycerol (DMPG) show that only the CHARMM force field describes the conformation and interactions of PG headgroups accurately. The other two models do not reproduce the native network of hydrogen bonds, suggesting the presence of biases in their conformational and nonbonded interaction properties. The CHARMM model is further validated in the biologically relevant liquid crystal phase by comparing experimental small-angle X-ray scattering spectra from DMPG unilamellar vesicles with data calculated from fluid bilayer simulations. The good agreement found in this model-free comparison implies that liquid crystal PG bilayers as described by CHARMM exhibit realistic bilayer thickness and lateral packing. Last, this model is used to simulate a fluid bilayer of palmitoyl-oleoyl-phosphatidylglycerol (POPG). The resulting view of POPG bilayer structure is at variance with that proposed previously based on simulations, in particular with respect to lateral packing of headgroups and the role of counterions.
Using first principles molecular dynamics simulation, we have studied a fluoride anion embedded in a periodically replicated water slab composed of 215 water molecules to mimic both bulk and interfacial solvation. In contrast to some recent experiments, our findings suggest that there are only small structural changes for fluoride and its first solvation shell in the bulk. Moreover, the presence of fluoride does not significantly alter the rotational dynamics of nearby water. In addition, we have computed the molecular dipole moments using Wannier centers. At the interface, the presence of fluoride increases the molecular dipole moments of nearby water molecules, whereas in the bulk the dipole moments for water appear to be essentially invariant to the presence of fluoride in the vicinity. Previous studies of the air-water interface have showed interfacial water to have higher average HOMO energies and thus likely to be more prone to electrophilic attack. With the addition of fluoride, the most likely reactive site for electrophilic reactions shifts to the anion. This finding could explain the known large increase in reaction rates for heterogeneous process of interest in atmospheric science. The reactive properties of other anions near the air-water interface are of general interest in heterogeneous chemistry and can be elucidated using a similar type of analysis as performed here for the fluoride anion.
air-water; liquid-vapor; interface; fluoride; halides
Early transition events of the voltage sensor (VS) of Kv1.2 potassium channel embedded in a lipid membrane are triggered using full atomistic molecular dynamics (MD) simulations. When subject to an applied hyperpolarized transmembrane (TM) voltage, the VS undergoes conformational changes and reaches a stable kinetic intermediate state, β’, within 20 ns. The gating charge (~2e) associated with this fast transition results mainly from salt-bridge rearrangements involving negative charges in S2 and S3 and all but the two top residues R294 and R297 of S4. Interactions of the latter with phospho-moieties of the lipid head groups appear to stabilize the kinetic state β’
Self-assembly at a liquid-liquid interface is a powerful experimental route to novel nanomaterials. We report herein a computational study of peptide nanotube formation at an oil-water interface. We probe interfacial self-assembly and nanotube formation of the cyclic octapeptide, cyclo [(-L-Trp-D-Leu-)4] as an illustrative example. Individual peptide rings are rapidly adsorbed at the liquid-liquid interface where they self-assemble. Monomeric and dimeric peptide rings lie with their molecular planes mostly parallel to the interface. Longer oligomeric nanotubes are increasingly tilted at the interface and grow by an Oswald ripening mechanism to eventually align their tube axis parallel to the interface. The present results on nanotube assembly suggest that computation will be a useful complement to experiment in understanding the nature of self-assembly of nanomaterials at liquid-liquid interfaces.
Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and hydrolyzes the phosphodiester linkages that form the backbone of the RNA strand in RNA·DNA hybrids. This enzyme is implicated in replication initiation and DNA topology restoration and represents a very promising target for anti-HIV drug design. Structural information has been provided by high-resolution crystal structures of the complex RNase H/RNA·DNA from Bacillus halodurans (Bh), which reveals that two metal ions are required for formation of a catalytic active complex. Here, we use classical force field-based and quantum mechanics/molecular mechanics calculations for modeling the nucleotidyl transfer reaction in RNase H, clarifying the role of the metal ions and the nature of the nucleophile (water versus hydroxide ion). During the catalysis, the two metal ions act cooperatively, facilitating nucleophile formation and stabilizing both transition state and leaving group. Importantly, the two Mg2+ metals also support the formation of a meta-stable phosphorane intermediate along the reaction, which resembles the phosphorane intermediate structure obtained only in the debated β-phosphoglucomutase crystal. The nucleophile formation (i.e., water deprotonation) can be achieved in situ, after migration of one proton from the water to the scissile phosphate in the transition state. This proton transfer is actually mediated by solvation water molecules. Due to the highly conserved nature of the enzymatic bimetal motif, these results might also be relevant for structurally similar enzymes belonging to the NT superfamily.
Metallo β-lactamases (MβL's) are enzymes naturally evolved by bacterial strains under the evolutionary pressure of β-lactam antibiotic clinical use. They have a broad substrate spectrum and are resistant to all the clinically useful inhibitors, representing a potential risk of infection if massively disseminated. MβL's scaffold is designed to accommodate one or two zinc ions able to activate a nucleophilic hydroxide for the hydrolysis of the β-lactam ring. The role of zinc content on binding and reactive mechanism of action has been the subject of debate and still remains an open issue despite the large amount of data acquired. We report herein a study of the reaction pathway for binuclear CcrA from Bacteroides fragilis using density functional theory based quantum mechanics-molecular mechanics dynamical modeling. CcrA is the prototypical binuclear enzyme belonging to B1 MβL family, which includes several harmful chromosomally-encoded and transferable enzymes. The involvement of a second zinc ion in the catalytic mechanism lowers the energetic barrier for β-lactam hydrolysis, preserving the essential binding features found in mononuclear B1 enzymes (BcII from Bacillus cereus) while providing a more efficient single-step mechanism. Overall, this study suggests that uptake of a second equivalent zinc ion is evolutionary favored.
metallo β-lactamases; β-lactams; dizinc; monozinc; metalloproteins; metalloenzymes; QM-MM; molecular dynamics