Conformational free-energy landscapes of a Na+/Ca2+ exchanger explain its alternating-access mechanism and functional specificity

Secondary-active transporters catalyze the movement of myriad substances across all cellular membranes, typically against opposing concentration gradients, and without consuming any ATP. To do so, these proteins employ an intriguing structural mechanism evolved to be activated only upon recognition or release of the transported species. We examine this self-regulated mechanism using a homolog of the cardiac Na+/Ca2+ exchanger as a model system. Using advanced computer simulations, we map out the complete functional cycle of this transporter, including unknown conformations that we validate against existing experimental data. Calculated free-energy landscapes reveal why this transporter functions as an antiporter rather than a symporter, why it specifically exchanges Na+ and Ca2+, and why the stoichiometry of this exchange is exactly 3:1. We also rationalize why the protein does not exchange H+ for either Ca2+ or Na+, despite being able to bind H+ and its high similarity with H+/Ca2+ exchangers. Interestingly, the nature of this transporter is not explained by its primary structural states, known as inward- and outward-open conformations; instead, the defining factor is the feasibility of conformational intermediates between those states, wherein access pathways leading to the substrate binding sites become simultaneously occluded from both sides of the membrane. This analysis offers a physically coherent, broadly transferable route to understand the emergence of function from structure among secondary-active membrane transporters.

Conformational free-energy landscapes of a Na+/Ca2+ exchanger explain its alternating-access mechanism and functional specificity

Secondary-active transporters catalyze the movement of myriad substances across all cellular membranes, typically against opposing concentration gradients, and without consuming any ATP. To do so, these proteins employ an intriguing structural mechanism evolved to be activated only upon recognition or release of the transported species. We examine this self-regulated mechanism using a homolog of the cardiac Na+/Ca2+ exchanger as a model system. Using advanced computer simulations, we map out the complete functional cycle of this transporter, including unknown conformations that we validate against existing experimental data. Calculated free-energy landscapes reveal why this transporter functions as an antiporter rather than a symporter, why it specifically exchanges Na+ and Ca2+, and why the stoichiometry of this exchange is exactly 3:1. We also rationalize why the protein does not exchange H+ for either Ca2+ or Na+, despite being able to bind H+ and its high similarity with H+/Ca2+ exchangers. Interestingly, the nature of this transporter is not explained by its primary structural states, known as inward- and outward-open conformations; instead, the defining factor is the feasibility of conformational intermediates between those states, wherein access pathways leading to the substrate binding sites become simultaneously occluded from both sides of the membrane. This analysis offers a physically-coherent, broadly transferable route to understand the emergence of function from structure among secondary-active membrane transporters.

Differential ion dehydration energetics explains selectivity in the non-canonical lysosomal K+ channel TMEM175

Structures of the human lysosomal K⁺ channel transmembrane protein 175 (TMEM175) in open and closed states revealed a novel architecture lacking the canonical K⁺ selectivity filter motif present in previously known K⁺ channel structures. A hydrophobic constriction composed of four isoleucine residues was resolved in the pore and proposed to serve as the gate in the closed state, and to confer ion selectivity in the open state. Here, we achieve higher-resolution structures of the open and closed states and employ molecular dynamics simulations to analyze the conducting properties of the putative open state, demonstrating that it is permeable to K⁺ and, to a lesser degree, also Na⁺. Both cations must dehydrate significantly to penetrate the narrow hydrophobic constriction, but ion flow is assisted by a favorable electrostatic field generated by the protein that spans the length of the pore. The balance of these opposing energetic factors explains why permeation is feasible, and why TMEM175 is selective for K⁺ over Na⁺, despite the absence of the canonical selectivity filter. Accordingly, mutagenesis experiments reveal an exquisite sensitivity of the channel to perturbations that mitigate the constriction. Together, these data reveal a novel mechanism for selective permeation of ions by TMEM175 that is unlike that of other K⁺ channels.

Force-Correction Analysis Method for Derivation of Multidimensional Free-Energy Landscapes from Adaptively Biased Replica Simulations

A methodology is proposed for the calculation of multidimensional free-energy landscapes of molecular systems, based on analysis of multiple molecular dynamics trajectories wherein adaptive biases have been applied to enhance the sampling of different collective variables. In this approach, which we refer to as the Force-Correction Analysis Method (FCAM), local averages of the total and biasing forces are evaluated post hoc, and the latter are subtracted from the former to obtain unbiased estimates of the mean force across collective-variable space. Multidimensional free-energy surfaces and minimum free-energy pathways are then derived by integrating the mean-force landscape with a kinetic Monte Carlo algorithm. To evaluate the proposed method, a series of numerical tests and comparisons with existing approaches were carried out for small molecules, peptides, and proteins, based on all-atom trajectories generated with standard, concurrent, and replica-exchange metadynamics in collective-variable spaces ranging from one to six dimensional. The tests confirm the correctness of the FCAM formulation and demonstrate that calculated mean forces and free energies converge rapidly and accurately, outperforming other methods used to unbias this kind of simulation data.

The Italian version of the Unité Rhumatologique des Affections de la Main (URAM) for Dupuytren's disease: The URAM-I(10)

Introduction

Several general hand functional assessment tools for Dupuytren's disease have been reported, but none of the patient-reported-outcome measures specific to Dupuytren's disease-associated disabilities are available in the Italian language. The purpose of this study was to culturally adapt the Unité Rhumatologique des Affections de la Main (URAM) into Italian (URAM-I) and determine its measurement properties.

Methods

Cross-cultural adaptation was performed according to the current guidelines. Construct validity (convergent and divergent validity) was measured by comparing the URAM-I with the Pain-Rated Wrist/Hand Evaluation (PRWHE-I), Short-Form 36 (SF-36-I) scale and finger range of motion, respectively. Factor analysis was used to investigate the URAM-I's internal structure. Reliability was assessed by internal consistency (Cronbach's alpha) and test-retest reliability by Intra-Class Correlation Coefficient (ICC).

Results

This study included 96 patients (males = 85%, age = 66.8 ± 9.3). Due to the cultural adaptation, we divided the original item #1 into two separate items, thus generating the URAM-I(10). Convergent validity analysis showed a strong positive (r = 0.67), significant (p < 0.01) Pearson's correlation with the PRWHE-I. Divergent validity analysis showed a weak, negative (r < 0.3) and not significant correlation with the SF-36-I subscales, except for the physical pain subscale (r = -0.21, p < 0.05). Factor analysis revealed a 2-factor, 4-item solution that explained 76% of the total variance. The URAM-I(10) demonstrated high internal consistency (α = 0.94) and high test-retest reliability (ICC = 0.97).

Conclusion

The URAM-I(10) demonstrates moderate construct validity, high internal consistency and test-retest reliability, and showed a 2-factor internal structure. Its evaluative use can be suggested for the Italian Dupuytren's population.

Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0]

Hydrogen-deuterium exchange (HDX) is a comprehensive yet detailed probe of protein structure and dynamics and, coupled to mass spectrometry, has become a powerful tool for investigating an increasingly large array of systems. Computer simulations are often used to help rationalize experimental observations of exchange, but interpretations have frequently been limited to simple, subjective correlations between microscopic dynamical fluctuations and the observed macroscopic exchange behavior. With this in mind, we previously developed the HDX ensemble reweighting approach and associated software, HDXer, to aid the objective interpretation of HDX data using molecular simulations. HDXer has two main functions; first, to compute H-D exchange rates that describe each structure in a candidate ensemble of protein structures, for example from molecular simulations, and second, to objectively reweight the conformational populations present in a candidate ensemble to conform to experimental exchange data. In this article, we first describe the HDXer approach, theory, and implementation. We then guide users through a suite of tutorials that demonstrate the practical aspects of preparing experimental data, computing HDX levels from molecular simulations, and performing ensemble reweighting analyses. Finally we provide a practical discussion of the capabilities and limitations of the HDXer methods including recommendations for a user's own analyses. Overall, this article is intended to provide an up-to-date, pedagogical counterpart to the software, which is freely available at https://github.com/Lucy-Forrest-Lab/HDXer.

Evaluation of colistin consumption in swine and poultry of Marche region during the 2017-2019 period

In Italy, the National Plan against Antimicrobial Resistance (PNCAR 2017-2020) involves both human and veterinary sectors. The last one was requested to reduce colistin consumption, a first choice antibiotic for human health. Indeed, the Plan defines specific limits to reach within 2020. In Marche region, there is a project from 2017, consisting in monitoring antibiotic consumption in livestock, with particular reference to Critically Important Antimicrobials (CIAs), like colistin. The project represents an AMR stewardship, which involves regional Veterinary Services, veterinary professionals and the IZS Umbria e Marche, developing a specific training and education path ad hoc.

In this work, we have considered data coming from swine and poultry prescriptions of Marche region in the 2017-2019 period, using these for the calculation of ADDD (Animal Defined Daily Doses), a method already used in human. In practice, we have first established DDDvet values, as suggested by ESVAC, obtained from the Italian drugs containing colistin made for the considered species.

Colistin prescription in swine reduced of 97% (from 20.60 in 2017 to 0.69 DDD/1000 animals-die in 2019). In poultry, a reduction of 69% was obtained (from 5.07 in 2017 to 1.56 DDD/1000 animals-die in 2019). Then, there was an evidence of reduction more than 70% in colistin consumption, demonstrating the importance of the education and awareness program sponsored by Competent Authorities and the other stakeholders involved. The used method of calculation (ESVAC) is different from the currently applied one, as it consists of standardized unity of measures, using prescription data rather than sales ones.

Monitoring antibiotic consumption both in human and veterinary sector is essential to understand AMR, as well is important the possibility to compare the data to each other. The present work demonstrate that, also in veterinary, is possible to apply the DDD-method to evaluate antibiotic consumption, like colistin.

Key messages

Colistin consumption has reduced in swine and poultry sectors in the 2017-2019 period. A standardized method of calculation of antibiotic consumption in animals is strongly needed.

Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles

Hydrogen-deuterium exchange combined with mass spectrometry (HDX-MS) is a widely applied biophysical technique that probes the structure and dynamics of biomolecules without the need for site-directed modifications or bio-orthogonal labels. The mechanistic interpretation of HDX data, however, is often qualitative and subjective, owing to a lack of quantitative methods to rigorously translate observed deuteration levels into atomistic structural information. To help address this problem, we have developed a methodology to generate structural ensembles that faithfully reproduce HDX-MS measurements. In this approach, an ensemble of protein conformations is first generated, typically using molecular dynamics simulations. A maximum-entropy bias is then applied post hoc to the resulting ensemble such that averaged peptide-deuteration levels, as predicted by an empirical model, agree with target values within a given level of uncertainty. We evaluate this approach, referred to as HDX ensemble reweighting (HDXer), for artificial target data reflecting the two major conformational states of a binding protein. We demonstrate that the information provided by HDX-MS experiments and by the model of exchange are sufficient to recover correctly weighted structural ensembles from simulations, even when the relevant conformations are rarely observed. Degrading the information content of the target data—e.g., by reducing sequence coverage, by averaging exchange levels over longer peptide segments, or by incorporating different sources of uncertainty—reduces the structural accuracy of the reweighted ensemble but still allows for useful insights into the distinctive structural features reflected by the target data. Finally, we describe a quantitative metric to rank candidate structural ensembles according to their correspondence with target data and illustrate the use of HDXer to describe changes in the conformational ensemble of the membrane protein LeuT. In summary, HDXer is designed to facilitate objective structural interpretations of HDX-MS data and to inform experimental approaches and further developments of theoretical exchange models.

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics

We report a methodology to calculate the free energy of a shape transformation in a lipid membrane directly from a molecular dynamics simulation. The bilayer need not be homogeneous or symmetric and can be atomically detailed or coarse grained. The method is based on a collective variable that quantifies the similarity between the membrane and a set of predefined density distributions. Enhanced sampling of this "Multi-Map" variable re-shapes the bilayer and permits the derivation of the corresponding potential of mean force. Calculated energies thus reflect the dynamic interplay of atoms and molecules, rather than postulated effects. Evaluation of deformations of different shape, amplitude, and range demonstrates that the macroscopic bending modulus assumed by the Helfrich-Canham model is increasingly unsuitable below the 100-Å scale. In this range of major biological significance, direct free-energy calculations reveal a much greater plasticity. We also quantify the stiffening effect of cholesterol on bilayers of different composition and compare with experiments. Lastly, we illustrate how this approach facilitates analysis of other solvent reorganization processes, such as hydrophobic hydration. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.

Molecular mechanisms of human P2X3 receptor channel activation and modulation by divalent cation bound ATP

P2X3 receptor channels expressed in sensory neurons are activated by extracellular ATP and serve important roles in nociception and sensory hypersensitization, making them attractive therapeutic targets. Although several P2X3 structures are known, it is unclear how physiologically abundant Ca²⁺-ATP and Mg²⁺-ATP activate the receptor, or how divalent cations regulate channel function. We used structural, computational and functional approaches to show that a crucial acidic chamber near the nucleotide-binding pocket in human P2X3 receptors accommodates divalent ions in two distinct modes in the absence and presence of nucleotide. The unusual engagement between the receptor, divalent ion and the γ-phosphate of ATP enables channel activation by ATP-divalent complex, cooperatively stabilizes the nucleotide on the receptor to slow ATP unbinding and recovery from desensitization, a key mechanism for limiting channel activity. These findings reveal how P2X3 receptors recognize and are activated by divalent-bound ATP, aiding future physiological investigations and drug development.

Structural Characterization of Biomolecules through Atomistic Simulations Guided by DEER Measurements

Double electron-electron resonance (DEER) is a popular technique that exploits attached spin labels to probe the collective dynamics of biomolecules in a native environment. Like most spectroscopic approaches, DEER detects an ensemble of states accounting for biomolecular dynamics as well as the labels' intrinsic flexibility. Hence, the DEER data alone do not provide high-resolution structural information. To disentangle this variability, we introduce a minimally biased simulation method to sample a structural ensemble that reproduces multiple experimental signals within the uncertainty. In contrast to previous approaches, our method targets the raw data themselves, and thereby it brings forth an unbiased molecular interpretation of the experiments. After validation on the T4 lysozyme, we apply this technique to interpret recent DEER experiments on a membrane transporter binding protein (VcSiaP). The results highlight the large-scale conformational movement that occurs upon substrate binding and reveal that the unbound VcSiaP is more open in solution than the X-ray structure.

Confidence Analysis of DEER Data and Its Structural Interpretation with Ensemble-Biased Metadynamics

Given its ability to measure multicomponent distance distributions between electron-spin probes, double electron-electron resonance (DEER) spectroscopy has become a leading technique to assess the structural dynamics of biomolecules. However, methodologies to evaluate the statistical error of these distributions are not standard, often hampering a rigorous interpretation of the experimental results. Distance distributions are often determined from the experimental DEER data through a mathematical method known as Tikhonov regularization, but this approach makes rigorous error estimates difficult. Here, we build upon an alternative, model-based approach in which the distance probability distribution is represented as a sum of Gaussian components, and use propagation of errors to calculate an associated confidence band. Our approach considers all sources of uncertainty, including the experimental noise, the uncertainty in the fitted background signal, and the limited time span of the data collection. The resulting confidence band reveals the most and least reliable features of the probability distribution, thereby informing the structural interpretation of DEER experiments. To facilitate this interpretation, we also generalize the molecular simulation method known as ensemble-biased metadynamics (EBMetaD). This method, originally designed to generate maximal-entropy structural ensembles consistent with one or more probability distributions, now also accounts for the uncertainty in those target distributions exactly as dictated by their confidence bands. After careful benchmarks, we demonstrate the proposed techniques using DEER results from spin-labeled T4 lysozyme.

The prokaryotic Na+/Ca2+ exchanger NCX_Mj transports Na+ and Ca2+ in a 3:1 stoichiometry

Sodium–calcium exchangers contribute to the generation of intracellular Ca²⁺ signals in numerous physiological processes. Shlosman et al. determine the ion stoichiometry of the only sodium–calcium exchanger of known atomic structure, revealing its functional similarity to mammalian exchangers.

Intracellular Ca²⁺ signals control a wide array of cellular processes. These signals require spatial and temporal regulation of the intracellular Ca²⁺ concentration, which is achieved in part by a class of ubiquitous membrane proteins known as sodium–calcium exchangers (NCXs). NCXs are secondary-active antiporters that power the translocation of Ca²⁺ across the cell membrane by coupling it to the flux of Na⁺ in the opposite direction, down an electrochemical gradient. Na⁺ and Ca²⁺ are translocated in separate steps of the antiport cycle, each of which is thought to entail a mechanism whereby ion-binding sites within the protein become alternately exposed to either side of the membrane. The prokaryotic exchanger NCX_Mj, the only member of this family with known structure, has been proposed to be a good functional and structural model of mammalian NCXs; yet our understanding of the functional properties of this protein remains incomplete. Here, we study purified NCX_Mj reconstituted into liposomes under well-controlled experimental conditions and demonstrate that this homologue indeed shares key functional features of the NCX family. Transport assays and reversal-potential measurements enable us to delineate the essential characteristics of this antiporter and establish that its ion-exchange stoichiometry is 3Na⁺:1Ca²⁺. Together with previous studies, this work confirms that NCX_Mj is a valid model system to investigate the mechanism of ion recognition and membrane transport in sodium–calcium exchangers.

Atomistic simulations indicate the c-subunit ring of the F1Fo ATP synthase is not the mitochondrial permeability transition pore

Pathological metabolic conditions such as ischemia induce the rupture of the mitochondrial envelope and the release of pro-apoptotic proteins, leading to cell death. At the onset of this process, the inner mitochondrial membrane becomes depolarized and permeable to osmolytes, proposedly due to the opening of a non-selective protein channel of unknown molecular identity. A recent study purports that this channel, referred to as Mitochondrial Permeability Transition Pore (MPTP), is formed within the c-subunit ring of the ATP synthase, upon its dissociation from the catalytic domain of the enzyme. Here, we examine this claim for two c-rings of different lumen width, through calculations of their ion conductance and selectivity based on all-atom molecular dynamics simulations. We also quantify the likelihood that the lumen of these c-rings is in a hydrated, potentially conducting state rather than empty or blocked by lipid molecules. These calculations demonstrate that the structure and biophysical properties of a correctly assembled c-ring are inconsistent with those attributed to the MPTP.

DOI:http://dx.doi.org/10.7554/eLife.23781.001

Relationship between emotional distress in caregivers and health status in persons with multiple sclerosis

Caregivers of persons with multiple sclerosis (MS) exhibit less satisfaction with quality of life with respect to the general population. To assess the relationship between depression in caregivers and health status profiles of MS patients, we examined data from 133 patients and their respective caregivers, as a part of a prospective randomized trial aimed to investigate the effectiveness of home-based care. Patients were evaluated at baseline and one year later with measures of physical and psychological impairment and health status (SF-36 Health Survey). Caregivers’ psychological morbidity was assessed by the Profile of Mood State (POMS) at the same time points. An improvement of patients’ health status as measured in four out of eight SF-36 dimensions was observed over the study period, while psychological morbidity of their caregivers did not change significantly. Depression in caregivers was related to physical, emotional and health status of the patients at baseline and/or at 12-month follow-up. Changes in the degree of depression of caregivers were also associated with changes in disability and health status of the patients. This study confirms and extends in a home-care setting previous findings on relationships between patients’ status and depression in caregivers. It suggests that the caregiver is an appropriate and independent target for more focused therapeutic strategies.

Silver- versus gold-catalyzed sequential oxidative cyclization of unprotected 2-alkynylanilines with oxone

Divergent catalytic activity of gold and silver complexes towards domino oxidative cyclization reactions of unprotected 2-alkynylanilines.

Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg(2+) through the SOMA string method

The atomic mechanisms of isomerization of ATP-Mg(2+) in solution are characterized using the recently developed String Method with Optimal Molecular Alignment (SOMA) and molecular-dynamics simulations. Bias-Exchange Metadynamics simulations are first performed to identify the primary conformers of the ATP-Mg(2+) complex and their connectivity. SOMA is then used to elucidate the minimum free-energy path (MFEP) for each transition, in a 48-dimensional space. Analysis of the per-atom contributions to the global free-energy profiles reveals that the mechanism of these transitions is controlled by the Mg(2+) ion and its coordinating oxygen atoms in the triphosphate moiety, as well as by the ion-hydration shell. Metadynamics simulations in path collective variables based on the MFEP demonstrate these isomerizations proceed across a narrow channel of configurational space, thus validating the premise underlying SOMA. This study provides a roadmap for the examination of conformational changes in biomolecules, based on complementary enhanced-sampling techniques with different strengths. © 2015 Wiley Periodicals, Inc.

Following easy slope paths on a free energy landscape: the case study of the Trp-cage folding mechanism

In this work a new method for the automatic exploration and calculation of multidimensional free energy landscapes is proposed. Inspired by metadynamics, it uses several collective variables that are relevant for the investigated process and a bias potential that discourages the sampling of already visited configurations. The latter potential allows escaping a local free energy minimum following the direction of slow motions. This is different from metadynamics in which there is no specific direction of the biasing force and the computational effort increases significantly with the number of collective variables. The method is tested on the Ace-Ala3-Nme peptide, and then it is applied to investigate the Trp-cage folding mechanism. For this protein, within a few hundreds of nanoseconds, a broad range of conformations is explored, including nearly native ones, initiating the simulation from a completely unfolded conformation. Finally, several folding/unfolding trajectories give a systematic description of the Trp-cage folding pathways, leading to a unified view for the folding mechanisms of this protein. The proposed mechanism is consistent with NMR chemical shift data at increasing temperature and recent experimental observations pointing to a pivotal role of secondary structure elements in directing the folding process toward the native state.

Two-state dynamics of the SH3-SH2 tandem of Abl kinase and the allosteric role of the N-cap

The regulation and localization of signaling enzymes is often mediated by accessory modular domains, which frequently function in tandems. The ability of these tandems to adopt multiple conformations is as important for proper regulation as the individual domain specificity. A paradigmatic example is Abl, a ubiquitous tyrosine kinase of significant pharmacological interest. SH3 and SH2 domains inhibit Abl by assembling onto the catalytic domain, allosterically clamping it in an inactive state. We investigate the dynamics of this SH3-SH2 tandem, using microsecond all-atom simulations and differential scanning calorimetry. Our results indicate that the Abl tandem is a two-state switch, alternating between the conformation observed in the structure of the autoinhibited enzyme and another configuration that is consistent with existing scattering data for an activated form. Intriguingly, we find that the latter is the most probable when the tandem is disengaged from the catalytic domain. Nevertheless, an amino acid stretch preceding the SH3 domain, the so-called N-cap, reshapes the free-energy landscape of the tandem and favors the interaction of this domain with the SH2-kinase linker, an intermediate step necessary for assembly of the autoinhibited complex. This allosteric effect arises from interactions between N-cap and the SH2 domain and SH3-SH2 connector, which involve a phosphorylation site. We also show that the SH3-SH2 connector plays a determinant role in the assembly equilibrium of Abl, because mutations thereof hinder the engagement of the SH2-kinase linker. These results provide a thermodynamic rationale for the involvement of N-cap and SH3-SH2 connector in Abl regulation and expand our understanding of the principles of modular domain organization.

Metadynamics convergence law in a multidimensional system

Metadynamics is a powerful sampling technique that uses a nonequilibrium history-dependent process to reconstruct the free-energy surface as a function of the relevant collective variables s . In Bussi [Phys. Rev. Lett. 96, 090601 (2006)] it is proved that, in a Langevin process, metadynamics provides an unbiased estimate of the free energy F(s) . We here study the convergence properties of this approach in a multidimensional system, with a Hamiltonian depending on several variables. Specifically, we show that in a Monte Carlo metadynamics simulation of an Ising model the time average of the history-dependent potential converge to F(s) with the same law of an umbrella sampling performed in optimal conditions (i.e., with a bias exactly equal to the negative of the free energy). Remarkably, after a short transient, the error becomes approximately independent on the filling speed, showing that even in out-of-equilibrium conditions metadynamics allows recovering an accurate estimate of F(s) . These results have been obtained introducing a functional form of the history-dependent potential that avoids the onset of systematic errors near the boundaries of the free-energy landscape.

Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations

The binding mechanism of a peptide substrate (Thr-Ile-Met-Met-Gln-Arg, cleavage site p2-NC of the viral polyprotein) to wild-type HIV-1 protease has been investigated by 1.6 micros biased all-atom molecular dynamics simulations in explicit water. The configuration space has been explored biasing seven reaction coordinates by the bias-exchange metadynamics technique. The structure of the Michaelis complex is obtained starting from the substrate outside the enzyme within a backbone rmsd of 0.9 A. The calculated free energy of binding is -6 kcal/mol, and the kinetic constants for association and dissociation are 1.3 x 10(6) M(-1) s(-1) and 57 s(-1), respectively, consistent with experiments. In the main binding pathway, the flaps of the protease do not open sizably. The substrate slides inside the enzyme cavity from the tight lateral channel. This may contrast with the natural polyprotein substrate which is expected to bind by opening the flaps. Thus, mutations might influence differently the binding kinetics of peptidomimetic ligands and of the natural substrate.

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.

Exploring the folding free energy landscape of insulin using bias exchange metadynamics

The bias exchange metadynamics (BE-META) technique was applied to investigate the folding mechanism of insulin, one of the most studied and biologically important proteins. The BE-META simulations were performed starting from an extended conformation of chain B of insulin, using only eight replicas and seven reaction coordinates. The folded state, together with the intermediate states along the folding pathway were identified and their free energy was determined. Three main basins were found separated from one another by a large free energy barrier. The characteristic native fold of chain B was observed in one basin, while the other two most populated basins contained "molten-globule" conformations stabilized by electrostatic and hydrophobic interactions, respectively. Transitions between the three basins occur on the microsecond time scale. The implications and relevance of this finding to the folding mechanisms of insulin were investigated.

Cyanobacteria from benthic mats of Antarctic lakes as a source of new bioactivities

AIMS

To exploit the cyanobacterial diversity of microbial mats growing in the benthic environment of Antarctic lakes for the discovery of novel antibiotic and antitumour activities.

METHODS AND RESULTS

In all, 51 Antarctic cyanobacteria isolated from benthic mats were cultivated in the laboratory by optimizing temperature, irradiance and mixing. Productivity was generally very low (</=60 mg l(-1) d(-1)) with growth rates (mu) in the range of 0.02-0.44 d(-1). Growth rates were limited by photosensitivity, sensitivity to air bubbling, polysaccharide production or cell aggregation. Despite this, 126 extracts were prepared from 48 strains and screened for antimicrobial and cytotoxic activities. Seventeen cyanobacteria showed antimicrobial activity (against the Gram-positive Staphylococcus aureus, the filamentous fungus Aspergillus fumigatus or the yeast Cryptococcus neoformans), and 25 were cytotoxic. The bioactivities were not in accordance with the phylogenetic grouping, but rather strain-specific. One active strain was cultivated in a 10-l photobioreactor.

CONCLUSIONS

Isolation and mass cultivation of Antarctic cyanobacteria and LC-MS (liquid chromatography/mass spectrometry) fractionation of extracts from a subset of those strains (hits) that exhibited relatively potent antibacterial and/or antifungal activities, evidenced a chemical novelty worthy of further investigation.

SIGNIFICANCE AND IMPACT OF THE STUDY

Development of isolation, cultivation and screening methods for Antarctic cyanobacteria has led to the discovery of strains endowed with interesting antimicrobial and antitumour activities.

Newly isolated Streptomyces spp. as enantioselective biocatalysts: hydrolysis of 1,2-O-isopropylidene glycerol racemic esters

AIMS

To identify microbial strains with esterase activity able to enantioselectively hydrolyse esters of (R,S)-1,2-O-isopropylidene glycerol.

METHODS AND RESULTS

The microbial hydrolysis of various racemic esters of 1,2-O-isopropylidene glycerol (IPG) was attempted by screening among Streptomyces spp. previously selected on the basis of their carboxylesterase activity. The best results were observed in the hydrolysis of butyrate ester and two strains appeared promising as they showed opposite enantioselectivity: Streptomyces sp. 90852 gave predominantly (S)-IPG, while strain 90930 mostly gave the R-alcohol. Streptomyces sp. 90930 was identified as Streptomyces violaceusniger, whereas Streptomyces sp. 90852 is a new species belonging to the Streptomyces violaceus taxon. The carboxylesterase belonging to strain 90852 gave a maximum value of enantiomeric ratio (E) of 14-16. This strain was lyophilized and used as dry mycelium for catalysing the synthesis of isopropylidene glycerol butyrate in heptane showing reaction rate and enantioselectivity (E = 6.6) lower than what observed for the hydrolysis.

CONCLUSIONS

A new esterase with enantioselective activity towards (R,S)-IPG butyrate has been selected. The best enantioselectivity is similar or even better than the highest reported value in the literature with commercial enzymes. The enzyme is produced by a new species belonging to the S. violaceus taxon.

SIGNIFICANCE AND IMPACT OF THE STUDY

New esterases from streptomycetes can be employed for the enantioselective hydrolysis of chiral esters derived from primary alcohols, not efficiently resolved with commercial enzymes.

Myxobacteria isolated in Israel as potential source of new anti-infectives

AIMS

To evaluate the patterns of the production of antimicrobial compounds by Israeli myxobacteria newly isolated from soil samples and barks by a battery of isolation and purification methods.

METHODS AND RESULTS

A total of 100 myxobacteria belonging to five of the 12 described genera, were isolated from 48 soil and 45 tree bark samples collected in different areas inside the State of Israel. Four isolation methods based on the peculiar metabolic and cell cycle aspects of myxobacteria, were combined with purification procedures and optimization of cultivation conditions. Ninety-seven strains were fermented and screened for antimicrobial activities. Production of antimicrobial activities was detected in 62 isolates. More than 50% of the collection (54 strains) was able to inhibit Escherichia coli growth.

CONCLUSIONS

The results of this study support the idea that myxobacterial strains can be isolated from particular habitats and then cultivated and screened for their capacity to produce secondary metabolites endowed with antibacterial and antifungal activities. Myxovirescin, a typical poliketide myxobacterial antibiotic, has been identified in one Israeli isolate. Althiomycin, a thiazolyl peptide, which inhibits prokaryotic protein synthesis, usually produced by actinomycetes, was detected in three strains selected in this study.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results confirm that myxobacteria are prolific producers of a variety of bioactive secondary metabolites including antibacterial and antifungal compounds, being their high frequency of anti-Gram-negative activities particularly appealing for the current anti-infective research. So far their screening has often been hampered because their isolation is time-consuming and are quite difficult to handle and cultivate. In this paper we demonstrate that a proper combination of isolation, purification and cultivation methods allow their pharmaceutical exploitation.

Theoretical modeling of vibroelectronic quantum states in complex molecular systems: Solvated carbon monoxide, a test case

In this paper we extend the perturbed matrix method by explicitly including the nuclear degrees of freedom, in order to treat quantum vibrational states in a perturbed molecule. In a previous paper we showed how to include, in a simple way, nuclear degrees of freedom for the calculation of molecular polarizability. In the present work we extend and generalize this approach to model vibroelectronic transitions, requiring a more sophisticated treatment.

Ground and excited electronic state thermodynamics of aqueous carbon monoxide: a theoretical study

By using the quasi Gaussian entropy theory in combination with molecular dynamics simulations and the perturbed matrix method, we investigate the ground and excited state thermodynamics of aqueous carbon monoxide. Results show that the model used is rather accurate and provides a great detail in the description of the excitation thermodynamics.

Adsorption, diffusion, and recombination of hydrogen on pure and boron-doped graphite surfaces

Boron inserted as impurity by substitution of carbon atoms in graphite is known to modify the reactivity of the surface in interaction with hydrogen. Boron induces a better H retention capability in graphite while it makes easier the recombination into molecular hydrogen under heating in thermal-desorption experimental conditions. It has already been calculated that boron modifies the electronic structure of the surface, which results in an increase of the adsorption energy for H. This result seems in good agreement with the better retention for H in doped graphite, but contradictory with the easier recombination observed. The aim of this work is to dismiss this contradiction by elucidating the modifications induced by boron in the recombination mechanism. We studied the diffusion of H on pure and boron-doped graphite in the density functional theory framework. We determined a diffusionlike mechanism leading to molecular hydrogen formation. Finally, we have shown the fundamental modifications induced by boron on the [0001] graphite surface reactivity. From these calculations it stands out that recombination is the result of desorption on pure graphite and diffusion on B-doped surfaces, while the activation energy for the rate limiting step is half reduced by boron. The results are compared to experimental observations. The connection between the cluster and periodic quantum modes for graphite is also discussed.

Testosterone amplifies excitotoxic damage of cultured oligodendrocytes

An overactivation of alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate (AMPA)/kainate receptors has been implicated in the pathophysiology of oligodendrocyte damage in demyelinating disorders of the CNS. We decided to examine the effect of testosterone on excitotoxic death of oligodendrocytes because a gender difference exists in the incidence and disease course of multiple sclerosis. Short-term pure cultures of oligodendrocytes (4 days in vitro) were exposed to a brief pulse with kainate or AMPA + cyclothiazide for the induction of excitotoxicity. Exposure to testosterone enantate was slightly toxic per se and amplified both AMPA and kainate toxicity. Testosterone treatment induced all gene targets of p53, and amplified the induction of these genes induced by kainate. The effect of testosterone was mediated by the activation of androgen receptors and was resistant to the aromatase inhibitors, dl-aminoglutethimide and 4-hydroxyandrost-4-ene-3,17-dione. Testosterone treatment also potentiated the stimulation of 45Ca2+ influx induced by AMPA + cyclothiazide or kainate without changing the expression of the glutamate receptor (GluR) 1, -2/3, and -4 subunits of AMPA receptors or the GluR6/7 subunits of kainate receptors. We conclude that testosterone amplifies excitotoxic damage of oligodendrocytes acting at an early step of the death cascade triggered by AMPA/kainate receptors.

Exposure to 900 MHz electromagnetic field induces an unbalance between pro-apoptotic and pro-survival signals in T-lymphoblastoid leukemia CCRF-CEM cells

It has been recently established that low-frequency electromagnetic field (EMFs) exposure induces biological changes and could be associated with increased incidence of cancer, while the issue remains unresolved as to whether high-frequency EMFs can have hazardous effect on health. Epidemiological studies on association between childhood cancers, particularly leukemia and brain cancer, and exposure to low- and high-frequency EMF suggested an etiological role of EMFs in inducing adverse health effects. To investigate whether exposure to high-frequency EMFs could affect in vitro cell survival, we cultured acute T-lymphoblastoid leukemia cells (CCRF-CEM) in the presence of unmodulated 900 MHz EMF, generated by a transverse electromagnetic (TEM) cell, at various exposure times. We evaluated the effects of high-frequency EMF on cell growth rate and apoptosis induction, by cell viability (MTT) test, FACS analysis and DNA ladder, and we investigated pro-apoptotic and pro-survival signaling pathways possibly involved as a function of exposure time by Western blot analysis. At short exposure times (2-12 h), unmodulated 900 MHz EMF induced DNA breaks and early activation of both p53-dependent and -independent apoptotic pathways while longer continuous exposure (24-48 h) determined silencing of pro-apoptotic signals and activation of genes involved in both intracellular (Bcl-2) and extracellular (Ras and Akt1) pro-survival signaling. Overall our results indicate that exposure to 900 MHz continuous wave, after inducing an early self-defense response triggered by DNA damage, could confer to the survivor CCRF-CEM cells a further advantage to survive and proliferate.

A search for a strong physisorption site for H[sub 2] in Li-doped porous carbons

The mechanism of hydrogen absorption between two coronene molecules has been studied by first principle calculations. Examination of different sites for H(2) molecule confirmed the classical picture of physisorption. We have also considered molecular hydrogen adsorption in a charged carbon structure achieved by doping with lithium at a density corresponding to the intercalate compound LiC(6). We have performed different types of calculations [Hartree-Fock and density functional theory (DFT)] for various atomic basis sets using CRYSTAL98, GAUSSIAN98, and DMOL3 codes. B3LYP-DFT (B3LYP-three-parameter functional of Backe, Lee, Yang and Parr) energy minimization calculations unravel that there is a stable adsorption site for molecular hydrogen in Li-doped sp(2) carbon structure. These calculations also give an insight into the atomic configurations of interlayer species (H(2) and Li) as the interlayer spacing increases. It can be shown that large changes occur in the positions and electronic properties of interlayer species. Hydrogen molecule does not show any tendency for dissociation and adopts a position in the interlayer void that is deeply related to that of lithium ions. We have evidenced a rather large charge transfer from lithium and capping hydrogen species on neighboring slab carbon atoms that induce the stabilization of molecular hydrogen. We have also found that rotating one carbon layer with respect to the other one (at constant interlayer distance) does not change the adsorption energy to a large extent. The best adsorption site is about five times deeper than the physisorption site found in the undoped case and occurs at an interlayer separation of 5.5+/-0.5 A. The corresponding atomic configuration consists in a hydrogen molecule standing (nearly) perpendicular to the plane surface surrounded by the three lithium ions in a configuration close to that of the LiC(6) intercalation compound.