Search

SARS-CoV-2 triggered a worldwide pandemic disease, COVID-19, for which an effective treatment has not yet been settled. Among the most promising targets to fight this disease is SARS-CoV-2 main protease (Mpro), which has been extensively studied in the last few months. There is an urgency for developing effective computational protocols that can help us tackle these key viral proteins. Hence, we have put together a robust and thorough pipeline of in silico protein–ligand characterization methods to address one of the biggest biological problems currently plaguing our world. These methodologies were used to characterize the interaction of SARS-CoV-2 Mpro with an α-ketoamide inhibitor and include details on how to upload, visualize, and manage the three-dimensional structure of the complex and acquire high-quality figures for scientific publications using PyMOL (Protocol 1); perform homology modeling with MODELLER (Protocol 2); perform protein–ligand docking calculations using HADDOCK (Protocol 3); run a virtual screening protocol of a small compound database of SARS-CoV-2 candidate inhibitors with AutoDock 4 and AutoDock Vina (Protocol 4); and, finally, sample the conformational space at the atomic level between SARS-CoV-2 Mpro and the α-ketoamide inhibitor with Molecular Dynamics simulations using GROMACS (Protocol 5). Guidelines for careful data analysis and interpretation are also provided for each Protocol.

Membrane pan-assay interference compounds (PAINS) are a class of molecules that interact nonspecifically with lipid bilayers and alter their physicochemical properties. An early identification of these compounds avoids chasing false leads and the needless waste of time and resources in drug discovery campaigns. In this work, we optimized an

The natural polyphenolic compound Rottlerin (RoT) showed anticancer properties in a variety of human cancers through the inhibition of several target molecules implicated in tumorigenesis, revealing its potential as an anticancer agent. Aquaporins (AQPs) are found overexpressed in different types of cancers and have recently emerged as promising pharmacological targets. Increasing evidence suggests that the water/glycerol channel aquaporin-3 (AQP3) plays a key role in cancer and metastasis. Here, we report the ability of RoT to inhibit human AQP3 activity with an IC50 in the micromolar range (22.8 ± 5.82 µM for water and 6.7 ± 2.97 µM for glycerol permeability inhibition). Moreover, we have used molecular docking and molecular dynamics simulations to understand the structural determinants of RoT that explain its ability to inhibit AQP3. Our results show that RoT blocks AQP3-glycerol permeation by establishing strong and stable interactions at the extracellular region of AQP3 pores interacting with residues essential for glycerol permeation. Altogether, our multidisciplinary approach unveiled RoT as an anticancer drug against tumors where AQP3 is highly expressed providing new information to aquaporin research that may boost future drug design.

This article belongs to the Collection State-of-the-Art Biochemistry in Spain., Phenylketonuria (PKU) is a rare metabolic disease caused by variations in a human gene, PAH, encoding phenylalanine hydroxylase (PAH), and the enzyme converting the essential amino acid phenylalanine into tyrosine. Many PKU-causing variations compromise the conformational stability of the encoded enzyme, decreasing or abolishing its catalytic activity, and leading to an elevated concentration of phenylalanine in the blood, which is neurotoxic. Several therapeutic approaches have been developed to treat the more severe manifestations of the disorder, but they are either not entirely effective or difficult to adhere to throughout life. In a search for novel pharmacological chaperones to treat PKU, a lead compound was discovered (compound IV) that exhibited promising in vitro and in vivo chaperoning activity on PAH. The structure of the PAH-IV complex has been reported. Here, using alchemical free energy calculations (AFEC) on the structure of the PAH-IV complex, we design a new generation of compound IV-analogues with a higher affinity for the enzyme. Seventeen novel analogues were synthesized, and thermal shift and isothermal titration calorimetry (ITC) assays were performed to experimentally evaluate their stabilizing effect and their affinity for the enzyme. Most of the new derivatives bind to PAH tighter than lead compound IV and induce a greater thermostabilization of the enzyme upon binding. Importantly, the correspondence between the calculated alchemical binding free energies and the experimentally determined ΔΔGb values is excellent, which supports the use of AFEC to design pharmacological chaperones to treat PKU using the X-ray structure of their complexes with the target PAH enzyme., This research was funded by MINECO, Spain, grants BFU2016-78232-P and PID2019-107293GB-I00; EU (Interreg-SUDOE), grant NEUROMED; FECYT-PRECIPITA; and Gobierno de Aragón, Spain, grants LMP30_18 and E45_20R. M.C.-G. was recipient of a predoctoral contract from Gobierno de Aragón, Spain.

Membrane Pan-Assay INterference compoundS (PAINS) are a class of molecules that interact non-specifically with lipid bilayers and alter their physicochemical properties. An early identification of these compounds avoids chasing false leads and the needless waste of time and resources in drug discovery campaigns. In this work, we optimized an in silico protocol based on umbrella sampling (US)/MD simulations to discriminate between compounds with different membrane PAINS behavior. We showed that the method is quite sensitive to membrane thickness fluctuations, which was mitigated by changing the US-reference position to the P-atoms of the closest interacting monolayer. The computational efficiency was improved further by decreasing the number of umbrellas and adjusting their strength and position in our US scheme. The ISDM-calculated membrane permeability coefficients confirmed that resveratrol and curcumin have distinct membrane PAINS characteristics and indicate a misclassification of nothofagin in a previous work. Overall, we have presented here a promising in silico protocol which can be adopted as a future reference method to identify membrane PAINS.

Cystic Fibrosis (CF) is a genetic disease caused by mutations in the gene encoding the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) channel. Currently, more than 2100 variants have been identified in the gene, with a large number being very rare. The approval of modulators that act on mutant CFTR protein, correcting its molecular defect and thus alleviating the burden of the disease, revolutionized the field of CF. However, these drugs do not apply to all patients with CF, especially those with rare mutations—for which there is a lack of knowledge on the molecular mechanisms of the disease and the response to modulators. In this work, we evaluated the impact of several rare putative class II mutations on the expression, processing, and response of CFTR to modulators. Novel cell models consisting of bronchial epithelial cell lines expressing CFTR with 14 rare variants were created. The variants studied are localized at Transmembrane Domain 1 (TMD1) or very close to the signature motif of Nucleotide Binding Domain 1 (NBD1). Our data show that all mutations analyzed significantly decrease CFTR processing and while TMD1 mutations respond to modulators, those localized in NBD1 do not. Molecular modeling calculations confirm that the mutations in NBD1 induce greater destabilization of CFTR structure than those in TMD1. Furthermore, the structural proximity of TMD1 mutants to the reported binding site of CFTR modulators such as VX-809 and VX-661, make them more efficient in stabilizing the CFTR mutants analyzed. Overall, our data suggest a pattern for mutation location and impact in response to modulators that correlates with the global effect of the mutations on CFTR structure.

Pan-assay interference compounds (PAINS) are promiscuous molecules with multiple behaviors that interfere with assay readouts. Membrane PAINS are a subset of these compounds that influence the function of membrane proteins by nonspecifically perturbing the lipid membranes that surround them. Here, we describe a computational protocol to identify potential membrane PAINS molecules by calculating the effect that a given compound has on the bilayer deformation propensity.

Quadruplex-interactive small molecules have a wide potential application, not only as drugs but also as sensors of quadruplexes structures. The purpose of this work is the synthesis of analogues of the bis-methylquinolinium-pyridine-2,6-dicarboxamide G4 ligand 360A, to identify relevant structure-activity relationships to apply to the design of other G4-interactive small molecules bearing bis-quinoline or bis-isoquinoline moieties. Thermal denaturation experiments revealed that non-methylated derivatives with a relative 1,4 position between the amide linker and the nitrogen of the quinoline ring are moderate G4 stabilizers, with a preference for the hybrid h-Telo G4. Insertion of a positive charge upon methylation of quinoline/isoquinoline nitrogen increases compounds capacity to selectively stabilize G4s compared to duplex DNA, with a preference for parallel structures. Among these, compounds having a relative 1,3-position between the charged methylquinolinium/isoquinolinium nitrogen and the amide linker are the best G4 stabilizers. More interestingly, these ligands showed different capacities to selectively block DNA polymer-ization in a PCR-stop assay and to induce G4 conformation switches of hybrid h-Telo G4. Mo-lecular dynamic simulations with the parallel k-RAS G4 structure showed that the relative spatial orientation of the two methylated quinoline/isoquinoline rings determines the ligands mode and strength of binding to G4s.

Pan-assay interference compounds (PAINS) are promiscuous molecules with multiple behaviors that interfere with assay readouts. Membrane PAINS are a subset of these compounds that influence the function of membrane proteins by nonspecifically perturbing the lipid membranes that surround them. Here, we describe a computational protocol to identify potential membrane PAINS molecules by calculating the effect that a given compound has on the bilayer deformation propensity.

Tuberculosis remains one of the top causes of death worldwide, and combating its spread has been severely complicated by the emergence of drug-resistance mutations, highlighting the need for more effective drugs. Despite the resistance to isoniazid (INH) arising from mutations in the katG gene encoding the catalase-peroxidase KatG, most notably the S315T mutation, this compound is still one of the most powerful first-line antitubercular drugs, suggesting further pursuit of the development of tailored INH derivatives. The N′-acylated INH derivative with a long alkyl chain (INH-C10) has been shown to be more effective than INH against the S315T variant of Mycobacterium tuberculosis, but the molecular details of this activity enhancement are still unknown. In this work, we show that INH N′-acylation significantly reduces the rate of production of both isonicotinoyl radical and isonicotinyl–NAD by wild type KatG, but not by the S315T variant of KatG mirroring the in vivo effectiveness of the compound. Restrai...

Aquaporins (AQPs) are a family of 13 small integral membrane proteins, whose primary function is to facilitate the passive transport of water across the plasma membrane of the cell, in response to osmotic gradients created by the active transport of solutes. These small membrane-spanning proteins assemble as homotetramers in which each monomer is composed by an extracellular and cytoplasmic vestibule connected by a central amphipathic pore region in a barrel like arrangement. [2]These proteins are widely expressed throughout the animal and plant kingdom, being localized in the plasma membrane and in the cytoplasmic compartments, particularly in cell types that are involved in fluid transport. AQPs have been proven to play key roles in tumor biology, including histological tumor grade, proliferation, migration, angiogenesis, or tumor-associated edema, namely due to its over-expression when compared to normal tissues. Therefore, AQPs can work as potential diagnostic and therapeutic targets in anticancer treatment, since their inhibition in endothelial and tumor cells might limit tumor growth and spread. [3] Unfortunately, the hit rate for the identification of small-molecule AQP modulators appears to be very low when compared to other membrane proteins, and the few available pharmacological modulators lack specificity or show high toxicity. [1] One of the possible explanations for this low druggability is the small size of the functional AQP monomer and its small pore diameter. Nonetheless, the continuous growing of structure/function knowledge on AQPs, particularly the atomic-level geometry of specific hydrophobic and hydrophilic residues in the pore region, makes AQPs a promising therapeutic target to be used in future computational drug discovery campaigns. [2] However, in order to achieve successful results, new and innovative approaches and methods must also be developed. Consequently, we are currently developing a new computational workflow based on several distinct methods that combine innovative ligand and structure-based approaches to identify new AQP modulators. In this work, we will present the first steps of the developed protocol, focusing our studies on AQP – subtype 1. [1] Castle, N. A. (2005). Aquaporins as targets for drug discovery. Drug Discovery Today, 10(7), 485–493.[2] Verkman, A. S., Anderson, M. O., & Papadopoulos, M. C. (2014). Aquaporins: important but elusive drug targets. Nature Reviews Drug Discovery, 13(4), 259–277.[3] Wang, J., Feng, L., Zhu, Z., Zheng, M., Wang, D., Chen, Z., & Sun, H. (2015). Aquaporins as diagnostic and therapeutic targets in cancer: How far we are? Journal of Translational Medicine, 13(96).

Catechins are molecules with potential use in different pathologies such as diabetes and cancer, but their pharmaceutical applications are often hindered by their instability in the bloodstream. This issue can be circumvented using liposomes as their nanocarriers for in vivo delivery. In this work, we studied the molecular details of (-)-epigallocatechin-3-gallate (EGCG) interacting with 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) monolayer/bilayer systems to understand the catechin loading ability and liposome stability, using experimental and computational techniques. The molecular dynamics simulations show the EGCG molecules deep inside the lipid bilayer, positioned below the lipid ester groups, generating a concentration-dependent lipid condensation. This effect was also inferred from the surface pressure isotherms of DMPC monolayers. In the polarization-modulated infrared reflection absorption spectra assays, the predominant effect at higher concentrations of EGCG (e.g., 20 mol %) was an increase in lipid tail disorder. The steady-state fluorescence data confirmed this disordered state, indicating that the catechin-induced liposome aggregation outweighs the condensation effects. Therefore, by adding more than 10 mol % EGCG to the liposomes, a destabilization of the vesicles occurs with the ensuing release of entrapped catechins. The loading capacity for DMPC seems to be limited by its disordered lipid arrangements, typical of a fluid phase. To further increase the clinical usefulness of liposomes, lipid bilayers with more stable and organized assemblies should be employed to avoid aggregation at large concentrations of catechin.

With the recent increase in computing power, the molecular modeling community is now more focused on improving the accuracy and overall quality of biomolecular simulations. For the available simulation packages, force fields, and all other associated methods used, this relates to how well they describe the conformational space and thermodynamic properties of a biomolecular system. The parameter sets of GROMOS force fields have been parametrized and validated with the reaction field (RF) method using charge groups and a twin-range cutoff scheme (0.8/1.4 nm). However, the most recent versions of GROMACS (since v.2016) discontinued the support for charge groups. To take full advantage of the newer and faster versions of this software package with GROMOS 54A7 and RF, we need to evaluate the impact of using a single cutoff scheme (vs twin-range) and of using the Verlet list update method (which is atomistic) compared to the group-based cutoff scheme. Our results show that the GROMOS 54A7 force field seems cons...

With the recent increase in computing power, the molecular modeling community is now more focused on improving the accuracy and overall quality of biomolecular simulations. For the available simulation packages, force fields, and all other associated methods used, this relates to how well they describe the conformational space and thermodynamic properties of a biomolecular system. The parameter sets of GROMOS force fields have been parametrized and validated with the reaction field (RF) method using charge groups and a twin-range cutoff scheme (0.8/1.4 nm). However, the most recent versions of GROMACS (since v.2016) discontinued the support for charge groups. To take full advantage of the newer and faster versions of this software package with GROMOS 54A7 and RF, we need to evaluate the impact of using a single cutoff scheme (vs twin-range) and of using the Verlet list update method (which is atomistic) compared to the group-based cutoff scheme. Our results show that the GROMOS 54A7 force field seems consistent with a single cutoff, since the resulting conformation and protonation ensembles were indistinguishable. The GROMOS parametrization procedure was also reproduced using an atomistic cutoff scheme, and we have observed that the hydration free energy values of small amino acid side-chain analogues were similar to the ones obtained with the group-based protocol. We do observe a small impact of the atomistic cutoff scheme in the conformational space of the model systems studied (G1-PAMAM and DMPC). However, since the structural properties of these systems are well converged for the cutoff range used (1.4-2.0 nm), unlike with the group-based cutoff schemes, we are confident that the atomistic cutoff can be adopted with RF for MD and constant-pH MD biomolecular simulations using the GROMOS 54A7 force field.

UID/ MAR/04292/2013 Acknowledgments : The authors acknowledge financial support from Fundação para a Ciência e a Tecnologia through grant SFRH/BPD/110491/2015, and projects UID/Multi/04046/2013, UID/MULTI/00612/2013, UID/MAR/04292/2013 and PTDC/QEQ-COM/5904/2014. This work was done within the scope of the protocol established between FCUL, the Forensic Science Laboratory from Portuguese Criminal Police and FFUP. The authors wish to thank Mariana Pereira, Joana Alegre and Andreia Alexandre for the technical lab support at Laboratório de Polícia Científica da Polícia Judiciária The emergence of potentially dangerous new psychoactive substances (NPS) imposes enormous challenges on forensic laboratories regarding their rapid and unambiguous identification. Access to comprehensive databases is essential for a quick characterization of these substances, allowing them to be categorized according to national and international legislations. In this work, it is reported the synthesis and structural characterization by NMR and MS of a library encompassing 21 cathinones, 4 of which are not yet reported in the literature, but with structural characteristics that make them a target for clandestine laboratories. This in-house library will be an important tool accessible to forensic laboratories, for the quick identification of seized NPS. The in vitro cytotoxicity of all cathinones was assessed in HepG2 cells, to have a preliminary but effective indication of their human hepatotoxicity potential. The two new cathinones DMB (8) and DMP (9) were the more cytotoxic, followed by the already seized mephedrone (2), 3,4-DMMC (3), 4-MDMC (7), NEB (12) with EC50 values ranging from 0.81 mM for (3) to 1.28 mM for (2). Results suggest an increase of cytotoxicity with the increase of the chain length of the acyl moiety and with the substitution (with one or two methyl groups) in the aromatic ring. The nature of the amine moiety seems to play only a minor role in the cytotoxic effect. Molecular dynamics simulations were performed to evaluate the molecular details related with the observed cytotoxicities. Although these studies indicated that cathinones are able to cross lipid bilayers with relative ease, when in their neutral forms, it was observed only a partial correlation between lipophilicity and cytotoxicity, indicating that membrane trafficking may not be the only key factor influencing the bioactivity of these compounds. This work is a valuable contribution to the forensic science field since a quick identification of novel cathinones is urgent to match their rapid increase in the market. info:eu-repo/semantics/publishedVersion

Tuberculosis remains one of the top causes of death worldwide, and combating its spread has been severely complicated by the emergence of drug-resistance mutations, highlighting the need for more effective drugs. Despite the resistance to isoniazid (INH) arising from mutations in the katG gene encoding the catalase-peroxidase KatG, most notably the S315T mutation, this compound is still one of the most powerful first-line antitubercular drugs, suggesting further pursuit of the development of tailored INH derivatives. The N'-acylated INH derivative with a long alkyl chain (INH-C

Bioactive compounds, such as isorhamnetin and piscidic acid, were obtained from decoctions of cladodes (stem pads from Opuntia ficus-indica). The effect of these phenolic compounds, in a fiber-free extract, were evaluated as inhibitors of cholesterol permeation through a Caco-2 cell monolayer and as 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor. A reduction of 38% in cholesterol permeation through the Caco-2 cell monolayer was obtained, and the phenolic compounds all permeated between 6 and 9%. A mixture of these compounds showed an IC50 of 20.3 mu g/mL as an enzyme inhibitor, whereas piscidic acid alone showed an IC50 of 149.6 mu g/mL; this was slightly outperformed by the isorhamnetin derivatives. Docking studies confirmed that both piscidic acid and isorhamnetin derivatives, present in the decoction, could adequately bind to the enzyme active site. These results reveal that O. ficus-indica, and cladodes derived there from, is a promising plant for use in the development of new functional foods and pharmaceutical products. info:eu-repo/semantics/publishedVersion

The unusual Met-Tyr-Trp adduct composed of cross-linked side chains along with an associated mobile Arg is essential for catalase activity in catalase-peroxidases. In addition, acidic residues in the entrance channel, in particular an Asp and a Glu ∼7 and ∼15 Å, respectively, from the heme, significantly enhance catalase activity. The mechanism by which these channel carboxylates influence catalase activity is the focus of this work. Seventeen new variants with fewer and additional acidic residues have been constructed and characterized structurally and for enzymatic activity, revealing that their effect on activity is roughly inversely proportional to their distance from the heme and adduct, suggesting that the electrostatic potential of the heme cavity may be affected. A discrete group of protonable residues are contained within a 15 Å sphere surrounding the heme iron, and a computational analysis reveals that the pKa of the distal His112, alone, is modulated within the pH range of catalase activity by the remote acidic residues in a pattern consistent with its protonated form having a key role in the catalase reaction cycle. The electrostatic potential also impacts the catalatic reaction through its influence on the charged status of the Met-Tyr-Trp adduct., This work was supported by a Discovery Grant 9600 from the Natural Sciences and Engineering Research Council (NSERC) of Canada (to P.C.L.) and the Canada Research Chair Program (to P.C.L.). The Canadian Light Source is supported by the Natural Sciences and Engineering Research Council of Canada, the National Research Council Canada, the Canadian Institutes of Health Research, the Province of Saskatchewan, Western Economic Diversification Canada, and the University of Saskatchewan. We also acknowledge financial support from the Portuguese Fundaca̧ o para a Ciencia e a Tecnologia through ̂ Project UID/MULTI/00612/2013.

During the infection process, the influenza fusion peptide (FP) inserts into the host membrane, playing a crucial role in the fusion process between the viral and host membranes. In this work we used a combination of simulation and experimental techniques to analyse the molecular details of this process, which are largely unknown. Although the FP structure has been obtained by NMR in detergent micelles, there is no atomic structure information in membranes. To answer this question, we performed bias-exchange metadynamics (BE-META) simulations, which showed that the lowest energy states of the membrane-inserted FP correspond to helical-hairpin conformations similar to that observed in micelles. BE-META simulations of the G1V, W14A, G12A/G13A and G4A/G8A/G16A/G20A mutants revealed that all the mutations affect the peptide’s free energy landscape. A FRET-based analysis showed that all the mutants had a reduced fusogenic activity relative to the WT, in particular the mutants G12A/G13A and G4A/G8A/G16A/G20A. According to our results, one of the major causes of the lower activity of these mutants is their lower membrane affinity, which results in a lower concentration of peptide in the bilayer. These findings contribute to a better understanding of the influenza fusion process and open new routes for future studies.

The emergence of an influenza pandemic is one of the biggest health threats of our time and there is an urgent need to develop vaccines and drugs against a broad spectrum of influenza viruses (IV). A promising strategy to combat IV is to inactivate the fusion process between the viral and host membranes, which is mediated by the surface protein hemagglutinin (HA). During this process, the N-terminal region of HA, known as fusion peptide (FP), inserts into the host membrane. Although it has been shown that the FP plays a crucial role in the fusion process, the molecular effect of the peptide remains unclear. To analyse the molecular determinants underlying the IV FP, we used state of the art simulation techniques, including metadynamics and constant pH molecular dynamics. The simulation results were combined spectroscopic methods to analyse the peptide's affinity for lipid membranes and its ability to promote lipid-mixing. This allowed us to obtain a detailed molecular characterization of the peptide's conformational properties and its effect on the host membrane. Our work also sheds light into the effect of mutations and external conditions, such as pH, on the FP activity. These results can be useful for the design of novel therapies against this devastating pathogen.

Glucose-6-phosphate isomerase (GPI) deficiency cause hereditary nonspherocytic hemolytic anemia (HNSHA) of variable severity in individuals homozygous or compound heterozygous for mutations in GPI gene. This work presents clinical features and genotypic results of two patients of Portuguese origin with GPI deficiency. The patients suffer from a mild hemolytic anemia (Hb levels ranging from 10 to 12.7g/mL) associated with macrocytosis, reticulocytosis, hyperbilirubinemia, hyperferritinemia and slight splenomegaly. Genomic DNA sequencing revealed in one patient homozygosity for a new missense mutation in exon 3, c.260G>C (p.Gly87Ala), and in the second patient compound heterozygosity for the same missense mutation (p.Gly87Ala), along with a frameshift mutation resulting from a single nucleotide deletion in exon 14, c.1238delA (p.Gln413Arg fs*24). Mutation p.Gln413Arg fs*24 is the first frameshift null mutation to be described in GPI deficiency. Molecular modeling suggests that the structural change induced by the p.Gly87Ala pathogenic variant has direct impact in the structural arrangement of the region close to the active site of the enzyme.

Flavodiiron proteins (FDPs) are present in organisms from all domains of life and have been described so far to be involved in the detoxification of oxygen or nitric oxide (NO), acting as O2 and/or NO reductases. The Escherichia coli FDP, named flavorubredoxin (FlRd), is the most extensively studied FDP. Biochemical and in vivo studies revealed that FlRd is involved in NO detoxification as part of the bacterial defense mechanisms against reactive nitrogen species. E. coli FlRd has a clear preference for NO as a substrate in vitro, exhibiting a very low reactivity toward O2. To contribute to the understanding of the structural features defining this substrate selectivity, we determined the crystallographic structure of E. coli FlRd, both in the isolated and reduced states. The overall tetrameric structure revealed a highly conserved flavodiiron core domain, with a metallo-β-lactamase-like domain containing a diiron center, and a flavodoxin domain with a flavin mononucleotide cofactor. The metal center in the oxidized state has a μ-hydroxo bridge coordinating the two irons, while in the reduced state, this moiety is not detected. Since only the flavodiiron domain was observed in these crystal structures, the structure of the rubredoxin domain was determined by NMR. Tunnels for the substrates were identified, and through molecular dynamics simulations, no differences for O2 or NO permeation were found. The present data represent the first structure for a NO-selective FDP.

The peptide Ac-(cyclo-2,6)-R[KAAAD]-NH2 (cyc-RKAAAD) is a short cyclic peptide known to adopt a remarkably stable single turn α-helix in water. Due to its simplicity and the availability of thermodynamic and kinetic experimental data, cyc-RKAAAD poses as an ideal model for evaluating the aptness of current molecular dynamics (MD) simulation methodologies to accurately sample conformations that reproduce experimentally observed properties. In this work, we extensively sample the conformational space of cyc-RKAAAD using microsecond-timescale MD simulations. We characterize the peptide conformational preferences in terms of secondary structure propensities and, using Cartesian-coordinate principal component analysis (cPCA), construct its free energy landscape, thus obtaining a detailed weighted discrimination between the helical and nonhelical subensembles. The cPCA state discrimination, together with a Markov model built from it, allowed us to estimate the free energy of unfolding (-0.57 kJ/mol) and the relaxation time (∼0.435 μs) at 298.15 K, which are in excellent agreement with the experimentally reported values (-0.22 kJ/mol and 0.42 μs, Serrano, A. L.; Tucker, M. J.; Gai, F. J. Phys. Chem. B, 2011, 115, 7472-7478.). Additionally, we present simulations conducted using two enhanced sampling methods: replica-exchange molecular dynamics (REMD) and bias-exchange metadynamics (BE-MetaD). We compare the free energy landscape obtained by these two methods with the results from MD simulations and discuss the sampling and computational gains achieved. Overall, the results obtained attest to the suitability of modern simulation methods to explore the conformational behavior of peptide systems with a high level of realism.

Poisson-Boltzmann (PB) models are a fast and common tool for studying electrostatic processes in proteins, particularly their ionization equilibrium (protonation and/or reduction), often yielding quite good results when compared with more detailed models. Yet, they are conceptually very simple and necessarily approximate, their empirical character being most evident when it comes to the choice of the dielectric constant assigned to the protein region. The present study analyzes several factors affecting the ability of PB-based methods to model protein ionization equilibrium. We give particular attention to a suggestion made by Warshel and co-workers (e.g., Sham et al. J. Phys. Chem. B 1997, 101, 4458) of using different protein dielectric constants for computing the individual (site) and the pairwise (site-site) terms of the ionization free energies. Our prediction of pK(a) values for several proteins indicates that no advantage is obtained by such a procedure, even for sites that are buried and/or display large pK(a) shifts relative to the solution values. In particular, the present methodology gives the best predictions using a dielectric constant around 20, for shifted/buried and nonshifted/exposed sites alike. The similarities and differences between the PB model and Warshel's PDLD/S model are discussed, as well as the reasons behind their apparently discrepant results. The present PB model is shown to predict also good reduction potentials in redox proteins.

The interaction and electron transfer (ET) between rubredoxin (Rd) and rubredoxin:oxygen oxidoreductase (ROO) from Desulfovibrio gigas is studied by molecular modelling techniques. Experimental kinetic assays using recombinant proteins show that the Rd reoxidation by ROO displays a bell-shaped dependence on ionic strength, suggesting a non-trivial electrostatic dependence of the interaction between these two proteins. Rigid docking studies reveal a prevalence for Rd to interact, in a very specific way, with the surface of the ROO dimer near its FMN cofactors. The optimization of the lowest energy complexes, using molecular dynamics simulation, shows a very tight interaction between the surface of the two proteins, with a high probability for Rd residues (but not the iron centre directly) to be in direct contact with the FMN cofactors of ROO. Both electrostatics and van der Waals interactions contribute to the final energy of the complex. In these complexes, the major contributions for complex formation are polar interactions between acidic residues of Rd and basic residues of ROO, plus substantial non-polar interactions between different groups. Important residues for this process are identified. ET estimates (using the Pathways model), in the optimized lowest energy complexes, suggest that these configurations are efficient for transferring electrons. The experimental bell-shaped dependence of kinetics on ionic strength is analysed in view of the molecular modelling results, and hypotheses for the molecular basis of this phenomenon are discussed.

Like all enveloped viruses, influenza virus enters the host cell by fusing its membrane with the host membrane, in a process mediated by the hemagglutinin (HA) glycoprotein. HA is a homotrimeric protein comprised by a soluble part (which contains the receptor binding site and the fusion peptide) and a transmembrane (TM) peptide. The TM peptide attaches the protein to the viral membrane and is also thought to play a role in the fusion process. Although this peptide has been gaining considerable attention in recent years, its 3D structure and the molecular determinants of membrane insertion remain unknown.To analyze the structural determinants of membrane insertion of the TM peptide, we simulated this peptide in the presence of a DMPC bilayer [1]. We observed that the peptide adopts a mainly helical conformation and inserts in the membrane with a tilt angle of ∼64°. Simulations with mutant forms of the TM peptide revealed that mutations of Trp 24 and Tyr 5 found in the C-terminal and N-terminal regions, respectively, affect the helicity and consequently the peptide arrangement inside the membrane bilayer. Since HA is a trimer, we also performed simulations with three copies of the TM peptide embedded in a membrane. The simulations showed that the three peptides assemble in a triangular arrangement that approximately matches the positions where they should attach to the available crystallographic structure of the soluble part of HA.1. B. L. Victor, A. M. Baptista and C. M. Soares, J Chem Inf Model, 2012, 52, 3001-3012.

Membrane fusion is a process involved in a high range of biological functions, going from viral infections to neurotransmitter release. Fusogenic proteins increase the slow rate of fusion by coupling energetically downhill conformational changes of the protein to the kinetically unfavorable fusion of the membrane lipid bilayers. Hemagglutinin is an example of a fusogenic protein, which promotes the fusion of the membrane of the influenza virus with the membrane of the target cell. The N-terminus of the HA2 subunit of this protein contains a fusion domain described to act as a destabilizer of the target membrane bilayers, leading eventually to a full fusion of the two membranes. On the other hand, the C-terminus of the same subunit contains a helical transmembrane domain which was initially described to act as the anchor of the protein to the membrane of the virus. However, in recent years the study of this peptide segment has been gaining more attention since it has also been described to be involved in the membrane fusion process. Yet, the structural characterization of the interaction of such a protein domain with membrane lipids is still very limited. Therefore, in this work, we present a study of this transmembrane peptide domain in the presence of DMPC membrane bilayers, and we evaluate the effect of several mutations, and the effect of peptide oligomerization in this interaction process. Our results allowed us to identify and confirm amino acid residue motifs that seem to regulate the interaction between the segment peptide and membrane bilayers. Besides these sequence requirements, we have also identified length and tilt requirements that ultimately contribute to the hydrophobic matching between the peptide and the membrane. Additionally, we looked at the association of several transmembrane peptide segments and evaluated their direct interaction and stability inside a membrane bilayer. From our results we could conclude that three independent TM peptide segments arrange themselves in a parallel arrangement, very similarly to what is observed for the C-terminal regions of the hemagglutinin crystallographic structure of the protein, to where the segments are attached.

Molecular dynamics simulation studies of rubredoxin from Desulfovibrio gigas (RDG) were used to characterize the molecular mechanism of thermal stabilization by the compatible solute (CS) diglycerol-phospate (DGP). DGP is a negatively charged CS that accumulates under salt stress in Archaeoglobus fulgidus. Experimental results show that a 100 mM DGP solution exerts a strong protection effect in the half-life of RDG at 363 K (Lamosa et al., Appl Environ Microbiol 2000;66:1974-1979). RDG was simulated in four aqueous solutions at 300 and 363 K: pure aqueous media, 100 mM DGP, 100 mM NaCl, and 500 mM DGP. Our work shows that the 100 mM DGP solution is able to maintain the average protein structure when the temperature is increased, preventing the occurrence of large-scale deviation of a mobile loop involved in the first steps of RDG unfolding. The molecular mechanism of thermal denaturation protection by DGP seems to involve the direct interaction between the protein and the CS by hydrogen bond interactions near the mobile loop. Several clusters of DGP molecules are formed and preferentially localized at neutral electrostatic regions of the surface. The increase of DGP concentration to 500 mM did not yield better stabilization of the protein suggesting that the thermal protective role of this charged CS is achieved at low concentrations, as shown experimentally.

Superoxide reductases (SORs) are antioxidant enzymes present in many prokaryotes, either anaerobes or microaerophiles, which detoxify superoxide by reducing it to hydrogen peroxide. The reaction mechanism involves the diffusion-limited encounter of superoxide with the reduced iron site and concomitant formation of an Fe(3+)-(hydro)peroxo adduct that, upon protonation, leads to the formation of hydrogen peroxide. By the end of this process, a glutamate residue coordinates the ferric ion, acting as a sixth ligand. Although this residue is able to shuttle protons to the intermediate at low pH, it seems to have a minor relevance to the overall reduction mechanism. Nevertheless, this ligand is conserved in most SORs known thus far, with the notable exception of neelaredoxin from Nanoarchaeum equitans. The protein of this organism was cloned and overexpressed, and its spectroscopic characterization revealed distinct pH-equilibrium properties in comparison with those of glutamate-containing SORs. A three-dimensional model of this protein was generated in an effort to identify structural properties that could explain these distinct features. Pulse radiolysis measurements showed that the efficiency of this enzyme in reducing superoxide is comparable to that of glutamate-containing SORs, thus definitely ruling out the requirement for such a ligand in the reduction mechanism.

Influenza virus is responsible for worldwide outbreaks of flu, causing hundreds of thousands of deaths every year, which rise to millions in pandemic years. In order to infect the host cells, influenza virus promotes the fusion of the viral and host membranes. This process is mediated by hemagglutinin (HA), a glycoprotein located on the surface of the viral envelope. Influenza HA has a highly conserved N-terminal domain, comprising ∼20 residues, which inserts into the host membrane. This region is critical for destabilizing target membranes during the fusion process and is known as fusion peptide (FP).To elucidate the molecular determinants that lead to the destabilization of biological membranes by the FP, we used a molecular dynamics (MD) approach. We performed simulations with the wild type and four different FP mutants: G1V, W14A, G4A/G8A/G16A/G20A, and G12A/G13A, which are known or expected to have an impaired fusogenic activity. Our aim is to understand how these mutations affect the conformational distribution of the peptide and its ability to destabilize the membrane.Given that lipid membranes are very viscous, it is difficult to obtain reasonable sampling using standard MD. Therefore, in addition to standard MD simulations, we also performed bias-exchange metadynamics simulations, both in water and in a DMPC membrane. These simulations enable us to compare the energy landscapes of the wild type and mutant peptides and explain how these mutations affect the fusogenic ability of the peptide.

Heme-copper oxidases are membrane proteins found in the respiratory chain of aerobic organisms. They are the terminal electron acceptors coupling the translocation of protons across the membrane with the reduction of oxygen to water. Because the catalytic process occurs in the heme cofactors positioned well inside the protein matrix, proton channels must exist. However, due to the high structural divergence among this kind of proteins, the proton channels previously described are not necessarily conserved. In this work we modeled the structure of the quinol oxidase from Acidianus ambivalens using comparative modeling techniques for identifying proton channels. Additionally, given the high importance that water molecules may have in this process, we have developed a methodology, within the context of comparative modeling, to identify high water probability zones and to deconvolute them into chains of ordered water molecules. From our results, and from the existent information from other proteins from the same superfamily, we were able to suggest three possible proton channels: one K-, one D-, and one Q-spatial homologous proton channels. This methodology can be applied to other systems where water molecules are important for their biological function.