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Context Follicle-stimulating hormone (FSH) plays an essential role in gonadal function. Loss-of-function mutations in the follicle-stimulating hormone receptor (FSHR) are an infrequent cause of primary ovarian failure. Objective To analyze the molecular physiopathogenesis of a novel mutation in the FSHR identified in a woman with primary ovarian failure, employing in vitro and in silico approaches, and to compare the features of this dysfunctional receptor with those shown by the trafficking-defective D408Y FSHR mutant. Methods Sanger sequencing of the FSHR cDNA was applied to identify the novel mutation. FSH-stimulated cyclic adenosine monophosphate (cAMP) production, ERK1/2 phosphorylation, and desensitization were tested in HEK293 cells. Receptor expression was analyzed by immunoblotting, receptor-binding assays, and flow cytometry. Molecular dynamics simulations were performed to determine the in silico behavior of the mutant FSHRs. Results A novel missense mutation (I423T) in the second transmembrane domain of the FSHR was identified in a woman with normal pubertal development but primary amenorrhea. The I423T mutation slightly impaired plasma membrane expression of the mature form of the receptor and severely impacted on cAMP/protein kinase A signaling but much less on β-arrestin-dependent ERK1/2 phosphorylation. Meanwhile, the D408Y mutation severely affected membrane expression, with most of the FSH receptor located intracellularly, and both signal readouts tested. Molecular dynamics simulations revealed important functional disruptions in both mutant FSHRs, mainly the loss of interhelical connectivity in the D408Y FSHR. Conclusions Concurrently, these data indicate that conformational differences during the inactive and active states account for the distinct expression levels, differential signaling, and phenotypic expression of the I423T and D408Y mutant FSHRs.

Absorption of bioactive peptides in the intestinal epithelium take place in the apical or the basolateral tight junctions of the cells. Depending on the peptide size and hydrophobicity, translocation mechanisms involve processes of passive diffusion, active transport by peptide-cotransporters such as members of the PepT family, and transcytosis by internalization vesicles. In this work, we investigated passive diffusion of bioactive peptides of 6, 17, and 30 amino acids into lipid bilayers of (POPC) phospholipid molecules. We initially selected these three peptides because such fragments are produced by partial hydrolysis of β-casein (BCN), and because of their physiological functions: BCN6 is an agonist of opioid receptors; BCN17 is an inhibitor of thrombin and angiotensin-converting enzymes, and BCN30 promotes secretion of the protective mucin barrier in the intestine. Our computational set up consisted of unbiased equilibrium molecular dynamics simulations, at the μs-time scale, using an all-atom force field. Each peptide was allowed to freely fold and unfold, as well as enter and exit the lipid bilayer, which allows determination of peptide affinity for the bilayer interface and hydrophobic core. Passive internalization of BCN6 (YPVEPF), BCN17 (YQEPVLGPVR GPFPIIV), and BCN30 (GVSKVKEAMA PKHKEMPFPK YPVEPFTESQ) displayed different dynamics at the bilayer interface: the BCN6 peptide attached and detached throughout the simulation trajectory; BCN17 and BCN30 attached irreversibly to the bilayer interface, respectively, with N- and C-terminus fragments in close contact with lipid molecules. Quenching of tyrosine fluorescence data suggest interfacial interactions of BCN6, BCN17 and BCN30 in POPC lipid bilayers, consistent with the proposed modeling set up. This approach gave valuable information of peptide insertion and folding at a lipid bilayer, allowing to explore the initial stages of the peptide adsorption at the interface, and providing a model for evaluation of amphipathic properties of potential biofunctional peptides.

Objective: Whey proteins, as β-lactoglobulin, have biological activity. Controlled hydrolysis of this protein could generate peptides with some biological function. The aim of this work was to analyze the peptides resulting from the in vitro hydrolysis with chymotrypsin in order to evaluate the presence of bioactive peptides. Design/methodology/approach: Chymotrypsin was used in the hydrolysis of β-lactoglobulin, and its peptides were evaluated by ultrafiltration, electrophoresis, and mass spectrometry. Findings/conclusion: Results showed that 2 h of chymotrypsin hydrolysis (T1) released peptides with molecular weight values of 8 and 9 KDa, while 4 h of hydrolysis (T2) produced peptides with molecular mass weight values of 7 and 5 KDa. The mass spectrometry (MALDI-TOF) showed six peaks and five of them were comparable with those obtained by in silico hydrolysis results (done previously by Fonseca Ayala, 2018). The identified peptides (DTDYK, DAQSAPL and LKPTPEGDL) in the fraction

Background: Neutrophil extracellular traps (NETs) from patients with Systemic Lupus Erythematosus (SLE) are characterized by lower ubiquitylation and myeloperoxidase (MPO) as a substrate. The structural and functional effect of such modification and if there are additional post-translational modifications (PTMs) are unknown.Methods: To assess the expression and functional role of PTMs in NETs of patients with SLE; reactivation, proliferation and cytokine production was evaluated by flow cytometry using co-cultures with dendritic cells (DC) and CD4+ from SLE patients and healthy controls. The impact of ubiquitylation on MPO was assessed by molecular dynamics. The expression of ISG15 in NETs was evaluated by immunofluorescence and Western Blot.Results: Fifteen patients with SLE and 10 healthy controls were included. In the co-cultures of CD4+ lymphocytes with DC stimulated with ubiquitylated MPO or recombinant MPO, a higher expression of IFNγ and IL17A was found in CD4+ from SLE patients (p + lymphocytes, while the opposite was documented in controls (p Conclusion: The ubiquitylated MPO has a differential effect on the induction of reactivation and proliferation of CD4+ lymphocytes in patients with SLE, which may be related to structural changes by ubiquitylation at the catalytic site of MPO. Besides a lower ubiquitylation pattern, NETs of patients with SLE are characterized by the expression of H2B conjugated with ISG15, and the induction of IFNγ by Th1 cells.

Misfolding of G protein-coupled receptors (GPCRs) caused by mutations frequently leads to disease due to intracellular trapping of the conformationally abnormal receptor. Several endocrine diseases due to inactivating mutations in GPCRs have been described, including X-linked nephrogenic diabetes insipidus, thyroid disorders, familial hypocalciuric hypercalcemia, obesity, familial glucocorticoid deficiency [melanocortin-2 receptor, MC2R (also known as adrenocorticotropin receptor, ACTHR), and reproductive disorders. In these mutant receptors, misfolding leads to endoplasmic reticulum retention, increased intracellular degradation, and deficient trafficking of the abnormal receptor to the cell surface plasma membrane, causing inability of the receptor to interact with agonists and trigger intracellular signaling. In this review, we discuss the mechanisms whereby mutations in GPCRs involved in endocrine function in humans lead to misfolding, decreased plasma membrane expression of the receptor protein, and loss-of-function diseases, and also describe several experimental approaches employed to rescue trafficking and function of the misfolded receptors. Special attention is given to misfolded GPCRs that regulate reproductive function, given the key role played by these particular membrane receptors in sexual development and fertility, and recent reports on promising therapeutic interventions targeting trafficking of these defective proteins to rescue completely or partially their normal function.

Women with inactivating mutations in the FSHR may exhibit an array of phenotypes, from lack of pubertal development, primary amenorrhea, and complete insensitivity to FSH, to secondary amenorrhea and premature ovarian failure. In contrast to the LHCGR, only 19 inactivating mutations in the FSHR have been described to date. We report herein the case of a 22 year old women who presented with normal pubertal development but primary amenorrhea, associated with elevated serum FSH and LH levels (27-30 IU/L), low serum estradiol (E2) (21-40 pg/ml) and normal serum AMH (2.2-2.5 ng/ml) levels. After administration of recombinant FSH (total dose 1425 IU/9 days) serum E2 levels rose from 20 to 65 pg/ml with a parallel increase in number (from 5 to 17 follicles) and size (from 3 to 10 mm diameter) of follicles, and ovarian volumes (from 4 to 10 cm3). Sequencing of the FSHR revealed a new homozygous mutation in codon 423, where ATC was changed to ACC, generating the Ile423Thr substitution at the junction of the transmembrane domain (TM) 2 and the exo-loop (EL) 1 of the FSHR. The mother and two half-brothers were heterozygous for the same mutation. The molecular physiopathogenesis of the novel Ile423Thr mutation was analyzed by a series of in silico and in vitro biochemical studies in HEK293 cells transiently expressing either the wild-type (Wt) FSHR or the Ile423Thr mutant cloned into the pSG5 vector, and the results were compared with those obtained in cells transfected with the expression-deficient Asp408Tyr mutant, which leads to a more severe form of hypergonadotropic hypogonadism (1). Compared with the Wt FSHR, the plasma membrane expression of the mature (~80 kDa) form of the Ile423Thr mutant was slightly reduced, while that of the Asp408Tyr mutant was remarkably low, as disclosed by immunoblotting. A dissociation in the responses to FSH-stimulated signaling between the mutant receptors was found: compared with the Wt FSHR, FSH-stimulated cAMP production and ERK phosphorylation were reduced by 67% and 27% in the Ile423Thr mutant and by 52% and 43% in the Asp408Tyr FSHR, respectively. In silico molecular dynamics simulations of the FSHRs in an explicit membrane environment unveiled important differences in the behavior of both mutants vs the Wt receptor, particularly in the interhelical interactions of Thr423 with TM7 and EL2, and Tyr408 with TMs 5 and 7. Concurrently, these data suggest that conformational differences during the inactive (particularly during trafficking of the receptor proteins from the endoplasmic reticulum to the plasma membrane) and active (agonist-occupied receptor) states, account for the distinct expression levels and differential signaling exhibited by the Ile423Thr and Asp408Tyr mutant FSHRs. (1) Bramble MS, et al. A novel follicle-stimulating hormone receptor mutation causing primary ovarian failure: a fertility application of whole exome sequencing. Hum. Reprod. 2016; 31;905-914.

The follicle-stimulating hormone receptor (FSHR) plays a crucial role in reproduction. This structurally complex receptor is a member of the G-protein coupled receptor (GPCR) superfamily of membrane receptors. As with the other structurally similar glycoprotein hormone receptors (the thyroid-stimulating hormone and luteinizing hormone-chorionic gonadotropin hormone receptors), the FSHR is characterized by an extensive extracellular domain, where binding to FSH occurs, linked to the signal specificity subdomain or hinge region. This region is involved in ligand-stimulated receptor activation whereas the seven transmembrane domain is associated with receptor activation and transmission of the activation process to the intracellular loops comprised of amino acid sequences, which predicate coupling to effectors, interaction with adapter proteins, and triggering of downstream intracellular signaling. In this review, we describe the most important structural features of the FSHR intimately involved in regulation of FSHR function, including trafficking, dimerization, and oligomerization, ligand binding, agonist-stimulated activation, and signal transduction.

Follicle-stimulating hormone receptor (FSHR) is a G-protein coupled receptor (GPCR) and a prototype of the glycoprotein hormone receptors subfamily of GPCRs. Structural data of the FSHR ectodomain in complex with follicle-stimulating hormone suggests a “pull and lift” activation mechanism that triggers a conformational change on the seven α-helix transmembrane domain (TMD). To analyze the conformational changes of the FSHR TMD resulting from sequence variants associated with reproductive impairment in humans, we set up a computational approach combining helix modeling and molecular simulation methods to generate conformational ensembles of the receptor at room (300 K) and physiological (310 K) temperatures. We examined the receptor dynamics in an explicit membrane environment of polyunsaturated phospholipids and solvent water molecules. The analysis of the conformational dynamics of the functional (N680 and S680) and dysfunctional (mutations at D408) variants of the FSHR allowed us to validate the FSHR-TMD model. Functional variants display a concerted motion of flexible intracellular regions at TMD helices 5 and 6. Disruption of side chain interactions and conformational dynamics were detected upon mutation at D408 when replaced with alanine, arginine, or tyrosine. Dynamical network analysis confirmed that TMD helices 2 and 5 may share communication pathways in the functional FSHR variants, whereas no connectivity was detected in the dysfunctional mutants, indicating that the global dynamics of the FSHR was sensitive to mutations at amino acid residue 408, a key position apparently linked to misfolding and variable cell surface plasma membrane expression of FSHRs with distinct mutations at this position.

Translocation of negatively charged ions across cell membranes by ion pumps raises the question as to how protein interactions control the location and dynamics of the ion. Here we address this question by performing extensive molecular dynamics simulations of wild type and mutant halorhodopsin, a seven-helical transmembrane protein that translocates chloride ions upon light absorption. We find that inter-helical hydrogen bonds mediated by a key arginine group largely govern the dynamics of the protein and water groups coordinating the chloride ion.

Posttranslational modifications occurring during the biosynthesis of G protein-coupled receptors include glycosylation and palmitoylation at conserved cysteine residues located in the carboxyl-terminus (Ctail) of the receptor. In a number of these receptors, these modifications play an important role in receptor function and particularly, in intracellular trafficking. In the present study, the three cysteine residues present in the carboxyl-terminus of the human FSHR were replaced with glycine by site-directed mutagenesis. Wild-type and mutant (Cys627/629/655Gly) FSHRs were then transiently expressed in HEK-293 cells and analyzed for cell-surface plasma membrane expression, agonist-stimulated signaling and internalization, and postendocytic processing in the abscence and presence of lysosome and/or proteasome inhibitors. Compared with the wild-type FSHR, the triple mutant FSHR exhibited ~70% reduction in plasma membrane expression as well as a profound attenuation in agonist-stimulated cAMP production and ERK1/2 phosphorylation. Incubation of HEK-293 cells expressing the wild-type FSHR with 2-bromopalmitate (palmitoylation inhibitor) for 6 h, decreased plasma membrane expression of the receptor by ~30%. The internalization kinetics and β-arrestin 1 and 2 recruitment were similar between the wild-type and triple mutant FSHR as disclosed by assays performed in non-equilibrium binding conditions and by confocal microscopy. Cells expressing the mutant FSHR recycled the internalized FSHR back to the plasma membrane less efficiently than those expressing the wild-type FSHR, an effect that was counteracted by proteasome but not by lysosome inhibition. These results indicate that replacement of the cysteine residues present in the carboxyl-terminus of the FSHR, impairs receptor trafficking from the endoplasmic reticulum/Golgi apparatus to the plasma membrane and its recycling from endosomes back to the cell surface following agonist-induced internalization. Since in the FSHR these cysteine residues are S-palmitoylated, the data presented emphasize on this posttranslational modification as an important factor for both upward and downward trafficking of this receptor.

In the present study, we analyzed the role of Lys191 on function, structure, and dynamic behavior of the human GnRH receptor (hGnRHR) and the formation of the Cys14–Cys200 bridge, which is essential for receptor trafficking to the plasma membrane. Several mutants were studied; mutants lacked either the Cys14–Cys200 bridge, Lys191 or both. The markedly reduced expression and function of a Cys14Ser mutant lacking the 14–200 bridge, was nearly restored to wild-type/ΔLys191 levels upon deletion of Lys191. Lys191 removal resulted in changes in the dynamic behavior of the mutants as disclosed by molecular dynamics simulations: the distance between the sulfur- (or oxygen-) sulfur groups of Cys (or Ser)14 and Cys200 was shorter and more constant, and the conformation of the NH2-terminus and the exoloop 2 exhibited fewer fluctuations than when Lys191 was present. These data provide novel information on the role of Lys191 in defining an optimal configuration for the hGnRHR intracellular trafficking and function.

In the present study, a model for the human gonadotropin-releasing hormone receptor embedded in an explicit lipid bilayer was developed. The final conformation was obtained by extensive molecular dynamics simulations of a homology model based on the bovine rhodopsin crystal structure. The analysis of the receptor structure allowed us to detect a number of specific contacts between different amino acid residues, as well as water- and lipid-mediated interactions. These interactions were stable in six additional independent 35 ns long simulations at 310 and 323 K, which used the refined model as the starting structure. All loops, particularly the extracellular loop 2 and the intracellular loop 3, exhibited high fluctuations, whereas the transmembrane helices were more static. Although other models of this receptor have been previously developed, none of them have been subjected to extensive molecular dynamics simulations, and no other three-dimensional structure is publicly available. Our results suggest that the presence of ions as well as explicit solvent and lipid molecules are critical for the structure of membrane protein models, and that molecular dynamics simulations are certainly useful for their refinement.

The carboxyl-terminal segment of G protein-coupled receptors has one or more conserved cysteine residues that are potential sites for palmitoylation. This posttranslational modification contributes to membrane association, internalization, and membrane targeting of proteins. In contrast to other members of the glycoprotein hormone receptor family (the LH and thyroid-stimulating hormone receptors), it is not known whether the follicle-stimulating hormone receptor (FSHR) is palmitoylated and what are the effects of abolishing its potential palmitoylation sites. In the present study, a functional analysis of the FSHR carboxyl-terminal segment cysteine residues was carried out. We constructed a series of mutant FSHRs by substituting cysteine residues with alanine, serine, or threonine individually and together at positions 629 and 655 (conserved cysteines) and 627 (nonconserved). The results showed that all three cysteine residues are palmitoylated but that only modification at Cys629 is functionally relevant. The lack of palmitoylation does not appear to greatly impair coupling to G(s) but, when absent at position 629, does significantly impair cell surface membrane expression of the partially palmitoylated receptor. All FSHR Cys mutants were capable of binding agonist with the same affinity as the wild-type receptor and internalizing on agonist stimulation. Molecular dynamics simulations at a time scale of approximately 100 nsec revealed that replacement of Cys629 resulted in structures that differed significantly from that of the wild-type receptor. Thus, deviations from wild-type conformation may potentially contribute to the severe impairment in plasma membrane expression and the modest effects on signaling exhibited by the receptors modified in this particular position.

Membrane proteins perform relevant physiological functions by means of intricate conformational changes in a hydrophobic environment. Lipid bilayers and embedded proteins, therefore, play a functional role in biomembranes, where the interplay of interactions keeps a delicate balance between cell barriers and selective transducers, transporters, pores, channels, etc. Molecular dynamics and experimental methods (e.g. X-ray diffraction, neutron scattering, nuclear magnetic resonance, infrared spectroscopy, dielectric relaxation spectroscopy, among others) encompass a set of tools to determine the relevant properties that make biomembranes so efficient for preserving life. In this chapter, I provide a perspective on studies that combine experimental methods and molecular dynamics approaches to decipher couplings of membrane proteins and lipid bilayers.

Isothermal–isobaric ensamble Monte Carlo simulations have been carried out for a dilute NaCl aqueous solution at 25 °C and 1 atm, using the transferable intermolecular potential 4-point-fluctuating charge (TIP4P-FQ) water model. The thermodynamic properties such as energy, density and enthalpy of solution were calculated. Structural features of the solvation shells around the Na+ and Cl− ions were studied by analyzing the radial distribution functions, the orientational distribution functions, the shell average of the number of water H-bonds and the shell average of the water electric dipole moment. Contributions of the ion, the first shell and bulk water molecules interactions to the total energy were analyzed in terms of the solvation shell structure around the sodium and chlorine ions in solution. The TIP4P-FQ model allows studying water polarization, which cannot be analyzed by means of the rigid models. Evidence of a more ordered structure around the sodium ion than around the chlorine ion is found. Water molecules noticeably increase their dipole moment in the first solvation shell and long-range effects are observed in the bulk water molecules due to the presence of both ions in the solution.

The exploration of novel antibiotic resistance determinants in a particular environment may be limited because of the presence of uncultured microorganisms. In this work, a culture-independent approach based on functional metagenomics was applied to search for chloramphenicol resistance genes in agro-industrial wastewater in Lerma de Villada, Mexico. To this end, a metagenomic library was generated in Escherichia coli DH10B containing DNA isolated from environmental samples of the residual arsenic-enriched (10 mg/ml) effluent. One resistant clone was detected in this library and further analyzed. An open reading frame similar to a multidrug resistance protein from Aeromonas salmonicida and responsible for chloramphenicol resistance was identified, sequenced, and found to encode a member of the major facilitator superfamily (MFS). Our results also showed that the expression of this gene restored streptomycin sensitivity in E. coli DH10B cells. To gain further insight into the phenotype of this MFS family member, we developed a model of the membrane protein multiporter that, in addition, may serve as a template for developing new antibiotics.

The pathogenic mechanisms whereby the Thr104Ile and Tyr108Cys mutations in the gonadotropin-releasing hormone receptor (GnRHR) gene cause hypogonadotropic hypogonadism in humans are unknown. Transient expression of Thr104Ile and Tyr108Cys mutants in COS-7 cells revealed that both GnRHR mutants neither bind nor respond to agonist. Removal of Lys191 rescued function of both mutants, while addition of a carboxyl-terminal targeting sequence only rescued function of the Thr104Ile mutant. Exposure to the pharmacoperone In3 rescued almost completely Thr104Ile mutant function to wild-type levels, whereas rescue was partial for the Tyr108Cys GnRHR. Additional mutations that block formation of bridges involving Cys108 showed that a Cys108-Cys200 disulfide bridge is the predominant moiety formed in the Tyr108Cys mutant. Thr104Ile and Tyr108Cys GnRHRs are misfolded structures whose function is rescuable by genetic and/or pharmacological strategies. The Tyr108Cys mutant forms an aberrant disulfide bridge that prevents formation of the required Cys14-Cys200 bridge essential for GnRHR plasma membrane expression.

A central feature of the lipid raft concept is the formation of cholesterol-rich lipid domains. The introduction of relatively rigid cholesterol molecules into fluid liquid-disordered (Ld) phospholipid bilayers can produce liquid-ordered (Lo) mixtures in which the rigidity of cholesterol causes partial ordering of the flexible hydrocarbon acyl chains of the phospholipids. Several lines of evidence support this concept, but direct structural information about Lo membranes is lacking. Here we present the structure of Lo membranes formed from cholesterol and dioleoylphosphatidylcholine (DOPC). Specific deuteration of the DOPC acyl-chain methyl groups and neutron diffraction measurements reveal an extraordinary disorder of the acyl chains of neat Ld DOPC bilayers. The disorder is so great that >20% of the methyl groups are in intimate contact with water in the bilayer interface. The ordering of the DOPC acyl chains by cholesterol leads to retraction of the methyl groups away from the interface. Molecular dynamics simulations based on experimental systems reveal asymmetric transbilayer distributions of the methyl groups associated with each bilayer leaflet.

The light-induced isomerization of the retinal from 11-cis to all-trans triggers changes in the conformation of visual rhodopsins that lead to the formation of the activated state, which is ready to interact with the G protein. To begin to understand how changes in the structure and dynamics of the retinal are transmitted to the protein, we performed molecular dynamics simulations of squid rhodopsin with 11-cis and all-trans retinal, and with two different force fields for describing the retinal molecule. The results indicate that structural rearrangements in the binding pocket, albeit small, propagate toward the cytoplasmic side of the protein, and affect the dynamics of internal water molecules. The sensitivity of the active-site interactions on the retinal force-field parameters highlights the coupling between the retinal molecule and its immediate protein environment.

The carboxyl-terminal segment of G protein-coupled receptors has one or more conserved cysteine residues that are potential sites for palmitoylation. This posttranslational modification contributes to membrane association, internalization, and membrane targeting of proteins. In contrast to other members of the glycoprotein hormone receptor family (the LH and thyroid-stimulating hormone receptors), it is not known whether the follicle-stimulating hormone receptor (FSHR) is palmitoylated and what are the effects of abolishing its potential palmitoylation sites. In the present study, a functional analysis of the FSHR carboxyl-terminal segment cysteine residues was carried out. We constructed a series of mutant FSHRs by substituting cysteine residues with alanine, serine, or threonine individually and together at positions 629 and 655 (conserved cysteines) and 627 (nonconserved). The results showed that all three cysteine residues are palmitoylated but that only modification at Cys629 is functionally relevant. The lack of palmitoylation does not appear to greatly impair coupling to G(s) but, when absent at position 629, does significantly impair cell surface membrane expression of the partially palmitoylated receptor. All FSHR Cys mutants were capable of binding agonist with the same affinity as the wild-type receptor and internalizing on agonist stimulation. Molecular dynamics simulations at a time scale of approximately 100 nsec revealed that replacement of Cys629 resulted in structures that differed significantly from that of the wild-type receptor. Thus, deviations from wild-type conformation may potentially contribute to the severe impairment in plasma membrane expression and the modest effects on signaling exhibited by the receptors modified in this particular position.

Membrane proteins perform important physiological functions since they act as sensors for extra-cellular stimuli and gates for transport and communication. However, the basic forces and principles that drive membrane protein folding and assembly remain elusive. The key to the thermodynamic stability of membrane proteins is the complex physiochemical environment of the lipid bilayer. At the most basic level the hydrophobic core of the bilayer has been used to develop hydrophobicity scales that can identify putative transmembrane helices in membrane proteins. Recent refinements have utilized the realization that different amino acid types have strong preferences for particular insertion depths along the membrane normal, allowing a more detailed prediction and differentiation of buried, interfacial, and loop segments.However, prediction of beta-barrel membrane protein segments has so far resisted this analysis. This was primarily due to a lack of sufficient high resolution structures. Here we extend a method previously developed and successfully applied to alpha-helical membrane proteins to beta-barrels. We report the distribution of amino acids along the membrane normal for beta-barrels and compare the differences to alpha-helical proteins. For both protein types membrane interfaces are dominated by small residues such as glycine, alanine, and serine. Charged residues displayed non-symmetric distributions with charged residues generally preferring the intracellular interface. This effect was more prominent for Arg and Lys resulting in a direct confirmation of the positive inside rule. Even though there are many similarities the overall distributions are remarkably different between alpha and beta proteins, with beta-barrels displaying a much narrower hydrophobic core. We confirm that hydrophobic residues are the main driving force behind membrane protein insertion, while polar, charged and aromatic residues were found to be important for the correct orientation of the helix inside the membrane.

Xanthorhodopsin (xR), a light-driven proton pump, is unique among the rhodopsin family because it contains not one, but two strongly interacting chromophores, the retinal and a carotenoid. The carotenoid is bound to the protein and acts as a light-harvesting antenna, transferring energy to the retinal with ∼40% quantum efficiency (Balashov et al., Science309, 2005). Unlike photosynthetic complexes in which excitation energy transfer (EET) occurs from a large collection of antennas to a reaction center, the EET in xR occurs directly between the retinal and a single bound carotenoid. Thus, xR serves as a simple (and computationally accessible, albeit challenging) model system for understanding EET in light-harvesting systems. Here, we present the results of long (aggregate length > 350 ns) classical molecular dynamics (MD) simulations, starting from the x-ray crystal structure of xR (Luecke et al., PNAS 105, 2008), coupled with single-point quantum mechanical (DFT) calculations performed on hundreds of simulation snapshots, to address two points. First, because the resolution of the crystal structure is not sufficiently high to resolve protons, the protonation state of the counterion complex (specifically, the His62-Asp96 pair) is unknown, so we ran four MD simulations in parallel, each with a different combination of protonation states for the His-Asp pair. The MD simulations, as well as DFT calculations of the retinal excited state energies, identify a single state that is most consistent with experimental data. Second, we probe the effects of small structural changes, which occur within the context of a thermally disordered lipid (POPC) bilayer, on the retinal excitation energies, and we conclude that the environment could play an important role in the EET between the bound carotenoid and the retinal.

Diabetes mellitus is one of the most common diseases in the world. Currently around 3% of the global population suffers from diabetes and this is expected to double by 2030. During hyperglycemic episodes, protein glycation may occur on lysine residues. Decrease of biological activity as a direct effect of glycation has been shown on calmodulin, superoxide dismutase and calcium ATPase on human erythrocytes. In this work, we evaluated the structural and dynamical effects due to lysine glycation on human acetylcholinesterase and butyrylcholinesterase. Four probable sites were tested and analyzed for each cholinesterase by molecular dynamics simulations, using the CHARMM27 forcefield in NAMD at 298K, for 25ns on each model. The cumulative effect of each site was studied comparing it to the native, unglycated protein structure. The structural and dynamic consequences due to lysine glycation on the conformation of the choline binding site are reported.Funding: Macroproyecto de Tecnologias de la Informacion y la Computacion (UNAM), Centro Nacional de Supercomputo (IPICYT), Supercomputadora Aitzaloa (UAM). Postdoctoral Funding (CONACYT).

Understanding the mechanism of G-protein coupled receptors action is of major interest for drug design. The visual rhodopsin is the prototype structure for the family A of G-protein coupled receptors. Upon photoisomerization of the covalently bound retinal chromophore, visual rhodopsins undergo a large-scale conformational change that prepares the receptor for a productive interaction with the G-protein. The mechanism by which the local perturbation of the retinal cis-trans isomerization is transmitted throughout the protein is not well understood. The crystal structure of the visual rhodopsin from squid solved recently suggests that a chain of water molecules extending from the retinal toward the cytoplasmic side of the protein may play a role in the signal transduction from the all-trans retinal geometry to the activated receptor. As a first step toward understanding the role of water in rhodopsin function, we performed a molecular dynamics simulation of squid rhodopsin embedded in a hydrated bilayer of polyunsaturated lipid molecules. The simulation indicates that the water molecules present in the crystal structure participate in favorable interactions with side chains in the interhelical region and form a persistent hydrogen-bond network in connecting Y315 to W274 via D80.

The structural similarity between many G-protein coupled receptors and their extraordinary relevance for drug development sparks significant interest in their activation mechanism and dynamics. Rhodopsins play an especially important role in experimental studies, because their activation can be triggered in a very controlled way via photoexcitation of the covalently bound cofactor retinal.The successful crystallization of intermediates along the pathway to activation, which were trapped using low temperatures and specific lipid environments, provides a detailed view of some of the initial steps occurring on the picosecond to nanosecond timescale. However, structural information for later intermediates, appearing on the microsecond to millisecond timescale, is still limited.Developments of new computational platforms now allow the challenging timescale ranging from 1-10 microseconds to be explored with atomistic computer simulations. Here we report on a set of molecular dynamics simulations of squid rhodopsin for which crystal structures of activation intermediates have begun to be available recently (e.g., 3AYM in the PDB). Our simulations start from a model of the batho state right after the photoexcitation and describe the structural evolution over a timescale of 5.5 microseconds, allowing us to observe the formation of the meta-I preactivated state featuring significant deformations of helices V and VI. Besides obtaining structural information, observing the dynamics of the structural transitions allows us to identify a reaction coordinate for the activation mechanism. By comparing simulations with different force field parameters for the retinal cofactor, we also obtain additional information on the coupling of specific degrees of freedom of the retinal to the rest of protein.This work was supported by the NSF (grant CHE-0750175). We are grateful for an allocation of computer time on Anton at the Pittsburgh Supercomputing Center (supported by the NIH).