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1.
J Chem Phys ; 160(14)2024 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-38591687

RESUMO

The pervasive presence of nanoplastics (NPs) in the environment has gained increasing attention due to their accumulation in living organisms. These emerging contaminants inevitably interact with extracellular polymeric substances along respiratory or gastrointestinal tracts, and diverse organic coating on the surface of NPs, known as bio- or eco-corona, is formed. Although its impact on altering the NP properties and potential cell internalization has been extensively examined, studies on its role in NP partitioning in the cell membrane are elusive yet. In this work, molecular dynamics is used to investigate the formation of chitosan (CT) corona centered on a polyvinyl chloride (PVC) nanoparticle and the uptake of the resulting complex onto lipid membranes. Coarse-grained models compatible with the newly developed Martini 3.0 force field are implemented for the two polymers employing the atomistic properties as targets in the parameterization. The reliability of the coarse-grained polymer models is demonstrated by reproducing the structural properties of the PVC melt and of solvated CT strands, as well as by determining the conformation adopted by the latter at the NP surface. Results show that the spontaneous binding of CT chains of high and intermediate protonation degrees led to the formation of soft and hard corona that modulates the interaction of PVC core with model membranes. The structural changes of the corona adsorbed at the lipid-water interface enable a subsequent transfer of the NP to the center of the saturated lipid membranes and a complete or partial transition to a snorkel conformation depending on the hydrophilic/hydrophobic balance in the CT-PVC complex. Overall, the computational investigation of the coarse-grained model system provides implications for understanding how the eco-corona development influences the uptake and implicit toxicology of NPs.


Assuntos
Bicamadas Lipídicas , Nanopartículas , Bicamadas Lipídicas/química , Cloreto de Polivinila , Reprodutibilidade dos Testes , Nanopartículas/química , Carboidratos
2.
Biochem Biophys Res Commun ; 709: 149806, 2024 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-38579619

RESUMO

Differential Scanning Calorimetry (DSC) is a central technique in investigating drug - membrane interactions, a critical component of pharmaceutical research. DSC measures the heat difference between a sample of interest and a reference as a function of temperature or time, contributing essential knowledge on the thermally induced phase changes in lipid membranes and how these changes are affected by incorporating pharmacological substances. The manuscript discusses the use of phospholipid bilayers, which can form structures like unilamellar and multilamellar vesicles, providing a simplified yet representative membrane model to investigate the complex dynamics of how drugs interact with and penetrate cellular barriers. The manuscript consolidates data from various studies, providing a comprehensive understanding of the mechanisms underlying drug - membrane interactions, the determinants that influence these interactions, and the crucial role of DSC in elucidating these components. It further explores the interactions of specific classes of drugs with phospholipid membranes, including non-steroidal anti-inflammatory drugs, anticancer agents, natural products with antioxidant properties, and Alzheimer's disease therapeutics. The manuscript underscores the critical importance of DSC in this field and the need for continued research to improve our understanding of these interactions, acting as a valuable resource for researchers.


Assuntos
Antineoplásicos , Bicamadas Lipídicas , Varredura Diferencial de Calorimetria , Bicamadas Lipídicas/química , Fosfolipídeos/química , Membranas Artificiais , Lipossomos/química
3.
Langmuir ; 40(15): 8248-8259, 2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38578277

RESUMO

A model bilayer of the outer membrane (OM) of Gram-negative bacteria, composed of lipid A and 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE), was assembled on the ß-Tg modified gold (111) single crystal surface using a combination of Langmuir-Blodgett and Langmuir-Schaefer transfer. Electrochemical and spectroscopic methods were employed to study the properties of the model bilayer and its interaction with polymyxin. The model bilayer is stable on the gold surface in the transmembrane potential region between 0.0 and -0.7 V. The presence of Mg2+ coordinates with the phosphate and carboxylate groups in the leaflet of lipid A and stabilizes the structure of the model bilayer. Polymyxin causes the model bilayer leakage and damage in the transmembrane potential region between 0.2 and -0.4 V. At transmembrane potentials lower than -0.5 V, polymyxin does not affect the membrane integrity. Polymyxin binds to the phosphate and carboxylate groups in lipid A molecules and causes the increase of the tilt angle of acyl chains and the decrease of the tilt of the C═O bond. The results in this paper indicate that the antimicrobial activity of polymyxin depends on the transmembrane potential at the model bilayer and provides useful information for the development of new antibiotics.


Assuntos
Antibacterianos , Bicamadas Lipídicas , Antibacterianos/farmacologia , Bicamadas Lipídicas/química , Lipídeo A , Polimixinas/farmacologia , Bactérias Gram-Negativas , Ouro/química , Fosfatos
4.
Langmuir ; 40(15): 7883-7895, 2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38587263

RESUMO

N-Acylated amino acids and neurotransmitters in mammals exert significant biological effects on the nervous system, immune responses, and vasculature. N-Acyl derivatives of γ-aminobutyric acid (N-acyl GABA), which belong to both classes mentioned above, are prominent among them. In this work, a homologous series of N-acyl GABAs bearing saturated N-acyl chains (C8-C18) have been synthesized and characterized with respect to self-assembly, thermotropic phase behavior, and supramolecular organization. Differential scanning calorimetric studies revealed that the transition enthalpies and entropies of N-acyl GABAs are linearly dependent on the acyl chain length. The crystal structure of N-tridecanoyl GABA showed that the molecules are packed in bilayers with the acyl chains aligned parallel to the bilayer normal and that the carboxyl groups from opposite layers associate to form dimeric structures involving strong O-H···O hydrogen bonds. In addition, N-H···O and C-H···O hydrogen bonds between amide moieties of adjacent molecules within each layer stabilize the molecular packing. Powder X-ray diffraction studies showed odd-even alternation in the d spacings, suggesting that the odd chain and even chain compounds pack differently. Equimolar mixtures of N-palmitoyl GABA and dipalmitoylphosphatidylcholine (DPPC) were found to form stable unilamellar vesicles with diameters of ∼300-340 nm, which could encapsulate doxorubicin, an anticancer drug, with higher efficiency and better release characteristics than DPPC liposomes at physiologically relevant pH. These liposomes exhibit faster release of doxorubicin at acidic pH (<7.0), indicating their potential utility as drug carriers in cancer chemotherapy.


Assuntos
1,2-Dipalmitoilfosfatidilcolina , Lipossomos , Animais , 1,2-Dipalmitoilfosfatidilcolina/química , Termodinâmica , Doxorrubicina , Ácido gama-Aminobutírico , Varredura Diferencial de Calorimetria , Bicamadas Lipídicas/química , Mamíferos
5.
Proc Natl Acad Sci U S A ; 121(17): e2319476121, 2024 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-38621120

RESUMO

Glycerophospholipids are synthesized primarily in the cytosolic leaflet of the endoplasmic reticulum (ER) membrane and must be equilibrated between bilayer leaflets to allow the ER and membranes derived from it to grow. Lipid equilibration is facilitated by integral membrane proteins called "scramblases." These proteins feature a hydrophilic groove allowing the polar heads of lipids to traverse the hydrophobic membrane interior, similar to a credit card moving through a reader. Nevertheless, despite their fundamental role in membrane expansion and dynamics, the identity of most scramblases has remained elusive. Here, combining biochemical reconstitution and molecular dynamics simulations, we show that lipid scrambling is a general feature of protein insertases, integral membrane proteins which insert polypeptide chains into membranes of the ER and organelles disconnected from vesicle trafficking. Our data indicate that lipid scrambling occurs in the same hydrophilic channel through which protein insertion takes place and that scrambling is abolished in the presence of nascent polypeptide chains. We propose that protein insertases could have a so-far-overlooked role in membrane dynamics as scramblases.


Assuntos
Proteínas de Membrana , Peptídeos , Membrana Celular/metabolismo , Proteínas de Membrana/metabolismo , Peptídeos/metabolismo , Membranas/metabolismo , Lipídeos , Bicamadas Lipídicas/química
6.
Biophys Chem ; 309: 107231, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38569455

RESUMO

Nanodisc technology is increasingly being used in structural, biochemical and biophysical studies of membrane proteins. The computational approaches have revealed many important features of nanodisc assembly, structures and dynamics. Therefore, we reviewed the application of computational approaches, especially molecular modeling and molecular dyncamics (MD) simulations, to characterize nanodiscs, including the structural models, assembly and disassembly, protocols for modeling, structural properties and dynamics, and protein-lipid interactions in nanodiscs. More amazing computational studies about nanodiscs are looked forward to in the future.


Assuntos
Nanoestruturas , Nanoestruturas/química , Bicamadas Lipídicas/química , Proteínas de Membrana/química , Modelos Moleculares
7.
Biophys Chem ; 309: 107233, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38579435

RESUMO

Emodin is a natural anthraquinone derivative found in nature, widely known as an herbal medicine. Here, the partition, location, and interaction of emodin with lipid membranes of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) are experimentally investigated with different techniques. Our studies have considered the neutral form of emodin (EMH) and its anionic/deprotonated form (EM-), and their interaction with a more and less packed lipid membrane, DMPC at the gel and fluid phases, respectively. Though DSC results indicate that the two species, EMH and EM-, similarly disrupt the packing of DMPC bilayers, spin labels clearly show that EMH causes a stronger bilayer disruption, both in gel and fluid DMPC. Fluorescence spectroscopy shows that both EMH and EM- have a high affinity for DMPC: the binding of EM- to both gel and fluid DMPC bilayers was found to be quite similar, and similar to that of EMH to gel DMPC, Kp = (1.4 ± 0.3)x103. However, EMH was found to bind twice more strongly to fluid DMPC bilayers, Kp = (3.2 ± 0.3)x103. Spin labels and optical absorption spectroscopy indicate that emodin is located close to the lipid bilayer surface, and suggest that EM- is closer to the lipid/water interface than EMH, as expected. The present studies present a relevant contribution to the current understanding of the effect the two species of emodin, EMH and EM-, present on different microregions of an organism, as local pH values can vary significantly, can cause in a neutral lipid membrane, either more or less packed, liked gel and fluid DMPC, respectively, and could be extended to lipid domains of biological membranes.


Assuntos
Emodina , Dimiristoilfosfatidilcolina/química , Bicamadas Lipídicas/química , Marcadores de Spin
8.
J Phys Chem B ; 128(16): 3833-3843, 2024 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-38603528

RESUMO

The construction of the stratum corneum (SC) is crucial to the problems of transdermal drug delivery. SC consists of the keratinocyte layers and the lipid matrix surrounding it. Among them, the lipid matrix is the barrier for many exogenous molecules, mainly composed of ceramides (CERs), free fatty acids (FFA), and cholesterol (CHOL). In this work, we developed single-component (CERs, CER-NS, and CER-EOS) and six three-component models, and each model was simulated by using the GROMOS-54A7 force field. Short-period phase (SPP) and long-period phase (LPP) systems were established separately, and area per lipid (APL), thickness, order of carbon chain (SCD), and density distribution were analyzed. The transition of CER-NS and CER-EOS in LPP was observed. The results of hydrogen bonds in the lipid systems indicated that a strong hydrogen-bond network was formed between the skin-lipid bilayers. Umbrella sampling method simulations were performed to calculate the free energy change of ethanol moving into the skin-lipid bilayer. The results revealed that ethanol molecules pulled some water molecules into the membrane when they passed through SPP-1. Our findings provided some insights and models of the stratum corneum that could be used for the subsequent mechanism of macromolecule permeation through membranes in drugs, cosmetics, and so on.


Assuntos
Ceramidas , Bicamadas Lipídicas , Simulação de Dinâmica Molecular , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Ceramidas/química , Ceramidas/metabolismo , Ligação de Hidrogênio , Colesterol/química , Colesterol/metabolismo , Epiderme/metabolismo , Epiderme/química , Etanol/química , Ácidos Graxos não Esterificados/química , Ácidos Graxos não Esterificados/metabolismo , Pele/metabolismo , Pele/química , Humanos
9.
Nat Commun ; 15(1): 3162, 2024 Apr 11.
Artigo em Inglês | MEDLINE | ID: mdl-38605024

RESUMO

The organization of membrane proteins between and within membrane-bound compartments is critical to cellular function. Yet we lack approaches to regulate this organization in a range of membrane-based materials, such as engineered cells, exosomes, and liposomes. Uncovering and leveraging biophysical drivers of membrane protein organization to design membrane systems could greatly enhance the functionality of these materials. Towards this goal, we use de novo protein design, molecular dynamic simulations, and cell-free systems to explore how membrane-protein hydrophobic mismatch could be used to tune protein cotranslational integration and organization in synthetic lipid membranes. We find that membranes must deform to accommodate membrane-protein hydrophobic mismatch, which reduces the expression and co-translational insertion of membrane proteins into synthetic membranes. We use this principle to sort proteins both between and within membranes, thereby achieving one-pot assembly of vesicles with distinct functions and controlled split-protein assembly, respectively. Our results shed light on protein organization in biological membranes and provide a framework to design self-organizing membrane-based materials with applications such as artificial cells, biosensors, and therapeutic nanoparticles.


Assuntos
Células Artificiais , Proteínas de Membrana , Membrana Celular/metabolismo , Membranas/metabolismo , Proteínas de Membrana/metabolismo , Lipossomos , Bicamadas Lipídicas/química
10.
J Phys Chem B ; 128(16): 3885-3897, 2024 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-38622775

RESUMO

Very few drugs have the necessary physicochemical properties to cross the skin's main permeability barrier, the stratum corneum (SC), in sufficient amounts. Propylene glycol (PG) is a chemical penetration enhancer that could be included in topical formulations in order to overcome the barrier properties of the skin and facilitate the transport of drugs across it. Experiments have demonstrated that PG increases the mobility and disorder of SC lipids and may extract cholesterol from the SC, but little is known about the molecular mechanisms of drug permeation enhancement by PG. In this work, we have performed molecular dynamics (MD) simulations to investigate the molecular-level effects of PG on the structure and properties of model SC lipid bilayers. The model bilayers were simulated in the presence of PG concentrations over the range of 0-100% w/w PG, using both an all-atom and a united atom force field. PG was found to localize in the hydrophilic headgroup regions at the bilayer interface, to occupy the lipid-water hydrogen-bonding sites, and to slightly increase lipid tail disorder in a concentration-dependent manner. We showed with MD simulation that PG enhances the permeation of small molecules such as water by interacting with the bilayer interface; the results of our study may be used to guide the design of formulations for transdermal drug delivery with enhanced skin permeation, as well as topical formulations and cosmetic products.


Assuntos
Bicamadas Lipídicas , Simulação de Dinâmica Molecular , Propilenoglicol , Pele , Propilenoglicol/química , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Pele/metabolismo , Pele/química , Ligação de Hidrogênio , Absorção Cutânea/efeitos dos fármacos
11.
ACS Appl Mater Interfaces ; 16(15): 18422-18433, 2024 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-38573069

RESUMO

DNA nanopores have emerged as powerful tools for molecular sensing, but the efficient insertion of large DNA nanopores into lipid membranes remains challenging. In this study, we investigate the potential of cell-penetrating peptides (CPPs), specifically SynB1 and GALA, to enhance the insertion efficiency of large DNA nanopores. We constructed SynB1- or GALA-functionalized DNA nanopores with an 11 nm inner diameter and visualized and quantified their membrane insertion using a TIRF microscopy-based single-liposome assay. The results demonstrated that incorporating an increasing number of SynB1 or GALA peptides into the DNA nanopore significantly enhanced the membrane perforation. Kinetic analysis revealed that the DNA nanopore scaffold played a role in prearranging the CPPs, which facilitated membrane interaction and pore formation. Notably, the use of pH-responsive GALA peptides allowed highly efficient and pH-controlled insertion of large DNA pores. Furthermore, single-channel recording elucidated that the insertion process of single GALA-modified nanopores into planar lipid bilayers was dynamic, likely forming transient large toroidal pores. Overall, our study highlights the potential of CPPs as insertion enhancers for DNA nanopores, which opens avenues for improved molecule sensing and the controlled release of cargo molecules.


Assuntos
Peptídeos Penetradores de Células , Nanoporos , Cinética , DNA/química , Bicamadas Lipídicas/química
12.
J Chem Inf Model ; 64(8): 3430-3442, 2024 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-38588472

RESUMO

Peptide dendrimers are a type of branched, symmetric, and topologically well-defined molecule that have already been used as delivery systems for nucleic acid transfection. Several of the most promising sequences showed high efficiency in many key steps of transfection, namely, binding siRNA, entering cells, and evading the endosome. However, small changes to the peptide dendrimers, such as in the hydrophobic core, the amino acid chirality, or the total available charges, led to significantly different experimental results with unclear mechanistic insights. In this work, we built a computational model of several of those peptide dendrimers (MH18, MH13, and MH47) and some of their variants to study the molecular details of the structure and function of these molecules. We performed CpHMD simulations in the aqueous phase and in interaction with a lipid bilayer to assess how conformation and protonation are affected by pH in different environments. We found that while the different peptide dendrimer sequences lead to no substantial structural differences in the aqueous phase, the total charge and, more importantly, the total charge density are key for the capacity of the dendrimer to interact and destabilize the membrane. These dendrimers become highly charged when the pH changes from 7.5 to 4.5, and the presence of a high charge density, which is decreased for MH47 that has four fewer titratable lysines, is essential to trigger membrane destabilization. These findings are in excellent agreement with the experimental data and help us to understand the high efficiency of some dendrimers and why the dendrimer MH47 is unable to complete the transfection process. This evidence provides further understanding of the mode of action of these peptide dendrimers and will be pivotal for the future design of new sequences with improved transfection capabilities.


Assuntos
Dendrímeros , Endossomos , Peptídeos , Dendrímeros/química , Endossomos/metabolismo , Peptídeos/química , Peptídeos/metabolismo , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Simulação de Dinâmica Molecular , Concentração de Íons de Hidrogênio , Eletricidade Estática , Modelos Moleculares
13.
Phys Chem Chem Phys ; 26(16): 12552-12563, 2024 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-38595108

RESUMO

Ganglioside GM1 is a class of glycolipids predominantly located in the nervous system. Comprising a ceramide anchor and an oligosaccharide chain containing sialic acid, GM1 plays a pivotal role in various cellular processes, including signal transduction, cell adhesion, and membrane organization. Moreover, GM1 has been implicated in the pathogenesis of several neurological disorders, such as Parkinson's disease, Alzheimer's disease, and stroke. In this study, by creating a neural cell model membrane simulation system and employing rigorous molecular models, we utilize a coarse-grained molecular dynamics approach to explore the structural and dynamic characteristics of multi-component neuronal plasma membranes at varying GM1 ganglioside concentrations. The simulation results reveal that as GM1 concentration increases, a greater number of hydrogen bonds form between GM1 molecules, resulting in the formation of larger clusters, which leads to reduced membrane fluidity, increased lipid ordering, decreased membrane thickness and surface area and higher levels of GM1 dissociation. Through a meticulous analysis, while considering GM1's structural attributes, we offer valuable insights into the structural and dynamic traits of the cell membrane. This study provides a robust methodology for exploring membrane characteristics and enhances our comprehension of GM1 molecules, serving as a resource for both experimental and computational researchers in this field.


Assuntos
Membrana Celular , Gangliosídeo G(M1) , Simulação de Dinâmica Molecular , Gangliosídeo G(M1)/química , Gangliosídeo G(M1)/metabolismo , Membrana Celular/química , Membrana Celular/metabolismo , Ligação de Hidrogênio , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo
14.
J Phys Chem B ; 128(15): 3652-3661, 2024 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-38576273

RESUMO

Many pharmaceutical drugs are known to interact with lipid membranes through nonspecific molecular interactions, which affect their therapeutic effect. Ibuprofen is a nonsteroidal anti-inflammatory drug (NSAID) and one of the most commonly prescribed. In the presence of cholesterol, lipid bilayers can separate into nanoscale liquid-disordered and liquid-ordered structures, the latter known as lipid rafts. Here, we study spin-labeled ibuprofen (ibuprofen-SL) in the model membrane consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and cholesterol in the molar ratio of (0.5-0.5xchol)/(0.5-0.5xchol)/xchol. Electron paramagnetic resonance (EPR) spectroscopy is employed, along with its pulsed version of double electron-electron resonance (DEER, also known as PELDOR). The data obtained indicate lateral lipid-mediated clustering of ibuprofen-SL molecules with a local surface density noticeably larger than that expected for random lateral distribution. In the absence of cholesterol, the data can be interpreted as indicating alternating clustering in two opposing leaflets of the bilayer. In the presence of cholesterol, for xchol ≥ 20 mol %, the results show that ibuprofen-SL molecules have a quasi-regular lateral distribution, with a "superlattice" parameter of ∼3.0 nm. This regularity can be explained by the entrapment of ibuprofen-SL molecules by lipid rafts known to exist in this system with the additional assumption that lipid rafts have a nanoscale substructure.


Assuntos
Ibuprofeno , Bicamadas Lipídicas , Espectroscopia de Ressonância de Spin Eletrônica , Bicamadas Lipídicas/química , Colesterol/química , Microdomínios da Membrana , Fosfatidilcolinas/química
15.
J Phys Chem Lett ; 15(16): 4515-4522, 2024 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-38634827

RESUMO

Cholesterol-rich lipid rafts are found to facilitate membrane fusion, central to processes like viral entry, fertilization, and neurotransmitter release. While the fusion process involves local, transient membrane dehydration, the impact of reduced hydration on cholesterol's structural organization in biological membranes remains unclear. Here, we employ confocal fluorescence microscopy and atomistic molecular dynamics simulations to investigate cholesterol behavior in phase-separated lipid bilayers under controlled hydration. We unveiled that dehydration prompts cholesterol release from raft-like domains into the surrounding fluid phase. Unsaturated phospholipids undergo more significant dehydration-induced structural changes and lose more hydrogen bonds with water than sphingomyelin. The results suggest that cholesterol redistribution is driven by the equalization of biophysical properties between phases and the need to satisfy lipid hydrogen bonds. This underscores the role of cholesterol-phospholipid-water interplay in governing cholesterol affinity for a specific lipid type, providing a new perspective on the regulatory role of cell membrane heterogeneity during membrane fusion.


Assuntos
Colesterol , Bicamadas Lipídicas , Simulação de Dinâmica Molecular , Água , Colesterol/química , Colesterol/metabolismo , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Água/química , Água/metabolismo , Microdomínios da Membrana/química , Microdomínios da Membrana/metabolismo , Ligação de Hidrogênio , Esfingomielinas/química , Esfingomielinas/metabolismo , Fusão de Membrana , Fosfolipídeos/química , Fosfolipídeos/metabolismo
16.
J Chem Inf Model ; 64(8): 3360-3374, 2024 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-38597744

RESUMO

HIV-1 Vpr is a multifunctional accessory protein consisting of 96 amino acids that play a critical role in viral pathogenesis. Among its diverse range of activities, Vpr can create a cation-selective ion channel within the plasma membrane. However, the oligomeric state of this channel has not yet been elucidated. In this study, we investigated the conformational dynamics of Vpr helices to model the ion channel topology. First, we employed a series of multiscale simulations to investigate the specific structure of monomeric Vpr in a membrane model. During the lipid bilayer self-assembly coarse grain simulation, the C-terminal helix (residues 56-77) effectively formed the transmembrane region, while the N-terminal helix exhibited an amphipathic nature by associating horizontally with a single leaflet. All-atom molecular dynamics (MD) simulations of full-length Vpr inside a phospholipid bilayer show that the C-terminal helix remains very stable inside the bilayer core in a vertical orientation. Subsequently, using the predicted C-terminal helix orientation and conformation, various oligomeric states (ranging from tetramer to heptamer) possibly forming the Vpr ion channel were built and further evaluated. Among these models, the pentameric form exhibited consistent stability in MD simulations and displayed a compatible conformation for a water-assisted ion transport mechanism. This study provides structural insights into the ion channel activity of the Vpr protein and the foundation for developing therapeutics against HIV-1 Vpr-related conditions.


Assuntos
Canais Iônicos , Bicamadas Lipídicas , Simulação de Dinâmica Molecular , Produtos do Gene vpr do Vírus da Imunodeficiência Humana , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Produtos do Gene vpr do Vírus da Imunodeficiência Humana/química , Produtos do Gene vpr do Vírus da Imunodeficiência Humana/metabolismo , Canais Iônicos/química , Canais Iônicos/metabolismo , Conformação Proteica , HIV-1/química
17.
Sci Adv ; 10(16): eadk0217, 2024 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-38630809

RESUMO

Biological phenomena, from enzymatic catalysis to synaptic transmission, originate in the structural transformations of biomolecules and biomolecular assemblies in liquid water. However, directly imaging these nanoscopic dynamics without probes or labels has been a fundamental methodological challenge. Here, we developed an approach for "electron videography"-combining liquid phase electron microscopy with molecular modeling-with which we filmed the nanoscale structural fluctuations of individual, suspended, and unlabeled membrane protein nanodiscs in liquid. Systematic comparisons with biochemical data and simulation indicate the graphene encapsulation involved can afford sufficiently reduced effects of the illuminating electron beam for these observations to yield quantitative fingerprints of nanoscale lipid-protein interactions. Our results suggest that lipid-protein interactions delineate dynamically modified membrane domains across unexpectedly long ranges. Moreover, they contribute to the molecular mechanics of the nanodisc as a whole in a manner specific to the protein within. Overall, this work illustrates an experimental approach to film, quantify, and understand biomolecular dynamics at the nanometer scale.


Assuntos
Elétrons , Nanoestruturas , Proteínas de Membrana/química , Simulação de Dinâmica Molecular , Microscopia Eletrônica , Lipídeos/química , Bicamadas Lipídicas/química , Nanoestruturas/química
18.
Methods Enzymol ; 696: 25-42, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38658082

RESUMO

Solid-state nuclear magnetic resonance (NMR) methods can probe the motions of membrane proteins in liposomes at the atomic level, and propel the understanding of biomolecular processes for which static structures cannot provide a satisfactory description. High-resolution crystallography snapshots have provided a structural basis for fluoride channels. NMR is a powerful tool to build upon these snapshots and depict a dynamic picture of fluoride channels in native-like lipid bilayers. In this contribution, we discuss solid-state and solution NMR experiments to detect fluoride binding and transport by fluoride channels. Ongoing developments in membrane protein sample preparation and ssNMR methodology, particularly in using 1H, 19F and 13C-detection schemes, offer additional opportunities to study structure and functional aspects of fluoride channels.


Assuntos
Fluoretos , Fluoretos/química , Fluoretos/metabolismo , Proteínas de Membrana/química , Proteínas de Membrana/metabolismo , Ressonância Magnética Nuclear Biomolecular/métodos , Ligação Proteica , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Lipossomos/química , Lipossomos/metabolismo , Espectroscopia de Ressonância Magnética/métodos
19.
Chem Rev ; 124(6): 3284-3330, 2024 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-38498932

RESUMO

It is well-known that aqueous dispersions of phospholipids spontaneously assemble into bilayer structures. These structures have numerous applications across chemistry and materials science and form the fundamental structural unit of the biological membrane. The particular environment of the lipid bilayer, with a water-poor low dielectric core surrounded by a more polar and better hydrated interfacial region, gives the membrane particular biophysical and physicochemical properties and presents a unique environment for chemical reactions to occur. Many different types of molecule spanning a range of sizes, from dissolved gases through small organics to proteins, are able to interact with membranes and promote chemical changes to lipids that subsequently affect the physicochemical properties of the bilayer. This Review describes the chemical reactivity exhibited by lipids in their membrane form, with an emphasis on conditions where the lipids are well hydrated in the form of bilayers. Key topics include the following: lytic reactions of glyceryl esters, including hydrolysis, aminolysis, and transesterification; oxidation reactions of alkenes in unsaturated fatty acids and sterols, including autoxidation and oxidation by singlet oxygen; reactivity of headgroups, particularly with reactive carbonyl species; and E/Z isomerization of alkenes. The consequences of reactivity for biological activity and biophysical properties are also discussed.


Assuntos
Bicamadas Lipídicas , Lipídeos de Membrana , Lipídeos de Membrana/química , Bicamadas Lipídicas/química , Membrana Celular/metabolismo , Membranas/metabolismo , Fosfolipídeos/metabolismo , Alcenos/metabolismo
20.
J Oleo Sci ; 73(4): 547-562, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38556288

RESUMO

Physicochemical investigations on the inclusion of anionic polyamidoaminesuccinamic acid dendrimer, generation 5 (PAMAM-SA, G5) with positively charged hybrid vesicles (HCV), prepared using soylecithin, ion pair amphiphile (IPA), cholesterol and dihexadecyldimethylammonium bromide, were investigated by dynamic light scattering, transmission electron/atomic force microscopy (TEM/AFM), differential scanning calorimetry, fluorescence spectroscopy and surface pressure-time isotherm studies. Adsorption of dendrimer onto vesicle surface and subsequent bilayer disruption strongly depends on the bilayer composition and dendrimer concentration. Change in the zeta potential value with increasing dendrimer concentration suggests the dendrimer-vesicle interaction to be electrostatic in nature. AFM studies also confirm the adsorption of dendrimer as well as hole formation in the bilayer. Impact of the inclusion of dendrimer into the bilayer were further investigated through differential scanning calorimetry by monitoring the chain melting temperature and enthalpy of the chain melting processes. Dendrimer at low concentration does not alter bilayer integrity, while hole formations are noted at higher dendrimer concentration. Fluorescence anisotropy studies confirm the adsorption and subsequent bilayer disruption due to dendrimer inclusion. Dendrimer induced vesicle disintegration kinetics conclusively illustrate the transformation of cationic bilayer to monolayer and thereby exposing the role of IPA. In vitro cytotoxicity studies on PAMAM-SA, G5 and HCVs mixtures against human breast cancer cell line suggest that dendrimer-liposome aggregates (dendriosomes) exhibit substantial anticancer activities with insignificant side effects. It is expected that the dendriosomes may have application to host and deliver anticancer drug in the field of targeted drug delivery.


Assuntos
Dendrímeros , Humanos , Dendrímeros/química , Bicamadas Lipídicas/química , Lipossomos , Sistemas de Liberação de Medicamentos , Adsorção
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