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1.
Cell ; 170(1): 172-184.e11, 2017 Jun 29.
Artículo en Inglés | MEDLINE | ID: mdl-28648660

RESUMEN

Membrane scission is essential for intracellular trafficking. While BAR domain proteins such as endophilin have been reported in dynamin-independent scission of tubular membrane necks, the cutting mechanism has yet to be deciphered. Here, we combine a theoretical model, in vitro, and in vivo experiments revealing how protein scaffolds may cut tubular membranes. We demonstrate that the protein scaffold bound to the underlying tube creates a frictional barrier for lipid diffusion; tube elongation thus builds local membrane tension until the membrane undergoes scission through lysis. We call this mechanism friction-driven scission (FDS). In cells, motors pull tubes, particularly during endocytosis. Through reconstitution, we show that motors not only can pull out and extend protein-scaffolded tubes but also can cut them by FDS. FDS is generic, operating even in the absence of amphipathic helices in the BAR domain, and could in principle apply to any high-friction protein and membrane assembly.


Asunto(s)
Endocitosis , Proteínas de la Membrana/química , Proteínas de la Membrana/metabolismo , Aciltransferasas/química , Aciltransferasas/metabolismo , Animales , Fenómenos Biomecánicos , Fricción , Humanos , Metabolismo de los Lípidos , Dominios Proteicos , Ratas
2.
Cell ; 149(1): 137-45, 2012 Mar 30.
Artículo en Inglés | MEDLINE | ID: mdl-22464326

RESUMEN

Functioning as key players in cellular regulation of membrane curvature, BAR domain proteins bend bilayers and recruit interaction partners through poorly understood mechanisms. Using electron cryomicroscopy, we present reconstructions of full-length endophilin and its N-terminal N-BAR domain in their membrane-bound state. Endophilin lattices expose large areas of membrane surface and are held together by promiscuous interactions between endophilin's amphipathic N-terminal helices. Coarse-grained molecular dynamics simulations reveal that endophilin lattices are highly dynamic and that the N-terminal helices are required for formation of a stable and regular scaffold. Furthermore, endophilin accommodates different curvatures through a quantized addition or removal of endophilin dimers, which in some cases causes dimerization of endophilin's SH3 domains, suggesting that the spatial presentation of SH3 domains, rather than affinity, governs the recruitment of downstream interaction partners.


Asunto(s)
Aciltransferasas/metabolismo , Aciltransferasas/química , Aciltransferasas/genética , Aciltransferasas/ultraestructura , Animales , Membrana Celular/química , Membrana Celular/metabolismo , Microscopía por Crioelectrón , Modelos Moleculares , Proteínas del Tejido Nervioso/química , Proteínas del Tejido Nervioso/genética , Proteínas del Tejido Nervioso/metabolismo , Dominios y Motivos de Interacción de Proteínas , Estructura Terciaria de Proteína , Ratas
3.
Proc Natl Acad Sci U S A ; 121(4): e2313737121, 2024 Jan 23.
Artículo en Inglés | MEDLINE | ID: mdl-38241438

RESUMEN

Nuclear import and uncoating of the viral capsid are critical steps in the HIV-1 life cycle that serve to transport and release genomic material into the nucleus. Viral core import involves translocating the HIV-1 capsid at the nuclear pore complex (NPC). Notably, the central channel of the NPC appears to often accommodate and allow passage of intact HIV-1 capsid, though mechanistic details of the process remain to be fully understood. Here, we investigate the molecular interactions that operate in concert between the HIV-1 capsid and the NPC that regulate capsid translocation through the central channel. To this end, we develop a "bottom-up" coarse-grained (CG) model of the human NPC from recently released cryo-electron tomography structure and then construct composite membrane-embedded CG NPC models. We find that successful translocation from the cytoplasmic side to the NPC central channel is contingent on the compatibility of the capsid morphology and channel dimension and the proper orientation of the capsid approach to the channel from the cytoplasmic side. The translocation dynamics is driven by maximizing the contacts between phenylalanine-glycine nucleoporins at the central channel and the capsid. For the docked intact capsids, structural analysis reveals correlated striated patterns of lattice disorder likely related to the intrinsic capsid elasticity. Uncondensed genomic material inside the docked capsid augments the overall lattice disorder of the capsid. Our results suggest that the intrinsic "elasticity" can also aid the capsid to adapt to the stress and remain structurally intact during translocation.


Asunto(s)
Cápside , VIH-1 , Humanos , Cápside/metabolismo , VIH-1/genética , Poro Nuclear/metabolismo , Proteínas de la Cápside/genética , Transporte Activo de Núcleo Celular , Proteínas de Complejo Poro Nuclear/metabolismo , Translocación Genética , Elasticidad
4.
Proc Natl Acad Sci U S A ; 120(27): e2305899120, 2023 07 04.
Artículo en Inglés | MEDLINE | ID: mdl-37364095

RESUMEN

Microtubules (MTs) are large cytoskeletal polymers, composed of αß-tubulin heterodimers, capable of stochastically converting from polymerizing to depolymerizing states and vice versa. Depolymerization is coupled with hydrolysis of guanosine triphosphate (GTP) within ß-tubulin. Hydrolysis is favored in the MT lattice compared to a free heterodimer with an experimentally observed rate increase of 500- to 700-fold, corresponding to an energetic barrier lowering of 3.8 to 4.0 kcal/mol. Mutagenesis studies have implicated α-tubulin residues, α:E254 and α:D251, as catalytic residues completing the ß-tubulin active site of the lower heterodimer in the MT lattice. The mechanism for GTP hydrolysis in the free heterodimer, however, is not understood. Additionally, there has been debate concerning whether the GTP-state lattice is expanded or compacted relative to the GDP state and whether a "compacted" GDP-state lattice is required for hydrolysis. In this work, extensive quantum mechanics/molecular mechanics simulations with transition-tempered metadynamics free-energy sampling of compacted and expanded interdimer complexes, as well as a free heterodimer, have been carried out to provide clear insight into the GTP hydrolysis mechanism. α:E254 was found to be the catalytic residue in a compacted lattice, while in the expanded lattice, disruption of a key salt bridge interaction renders α:E254 less effective. The simulations reveal a barrier decrease of 3.8 ± 0.5 kcal/mol for the compacted lattice compared to a free heterodimer, in good agreement with experimental kinetic measurements. Additionally, the expanded lattice barrier was found to be 6.3 ± 0.5 kcal/mol higher than compacted, demonstrating that GTP hydrolysis is variable with lattice state and slower at the MT tip.


Asunto(s)
Microtúbulos , Tubulina (Proteína) , Guanosina Trifosfato , Tubulina (Proteína)/química , Hidrólisis , Guanosina Difosfato/química , Microtúbulos/química
5.
J Biol Chem ; : 107456, 2024 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-38866325

RESUMEN

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N) and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we used several lipid binding assays and found the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, we show lipid binding occurs in the N protein C-terminal domain, which is supported by extensive in silico analysis. We demonstrate anionic lipid binding occurs for both the free and N oligomeric forms, suggesting N can associate with membranes in the nucleocapsid form. Based on these results, we present a lipid-dependent model based on in vitro, cellular and in silico data for the recruitment of N to assembly sites in the lifecycle of SARS-CoV-2.

6.
Proc Natl Acad Sci U S A ; 119(10): e2117781119, 2022 03 08.
Artículo en Inglés | MEDLINE | ID: mdl-35238630

RESUMEN

SignificanceThe mature capsids of HIV-1 are transiently stable complexes that self-assemble around the viral genome during maturation, and uncoat to release preintegration complexes that archive a double-stranded DNA copy of the virus in the host cell genome. However, a detailed view of how HIV cores rupture remains lacking. Here, we elucidate the physical properties involved in capsid rupture using a combination of large-scale all-atom molecular dynamics simulations and cryo-electron tomography. We find that intrinsic strain on the capsid forms highly correlated patterns along the capsid surface, along which cracks propagate. Capsid rigidity also increases with high strain. Our findings provide fundamental insight into viral capsid uncoating.


Asunto(s)
Cápside/fisiología , VIH-1/fisiología , Desencapsidación Viral , Cápside/química , Proteínas de la Cápside/química , Línea Celular , Tomografía con Microscopio Electrónico/métodos , Humanos , Simulación de Dinámica Molecular , Conformación Proteica
7.
Biophys J ; 123(1): 42-56, 2024 01 02.
Artículo en Inglés | MEDLINE | ID: mdl-37978800

RESUMEN

During the HIV-1 assembly process, the Gag polyprotein multimerizes at the producer cell plasma membrane, resulting in the formation of spherical immature virus particles. Gag-genomic RNA (gRNA) interactions play a crucial role in the multimerization process, which is yet to be fully understood. We performed large-scale all-atom molecular dynamics simulations of membrane-bound full-length Gag dimer, hexamer, and 18-mer. The inter-domain dynamic correlation of Gag, quantified by the heterogeneous elastic network model applied to the simulated trajectories, is observed to be altered by implicit gRNA binding, as well as the multimerization state of the Gag. The lateral dynamics of our simulated membrane-bound Gag proteins, with and without gRNA binding, agree with prior experimental data and help to validate our simulation models and methods. The gRNA binding is observed to affect mainly the SP1 domain of the 18-mer and the matrix-capsid linker domain of the hexamer. In the absence of gRNA binding, the independent dynamical motion of the nucleocapsid domain results in a collapsed state of the dimeric Gag. Unlike stable SP1 helices in the six-helix bundle, without IP6 binding, the SP1 domain undergoes a spontaneous helix-to-coil transition in the dimeric Gag. Together, our findings reveal conformational switches of Gag at different stages of the multimerization process and predict that the gRNA binding reinforces an efficient binding surface of Gag for multimerization, and also regulates the dynamic organization of the local membrane region itself.


Asunto(s)
Productos del Gen gag , VIH-1 , Productos del Gen gag del Virus de la Inmunodeficiencia Humana , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/química , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/metabolismo , Productos del Gen gag/química , Productos del Gen gag/genética , Productos del Gen gag/metabolismo , Genómica , VIH-1/metabolismo , ARN Viral/química , Ensamble de Virus
8.
Biophys J ; 2024 Jun 17.
Artículo en Inglés | MEDLINE | ID: mdl-38894540

RESUMEN

Actin filament networks are exposed to mechanical stimuli, but the effect of strain on actin filament structure has not been well established in molecular detail. This is a critical gap in understanding because the activity of a variety of actin-binding proteins has recently been determined to be altered by actin filament strain. We therefore used all-atom molecular dynamics simulations to apply tensile strains to actin filaments and find that changes in actin subunit organization are minimal in mechanically strained, but intact, actin filaments. However, a conformational change disrupts the critical D-loop to W-loop connection between longitudinal neighboring subunits, which leads to a metastable cracked conformation of the actin filament whereby one protofilament is broken prior to filament severing. We propose that the metastable crack presents a force-activated binding site for actin regulatory factors that specifically associate with strained actin filaments. Through protein-protein docking simulations, we find that 43 evolutionarily diverse members of the dual zinc-finger-containing LIM-domain family, which localize to mechanically strained actin filaments, recognize two binding sites exposed at the cracked interface. Furthermore, through its interactions with the crack, LIM domains increase the length of time damaged filaments remain stable. Our findings propose a new molecular model for mechanosensitive binding to actin filaments.

9.
Biophys J ; 2024 Mar 28.
Artículo en Inglés | MEDLINE | ID: mdl-38549372

RESUMEN

Phosphate, an essential metabolite involved in numerous cellular functions, is taken up by proton-coupled phosphate transporters of plants and fungi within the major facilitator family. Similar phosphate transporters have been identified across a diverse range of biological entities, including various protozoan parasites linked to human diseases, breast cancer cells with increased phosphate requirements, and osteoclast-like cells engaged in bone resorption. Prior studies have proposed an overview of the functional cycle of a proton-driven phosphate transporter (PiPT), yet a comprehensive understanding of the proposed reaction pathways necessitates a closer examination of each elementary reaction step within an overall kinetic framework. In this work, we leverage kinetic network modeling in conjunction with a "bottom-up" molecular dynamics approach to show how such an approach can characterize the proton-phosphate co-transport behavior of PiPT under different pH and phosphate concentration conditions. In turn, this allows us to reveal the prevailing reaction pathway within a high-affinity phosphate transporter under different experimental conditions and to uncover the molecular origin of the optimal pH condition of this transporter.

10.
Biophys J ; 123(3): 389-406, 2024 Feb 06.
Artículo en Inglés | MEDLINE | ID: mdl-38196190

RESUMEN

Although the structural rearrangement of the membrane-bound matrix (MA) protein trimers upon HIV-1 maturation has been reported, the consequences of MA maturation on the MA-lipid interactions are not well understood. Long-timescale molecular dynamics simulations of the MA multimeric assemblies of immature and mature virus particles with our realistic asymmetric membrane model have explored MA-lipid interactions and lateral organization of lipids around MA complexes. The number of stable MA-phosphatidylserine and MA-phosphatidylinositol 4,5-bisphosphate (PIP2) interactions at the trimeric interface of the mature MA complex is observed to be greater compared to that of the immature MA complex. Our simulations identified an alternative PIP2-binding site in the immature MA complex where the multivalent headgroup of a PIP2 lipid with a greater negative charge binds to multiple basic amino acid residues such as ARG3 residues of both the MA monomers at the trimeric interface and highly basic region (HBR) residues (LYS29, LYS31) of one of the MA monomers. Our enhanced sampling simulations have explored the conformational space of phospholipids at different binding sites of the trimer-trimer interface of MA complexes that are not accessible by conventional unbiased molecular dynamics. Unlike the immature MA complex, the 2' acyl tail of two PIP2 lipids at the trimeric interface of the mature MA complex is observed to sample stable binding pockets of MA consisting of helix-4 residues. Together, our results provide molecular-level insights into the interactions of MA trimeric complexes with membrane and different lipid conformations at the specific binding sites of MA protein before and after viral maturation.


Asunto(s)
VIH-1 , Simulación de Dinámica Molecular , VIH-1/metabolismo , Unión Proteica , Membranas/metabolismo , Lípidos , Membrana Celular/metabolismo
11.
J Am Chem Soc ; 146(2): 1612-1618, 2024 Jan 17.
Artículo en Inglés | MEDLINE | ID: mdl-38170906

RESUMEN

Amino acid ionic liquids (AAILs) are promising green materials for CO2 capture and conversion due to their large chemical structural tunability. However, the structural understanding of the AAILs underlying the CO2 reaction dynamics remains uncertain. Herein, we examine the steric effects of AAIL anions with various chemical structures on CO2 capture behavior. Based on ab initio free-energy sampling, we assess reaction mechanisms for carbamate formation via a two-step reaction pathway with a zwitterion intermediate undergoing dynamic proton transfer. Our results show that free-energy barriers for carbamate formation can be significantly reduced as the degree of steric hindrance of the anions decreases. Further analyses reveal that reduced steric hindrance of anions causes markedly stronger intermolecular interactions between zwitterion and anions, leading to an increased kinetically favorable intermolecular proton transfer for carbamate production. We also describe the correlation strength between intramolecular interactions within the zwitterion and intermolecular interactions between the zwitterion and anions. We conclude that the favored structural flexibility due to the less steric hindrance of the zwitterion leads to enhanced intermolecular interactions, facilitating proton transfer to nearby AAIL anions for carbamate formation. Our study provides invaluable insight into the influence of various degrees of steric hindrance of the AAIL anions governing CO2 chemisorption. These findings may aid in the design of optimal AAIL solvents for the CO2 capture process.

12.
J Am Chem Soc ; 146(15): 10342-10356, 2024 Apr 17.
Artículo en Inglés | MEDLINE | ID: mdl-38574341

RESUMEN

In acidic HZSM-5 zeolite, the reactivity of a methanol molecule interacting with the zeolite proton is amenable to modification via coadsorbing a stochiometric amount of an electron density donor E to form the [(E)(CH3OH)(HZ)] complex. The rate of the methanol in this complex undergoing dehydration to dimethyl ether was determined for a series of E with proton affinity (PA) ranging from 659 kJ mol-1 for C6F6 to 825 kJ mol-1 for C4H8O and was found to follow the expression: Ln(Rate) - Ln(RateN2) = ß(PA - PAN2)γ, where E = N2 is the reference and ß and γ are constants. This trend is probably due to the increased stability of the solvated proton in the [(E)(CH3OH)(HZ)] complex with increasing PA. Importantly, this is also observed in steady-state flow reactions when stoichiometric quantities of E are preadsorbed on the zeolite. As demonstrated with E being D2O, the effect on methanol reactivity diminishes when E is present in excess of the [(E)(CH3OH)(HZ)] complex. It is proposed that the methanol dehydration reaction involves [(E)(CH3OH)(CH3OH)(HZ)] as the transition state, which is supported by the isotopologue distribution of the initial dimethyl ether formed when a flow of CH3OH was passed over ZSM-5 containing one CD3OH per zeolite proton. The implication of this on the mechanism of catalytic methanol dehydration on HZSM-5 is discussed.

13.
Inorg Chem ; 63(24): 10897-10914, 2024 Jun 17.
Artículo en Inglés | MEDLINE | ID: mdl-38795015

RESUMEN

Contrast agents are important imaging probes in clinical MRI, allowing the identification of anatomic changes that otherwise would not be possible. Intensive research on the development of new contrast agents is being made to image specific pathological markers or sense local biochemical changes. The most widely used MRI contrast agents are based on gadolinium(III) complexes. Due to their very high charge density, they have low permeability through tight biological barriers such as the blood-brain barrier, hampering their application in the diagnosis of neurological disorders. In this study, we explore the interaction between the widely used contrast agent [Gd(DOTA)]- (Dotarem) and POPC lipid bilayers by means of molecular dynamics simulations. This metal complex is a standard reference where several chemical modifications have been introduced to improve key properties such as bioavailability and targeting. The simulations unveil detailed insights into the agent's interaction with the lipid bilayer, offering perspectives beyond experimental methods. Various properties, including the impact on global and local bilayer properties, were analyzed. As expected, the results indicate a low partition coefficient (KP) and high permeation barrier for this reference compound. Nevertheless, favorable interactions are established with the membrane leading to moderately long residence times. While coordination of one inner-sphere water molecule is maintained for the membrane-associated chelate, the physical-chemical attributes of [Gd(DOTA)]- as a MRI contrast agent are affected. Namely, increases in the rotational correlation times and in the residence time of the inner-sphere water are observed, with the former expected to significantly increase the water proton relaxivity. This work establishes a reference framework for the use of simulations to guide the rational design of new contrast agents with improved relaxivity and bioavailability and for the development of liposome-based formulations for use as imaging probes or theranostic agents.


Asunto(s)
Medios de Contraste , Membrana Dobles de Lípidos , Imagen por Resonancia Magnética , Simulación de Dinámica Molecular , Compuestos Organometálicos , Medios de Contraste/química , Imagen por Resonancia Magnética/métodos , Compuestos Organometálicos/química , Compuestos Organometálicos/síntesis química , Membrana Dobles de Lípidos/química , Fosfatidilcolinas/química , Compuestos Heterocíclicos
14.
Proc Natl Acad Sci U S A ; 118(49)2021 12 07.
Artículo en Inglés | MEDLINE | ID: mdl-34857630

RESUMEN

Water-assisted proton transport through confined spaces influences many phenomena in biomolecular and nanomaterial systems. In such cases, the water molecules that fluctuate in the confined pathways provide the environment and the medium for the hydrated excess proton migration via Grotthuss shuttling. However, a definitive collective variable (CV) that accurately couples the hydration and the connectivity of the proton wire with the proton translocation has remained elusive. To address this important challenge-and thus to define a quantitative paradigm for facile proton transport in confined spaces-a CV is derived in this work from graph theory, which is verified to accurately describe water wire formation and breakage coupled to the proton translocation in carbon nanotubes and the Cl-/H+ antiporter protein, ClC-ec1. Significant alterations in the conformations and thermodynamics of water wires are uncovered after introducing an excess proton into them. Large barriers in the proton translocation free-energy profiles are found when water wires are defined to be disconnected according to the new CV, even though the pertinent confined space is still reasonably well hydrated and-by the simple measure of the mere existence of a water structure-the proton transport would have been predicted to be facile via that oversimplified measure. In this paradigm, however, the simple presence of water is not sufficient for inferring proton translocation, since an excess proton itself is able to drive hydration, and additionally, the water molecules themselves must be adequately connected to facilitate any successful proton transport.


Asunto(s)
Transporte Iónico/fisiología , Protones , Agua/química , Antiportadores/metabolismo , Fenómenos Bioquímicos , Transporte Biológico/fisiología , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Modelos Teóricos , Simulación de Dinámica Molecular , Nanoestructuras , Nanotubos de Carbono , Termodinámica
15.
Proc Natl Acad Sci U S A ; 118(3)2021 01 19.
Artículo en Inglés | MEDLINE | ID: mdl-33397805

RESUMEN

The CA (capsid) domain of immature HIV-1 Gag and the adjacent spacer peptide 1 (SP1) play a key role in viral assembly by forming a lattice of CA hexamers, which adapts to viral envelope curvature by incorporating small lattice defects and a large gap at the site of budding. This lattice is stabilized by intrahexameric and interhexameric CA-CA interactions, which are important in regulating viral assembly and maturation. We applied subtomogram averaging and classification to determine the oligomerization state of CA at lattice edges and found that CA forms partial hexamers. These structures reveal the network of interactions formed by CA-SP1 at the lattice edge. We also performed atomistic molecular dynamics simulations of CA-CA interactions stabilizing the immature lattice and partial CA-SP1 helical bundles. Free energy calculations reveal increased propensity for helix-to-coil transitions in partial hexamers compared to complete six-helix bundles. Taken together, these results suggest that the CA dimer is the basic unit of lattice assembly, partial hexamers exist at lattice edges, these are in a helix-coil dynamic equilibrium, and partial helical bundles are more likely to unfold, representing potential sites for HIV-1 maturation initiation.


Asunto(s)
Proteínas de la Cápside/ultraestructura , Infecciones por VIH/genética , VIH-1/genética , Factor de Transcripción Sp1/ultraestructura , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/ultraestructura , Cápside/química , Cápside/ultraestructura , Proteínas de la Cápside/genética , Cristalografía por Rayos X , Infecciones por VIH/virología , Seropositividad para VIH , VIH-1/patogenicidad , VIH-1/ultraestructura , Humanos , Simulación de Dinámica Molecular , Multimerización de Proteína/genética , Proteolisis , Factor de Transcripción Sp1/química , Factor de Transcripción Sp1/genética , Virión/genética , Virión/patogenicidad , Ensamble de Virus/genética , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/química , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/genética
16.
Proc Natl Acad Sci U S A ; 118(25)2021 06 22.
Artículo en Inglés | MEDLINE | ID: mdl-34135124

RESUMEN

Phosphate is an indispensable metabolite in a wide variety of cells and is involved in nucleotide and lipid synthesis, signaling, and chemical energy storage. Proton-coupled phosphate transporters within the major facilitator family are crucial for phosphate uptake in plants and fungi. Similar proton-coupled phosphate transporters have been found in different protozoan parasites that cause human diseases, in breast cancer cells with elevated phosphate demand, in osteoclast-like cells during bone reabsorption, and in human intestinal Caco2BBE cells for phosphate homeostasis. However, the mechanism of proton-driven phosphate transport remains unclear. Here, we demonstrate in a eukaryotic, high-affinity phosphate transporter from Piriformospora indica (PiPT) that deprotonation of aspartate 324 (D324) triggers phosphate release. Quantum mechanics/molecular mechanics molecular dynamics simulations combined with free energy sampling have been employed here to identify the proton transport pathways from D324 upon the transition from the occluded structure to the inward open structure and phosphate release. The computational insights so gained are then corroborated by studies of D45N and D45E amino acid substitutions via mutagenesis experiments. Our findings confirm the function of the structurally predicted cytosolic proton exit tunnel and suggest insights into the role of the titratable phosphate substrate.


Asunto(s)
Basidiomycota/metabolismo , Proteínas Fúngicas/metabolismo , Proteínas de Transporte de Fosfato/metabolismo , Protones , Cristalografía por Rayos X , Citosol/metabolismo , Proteínas Fúngicas/química , Simulación de Dinámica Molecular , Mutagénesis , Proteínas de Transporte de Fosfato/química , Fosfatos/metabolismo , Conformación Proteica , Fuerza Protón-Motriz
17.
Biophys J ; 122(13): 2655-2674, 2023 07 11.
Artículo en Inglés | MEDLINE | ID: mdl-37218128

RESUMEN

In the late stages of the HIV-1 life cycle, membrane localization and self-assembly of Gag polyproteins induce membrane deformation and budding. Release of the virion requires direct interaction between immature Gag lattice and upstream ESCRT machinery at the viral budding site, followed by assembly of downstream ESCRT-III factors, culminating in membrane scission. However, molecular details of upstream ESCRT assembly dynamics at the viral budding site remain unclear. In this work, using coarse-grained (CG) molecular dynamics (MD) simulations, we investigated the interactions between Gag, ESCRT-I, ESCRT-II, and membrane to delineate the dynamical mechanisms by which upstream ESCRTs assemble templated by late-stage immature Gag lattice. We first systematically derived "bottom-up" CG molecular models and interactions of upstream ESCRT proteins from experimental structural data and extensive all-atom MD simulations. Using these molecular models, we performed CG MD simulations of ESCRT-I oligomerization and ESCRT-I/II supercomplex formation at the neck of the budding virion. Our simulations demonstrate that ESCRT-I can effectively oligomerize to higher-order complexes templated by the immature Gag lattice both in the absence of ESCRT-II and when multiple copies of ESCRT-II are localized at the bud neck. The ESCRT-I/II supercomplexes formed in our simulations exhibit predominantly columnar structures, which has important implications for the nucleation pathway of downstream ESCRT-III polymers. Importantly, ESCRT-I/II supercomplexes bound to Gag initiate membrane neck constriction by pulling the inner edge of the bud neck closer to the ESCRT-I headpiece ring. Our findings serve to elucidate a network of interactions between upstream ESCRT machinery, immature Gag lattice, and membrane neck that regulate protein assembly dynamics at the HIV-1 budding site.


Asunto(s)
VIH-1 , VIH-1/metabolismo , Productos del Gen gag/genética , Productos del Gen gag/metabolismo , Simulación de Dinámica Molecular , División Celular , Complejos de Clasificación Endosomal Requeridos para el Transporte/metabolismo
18.
Biophys J ; 122(6): 1068-1085, 2023 03 21.
Artículo en Inglés | MEDLINE | ID: mdl-36698313

RESUMEN

The triple glutamine (Q) mutant (QQQ) structure of a Cl-/H+ antiporter from Escherichia coli (ClC-ec1) displaying a novel backbone arrangement has been used to challenge the long-held notion that Cl-/H+ antiporters do not operate through large conformational motions. The QQQ mutant substitutes the glutamine residue for an external glutamate E148, an internal glutamate E203, and a third glutamate E113 that hydrogen-bonds with E203. However, it is unknown if QQQ represents a physiologically relevant state, as well as how the protonation of the wild-type glutamates relates to the global dynamics. We herein apply continuous constant-pH molecular dynamics to investigate the H+-coupled dynamics of ClC-ec1. Although any large-scale conformational rearrangement upon acidification would be due to the accumulation of excess charge within the protein, protonation of the glutamates significantly impacts mainly the local structure and dynamics. Despite the fact that the extracellular pore enlarges at acidic pHs, an occluded ClC-ec1 within the active pH range of 3.5-7.5 requires a protonated E148 to facilitate extracellular Cl- release. E203 is also involved in the intracellular H+ transfer as an H+ acceptor. The water wire connection of E148 with the intracellular solution is regulated by the charge states of the E113/E203 dyad with coupled proton titration. However, the dynamics extracted from our simulations are not QQQ-like, indicating that the QQQ mutant does not represent the behavior of the wild-type ClC-ec1. These findings reinforce the necessity of having a protonatable residue at the E203 position in ClC-ec1 and suggest that a higher level of complexity exists for the intracellular H+ transfer in Cl-/H+ antiporters.


Asunto(s)
Antiportadores , Proteínas de Escherichia coli , Antiportadores/genética , Antiportadores/metabolismo , Ácido Glutámico/química , Glutamina , Cloruros/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Protones , Canales de Cloruro/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo
19.
J Am Chem Soc ; 145(29): 15663-15667, 2023 Jul 26.
Artículo en Inglés | MEDLINE | ID: mdl-37439824

RESUMEN

Amino acid ionic liquids have received increasing attention as ideal candidates for the CO2 chemisorption process. However, the underlying molecular mechanisms, especially those involving proton transfer, remain unclear. In this work, we elucidate the atomistic-level reaction mechanisms responsible for carbamate formation during CO2 capture by amino acid ionic liquids through explicit ab initio molecular dynamics augmented by well-tempered metadynamics. The resulting ab initio free-energy sampling reveals a two-step reaction pathway in which a zwitterion, initially formed from the reaction between the anion of serine and CO2, undergoes a kinetically facile intermolecular proton transfer to the O atom of the COO- moiety in the nearby serine. Further analysis reveals that the significantly reduced free-energy barriers are attributed to enhanced intermolecular interaction between the zwitterion and serine, thus facilitating the kinetic favorability of the proton transfer, which governs the overall CO2 capture mechanism. This work provides valuable insight into the important mechanistic and kinetic features of these reactions from explicit condensed phase ab initio MD free-energy sampling of the CO2 capture process.

20.
Chem Rev ; 121(15): 9450-9501, 2021 08 11.
Artículo en Inglés | MEDLINE | ID: mdl-34213328

RESUMEN

The structure, chemistry, and charge of interfaces between materials and aqueous fluids play a central role in determining properties and performance of numerous water systems. Sensors, membranes, sorbents, and heterogeneous catalysts almost uniformly rely on specific interactions between their surfaces and components dissolved or suspended in the water-and often the water molecules themselves-to detect and mitigate contaminants. Deleterious processes in these systems such as fouling, scaling (inorganic deposits), and corrosion are also governed by interfacial phenomena. Despite the importance of these interfaces, much remains to be learned about their multiscale interactions. Developing a deeper understanding of the molecular- and mesoscale phenomena at water/solid interfaces will be essential to driving innovation to address grand challenges in supplying sufficient fit-for-purpose water in the future. In this Review, we examine the current state of knowledge surrounding adsorption, reactivity, and transport in several key classes of water/solid interfaces, drawing on a synergistic combination of theory, simulation, and experiments, and provide an outlook for prioritizing strategic research directions.

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