Search

We applied a new large two membrane model of human urea transporter B (UT-B) with urea concentration gradient between intracellular and extracellular solution to explore the structure and dynamics of urea permeation. The first solved human UT-B X-ray crystal structure (PDB 6QD5) was studied using atomistic force field based large scale molecular dynamics (MD) simulations. The urea binding sites in UT-B were identified by the combination of first principles molecular dynamics docking and hybrid steered molecular dynamics (hSMD). In the simulations, urea molecules bound to the two binding sites although urea molecules did not go through the channels. The potential of mean force (PMF) of urea along the channel was calculated by hSMD to investigate the selectivity of the urea permeation across the channel pore. The simulations provide an opportunity to explore the binding sites spontaneously to help understand the urea permeation gating and transportation mechanism. A clearer analysis of the selectivity filter is shown in more detail. We also furthered the research about small organic molecules in the specific environment, such as channels in this work. [ABSTRACT FROM AUTHOR]

Abstract The ubiquitous glucose transporter 1 (GLUT1) is physiologically and pathologically relevant in energy metabolism of the CNS, skeletal muscles, cancer cells etc. Extensive experiments on GLUT1 produced thorough understandings of its expressions, functions, and structures which were recently resolved to atomic accuracy. However, theoretical understandings are still controversial about how GLUT1 facilitates glucose diffusion across the cell membrane. Molecular dynamics (MD) simulations of the current literature have GLUT1 embedded in a symmetric bilayer of a single lipid type. They provide atomistic illustrations of the alternating access theory (AAT), but the simulation results are inconsistent with the undisputed experimental data of kinetics showing rapid transport of glucose at near-physiological temperatures, high Arrhenius activation barrier in zero-trans uptake, and large trans-acceleration at sub-physiological temperatures. In this research, we embedded GLUT1 in an asymmetric bilayer of multiple lipids to better mimic the erythrocyte membrane. We ran unbiased MD simulations at 37 °C and at 5 °C and found a new mechanism of glucose transport via GLUT1: The extracellular (EC) gate opened wide for EC glucopyranose at 37 °C and, only in the presence of intracellular (IC) glucose, at 5 °C. In the absence of IC glucose at 5 °C, the EC gate opened narrowly for acyclic glucose, gating out glucopyranose. This EC-gating mechanism is simpler than AAT and yet it well explains for the rapid glucose transport at near-physiological temperatures and large trans-acceleration at sub-physiological temperatures. It also explains why zero-trans uptake (involving the pyranose-to-aldehyde transformation) has an Arrhenius barrier ∼20 kcal/mol higher than the equilibrium exchange transport. Graphical abstract Image 1 Highlights • EC-gating activities found in unbiassed simulations of human GLUT1 in erythrocyte membrane. • EC-gating mechanism simpler than the alternating access mechanism for glucose transport. • EC-gate widely open for extracellular glucopyranose at physiological temperature. • EC-gating dependence on intracellular glucose at sub-physiological temperatures explaining full-range kinetics. [ABSTRACT FROM AUTHOR]

Glucose transporters (GLUTs), expressed in all types of human cells, are responsible for the uptake of sugars as the primary energy source for the normal functions of good cells and for the abnormal growth of cancer cells. The E. coli xylose permease (XylE), a homologue of human GLUTs, has been investigated more thoroughly than other major facilitator proteins in the current literature. In this paper, we present a molecular dynamics (MD) study of an all-atom model system to elucidate the atomistic details and the free-energy landscape along the path of binding a xylopyranose (XYP) from the extracellular space to the inside of the transporter protein XylE. From the MD simulations, the Gibbs free energy of binding was found to be − 4.4 kcal/mol in agreement with the experimental value of − 4.7 kcal/mol. The accuracy of our study is further shown in the computed hydration energy of XYP of − 14.6 kcal/mol in comparison with the experimental data of − 15.0 kcal/mol. Along the binding path, the Gibbs free energy of the XYP-XylE complex first rises from zero in the dissociated state to approximately 4 kcal/mol in the transition state (when XylE slightly increases its opening toward the extracellular side to accommodate XYP) before dropping down to − 9.0 kcal/mol in the bound state. These quantitative insights indicate the fast equilibration between the bound and the unbound states of XylE and XYP. They also serve as an atomistic-dynamic corroboration of the experimental conclusion that XylE is a high-affinity sugar transporter. [ABSTRACT FROM AUTHOR]

Amyloid-beta (Aβ) peptides, Aβ40 and the more neurotoxic Aβ42, have been the subject of many research efforts for Alzheimer's disease. In two recent independent investigations, the atomistic structure of Aβ42 fibril has been clearly established in the S-shaped conformation consisting of three β-sheets stabilized by salt bridges formed between the Lys28 sidechain and the C-terminus of Ala42. This structure distinctively differs from the long-known structure of Aβ40 in the β-hairpin shaped conformation consisting of two β-sheets. Recent in silico investigations based on all-atom models have reached closer agreement with the in vitro measurements of Aβ40 thermodynamics. In this study, we present an in silico investigation of Aβ42 thermodynamics. Using the established force field parameters in seven sets of all-atom simulations, we examined the stability of small Aβ42 oligomers in physiological saline. We computed the elongation affinity of the S-shaped Aβ42 fibril, reaching agreement with the experimental data. We also estimated the Arrhenius activation barrier along the elongation pathway (from the disordered conformation of a free Aβ42 peptide to its S-shaped conformation on a fibril) that amounts to about 16 kcal/mol, which is consistent with the experimental data. Based on these quantitative agreements, we conclude that aggregation of Aβ42 peptides into fibrils is thermodynamically slow without precipitation by extrinsic factors such as heparan sulfate proteoglycan and highlight the possibility to prevent Aβ42 aggregation by eliminating some precipitation factors or by increasing competitive agents to capture and transport free Aβ42 peptides from the cerebrospinal fluid. [ABSTRACT FROM AUTHOR]

Human carbonic anhydrase II (hCAII) represents an ultimate example of the perfectly efficient metalloenzymes, which is capable of catalyzing the hydration of carbon dioxide with a rate approaching the diffusion controlled limit. Extensive experimental studies of this physiologically important metalloprotein have been done to elucidate the fundamentals of its enzymatic actions: what residues anchor the Zn 2+ (or another divalent cation) at the bottom of the binding pocket; how the relevant residues work concertedly with the divalent cation in the reversible conversions between CO 2 and HCO 3 – ; what are the protonation states of the relevant residues and acetazolamide, an inhibitor complexed with hCAII, etc. In this article, we present a detailed computational study on the basis of the all-atom CHARMM force field where Zn 2+ is represented with a simple model of divalent cation using the transferrable parameters available from the current literature. We compute the hydration free energy of Zn 2+ , the characteristics of hCAII-Zn 2+ complexation, and the absolute free energy of binding acetazolamide to the hCAII-Zn 2+ complex. In each of these three problems, our computed results agree with the experimental data within the known margin of error without making any case-by-case adjustments to the parameters. The quantitatively accurate insights we gain in this all-atom molecular dynamics study should be helpful in the search and design of more specific inhibitors of this and other carbonic anhydrases. [ABSTRACT FROM AUTHOR]

Aquaporins and aquaglyceroporins (AQPs) are membrane channel proteins responsible for transport of water and for transport of glycerol in addition to water across the cell membrane, respectively. They are expressed throughout the human body and also in other forms of life. Inhibitors of human AQPs have been sought for therapeutic treatment for various medical conditions including hypertension, refractory edema, neurotoxic brain edema, and so forth. Conducting all-atom molecular dynamics simulations, we computed the binding affinity of acetazolamide to human AQP4 that agrees closely with in vitro experiments. Using this validated computational method, we found that 1,3-propanediol (PDO) binds deep inside the AQP4 channel to inhibit that particular aquaporin efficaciously. Furthermore, we used the same method to compute the affinities of PDO binding to four other AQPs and one aquaglyceroporin whose atomic coordinates are available from the protein data bank (PDB). For bovine AQP1, human AQP2, AQP4, AQP5, and Plasmodium falciparum PfAQP whose structures were resolved with high resolution, we obtained definitive predictions on the PDO dissociation constant. For human AQP1 whose PDB coordinates are less accurate, we estimated the dissociation constant with a rather large error bar. Taking into account the fact that PDO is generally recognized as safe by the US FDA, we predict that PDO can be an effective diuretic which directly modulates water flow through the protein channels. It should be free from the serious side effects associated with other diuretics that change the hydro-homeostasis indirectly by altering the osmotic gradients. [ABSTRACT FROM AUTHOR]

Nanometer-sized gold particles (AuNPs) are of peculiar interest because their behaviors in an aqueous solution are sensitive to changes in environmental factors including the size and shape of the solute ions. In order to determine these important characteristics, we performed all-atom molecular dynamics simulations on the icosahedral Au144 nanoparticles each coated with a homogeneous set of 60 thiolates (4-mercaptobenzoate, pMBA) in eight aqueous solutions having ions of varying sizes and shapes (Na+, K+, tetramethylamonium cation TMA+, tris-ammonium cation TRS+, Cl-, and OH-). For each solution, we computed the reversible work (potential of mean of force) to bring two nanoparticles together as a function of their separation distance. We found that the behavior of pMBA protected Au144 nanoparticles can be readily modulated by tuning their aqueous environmental factors (pH and solute ion combinations). We examined the atomistic details on how the sizes and shapes of solute ions quantitatively factor in the definitive characteristics of nanoparticle-environment and nanoparticle-nanoparticle interactions. We predict that tuning the concentrations of nonspherical composite ions such as TRS+ in an aqueous solution of AuNPs be an effective means to modulate the aggregation propensity desired in biomedical and other applications of small charged nanoparticles. [ABSTRACT FROM AUTHOR]

Mh OR5, an insect olfactory receptor (OR), has an occluded binding site for the odorant eugenol in both the open and closed states of the ion channel. We used atomistic molecular dynamics simulation (MD) and steered molecular dynamics to examine possible tunnels to the odorant binding site from the protein surface. Four high probability tunnels were identified in the MD results. Surprisingly, three of the tunnels connect the ligand binding site to the lipid bilayer. We found sharp 30%–50% increases or decreases in tunnel bottleneck areas over 70 nsec MD trajectories, both in the ligand-bound and unliganded OR structures. Steered MD showed that eugenol follows the tunnels to the protein surface, and the potential of mean force is quantitatively consistent with the known affinity of eugenol for Mh OR5. We examined AlphaFold-generated models of 21 other insect ORs, and we found that 19 had odorant binding sites and tunnels in similar positions to Mh OR5. The possibility of a tunnel between the odorant binding site and the lipid bilayer in insect ORs suggests new experiments to test molecular mechanisms for insect odorant reception. [Display omitted] • The insect olfactory receptor Mh OR5 was analyzed by molecular dynamics simulation. • Tunnels connect occluded ligand-binding sites to the exterior and to the lipid bilayer. • Tunnel bottlenecks undergo large area fluctuations over 5–10 ns. • Steered molecular dynamics shows ligand can enter or exit Mh OR5 via the tunnels. [ABSTRACT FROM AUTHOR]

Glucose transporter GLUT1 is ubiquitously expressed in the human body from the red cells to the blood-brain barrier to the skeletal muscles. It is physiologically relevant to understand how GLUT1 facilitates diffusion of glucose across the cell membrane. It is also pathologically relevant because GLUT1 deficiency causes neurological disorders and anemia and because GLUT1 overexpression fuels the abnormal growth of cancer cells. This article presents a quantitative investigation of GLUT1 based on all-atom molecular-dynamics (MD) simulations of the transporter embedded in lipid bilayers of asymmetric inner-and-outer-leaflet lipid compositions, subject to asymmetric intra-and-extra-cellular environments. This is in contrast with the current literature of MD studies that have not considered both of the aforementioned asymmetries of the cell membrane. The equilibrium (unbiased) dynamics of GLUT1 shows that it can facilitate glucose diffusion across the cell membrane without undergoing large-scale conformational motions. The Gibbs free-energy profile, which is still lacking in the current literature of GLUT1, quantitatively characterizes the diffusion path of glucose from the periplasm, through an extracellular gate of GLUT1, on to the binding site, and off to the cytoplasm. This transport mechanism is validated by the experimental data that GLUT1 has low water-permeability, uptake-efflux symmetry, and 10 kcal/mol Arrhenius activation barrier around 37 °C. [Display omitted] • Model system of two membrane patches asymmetric in EC and IC salines • Model RBC membrane asymmetric in inner and outer leaflet lipid compositions • EC-gating mechanism of GLUT1 in quantitative agreement with in vitro data on glucose transport and water permeation [ABSTRACT FROM AUTHOR]

In order to elucidate how phosphatidylserine (PS6) interacts with AQP5 in a cell membrane, we developed a hybrid steered molecular dynamics (hSMD) method that involved: (1) Simultaneously steering two centers of mass of two selected segments of the ligand, and (2) equilibrating the ligand-protein complex with and without biasing the system. Validating hSMD, we first studied vascular endothelial growth factor receptor 1 (VEGFR1) in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide (8ST), for which the binding energy is known fromin vitroexperiments. In this study, our computed binding energy well agreed with the experimental value. Knowing the accuracy of this hSMD method, we applied it to the AQP5-lipid-bilayer system to answer an outstanding question relevant to AQP5’s physiological function: Will the PS6, a lipid having a single long hydrocarbon tail that was found in the central pore of the AQP5 tetramer crystal, actually bind to and inhibit AQP5’s central pore under near-physiological conditions, namely, when AQP5 tetramer is embedded in a lipid bilayer? We found,in silico, using the CHARMM 36 force field, that binding PS6 to AQP5 was a factor of 3 million weaker than “binding” it in the lipid bilayer. This suggests that AQP5’s central pore will not be inhibited by PS6 or a similar lipid in a physiological environment. [ABSTRACT FROM PUBLISHER]

Measuring or computing the single-channel permeability of aquaporins/aquaglyceroporins (AQPs) has long been a challenge. The measured values scatter over an order of magnitude but the corresponding Arrhenius activation energies converge in the current literature. Osmotic flux through an AQP was simulated as water current forced through the channel by kilobar hydraulic pressure or theoretically approximated as single-file diffusion. In this paper, we report large scale simulations of osmotic current under sub M gradient through three AQPs (water channels AQP4 and AQP5 and glycerol-water channel GlpF) using the mature particle mesh Ewald technique (PME) for which the established force fields have been optimized with known accuracy. These simulations were implemented with hybrid periodic boundary conditions devised to avoid the artifactitious mixing across the membrane in a regular PME simulation. The computed single-channel permeabilities at 5 °C and 25 °C are in agreement with recently refined experiments on GlpF. The Arrhenius activation energies extracted from our simulations for all the three AQPs agree with the in vitro measurements. The single-file diffusion approximations from our large-scale simulations are consistent with the current literature on smaller systems. From these unambiguous agreements among the in vitro and in silico studies, we observe the quantitative accuracy of the all-atom force fields of the current literature for water-channel biology. We also observe that AQP4, that is particularly rich in the central nervous system, is more efficient in water conduction and more temperature-sensitive than other water-only channels (excluding glycerol channels that also conduct water when not inhibited by glycerol). [ABSTRACT FROM AUTHOR]

Computing the ligand-protein binding affinity (or the Gibbs free energy) with chemical accuracy has long been a challenge for which many methods/approaches have been developed and refined with various successful applications. False positives and, even more harmful, false negatives have been and still are a common occurrence in practical applications. Inevitable in all approaches are the errors in the force field parameters we obtain from quantum mechanical computation and/or empirical fittings for the intra- and inter-molecular interactions. These errors propagate to the final results of the computed binding affinities even if we were able to perfectly implement the statistical mechanics of all the processes relevant to a given problem. And they are actually amplified to various degrees even in the mature, sophisticated computational approaches. In particular, the free energy perturbation (alchemical) approaches amplify the errors in the force field parameters because they rely on extracting the small differences between similarly large numbers. In this paper, we develop a hybrid steered molecular dynamics (hSMD) approach to the difficult binding problems of a ligand buried deep inside a protein. Sampling the transition along a physical (not alchemical) dissociation path of opening up the binding cavity---pulling out the ligand---closing back the cavity, we can avoid the problem of error amplifications by not relying on small differences between similar numbers. We tested this new form of hSMD on retinol inside cellular retinol-binding protein 1 and three cases of a ligand (a benzylacetate, a 2-nitrothiophene, and a benzene) inside a T4 lysozyme L99A/M102Q(H) double mutant. In all cases, we obtained binding free energies in close agreement with the experimentally measured values. This indicates that the force field parameters we employed are accurate and that hSMD (a brute force, unsophisticated approach) is free from the problem of error amplification suffered by many sophisticated approaches in the literature. [ABSTRACT FROM AUTHOR]