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It is difficult to observe a spontaneous translocation of cell-penetrating peptides(CPPs) within a short time scale (e.g., a few hundred ns) in all-atom molecular dynamics(MD) simulations because the time required for the translocation of usual CPPs is on the order of minutes or so. In this work, we report a spontaneous translocation of a single Arg$_9$(R9) across a DOPC/DOPG(4:1) model membrane within an order of a few tens ns scale by using the weighted ensemble(WE) method. We identify how water molecules and the orientation of Arg$_9$ play a role in translocation. We also show how lipid molecules are transported along with Arg$_9$. In addition, we present free energy profiles of the translocation across the membrane using umbrella sampling and show that a single Arg$_9$ translocation is energetically unfavorable. We expect that the WE method can help study interactions of CPPs with various model membranes within MD simulation approaches., 8 pages, 6 figures with Supplementary Information

Hydrogel is in the spotlight as a useful biomaterial in the field of drug delivery and tissue engineering due to its similar biological properties to a native extracellular matrix (ECM). Herein, we proposed a ternary hydrogel of gellan gum (GG), silk fibroin (SF), and chondroitin sulfate (CS) as a biomaterial for cartilage tissue engineering. The hydrogels were fabricated with a facile combination of the physical and chemical crosslinking method. The purpose of this study was to find the proper content of SF and GG for the ternary matrix and confirm the applicability of the hydrogel in vitro and in vivo. The chemical and mechanical properties were measured to confirm the suitability of the hydrogel for cartilage tissue engineering. The biocompatibility of the hydrogels was investigated by analyzing the cell morphology, adhesion, proliferation, migration, and growth of articular chondrocytes-laden hydrogels. The results showed that the higher proportion of GG enhanced the mechanical properties of the hydrogel but the groups with over 0.75% of GG exhibited gelling temperatures over 40 °C, which was a harsh condition for cell encapsulation. The 0.3% GG/3.7% SF/CS and 0.5% GG/3.5% SF/CS hydrogels were chosen for the in vitro study. The cells that were encapsulated in the hydrogels did not show any abnormalities and exhibited low cytotoxicity. The biochemical properties and gene expression of the encapsulated cells exhibited positive cell growth and expression of cartilage-specific ECM and genes in the 0.5% GG/3.5% SF/CS hydrogel. Overall, the study of the GG/SF/CS ternary hydrogel with an appropriate content showed that the combination of GG, SF, and CS can synergistically promote articular cartilage defect repair and has considerable potential for application as a biomaterial in cartilage tissue engineering., This research was supported by the International Research and Development Program of the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT and Future Planning (NRF-2017K1A3A7A03089427) and by the bilateral cooperation Program of the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT and Future Planning (NRF-2019K2A9A1A06098563).

In multiple inflation scenario having two inflations with an intermediate matter-dominated phase, the power spectrum is estimated to be enhanced on scales smaller than the horizon size at the beginning of the second inflation, $k > k_{\rm b}$. We require $k_{\rm b} > 10 {\rm Mpc}^{-1}$ to make sure that the enhanced power spectrum is consistent with large scale observation of cosmic microwave background (CMB). We consider the CMB spectral distortions generated by the dissipation of acoustic waves to constrain the power spectrum. The $\mu$-distortion value can be $10$ times larger than the expectation of the standard $\Lambda$CDM model ($\mu_{\Lambda\mathrm{CDM}} \simeq 2 \times 10^{-8}$) for $ k_{\rm b} \lesssim 10^3 {\rm Mpc}^{-1}$, while the $y$-distortion is hardly affected by the enhancement of the power spectrum., Comment: 16 pages, 5 figures

Sodium-glucose transporters (SGLTs) facilitate the movement of water across the cell membrane, playing a central role in cellular homeostasis. Here, we present a detailed analysis of the mechanism of water permeation through the inward-facing state of vSGLT based on nearly 10 μs of molecular dynamics simulations. These simulations reveal the transient formation of a continuous water channel through the transporter that permits water to permeate the protein. Trajectories in which spontaneous release of galactose is observed, as well as those in which galactose remains in the binding site, show that the permeation rate, although modulated by substrate occupancy, is not tightly coupled to substrate release. Using a, to our knowledge, novel channel-detection algorithm, we identify the key residues that control water flow through the transporter and show that solvent gating is regulated by side-chain motions in a small number of residues on the extracellular face. A sequence alignment reveals the presence of two insertion sites in mammalian SGLTs that flank these outer-gate residues. We hypothesize that the absence of these sites in vSGLT may account for the high water permeability values for vSGLT determined via simulation compared to the lower experimental estimates for mammalian SGLT1.

Secondary active transporters, such as those that adopt the leucine-transporter fold, are found in all domains of life, and they have the unique capability of harnessing the energy stored in ion gradients to accumulate small molecules essential for life as well as expel toxic and harmful compounds. How these proteins couple ion binding and transport to the concomitant flow of substrates is a fundamental structural and biophysical question that is beginning to be answered at the atomistic level with the advent of high-resolution structures of transporters in different structural states. Nonetheless, the dynamic character of the transporters, such as ion/substrate binding order and how binding triggers conformational change, is not revealed from static structures, yet it is critical to understanding their function. Here, we report a series of molecular simulations carried out on the sugar transporter vSGLT that lend insight into how substrate and ions are released from the inward-facing state of the transporter. Our simulations reveal that the order of release is stochastic. Functional experiments were designed to test this prediction on the human homolog, hSGLT1, and we also found that cytoplasmic release is not ordered, but we confirmed that substrate and ion binding from the extracellular space is ordered. Our findings unify conflicting published results concerning cytoplasmic release of ions and substrate and hint at the possibility that other transporters in the superfamily may lack coordination between ions and substrate in the inward-facing state.

Membrane co-transport proteins that use a five-helix inverted repeat motif have recently emerged as one of the largest structural classes of secondary active transporters. However, despite many structural advances there is no clear evidence of how ion and substrate transport are coupled. Here we report a comprehensive study of the sodium/galactose transporter from Vibrio parahaemolyticus (vSGLT), consisting of molecular dynamics simulations, biochemical characterization and a new crystal structure of the inward-open conformation at a resolution of 2.7 Å. Our data show that sodium exit causes a reorientation of transmembrane helix 1 that opens an inner gate required for substrate exit, and also triggers minor rigid-body movements in two sets of transmembrane helical bundles. This cascade of events, initiated by sodium release, ensures proper timing of ion and substrate release. Once set in motion, these molecular changes weaken substrate binding to the transporter and allow galactose readily to enter the intracellular space. Additionally, we identify an allosteric pathway between the sodium-binding sites, the unwound portion of transmembrane helix 1 and the substrate-binding site that is essential in the coupling of co-transport.

This article reports an all-atom molecular dynamics simulation to study a model pulmonary surfactant film interacting with a carbonaceous nanoparticle. The pulmonary surfactant is modeled as a dipalmitoylphosphatidylcholine monolayer with a peptide consisting of the first 25 residues from surfactant protein B. The nanoparticle model with a chemical formula C188H53 was generated using a computational code for combustion conditions. The nanoparticle has a carbon cage structure reminiscent of the buckyballs with open ends. A series of molecular-scale structural and dynamical properties of the surfactant film in the absence and presence of nanoparticle are analyzed, including radial distribution functions, mean-square displacements of lipids and nanoparticle, chain tilt angle, and the surfactant protein B peptide helix tilt angle. The results show that the nanoparticle affects the structure and packing of the lipids and peptide in the film, and it appears that the nanoparticle and peptide repel each other. The ability of the nanoparticle to translocate the surfactant film is one of the most important predictions of this study. The potential of mean force for dragging the particle through the film provides such information. The reported potential of mean force suggests that the nanoparticle can easily penetrate the monolayer but further translocation to the water phase is energetically prohibitive. The implication is that nanoparticles can interact with the lung surfactant, as supported by recent experimental data by Bakshi et al.

Sodium-glucose transporters (SGLTs) mediate sugar transport as well as water flow across the cell membrane. Using a series of long molecular dynamics simulations generated on the special-purpose Anton supercomputer totaling nearly 16 microseconds in aggregate, we investigated the mechanism of water permeation through the inward-facing state of the bacterial sugar transporter vSGLT from Vibrio parahaemolyticus. Our simulations reveal conformational changes in the extracellular gate that create a transient water channel through the transporter. We developed a novel channel detection algorithm to characterize water pathways through the protein and identify key residues that control water flow. The simulations contain multiple, independent instances in which the galactose, initially bound to the transporter, spontaneously exits to solution. By comparing water flow through vSGLT when the sugar is bound, exiting and free in solution, we show that water flow, while modulated by galactose occupancy, is not coupled to substrate release.

In this work we report on a new QCD sum rule analysis to predict masses of the excited baryon states (e.g. Sigma(1620) and Lambda(1405)) by using multiquark interpolating fields ($(q\bar{q})(qqq)$). For the Sigma(1620) we consider the $\bar{K}N$, $\pi\Sigma$, and $\pi\Lambda$ (I=1) multiquark interpolating fields. The calculated mass from those multiquark states is about 1.592 GeV. For the Lambda(1405) we first show the result using the $\pi^+\Sigma^- + \pi^0\Sigma^0 + \pi^-\Sigma^+$ (I=0) multiquark interpolating field, and compare the calculated mass to that of our previous result using the $\pi^0\Sigma^0$ multiquark state. We then show that the mass 1.405 GeV is well reproduced when using the $\bar{K}N$ (I=0) multiquark state. The uncertainties in our sum rules are also discussed.

In the QCD sum rule approach we predict the $\Lambda$ (1405) mass by choosing the $\pi^0\Sigma^0$ multiquark interpolating field. It is found that the mass is about 1.419 GeV from $\Pi_1 (q^2)$ sum rule which is more reliable than $\Pi_q (q^2)$ sum rule, where $\Pi_q (q^2)$ and $\Pi_1 (q^2)$ are two invariant functions of the correlator $\Pi (q^2)$. We also present the sum rules for the $K^+ p$ and the $\pi^+\Sigma^+$ multiquark states, and compare to those for the $\pi^0\Sigma^0$ multiquark state. The mass of the $\Lambda$ (1600) can be also reproduced in our approach.

The coupling constants g_{\pi \Lambda \Sigma} and g_{K \Sigma \Xi} are calculated in the QCD sum rule approach using the three-point function method and taking into account the SU(3) symmetry breaking effects. The pattern of SU(3) breaking appears to be different from that based on SU(3) relations.

{ital g}{sub {ital KN}}{Lambda} and {ital g}{sub {ital KN}{Sigma}} are calculated using a QCD sum rule motivated method used by Reinders, Rubinstein, and Yazaki to extract hadron couplings to Goldstone bosons. The SU(3) symmetry breaking effects are taken into account by including the contributions from the strange quark mass and assuming different values for the strange and the up-down quark condensates. We find {ital g}{sub {ital KN}}{Lambda}/{radical}4{pi}={minus}1.96 and {ital g}{sub {ital KN}{Sigma}}/{radical}4{pi}=0.33. {copyright} {ital 1996 The American Physical Society.}

We present first results for masses of spin-3/2 baryons in lattice QCD, using a novel fat-link clover fermion action in which only the irrelevant operators are constructed using fat links. In the isospin-1/2 sector, we observe, after appropriate spin and parity projection, a strong signal for the J^P=3/2^- state, and find good agreement between the 1/2^+ mass and earlier nucleon mass simulations with a spin-1/2 interpolating field. For the isospin-3/2 Delta states, clear mass splittings are observed between the various 1/2^+/- and 3/2^+/- channels, with the calculated level orderings in good agreement with those observed empirically., Comment: 3 pages, 2 figures, Lattice2002(QCD Spectrum and Quark Masses)

We report N* masses in the spin 3/2 sector from a highly-improved anisotropic action. States with both positive and negative parity are isolated via a parity projection method. The extent to which spin projection is needed is examined. The gross features of the splittings from the nucleon ground state show a trend consistent with experimental results at the quark masses explored., Lattice2001(spectrum), 3 pages, 4 figures, new interpolating field

Voltage-gated potassium (Kv) channels control the electrical excitability of neurons and muscles. Despite this key role, how these channels open and close or gate is not fully understood. Gating is usually attributed to the bending and straightening of pore-lining helices at glycine and proline residues. In this work we focused on the role of proline in the Pro-Val-Pro (PVP) motif of the inner S6 helix in the Kv1.2 channel. We started by developing a simple hinged-rod model to fully explore the configurational space of bent helices and we related these configurations to the degree of pore opening. We then carried out fully atomistic simulations of the S6 helices and compared these simulations to the hinged-rod model. Both methods suggest that Kv1 channels are not tightly closed when the inner helices are straight, unlike what is seen in the non-PVP containing channels KcsA and KirBac. These results invite the possibility that the S6 helices may be kinked when Kv1 channels are closed. Our simulations indicate that the wild-type helix adopts multiple spatially distinct configurations, which is consistent with its role in adopting a closed state and an open state. The two most dominant configurational basins correspond to a 6 A movement of the helix tail accompanied by the PVP region undergoing a local alpha-helix to 3(10)-helix transition. We explored how single point mutations affect the propensity of the S6 helix to adopt particular configurations. Interestingly, mutating the first proline, P405 (P473 in Shaker), to alanine completely removed the bistable nature of the S6 helix possibly explaining why this mutation compromises the channel. Next, we considered four other mutations in the area known to affect channel gating and we saw similarly dramatic changes to the helix's dynamics and range of motion. Our results suggest a possible mechanism of helix pore closure and they suggest differences in the closed state of glycine-only channels, like KcsA, and PVP containing channels.

We present a new method to calculate Lyapunov exponents of rigid diatomic molecules in three dimensions (12N dimensional phase space). The spectra of Lyapunov exponents are obtained for 32 rigid diatomic molecules interacting through the Weeks-Chandler-Anderson(WCA) potential for various bond length and densities, and compared with those in Y.-H. Shin et al. [Phys. Rev. E 64, 041106 (2001)]. Our algorithm is easy to implement and total CPU time is relatively inexpensive., Comment: Accepted in Phys. Rev. E

Using a coarse-grained elastic model, we examine the bending properties of anti-parallel beta-sheets comprised of uniform amino-acid residues in vacuum as well as in explicit solvent. By comparing the conformational probability of the beta-sheet from molecular dynamics simulations with the same quantities obtained from the coarse-grained model, we compute the elastic bending constant, kappa. Equilibrium fluctuations of the beta-sheet and its response to external forces are well reproduced by a model with a uniform isotropic bending constant. An anisotropic bending model is also investigated, although the computed anisotropy is relatively weak and most of the observed properties are well described by an isotropic model. The presence of explicit solvent also lowers the bending constant. The sequence dependence of our result and its implications in protein conformational dynamics are discussed.

The elasticity of alpha-helices is examined using equilibrium molecular-dynamics simulations. From the statistics of curvatures and twists, we compute the elastic moduli of several representative alpha-helices, both in the presence and absence of aqueous solvent. We discover that the bending modulus (persistence length) of the helices is independent of the amino-acid sequence, although helices in water are slightly softer than in vacuum. The response of the helices under the action of an external force is also computed and compared with continuum mechanics predictions. Within the time scale of our simulation, we show that the properties of alpha-helices are well reproduced by an elastic and isotropic rod. The persistence length (bending modulus) of most alpha-helices in water or vacuum is approximately 100 nm, roughly twice that of DNA.

We present first results for masses of spin-3/2 N and Delta baryons in lattice QCD, using Fat-Link Irrelevant Clover (FLIC) fermions. Spin-3/2 interpolating fields providing overlap with both spin-3/2 and spin-1/2 states are considered. In the isospin-1/2 sector. we observe, after appropriate spin and parity projection, a strong signal for the J{sup P} = 3/2{sup -} state together with a weak but discernible signal for the 3/2{sup +} state with a mass splitting near that observed experimentally. We also find good agreement between the 1/2{sup {+-}} masses and earlier nucleon mass simulations with the standard spin-1/2 interpolating field. For the isospin-3/2 Delta states, clear mass splittings are observed between the various 1/2{sup {+-}} and 3/2{sup {+-}} channels, with the calculated level orderings in good agreement with those observed empirically.

We study charmonium using the standard relativistic formalism in the quenched approximation, on a set of lattices with isotropic lattice spacings ranging from 0.1 to 0.04 fm. We concentrate on the calculation of the hyperfine splitting between eta_c and J/psi, aiming for a controlled continuum extrapolation of this quantity. The splitting extracted from the non-perturbatively improved clover Dirac operator shows very little dependence on the lattice spacing for $a \leq 0.1$ fm. The dependence is much stronger for Wilson and tree-level improved clover operators, but they still yield consistent extrapolations if sufficiently fine lattices, $a \leq 0.07$ fm ($a M(\eta_c) \leq 1$), are used. Our result for the hyperfine splitting is 77(2)(6) MeV (where Sommer's parameter, r_0, is used to fix the scale). This value remains about 30% below experiment. Dynamical fermions and OZI-forbidden diagrams both contribute to the remainder. Results for the eta_c and J/psi wave functions are also presented., Comment: 22 pages, 7 figures

The responses of quark condensates to the chemical potential, as a function of temperature T and chemical potential \mu, are calculated within the Nambu--Jona-Lasinio (NJL) model. We compare our results with those from the recent lattice QCD simulations [QCD-TARO Collaboration, Nucl. Phys. B (Proc. Suppl.) 106, 462 (2002)]. The NJL model and lattice calculations show qualitatively similar behavior, and they will be complimentary ways to study hadrons at finite density. The behavior above T_c requires more elaborated analyses., Comment: 3 pages, 2 figs, based on a contribution to the Prof. Osamu Miyamura memorial symposium, Hiroshima University, Nov. 16-17, 2001; slightly revised, accepted for publication in Physical Review D

We present a framework to compute the responses of hadron masses to the chemical potential in lattice QCD simulations. As a first trial, the screening mass of the pseudoscalar meson and its first and second responses are evaluated. We present results on a $16\times 8^2\times 4$ lattice with two flavors of staggered quarks below and above $T_c$. The responses to both the isoscalar and isovector chemical potentials are obtained. They show different behavior in the low and the high temperature phases, which may be explained as a consequence of chiral symmetry breaking and restoration, respectively., Comment: 10 pages, 11 figures

We improve our previous QCD sum rule calculation on G(KN\Lambda) and G(KN\Sigma) coupling constants by including the contributions from higher dimensional condensates, and , in the OPE. It is found that the contribution of these condensates is non-negligible compared to that of the quark condensates. Using a best-fit analysis we find |G(KN\Lambda)| = 2.49 $\pm$ 1.25 and |G(KN\Sigma)| = 0.395 $\pm$ 0.377., Comment: revtex, 10 pages, 2 ps figures; substantial revision, results changed, to be published in Phys. Rev. C

We propose a new QCD sum rule analysis for the Lambda(1405) and the Sigma(1620). Using the I=0 and I=1 multiquark sum rules we predict their masses.

We report the results from 16 microseconds of molecular dynamics (MD) simulations carried out on vSGLT using the Anton supercomputer at the Pittsburgh Supercomputing Center. We observed multiple galactose unbinding events as well as instances in which the energizing sodium ion unbind and then rebind to the putative sodium binding site. Using umbrella sampling we calculated the potential of mean force (pmf) for all galactose unbinding trajectories. We will discuss the allosteric interaction between the ion and substrate and the potential for one to control the release of the other via the inner and outer gates.

Standard QCD sum-rule analyses of the nucleon mass give results that are inconsistent with chiral perturbation theory due to an overly simple continuum ansatz on the phenomenological side of the sum rule. We show that a careful treatment of the continuum, including $\pi$-$N$ states and other states with virtual pions, resolves the inconsistency associated with chiral logs., Comment: 10 pages, no figures

A number of recent high resolution structures suggest that a larger family of cation coupled substrate transporters share a common core architecture. At the molecular level, it is not known how this architecture enables them to harness the energy stored in ionic gradients to move small molecules across the membrane. We have studied the details of substrate and ion entry and exit to the cytoplasm of the galactose symporter vSGLT. We used equilibrium molecular dynamics (MD) simulations to determine the role of key residues in stabilizing galactose and sodium in their respective binding sites. The simulations show that the transporter is stable when simulated as a monomer having only small deviations from the x-ray structure. We also used steered MD simulations to pull galactose and sodium from their site into the cytoplasm to obtain the free energy for unbinding.

Continuum electrostatic approaches have been extremely successful at describing the charged nature of soluble proteins and how they interact with binding partners. However, it is unclear whether continuum methods can be used to quantitatively understand the energetics of membrane protein insertion and stability. Recent translation experiments suggest that the energy required to insert charged peptides into membranes is much smaller than predicted by present continuum theories. Atomistic simulations have pointed to bilayer inhomogeneity and membrane deformation around buried charged groups as two critical features that are neglected in simpler models. Here, we develop a fully continuum method that circumvents both of these shortcomings by using elasticity theory to determine the shape of the deformed membrane and then subsequently uses this shape to carry out continuum electrostatics calculations. Our method does an excellent job of quantitatively matching results from detailed molecular dynamics simulations at a tiny fraction of the computational cost. We expect that this method will be ideal for studying large membrane protein complexes.

It is well accepted that cotransporters facilitate water movement by two independent mechanisms: osmotic flow through a water channel in the protein and flow driven by ion/substrate cotransport. However, the molecular mechanism of transport-linked water flow is controversial. Some researchers believe that it occurs via cotransport, in which water is pumped along with the transported cargo, while others believe that flow is osmotic in response to an increase in intracellular osmolarity. In this letter, we report the results of a 200-ns molecular dynamics simulation of the sodium-dependent galactose cotransporter vSGLT. Our simulation shows that a significant number of water molecules cross the protein through the sugar-binding site in the presence as well as the absence of galactose, and 70–80 water molecules accompany galactose as it moves from the binding site into the intracellular space. During this event, the majority of water molecules in the pathway are unable to diffuse around the galactose, resulting in water in the inner half of the transporter being pushed into the intracellular space and replaced by extracellular water. Thus, our simulation supports the notion that cotransporters act as both passive water channels and active water pumps with the transported substrate acting as a piston to rectify the motion of water.

In human kidneys, the glomeruli filter about 54 g of urea from the blood each day and approximately 12-14 g of which is reabsorbed in the proximal tubule that is believed to be devoid of urea channels or uniporters. Experimental evidence suggests that human sodium-dependent glucose cotransporters (hSGLTs) may be involved in urea uptake. Our Molecular dynamics (MD) simulations with the inward-facing structure of vSGLT (PDB ID: 3DH4) resulted in permeation of a single urea molecule in presence of a bound galactose. Separately, long-timescale MD simulations (1.5 μs) performed on the Anton supercomputer in presence of urea did not result in any urea permeation event. During these simulations, sugar was observed to escape the binging pocket indicating that the presence of galctose in the binding pocket may facilitate urea escape to the periplasm. Here we present our results on the study of energetics of urea transport along the previously observed pathway. Umbrella sampling simulations are performed to calculate the potential of mean force (PMF) of urea exit. Separate sets of umbrella sampling simulations are performed in presence and absence of a bound galactose to investigate our hypothesis that the bound galactose facilitates urea permeation. Two different force field parameters for urea are used to inspect the validity of the previously observed urea permeation event.