- Abstract: A rigorous formulation of the solvation forces (first derivatives) associated with the electrostatic free energy calculated from numerical solutions of the linearized Poisson-Boltzmann equation on a discrete grid is described. The solvation forces are obtained from the formal solution of the linearized Poisson-Boltzmann equation written in terms of the Green function. An intermediate region for the solute-solvent dielectric boundary is introduced to yield a continuous solvation free energy... Show More
- Abstract: Recently, we presented a Green's function approach for the calculation of analytic continuum electrostatic solvation forces based on numerical solutions of the finite-difference Poisson–Botzmann (FDPB) equation [Im et al., Comp. Phys. Comm. 111 (1998) 59]. In this treatment the analytic forces were explicitly defined as the first derivative of the FDPB continuum electrostatic free energy with respect to the coordinates of the solute atoms. A smooth intermediate region for the solute–solvent... Show More
- Abstract: A computational algorithm based on Grand Canonical Monte Carlo (GCMC) and Brownian Dynamics (BD) is described to simulate the movement of ions in membrane channels. The proposed algorithm, GCMC/BD, allows the simulation of ion channels with a realistic implementation of boundary conditions of concentration and transmembrane potential. The method is consistent with a statistical mechanical formulation of the equilibrium properties of ion channels (; Biophys. J. 77:139-153). The GCMC/BD... Show More
- Abstract: There is no doubt that MD simulations in which water and lipid molecules are treated explicitly represent the most detailed method for studying ion channels. Nevertheless, this computationally intensive methodology often suffers from statistical uncertainties due to finite sampling. From this perspective, a continuum model can be very useful for examining various energetic factors arising from long-range electrostatic effects involved in the function of an ion channel. This review shows that... Show More
- Abstract: A general approach has been developed to allow accurate simulations of a small region part of a large macromolecular system while incorporating the influence of the remaining distant atoms with an effective boundary potential. The method is called the Generalized Solvent Boundary Potential (GSBP). By representing the surrounding solvent as a continuum dielectric, both the solvent-shielded static field from the distant atoms of the macromolecule and the reaction field from the dielectric... Show More
- Abstract: A general method has been developed to include the electrostatic reaction field in Brownian dynamics (BD) simulations of ions diffusing through complex molecular channels of arbitrary geometry. Assuming that the solvent is represented as a featureless continuum dielectric medium, a multipolar basis-set expansion is developed to express the reaction field Green’s function. A reaction field matrix, which provides the coupling between generalized multipoles, is calculated only once and stored... Show More
- Abstract: The atomic force microscope (AFM) was used to image native OmpF porin and to detect the electrostatic potential generated by the protein. To this end the OmpF porin trimers from Escherichia coli was reproducibly imaged at a lateral resolution of approximately 0.5 nm and a vertical resolution of approximately 0.1 nm at variable electrolyte concentrations of the buffer solution. At low electrolyte concentrations the charged AFM probe not only contoured structural details of the membrane... Show More
- Abstract: A 5 ns all-atom molecular dynamics trajectory of Escherichia coli OmpF porin embedded in an explicit dimyristoyl-phosphatidylcholine (DMPC) bilayer bathed by a 1 M [KCl] aqueous salt solution is generated to explore the microscopic details of the mechanism of ion permeation. The atomic model includes the OmpF trimer, 124 DMPC, 13470 water molecules as well as 231 K+ and 201 Cl-, for a total of 70,693 atoms. The structural and dynamical results are in excellent agreement with the X-ray data.... Show More
- Abstract: Three different theoretical approaches are used and compared to refine our understanding of ion permeation through the channel formed by OmpF porin from Escherichia coli. Those approaches are all-atom molecular dynamics (MD) in which ions, solvent, and lipids are represented explicitly, Brownian dynamics (BD) in which ions are represented explicitly, while solvent and lipids are represented as featureless dielectrics, and Poisson-Nernst-Planck (PNP) electrodiffusion theory in which both... Show More
- Abstract: The generalized solvent boundary potential (GSBP) method which can allow an efficient treatment of the long-range interactions by using explicit solvent MD in a small innner region and treatment of the outer region using an implicit solvent model was shown. Initial tests with all protein and solute atoms held fixed were used to examine the consistency of GSBP. The small variations with system size in the final charging free energy of aspartate demonstrates that the solvent-shielded static... Show More
- Abstract: Based on recent developments in generalized Born (GB) theory that employ rapid volume integration schemes (M. S. Lee, F. R. Salabury, Jr., and C. L. Brooks III, J Chem Phys 2002, 116, 10606) we have recast the calculation of the self-electrostatic solvation energy to utilize a simple smoothing function at the dielectric boundary. The present GB model is formulated in this manner to provide consistency with the Poisson-Boltzmann (PB) theory previously developed to yield numerically stable... Show More
- Abstract: Exploiting recent developments in generalized Born (GB) electrostatics theory, we have reformulated the calculation of the self-electrostatic solvation energy to account for the influence of biological membranes. Consistent with continuum Poisson-Boltzmann (PB) electrostatics, the membrane is approximated as an solvent-inaccessible infinite planar low-dielectric slab. The present membrane GB model closely reproduces the PB electrostatic solvation energy profile across the membrane. The... Show More
- Abstract: This study compares generalized Born (GB) and Poisson (PB) methods for calculating electrostatic solvation energies of proteins. A large set of GB and PB implementations from our own laboratories as well as others is applied to a series of protein structure test sets for evaluating the performance of these methods. The test sets cover a significant range of native protein structures of varying size, fold topology, and amino acid composition as well as nonnative extended and misfolded... Show More
- Abstract: In this paper we are investigating the effect of the dielectric environment on atomic Born radii used in generalized Born (GB) methods. Motivated by the Kirkwood expression for the reaction field of a single off-center charge in a spherical cavity, we are proposing extended formalisms for the calculation of Born radii as a function of external and internal dielectric constants. We demonstrate that reaction field energies calculated from environmentally dependent Born radii lead to much... Show More
- Abstract: The goal of this review is to establish a broad and rigorous theoretical framework to describe ion permeation through biological channels. This framework is developed in the context of atomic models on the basis of the statistical mechanical projection-operator formalism of Mori and Zwanzig. The review is divided into two main parts. The first part introduces the fundamental concepts needed to construct a hierarchy of dynamical models at different level of approximation. In particular, the... Show More
- Abstract: De novo folding simulations of the major pVIII coat protein from filamentous fd bacteriophage, using a newly developed implicit membrane generalized Born model and replica-exchange molecular dynamics, are presented and discussed. The quality of the predicted structures, judged by comparison of the root-mean-square deviations of a room temperature ensemble of conformations from the replica-exchange simulations and experimental structures from both solid-state NMR in lipid bilayers and... Show More
- Abstract: Identification of the molecular interaction governing ion conduction through biological pores is one of the most important goals of modern electrophysiology. Grand canonical Monte Carlo Brownian dynamics (GCMC/BD) and three-dimensional Poisson-Nernst-Plank (3d-PNP) electrodiffusion algorithms offer powerful and general approaches to study of ion permeation through wide molecular pores. A detailed analysis of ion flows through the staphylococcal alpha-hemolysin channel based on series of... Show More
- Abstract: NMR biomolecular structure calculations exploit simulated annealing methods for conformational sampling and require a relatively high level of redundancy in the experimental restraints to determine quality three-dimensional structures. Recent advances in generalized Born (GB) implicit solvent models should make it possible to combine information from both experimental measurements and accurate empirical force fields to improve the quality of NMR-derived structures. In this paper, we study... Show More
- Abstract: Since biomolecules exist in aqueous and membrane environments, the accurate modeling of solvation, and hydrogen bonding interactions in particular, is essential for the exploration of structure and function in theoretical and computational studies. In this chapter, we focus on alternatives to explicit solvent models and discuss recent advances in generalized Born (GB) implicit solvent theories. We present a brief review of the successes and shortcomings of the application of these theories... Show More
- Abstract: Determining an accurate initial native-like protein fold is one of the most important and time-consuming steps of de novo NMR structure determination. Here we demonstrate that high-quality native-like models can be rapidly generated from initial structures obtained using limited NOE assignments, through replica exchange molecular dynamics refinement with a generalized Born implicit solvent (REX/GB). Conventional structure calculations using an initial sparse NOE set were unable to identify a... Show More
Publications citing this author (10164)
- The accurate representation of the interactions between a lipid bilayer and an integral membrane protein, whether as an anchor to a bilayer or as an extensive membrane channel, is only possible within the context of explicit lipid representation. Established studies using implicit bilayers were able to account for the hydrophobic mismatch between TM domains and the system solvent, however, due to membrane deformation from lipid-protein rearrangement, the tight-coupling between protein structure and protein function can only be represented by explicit lipid bodies. The grand average of hydropathy (GRAVY)value for the wild-type and L98H mutant were-0.216
[Show abstract] [Hide abstract] ABSTRACT: Author Summary Cells in biological organisms have to be able to respond to mechanical forces during processes such as touch, hearing, pain sensation and tissue growth. One way this is achieved is through mechanosensitive ion channels, membrane embedded proteins that initiate electrical signalling upon tension within the cell or cell membrane. The malfunction of such channels is also associated with a range of diseases including muscular dystrophy and cardiac arrhythmia. In this manuscript, we study in detail the mechanosensitive channel of large conductance (MscL) from bacteria, a model system in which to understand the principles of mechanosensation. Despite many years of investigative work the details of how the protein senses tension in the surrounding membrane remain unknown. By combining structural data from experiments with computer simulation we are able to model the open channel structure of the protein and report previously unobserved structural changes that might present a new mechanism of sensing tension. The methods developed in this paper are not limited to the study of mechanosensitive ion channels and may be useful in understanding the structure and function of other membrane proteins.
- Gating is induced by tension in the surrounding lipid bilayer that triggers a large conformational change to form an open channel of approximately 30 A ˚ diameter6789. The structure and function of MscL, have been investigated extensively using a range of techniques including patch clamp studies (see [10,11] and  for reviews), mutation studies1213141516, FRET [9,17], EPR spectroscopy [7,18,19], structural modelling [20,21] and MD simulations2223242526272829303132. Based on the original crystal structure  and the large conductance of the pore it was initially thought the open pore is lined by all 10 TM helices.
[Show abstract] [Hide abstract] ABSTRACT: Myosin's actin-binding loop (loop 2) carries a charge opposite to that of its binding site on actin and is thought to play an important role in ionic interactions between the two molecules during the initial binding step. However, no subsequent role has been identified for loop 2 in actin-myosin binding. We used an optical trap to measure bond formation and bond rupture between actin and rigor heavy meromyosin when loaded perpendicular to the filament axis. We studied HMM with intact or proteolytically cleaved loop 2 at low and physiologic ionic strength. Here we show that the presence of intact loop 2 allows actomyosin bonds to form quickly and that they do so in a short-lived bound state. Increasing tensile load causes the transition to a long-lived state-the distinguishing behavior of a catch bond. When loop 2 was cleaved catch bond behavior was abrogated leaving only a long-lived state. These data suggest that in addition to its role in locating binding sites on actin, loop 2 is also a force-dependent inhibitor of the long-lived actomyosin complex. This may be important for reducing the duty ratio and increasing the shortening velocity of actomyosin at low forces.
- Electronic supplementary material The online version of this article (doi:10.1007/s10974-014-9375-z) contains supplementary material, which is available to authorized users. conformation upon actin-myosin binding, but its specific locations and interactions differ between studies (Liu et al. 2006; Lorenz and Holmes 2010). A recent high resolution cryo-EM-based model identifies potential electrostatic interactions between loop 2 on myosin and actin's N-terminus , putting loop 2 at the center of the actin-myosin interface (Behrmann et al. 2012).
[Show abstract] [Hide abstract] ABSTRACT: Purple membranes (PM) of the bacteria Halobacterium salinarum are a unique natural membrane where bacteriorhodopsin (BR) can convert photon energy and pump protons. Elucidating the electronic properties of biomembranes is critical for revealing biological mechanisms and developing new devices. We report here the electric properties of PMs studied by using multi-functional electric force microscopy (EFM) at the nanoscale. The topography, surface potential, and dielectric capacity of PMs were imaged and quantitatively measured in parallel. Two orientations of PMs were identified by EFM because of its high resolution in differentiating electrical characteristics. The extracellular (EC) sides were more negative than the cytoplasmic (CP) side by 8 mV. The direction of potential difference may facilitate movement of protons across the membrane and thus play important roles in proton pumping. Unlike the side-dependent surface potentials observed in PM, the EFM capacitive response was independent of the side and was measured to be at a dC/dz value of ~5.25 nF/m. Furthermore, by modification of PM with de novo peptides based on peptide-protein interaction, directional oriented PM assembly on silicon substrate was obtained for technical devices. This work develops a new method for studying membrane nanoelectronics and exploring the bioelectric application at the nanoscale.
- Probing the electric property at the nanometer scale is of fundamental interest because of the rich local structure of the membranes and the fact that many bioelectric phenomena occur at this level [24,25]. The AFM has been introduced to image and quantify the electrostatic properties of protein membranes at (sub-)nanometer resolution in buffer solution, which linked the structure and function relationship of native membrane proteins [26,27]. However, measurements for the electric properties of biomembranes when they are not suspended in an aqueous environment, but rather supported on a suitable substrate in air, are still lacking.
[Show abstract] [Hide abstract] ABSTRACT: Techniques of rare event dynamics were reviewed, including string methods, which will be implemented with the biochemical simulation packages. The existing methods were applied to study biological systems with relevance to drug design and drug metabolism. The rare event dynamics simulations were performed to understand the kinetic and thermodynamic free energy information on the drug binding sites in the M2 proton channel, the free energy of insertion and association of membrane proteins and membrane active peptides. Results give a theoretical framework to interpret and reconcile existing and often conflicting opinions.
- The gotten association free energy of GpA in micelles gives a good agreement with the experimental result . A framework of reaction coordinates which describes helix-helix distance and crossing angle was developed by Lee and Im . They applied external potential to those RCs to enhance sampling in MD simulations.
[Show abstract] [Hide abstract] ABSTRACT: The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions. By preparing multiple samples in each of which a different ion of the lanthanide series is introduced, it is possible to obtain multiple independent PCS datasets that can be used synergistically to generate protein structure ensembles (typically called bundles). For typical NMR-based determination of protein structure, it is necessary to perform an energetic refinement of such initial bundles to obtain final structures whose geometric quality is suitable for deposition in the PDB. This can be conveniently done by using restrained molecular dynamics simulations (rMD) in explicit solvent. However, there are no available protocols for rMD using multiple PCS datasets as part of the restraints. In this work, we extended the PCS module of the AMBER MD package to handle multiple datasets and tuned a previously developed protocol for NMR structure refinement to achieve consistent convergence with PCS restraints. Test calculations with real experimental data show that this new implementation delivers the expected improvement of protein geometry, resulting in final structures that are of suitable quality for deposition. Furthermore, we observe that also initial structures generated only with traditional restraints can be successfully refined using traditional and PCS restraints simultaneously.
- Aside from the accuracy and completeness of experimental data, the quality of NMR structures thus depends on the programs utilized in the generation of initial structures with simplified force fields and in their subsequent energetic refinement (Linge and Nilges 1999; Linge et al. 2003; Chen et al. 2004 ). In particular, as demonstrated by many studies, the quality of NMR structures can be improved by refinement either based on molecular dynamics simulations with state-of-the-art force field and explicit or, less often, implicit solvent (Xia et al. 2002; Linge et al. 2003; Chen et al. 2004; Feig et al. 2004; Jao et al. 2008 ). Other approaches based on structure rebuilding (Mao et al. 2014) or on the use of statistical potentials (Ryu et al. 2016) have been proposed.
[Show abstract] [Hide abstract] ABSTRACT: Antimicrobial peptides (AMPs) are small, naturally occurring peptides that exhibit strong antibacterial properties generally believed to be a result of selective bacterial membrane disruption. As a result, there has been significant interest in the development of therapeutic antibiotics based on AMPs; however, the poor understanding of the fundamental mechanism of action of these peptides has largely hampered such efforts. We present a summary of computational and theoretical investigations of protegrin, a particularly potent peptide that is both an excellent model for the mechanism of action of AMPs and a promising therapeutic candidate. Experimental investigations have shed light on many of the key steps in the action of protegrin: protegrin monomers are known to dimerize in various lipid environments; protegrin peptides interact strongly with lipid bilayer membranes, particularly anionic lipids; protegrins have been shown to form pores in lipid bilayers, which results in uncontrolled ion transport and may be a key factor in bacterial death. In this work, we present a comprehensive review of the computational and theoretical studies that have complemented and extended the information obtained from experimental work with protegrins, as well as a brief survey of the experimental biophysical studies that are most pertinent to such computational work. We show that a consistent, mechanistic description of the bactericidal mechanism of action of protegrins is emerging, and briefly outline areas where the current understanding is deficient. We hope that the research reviewed herein offers compelling evidence of the benefits of computational investigations of protegrins and other AMPs, as well as providing a useful guide to future work in this area.
- The work described herein spans a variety of computational studies aimed at understanding the mechanism of action of protegrin peptides and ultimately engineering novel therapeutics based on protegrin templates. The earliest MD simulations of protegrin peptides were conducted in lipid micelles [ that quantify peptide orientation in a lipid bilayer [67,86], adsorption  and dimerization . The properties of oligomeric protegrin pores have also been analyzed by several MD simulation studies [14,43,59], which confirmed their stability, demonstrated their ability to cause uncontrolled ion transport and showed a tendency for pore-lining lipids to tilt towards the peptides, favoring a toroidal or semi-toroidal arrangement.
[Show abstract] [Hide abstract] ABSTRACT: Ever since technologies enabled the characterization of eukaryotic plasma membranes, heterogeneities in the distributions of its constituents were observed. Over the years this led to the proposal of various models describing the plasma membrane organization such as lipid shells, picket-and-fences, lipid rafts, or protein islands, as addressed in numerous publications and reviews. Instead of emphasizing on one model we in this review give a brief overview over current models and highlight how current experimental work in one or the other way do not support the existence of a single overarching model. Instead, we highlight the vast variety of membrane properties and components, their influences and impacts. We believe that highlighting such controversial discoveries will stimulate unbiased research on plasma membrane organization and functionality, leading to a better understanding of this essential cellular structure.
- In cells, binding of proteins to charged headgroups of inner leaflet lipids is well-documented to control important cellular processes, e.g., phagocytosis (Botelho et al., 2000). In addition, peripheral protein interactions at the inner leaflet of the plasma membrane modulate localization and mobility of charged lipids, as well as some other, probably associated, molecules (Golebiewska et al., 2008Golebiewska et al., , 2011 Yeung et al., 2008). But whether such peripheral interactions can modulate the mobility of other membrane components (e.g., at the outer leaflet) and have a more general impact on the plasma membrane organization awaits its direct proof.
[Show abstract] [Hide abstract] ABSTRACT: In this work, we present pysimm, a python package designed to facilitate structure generation, simulation, and modification of molecular systems. pysimm provides a collection of simulation tools and smooth integration with highly optimized third party software. Abstraction layers enable a standardized methodology to assign various force field models to molecular systems and perform simple simulations. These features have allowed pysimm to aid the rapid development of new applications specifically in the area of amorphous polymer simulations.
- Bridging this gap helps to open up doors to many more researchers to utilize computational power to study polymer science. There is a plethora of software that exists to do various tasks associated with molecular simulations from highly optimized simulation packages such as LAMMPS , AMBER , GROMACS , CHARMM , HOOMD , OpenMM  and Cassandra  , to software designed to prepare systems for simulation such as AmberTools LEaP , PackMol , and mBuild , to computational chemistry packages such as RDKit  and OpenBabel  , to postprocessing software such as AmberTools CPPTRAJ , LAMMPS Pizza.py , PoreBlazer , VMD , PyMol  and MD- Traj , and software specifically designed to create polymer structures such as PolymerModeler , Polymatic  and As- semble!
[Show abstract] [Hide abstract] ABSTRACT: The effect of the incorporation of phosphorylated phospholamban (pPLN) and sarcolipin (SLN) in mercury-supported self-assembled lipid monolayers and in lipid bilayers tethered to mercury via a hydrophilic spacer was investigated by voltammetric techniques and electrochemical impedance spectroscopy. It was shown that pPLN and SLN do not permeabilize lipid bilayers toward ions at physiological pH. However, they exert a permeabilizing action toward inorganic monovalent cations such as K(+) and Tl(+), but not toward divalent cations such as Ca(2+) and Cd(2+), following a small decrease in pH. This behavior can be associated with their regulatory action on the Ca-ATPase of the sarcoplasmic reticulum (SERCA). SERCA pumps two Ca(2+) ions from the cytosol to the lumen of the sarcoplasmic reticulum (SR) and two protons in the opposite direction, causing a transient decrease of pH in the immediate vicinity of its cytoplasmic domain. This decrease is expected to activate the liberated pPLN molecules and SLN to make the SR membrane leakier toward K(+) and Na(+) and the SLN ion channel to translocate small inorganic anions, such as Cl(-). The effect of pPLN and SLN, which becomes synergic when they are both present in the SR membrane, is expected to favor a rapid equilibration of ions on both sides of the membrane.
- A molecular dynamics (MD) simulation of the PLN pentamer by Sansom et al.  yields a K + -pore interaction energy profile consistent with a cationselective pore. However, subsequent more sophisticated simulations [13,15,16] lead to the conclusion that the PLN pentamer is unlikely to function as an ion channel at physiological transmembrane potentials. We recently showed that, in principle, the PLN pentamer may act as a cation channel , as postulated by Oxenoid and Chou  and by Arkin at al. .
[Show abstract] [Hide abstract] ABSTRACT: Hydrophobic matching, lipid sorting, and protein oligomerization are key principles by which lipids and proteins organize in biological membranes. The Aquaporin-0 channel (AQP0), solved by electron crystallography (EC) at cryogenic temperatures, is one of the few protein-lipid complexes of which the structure is available in atomic detail. EC and room-temperature molecular dynamics (MD) of dimyristoylglycerophosphocholine (DMPC) annular lipids around AQP0 show similarities, however, crystal-packing and temperature might affect the protein surface or the lipids distribution. To understand the role of temperature, lipid phase, and protein mobility in the localization and ordering of AQP0-lipids, we used MD simulations of an AQP0-DMPC bilayer system. Simulations were performed at physiological and at DMPC gel-phase temperatures. To decouple the protein and lipid mobility effects, we induced gel-phase in the lipids or restrained the protein. We monitored the lipid ordering effects around the protein. Reducing the system temperature or inducing lipid gel-phase had a marginal effect on the annular lipid localization. However, restraining the protein mobility increased the annular lipid localization around the whole AQP0 surface, resembling EC. The distribution of the inter-phosphate and hydrophobic thicknesses showed that stretching of the DMPC annular layer around AQP0 surface is the mechanism that compensates the hydrophobic mismatch in this system. The distribution of the local area-per-lipid and the acyl-chain order parameters showed particular fluid- and gel-like areas that involved several lipid layers. These areas were in contact with the surfaces of higher and lower protein mobility, respectively. We conclude that the AQP0 surfaces induce specific fluid- and gel-phase prone areas. The presence of these areas might guide the AQP0 lipid sorting interactions with other membrane components, and is compatible with the squared array oligomerization of AQP0 tetramers separated by a layer of annular lipids.
- The local lipid ordering was estimated with g_lomepro (Gapsys et al., 2013) in a 100 × 100 grid. The calculated lipid properties were: inter-phosphorous (P–P), and hydrophobic thicknesses, the later using the carbon-2 average position from both acyl-chains (Kim et al., 2012); the area-per-lipid (APL), and the carbon-deuterium order parameters (S CD ). The interaction energies and protein fluctuations (RMSF) were estimated with Gromacs tools.
[Show abstract] [Hide abstract] ABSTRACT: The serotonin (5HT) transporter (SERT) is a member of neurotransmitter sodium symporter (NSS) family, which maintains neurotransmitter by reuptaking 5HT into synapses. Decrease in serotonin concentrations in synaptic clefts have been reported to cause psychological and neurological disorders. Therefore, inhibition of SERT is a potent strategy for the treatment of related diseases such as depression. In this study, approximately 260000 small molecules from an available chemical database have been virtually screened both at central and allosteric binding sites of SERT to identify potent novel candidate SERT inhibitors. A set of docking algorithms were used to predict binding modes and energies of compounds. Screening analyses led three top-ranked hit compounds (160234, Otava ID: 7118020138; 159166, Otava ID: 7117171303; and 69419, Otava ID: 118671819) for central binding site (S1) and one compound (93507, Otava ID: 6248262) for allosteric binding site (S2). These promising compounds are then subjected to long multiple molecular dynamics (MD) simulations to elucidate their structural and dynamical profiles at the binding cavities of SERT. Higher predicted binding affinities of identified compounds were also confirmed with binding free energy calculations (MM/GBSA) in comparison with the reference central and allosteric binding site inhibitors, paroxetine (8PR) and escitalopram (68P), respectively. To the best of our knowledge, the present work is the first structure-based high throughput virtual screening study reported using recently revealed crystal structure of SERT for screening inhibitors from chemical databases on S1 and S2 binding sites. Small molecule library screening study yielded candidate compounds both at central and allosteric binding site of SERT, and further experimentation may pave the way for developing novel strong inhibitors.
- In this way, the optimized side chain conformations of residues were determined.. Orientated complexes were embedded into the palmitoyloleoylphosphatidylcholine (POPC) membrane bilayer. 128 POPC molecules were included in the outer bilayer and 128 POPC molecules were used in the inner bilayer.
[Show abstract] [Hide abstract] ABSTRACT: The Na(+)/K(+)-pump maintains the physiological K(+) and Na(+) electrochemical gradients across the cell membrane. It operates via an 'alternating-access' mechanism, making iterative transitions between inward-facing (E1) and outward-facing (E2) conformations. Although the general features of the transport cycle are known, the detailed physicochemical factors governing the binding site selectivity remain mysterious. Free energy molecular dynamics simulations show that the ion binding sites switch their binding specificity in E1 and E2. This is accompanied by small structural arrangements and changes in protonation states of the coordinating residues. Additional computations on structural models of the intermediate states along the conformational transition pathway reveal that the free energy barrier toward the occlusion step is considerably increased when the wrong type of ion is loaded into the binding pocket, prohibiting the pump cycle from proceeding forward. This self-correcting mechanism strengthens the overall transport selectivity and protects the stoichiometry of the pump cycle.
- The coordinates of atoms in these extended region and those linked to them within three atomic bonds in the inner region were held fixed during the simulations. The rest of the system was considered the outer region, in which the atoms were removed and their impact on the inner region atoms was represented by the General Solvent Boundary Potential (GSBP) in the form of a solvent-shielded static field and a solvent-induced reaction field (Im et al., 2001). The reaction field arising from changes in charge distribution in the inner region was expressed in terms of a generalized multipole expansion using 11 spherical harmonic functions.
[Show abstract] [Hide abstract] ABSTRACT: Type III Secretion Systems (T3SS) are complex bacterial structures that provide gram-negative pathogens with a unique virulence mechanism whereby they grow a needle-like structure in order to inject bacterial effector proteins into the cytoplasm of a host cell. Numerous experiments have been performed to understand the structural details of this nanomachine during the past decade. Despite the concerted efforts of molecular and structural biologists, several crucial aspects of the assembly of this structure, such as the regulation of the length of the needle itself, remain unclear. In this work, we used a combination of mathematical and computational techniques to better understand length control based on the timing of substrate switching, which is a possible mechanism for how bacteria ensure that the T3SS needles are neither too short nor too long. In particular, we predicted the form of the needle length distribution based on this mechanism, and found excellent agreement with available experimental data from Salmonella typhimurium with only a single free parameter. Although our findings provide preliminary evidence in support of the substrate switching model, they also make a set of quantitative predictions that, if tested experimentally, would assist in efforts to unambiguously characterize the regulatory mechanisms that control the growth of this crucial virulence factor.
- As discussed above, in the alternative ruler protein mechanism, the eponymous ruler (e.g. YscP in Yersinia) is thought to anchor its C-terminus to the beginning of the needle in the secretion channel and measure the length of the needle; since the secretion channel is very narrow , the ruler will almost certainly block the secretion of other proteins during the time it is bound [5, 7]. This measurement is likely repeated several times during the course of needle growth, until the needle is long enough for the C-terminus of the ruler protein to be in proximity of the needle's end, which induces needle maturation and the end of needle polymerization [1, 13, 14].
[Show abstract] [Hide abstract] ABSTRACT: Among broadly neutralizing antibodies to HIV, 10E8 exhibits greater neutralizing breadth than most. Consequently, this antibody is the focus of prophylactic/therapeutic development. The 10E8 epitope has been identified as the conserved membrane proximal external region (MPER) of gp41 subunit of the envelope (Env) viral glycoprotein and is a major vaccine target. However, the MPER is proximal to the viral membrane and may be laterally inserted into the membrane in the Env prefusion form. Nevertheless, 10E8 has not been reported to have significant lipid-binding reactivity. Here we report x-ray structures of lipid complexes with 10E8 and a scaffolded MPER construct and mutagenesis studies that provide evidence that the 10E8 epitope is composed of both MPER and lipid. 10E8 engages lipids through a specific lipid head group interaction site and a basic and polar surface on the light chain. In the model that we constructed, the MPER would then be essentially perpendicular to the virion membrane during 10E8 neutralization of HIV-1. As the viral membrane likely also plays a role in selecting for the germline antibody as well as size and residue composition of MPER antibody complementarity determining regions, the identification of lipid interaction sites and the MPER orientation with regard to the viral membrane surface during 10E8 engagement can be of great utility for immunogen and therapeutic design.
- The putative transmembrane region model constructed solely to anchor the lipid bilayer was then used in membrane building with CHARMM . A rectangular box (x = y = 157.7 Å) was used to generate a heterogeneous bilayer containing 400 lipids on the upper leaflet and 434 lipids on the lower leaflet of the membrane, by replacement method . The HIV-1 membrane lipid composition  was taken into account when choosing the composition of the bilayer.