Monohydration selectivity mechanism of alkali cations in the potassium channel of excitable biomembranes

Nonempirical quantum chemical method Hartree–Fock–Roothan LCAO SCF MO in a two-exponent Dunning basis with the use of an extended set of Gaussian functions by Huzinaga–Dunning with consideration of electron correlation according to the Meller–Plesset theory of excitations of the second order was used to study monohydrates of Li⁺, Na⁺, K⁺, and HCOO^? ions. The indicated basis was supplemented with polarization functions of d-type on the O atom and of p-type on the hydrogen atom as well as with diffusion functions of p-type on the oxygen atom. It has been found that binding energies of the water molecule with Li⁺, Na⁺ appeared to be higher and with K⁺ lower than with HCOO^? · H₂O. Potential curve shapes of K⁺ + H₂O and HCOO^? + H₂O reactions are shown to be similar. The molecular mechanism of K⁺ channel selectivity of an excitable membrane is explained on the basis of the obtained calculations.     

Structural and functional consequences of an amide-to-ester substitution in the selectivity filter of a potassium channel

The selectivity filter of K(+) channels comprises four contiguous ion binding sites, S1 through S4. Structural and functional data indicate that the filter contains on average two K(+) ions at any given time and that these ions reside primarily in two configurations, namely to sites S1 and S3 or to sites S2 and S4. Maximum ion flux through the channel is expected to occur when the energy difference between these two binding configurations is zero. In this study, we have used protein semisynthesis to selectively perturb site 1 within the filter of the KcsA channel through use of an amide-to-ester substitution. The modification alters K(+) conduction properties. The structure of the selectivity filter is largely unperturbed by the modification, despite the loss of an ordered water molecule normally located just behind the filter. Introduction of the ester moiety was found to alter the distribution of K(+), Rb(+,) and Cs(+) within the filter, with the most dramatic change found for Rb(+). The redistribution of ions is associated with the appearance of a partially hydrated ion just external to the filter, at a position where no ion is observed in the wild-type channel. The appearance of this new ion-binding site creates a change in the distance between a pair of K(+) ions some fraction of the time, apparently leading to a reduction in the ion conduction rate. Importantly, this finding suggests that the selectivity filter of a potassium channel is optimized both in terms of absolute ion occupancy and in terms of the separation in distance between the conducting ions.     

The Effect of Fluoro Substitution upon the β‐Hairpin Fold of a β‐Tetrapeptide in Methanol

The importance of β‐peptides lies in their ability to mimic the conformational behavior of α‐peptides, even with a much shorter chain length, and in their resistance to proteases. To investigate the effect of substitution of β‐peptides on their dominant fold, we have carried out a molecular‐dynamics (MD) simulation study of two tetrapeptides, Ac‐(2R,3S)‐β^2,3hVal(αMe)‐(2S)‐β²hPhe‐(R)‐β³hLys‐(2R,3S)‐β^2,3‐Ala(αMe)‐NH₂, differing in the substitution at the C_α of Phe2 (pepF with F, and pepH with H). Three simulations, unrestrained (UNRES), using ³J‐coupling biasing with local elevation in combination with either instantaneous (INS) or time‐averaging (AVE) NOE distance restraining, were carried out for each peptide. In the unrestrained simulations, we find three (pepF) and two (pepH) NOE distance bound violations of maximally 0.22 nm that involve the terminal residues. The restrained simulations match both the NOE distance bounds and ³J‐values derived from experiment. The fluorinated peptide shows a slightly larger conformational variability than the non‐fluorinated one.     

Protein adsorption in porous adsorbent particles: A multiscale modeling study on inner radial humps in the concentration profiles of adsorbed protein induced by nonuniform ligand density distributions

Recently published results determined from molecular dynamics (MD) modeling and simulation studies have shown that the spatial distribution of the density of immobilized charged ligands in ion‐exchange porous adsorbent particles is most likely nonuniform and the adsorbent particles also exhibit local nonelectroneutrality. In this work, the functional forms of the nonuniform spatial distributions of the density of the immobilized ligands in four different porous adsorbent media that were determined by MD studies were employed in a macroscopic continuum model describing the transport and adsorption of a single protein in the porous particles of the four different adsorbent media. The results clearly show that inner radial humps in the concentration profiles of the adsorbed protein can occur when the spatial distribution of the density of the immobilized ligands in the porous adsorbent particles is nonuniform and also has local maxima or minima along the radial direction in the particle. The results also indicate that the rate at which the equilibrium condition is approached depends significantly on the functional form of the spatial distribution of the density of the immobilized ligands. When adsorption equilibrium has been reached, the concentration profile of the adsorbed protein exhibits the shape of the spatial distribution of the density of the immobilized ligands. The results suggest that the technique of confocal scanning laser microscopy could be used to measure the concentration profile of an adsorbed protein at equilibrium and this measurement could provide the spatial distribution of the density of the immobilized ligands, and such measurements could also be used for quality control of the adsorbent medium. The results in this work have also implications in the modeling, design, analysis, and quality control of systems involving biocatalysis. Furthermore, the results clearly indicate that it is very important to study the dynamic behavior of an adsorption system having a nonuniform spatial distribution in the density of the immobilized charged ligands and where (i) both monovalent and multivalent interactions between the single charged adsorbate and the immobilized charged ligands occur and (ii) the values of the pH and ionic strength are such that the electrophoretic effects are active.     

Computer simulation of the binding of amonafide and azonafide to DNA

Summary Intercalative binding of the antitumor drugs amonafide and azonafide to the oligonucleotide duplex d(GGCCGGCCGG)·d(CCGGCCGGCC) was compared using molecular dynamics in vacuum with the AMBER force field. A number of reasonable possible binding conformations were obtained, with the azonafide complexes favored over the amonafide complexes in net binding enthalpy. In comparison with amonafide, the larger chromophore of azonafide permits greater DNA distortion and wider side-chain swings, without falling out of the intercalation site. The best model obtained was used for further dynamics on amonafide and azonafide with solvent and counterions present, and again the azonafide complex had a more favorable enthalpy. Furthermore, the enthalpy change on going from solvent into the intercalation site was less unfavorable for azonafide. These results are consistent with the stronger DNA binding of azonafide compared to amonafide, as observed in relative melting transition temperature increases and tumor inhibition in cell cultures.     

Structure and ion selectivity of the open potential-dependent potassium channel

The structure and ion selectivity of the potential-dependent potassium channel is investigated. It is shown that the channel constructed by joining the α-subunit with the β-subunit concave, when the axial symmetry axes coincide, is the potential-dependent potassium channel in the open state.     

Electrophoretic ratcheting of spherical particles in well/channel microfluidic devices: Making particles move against the net field

We examine the electrophoresis of spherical particles in microfluidic devices made of alternating wells and narrow channels, including a system previously used to separate DNA molecules. Our computer simulations predict that such systems can be used to separate spherical particles of different sizes that share the same free-solution mobility. Interestingly, the electrophoretic velocity shows an inversion as the field intensity is increased: while small particles have higher velocities at low field, the situation is reversed at high fields with the larger particles then moving faster. The resulting nonlinearity suggests that asymmetric pulsed electric fields could be used to build separation ratchets: particles then have a net size-dependent velocity in the presence of a zero-mean external field. Exploiting the inversion mentioned above, we show how to design pulsed field sequences that make particles move against the mean field (an example of negative mobility). Finally, we demonstrate that it is possible to use pulsed fields to make particles of different sizes move in opposite directions, even though their charge have the same sign.     

On the dynamics of electrochemical ion-transfer reactions

A model electrochemical ion-transfer reaction is investigated by molecular dynamics simulations. Non-equilibrium solvation effects can lead to barrier recrossings when the ion passes the transition state. The resulting transmission coefficient, which measures the deviation of the rate from the predictions of the transition state theory, is in good agreement with the Grote–Hynes theory. By contrast, Kramers theory predicts a much lower rate constant. The reaction occurs in the polarization caging regime of Grote–Hynes theory, in which the solvent motion controls the advance of the reaction. Furthermore, the molecular friction depends strongly on the distance from the electrode.     

A GPU solvent–solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software

During the past few years, graphics processing units (GPUs) have become extremely popular in the high performance computing community. In this study, we present an implementation of an acceleration engine for the solvent–solvent interaction evaluation of molecular dynamics simulations. By careful optimization of the algorithm speed‐ups up to a factor of 54 (single‐precision GPU vs. double‐precision CPU) could be achieved. The accuracy of the single‐precision GPU implementation is carefully investigated and does not influence structural, thermodynamic, and dynamic quantities. Therefore, the implementation enables users of the GROMOS software for biomolecular simulation to run the solvent–solvent interaction evaluation on a GPU, and thus, to speed‐up their simulations by a factor 6–9. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Mechanisms of Biological Ion Transport — Carriers,Channels, and Pumps in Artificial Lipid Membranes

The cell membrane contains specific systems for passive and active transport of ions between the cytoplasm and the extracellular medium. For a number of small and medium-sized transport molecules like valinomycin and gramicidin A, extensive structural and kinetic data are available and it is possible in these cases to understand the transport function on the basis of their molecular structure. Incorporation into artificial bimolecular lipid membranes opens up the possibility of studying the kinetic properties of biological transport systems in detail.     

On Coarse-Graining by the Inverse Monte Carlo Method: Dissipative Particle Dynamics Simulations Made to a Precise Tool in Soft Matter Modeling

We present a promising coarse-graining strategy for linking micro- and mesoscales of soft matter systems. The approach is based on effective pairwise interaction potentials obtained from detailed atomistic molecular dynamics (MD) simulations, which are then used in coarse-grained dissipative particle dynamics (DPD) simulations. Here, the effective potentials were obtained by applying the inverse Monte Carlo method [Lyubartsev and Laaksonen, Phys. Rev. E. 52, 3730 (1995)] on a chosen subset of degrees of freedom described in terms of radial distribution functions. In our first application of the method, the effective potentials were used in DPD simulations of aqueous NaCl solutions. With the same computational effort we were able to simulate systems of one order of magnitude larger than the MD simulations. The results from the MD and DPD simulations are in excellent agreement.     

Local elevation: A method for improving the searching properties of molecular dynamics simulation

Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.     

Electrostatics of phosphatidic acid monolayers: Insights from computer simulations

In this paper, we argue that many of the fascinating electrostatic effects that take place in amphiphilic systems are strongly related to the particular organization of the oxygen atoms within each individual molecule. In particular, we focus on two effects: charge inversion and dielectric overscreening. For that purpose, we present molecular dynamics simulations of phosphatidic acid (DMPA²⁻) in the presence of divalent counterions. Our results show that the many oxygens present in DMPA²⁻ cooperatively create strong binding sites for counterions, which in some cases lead to charge inversion. We also present an analysis of the role of interfacial water and relate our analysis to the phenomenon of dielectric overscreening. Several experimental implications are discussed in the conclusions.     

In-silico structural analysis of E509K mutation in LARGE and T192M mutation in Alpha Dystroglycan in the inhibition of glycosylation of Alpha Dystroglycan by LARGE

Impaired glycosylation of cellular receptor Alpha Dystroglycan (α-DG) leads to dystroglycanopathy. Glycoprotein α-DG is the receptor protein in the Dystrophin Associated Protein Complex (DAPC), a macromolecular gathering on muscle cell membrane to form a bridge between extracellular matrix (ECM) and cellular actin cytoskeleton. Proper glycosylation of α-DG is mediated by the glycosylating enzyme LARGE. Mutations either in α-DG or in LARGE lead to improper glycosylations of α-DG thereby hampering the formation of final Laminin binding form α-DG resulting in dystroglycanopathy. In our current work, we explored the structural changes associated with the presence of mutations in α-DG as well as in the enzyme LARGE. We further extended our research to understand the effect of the mutations onto protein-enzyme interactions. Moreover, since LARGE transfers the sugar moiety (glucuronic acid; GlcA) onto α-DG, we tried to analyze what effect the mutation in LARGE confers on this enzyme ligand interaction. This work for the first time addressed the molecular changes occurring in the structures α-DG, LARGE and their interactions and shed lights on the as yet poorly understood mechanism behind the dystroglycanopathy onset.     

Atomistic Simulation Study of Calcium,Phosphate and Fluoride Ion Association to the Teleopeptide‐Tails of Collagen – Initial Steps to Biomineral Formation

The attachment of single ions to putative adsorption sites in the tails of collagen fibers is investigated by means of molecular dynamics simulations and discussed with respect to the very early steps of apatite/collagen biomineral formation. Our studies clearly demonstrate an increased flexibility of the tails of the triple‐helical collagen protein. Apart from the termini of the backbone, several side chains were also observed to be freely accessible to ion attachment from aqueous solution. The teleopeptide was systematically scanned for suitable adsorption sites for calcium, phosphate and fluoride ions. Association of these ions was then explored from potential of mean force calculations. The resulting energy profiles reveal a variety of favorable protein‐ion bonds and hint at the suitability of the collagen tails to promote apatite aggregation.     

Theoretical investigations on the interactions of glucokinase regulatory protein with fructose phosphates

Glucokinase (GK) plays a critical role in maintaining glucose homeostasis in the human liver and pancreas. In the liver, the activity of GK is modulated by the glucokinase regulatory protein (GKRP) which functions as a competitive inhibitor of glucose to bind to GK. Moreover, the inhibitory intensity of GKRP–GK is suppressed by fructose 1-phosphate (F1P), and reinforced by fructose 6-phosphate (F6P). Here, we employed a series of computational techniques to explore the interactions of fructose phosphates with GKRP. Calculation results reveal that F1P and F6P can bind to the same active site of GKRP with different binding modes, and electrostatic interaction provides a major driving force for the ligand binding. The presence of fructose phosphate severely influences the motions of protein and the conformational space, and the structural change of sugar phosphate influences its interactions with GKRP, leading to a large conformational rearrangement of loop2 in the SIS2 domain. In particular, the binding of F6P to GKRP facilitates the protruding loop2 contacting with GK to form the stable GK–GKRP complex. The conserved residues 179–184 of GKRP play a major role in the binding of phosphate group and maintaining the stability of GKRP. These results may provide deep insight into the regulatory mechanism of GKRP to the activity of GK.     

Molecular dynamics study of host–guest interactions in cyclodextrins: methodology and data analysis for a comparison with solution data and the solid-state structure

A general method is proposed to model the behavior of cyclodextrins (CDs) and of their inclusion compounds through energy minimizations and molecular dynamics (MD) simulations at a constant temperature. In this way, the formation of a host–guest compound is obtained starting from many trial geometries with the guest outside the CD cavity without any a priori assumption. The MD simulation results are analyzed through two functions: (i) the similarity maps of the root-mean-square distances between instantaneous conformations found in the MD runs to recognize different families of conformers; (ii) the pair distribution function PDF, yielding the probability density of finding appropriate atom pairs as a function of their distance at equilibrium. As an example, the inclusion compound formed by β-CD and (−)-menthol-β-d-glucoside is investigated. The lowest-energy inclusion compound is in good agreement with the results of single-crystal X-ray analysis, while at room temperature the MD runs show a closely similar arrangement with thermal fluctuations. In this case, the PDF between diagnostic hydrogen atoms of β-CD and of the guest molecule are fully consistent with the experimental NOE results obtained from NMR measurements in solution.