Structural organization of a chain molecule with specific charge distribution: A molecular dynamics study

We report the results of molecular dynamics simulations of a charged bead-monomer chain molecule with charge distribution adopted from immunoglobulin-binding domain B1 of protein-g. The beads of the model are connected by invariable bonds and interact with each other via the Coulomb potential. To study the low-temperature conformational space of the designed model we use standard canonical, microcanonical and multicanonical molecular dynamics simulations. We find that at low temperature T = T c the chain undergoes a continuous freezing transition into one of many low-energy conformations. Below T c the molecule is a compact globule composed of an inner core, containing mostly charged monomers, and an outer corona, consisting of all the rest neutral units. All frozen conformations have almost equal potential energy but differ in structure. The potential energy surface of the model does not posses a pronounced ground-state minimum--an essential feature of protein-like heteropolymers.     

A comparison of the interfacial interactions of the apoprotein from high density lipoprotein and beta-casein with phospholipids.

The conformations adopted by beta-casein and the total apoprotein from serum high density lipoprotein when spread at the air-water interface are compared; the monolayer data are consistent with the apoprotein being alpha-helical and the beta-casein being disordered with segments distributed in loops and trains. The penetration of these hydrophobic proteins into phosphatidylcholine monolayers in different physical states was investigated. More protein can penetrate into monolayers when they are in the liquid-expanded state; for penetration at constant total surface area the lateral compressibility of the lipid is an important factor. The charge and conformation of the polar group of the phospholipid does not have a major influence on the interaction. The mixed films of lipid and protein have a mosaic structure; probably the beta-casein is in a compressed state whereas the apoprotein is extended as alpha-helices in the plane of the interface. The chain-length depedences of the interaction of the apoprotein with phosphatidylcholine monolayers and bilayers are different; when the apoprotein binds to bilayers of shorter-chain phosphatidylcholines it alters the shape of the lipid-water interface whereas with monolayers the interface remains planar throughout.     

A comparison of the interfacial interactions of the apoprotein from high density lipoprotein and β-casein with phospholipids

The conformations adopted by β-casein and the total apoprotein from serum high density lipoprotein when spread at the air-water interface are compared; the monolayer data are consistent with the apoprotein being α-helical and the β-casein being disordered with segments distributed in loops and trains. The penetration of these hydrophobic proteins into phosphatidylcholine monolayers in different physical states was investigated. More protein can penetrate into monolayers when they are in the liquid-expanded state; for penetration at constant total surface area the lateral compressibility of the lipid is an important factor. The charge and conformation of the polar group of the phospholipid does not have a major influence on the interaction. The mixed films of lipid and protein have a mosaic structure; probably the β-casein is in a compressed state whereas the apoprotein is extended as α-helices in the plane of the interface. The chain-length dependences of the interaction of the apoprotein with phosphatidylcholine monolayers and bilayers are different; when the apoprotein binds to bilayers of shorter-chain phosphatidylcholines it alters the shape of the lipid-water interface whereas with monolayers the interface remains planar throughout.     

Surface charging by large multivalent molecules. Extending the standard Gouy-Chapman treatment.

Traditionally, Gouy-Chapman theory has been used to calculate the distribution of ions in the diffuse layer next to a charged surface. In recent years, the same theory has found application to adsorption (incorporation, partitioning) of charged peptides, hormones, or drugs at the membrane-water interface. Empirically it has been found that an effective charge, smaller than the physical charge, must often be used in the Gouy-Chapman formula. In addition, the large size of these molecules can be expected to influence their adsorption isotherms. To improve evaluation techniques for such experiments, comparatively simple extensions of the standard Gouy-Chapman formalism have been studied which are based on a discrete charge virial expansion. The model allows for the mobility of charged groups at the interface. It accounts for finite size of the adsorbed macromolecules and for discrete charge effects arising from pair interactions in the interface plane. In contrast to previous discrete charge treatments this model nearly coincides with the Gouy-Chapman formalism in the case where the adsorbing molecules are univalent. Large discrepancies are found for multivalent molecules. This could explain the reduced effective charges needed in the standard Gouy-Chapman treatment. The reduction factor can be predicted. The model is mainly limited to low surface coverage, typical for the adsorption studies in question.     

Ab initio self-consistent field and potential-dependent partial equalization of orbital electronegativity calculations of hydration properties of N-acetyl-N'-methyl-alanineamide

Using a recently developed parallel computation algorithm, ab initio self-consistent field (SCF) calculations were carried out to estimate the relative hydration energies for 12 low-energy conformations of N-acetyl-N'-methyl-alanineamide. The requisite SCF calculations were carried out using 6-31G and 6-31G* basis sets, both in the absence and presence of a perturbing potential arising from a model solvent. The alpha R, alpha L, polyproline II (PII), and pi helical conformations were preferentially stabilized by the solvent potential, whereas conformations with intramolecular hydrogen-bonding C5 and C7 were preferred in the gas phase. Average vicinal nmr coupling constants (JNH-C alpha H), calculated using the total energies of the various solvated conformations, were consistent with observed coupling constants for this peptide in aqueous solution. Substantial alteration of the solute charge density occurred upon equilibration with the reaction field, as was exemplified in changes both in the molecular dipole moments and in atom-centered multipoles, when the molecule was transferred from a medium of low dielectric constant to one of high dielectric constant. In order to model these changes in charge density with an empirical scheme, we have implemented a novel monopolar representation of the solute charge density based on a potential-dependent form of partial equalization of orbital electronegativities (PDPEOE). In the atom-centered point charge PDPEOE representation, charge flows from one region of the solute to another in response to external fields. Hydration energies calculated using the PDPEOE representation are similar to those calculated by the SCF procedure. Also, the PDPEOE calculations yielded changes in molecular dipole moments upon solvation that agreed closely with the changes in the calculated ab initio SCF dipole moments.     

Adhesion Signals of Phospholipid Vesicles at an Electrified Interface

General adhesion behavior of phospholipid vesicles was examined in a wide range of potentials at the mercury electrode by recording time-resolved adhesion signals. It was demonstrated that adhesion-based detection is sensitive to polar headgroups in phospholipid vesicles. We identified a narrow potential window around the point of zero charge of the electrode where the interaction of polar headgroups of phosphatidylcholine vesicles with the substrate is manifested in the form of bidirectional signals. The bidirectional signal is composed of the charge flow due to the nonspecific interaction of vesicle adhesion and spreading and of the charge flow due to a specific interaction of the negatively charged electrode and the most exposed positively charged choline headgroups. These signals are expected to appear only when the electrode surface charge density is less than the surface charge density of the choline groups at the contact interface. In comparison, for the negatively charged phosphatidylserine vesicles, we identified the potential window at the mercury electrode where charge compensation takes place, and bidirectional signals were not detected.     

Nonsequence-specific arginine interactions in the nucleosome core particle

We have analyzed the relative orientation of basic amino acid side chains towards DNA in the nucleosome core particle. The electric field created by DNA phosphates has no apparent preferential orientation: no favored orientation of the arginine guanidinium group is found. Arginine may be either directly hydrogen bonded to a phosphate oxygen or stabilized in the minor groove by van der Waals contacts and the local negative electric field. On the other hand, the phosphate oxygen atoms hydrogen bonded to arginines are always found close to the plane defined by the guanidinium group. Thus it can be concluded that the interactions of arginine are strongly directional, those of phosphate are not. We also find that a highly charged fragment of histone H2B, which is placed between two DNA turns, has a very variable conformation. An increase in protein positive charge density apparently allows multiple nonspecific protein conformations when interacting with DNA.     

The inhibition of a plant proteinase by lysine copolymers is modulated by the hydrophobicity of the interposed amino acid side chains

Summary One Lys/Phe copolymer and two series of copolymers of lysine with either alanine or tyrosine have been used as inhibitors of a plant proteinase that is known to be inhibited by polycationic inhibitors. The copolymers differ in the hydrophobicity of the non-lysine amino acid residue and the single members of each series differ from each other in their degree of polymerization and in their charge density, i.e., the frequency of occurrence of the lysine residue in the synthetic polyamino acid chain. All the tested copolymers show cooperative inhibition, with a Hill coefficient higher than 1. CD measurements indicate that the inhibition is realized through a conformational change of the enzyme molecule. Both the enzyme inhibition and the conformational change are supported by aspecific electrostatic binding between the positively charged groups of the lysine moiety and the negatively charged groups of the enzyme surface. In each series the inhibitory power increases with the charge density, while at the same charge density the inhibitory efficiency depends on the hydrophobicity of the side chain of the non-lysine amino acid in the order Phe>Tyr>Ala.     

Conformation and hydration of aspartame

Conformational free energy calculations using an empirical potential (ECEPP/2) and the hydration shell model were carried out on the neutral, acidic, zwitterionic, and basic forms of aspartame in the hydrated state. The results indicate that as the molecule becomes more charged, the number of low energy conformations becomes smaller and the molecule becomes less flexible. The calculated free energies of hydration of charged aspartames show that hydration has a significant effect on the conformation in solution. Only two feasible conformations were found for the zwitterionic form, and these are consistent with the conformations deduced from NMR and X-ray diffraction experiments. The calculated free energy difference between these two conformations was 1.25 kcal/mol. The less favored of the two solvated conformations can be expected to be stabilized by hydrophobic interaction of the phenyl groups in the crystal.     

Structure of valinomycin by molecular dynamics studies.

Valinomycin is an important ionophore which exhibits a high conformational flexibility. The study of various conformations adopted by this molecule together with the study of flexibility in a given conformation can throw light on the ion transport by the ionophore across the membrane. Molecular dynamics (MD) studies are ideal to characterize the flexibility in different parts of the molecule and can also give an idea of various conformations adopted by the molecule at a given temperature. Hence MD studies at 100K have been carried out on the minimized crystal structure of the molecule to scan the possible conformations in the neighbourhood of the well known 'bracelet' like structure of uncomplexed Valinomycin, Properties, like the flexibility, average values, r.m.s. fluctuations of the various intramolecular hydrogen bonds are discussed. Energy minimization has been carried out on selected MD simulated points to analyze the characteristics of the unique conformation adopted by this molecule at this temperature.     

Charge pairing of headgroups in phosphatidylcholine membranes: A molecular dynamics simulation study

Molecular dynamics simulation of the hydrated dimyristoylphosphatidylcholine (DMPC) bilayer membrane in the liquid-crystalline phase was carried out for 5 ns to study the interaction among DMPC headgroups in the membrane/water interface region. The phosphatidylcholine headgroup contains a positively charged choline group and negatively charged phosphate and carbonyl groups, although it is a neutral molecule as a whole. Our previous study (Pasenkiewicz-Gierula, M., Y. Takaoka, H. Miyagawa, K. Kitamura, and A. Kusumi. 1997. J. Phys. Chem. 101:3677-3691) showed the formation of water cross-bridges between negatively charged groups in which a water molecule is simultaneously hydrogen bonded to two DMPC molecules. Water bridges link 76% of DMPC molecules in the membrane. In the present study we show that relatively stable charge associations (charge pairs) are formed between the positively and negatively charged groups of two DMPC molecules. Charge pairs link 93% of DMPC molecules in the membrane. Water bridges and charge pairs together form an extended network of interactions among DMPC headgroups linking 98% of all membrane phospholipids. The average lifetimes of DMPC-DMPC associations via charge pairs, water bridges and both, are at least 730, 1400, and over 1500 ps, respectively. However, these associations are dynamic states and they break and re-form several times during their lifetime.     

Density functional theory for the nonspecific binding of salt to polyelectrolytes: thermodynamic properties

The thermodynamics of the nonspecific binding of salt to a polyelectrolyte molecule is studied using a density functional approach. The polyelectrolyte molecule is modeled as an infinite, inflexible, and impenetrable charged cylinder and the counterions and co-ions are modeled as charged hard spheres of equal diameter. The density functional theory is based on a hybrid approach where the hard-sphere contribution to the one-particle correlation function is evaluated nonperturbatively and the ionic contribution to the one-particle correlation function is evaluated perturbatively. The advantage of the approach is that analytical expressions are available for all the correlation functions. The calculated single ion preferential interaction coefficients, excess free energy, and activity coefficients show a nonmonotonic variation as a function of polyion charge in the presence of divalent ions. These properties display considerable departure from the predictions of the nonlinear Poisson-Boltzmann (NLPB) equation, with qualitative differences in some cases, which may be attributed to correlation effects neglected in the NLPB theory.     

Ions from the Hofmeister series and osmolytes: effects on proteins in solution and in the crystallization process

Sephadex G-10 gel sieving chromatography, Jones-Dole viscosity B coefficients, and solution neutron and X-ray diffraction are used to show that small ions of high charge density (e.g., sulfate, phosphate, the carboxylate, sodium, and fluoride) are strongly hydrated (kosmotropes) whereas large monovalent ions of low charge density (e.g., ammonium, chloride, potassium, and the positively charged amino acid side chains) are weakly hydrated (chaotropes). The heats of solution of the crystalline alkali halides are then used to show that only oppositely charged ions of equal water affinity spontaneously form inner sphere ion pairs, and that this controls ion binding to proteins. The net charge on a protein is a major determinant of its solubility. Finally, the surface potential difference and surface tension at an air-salt solution interface are used to generate a simple model for how ions affect protein stability and solubility through indirect interactions at the protein-solution interface. A few comments about small neutral osmolytes are also included.     

An X-ray diffraction analysis of oriented lipid multilayers containing basic proteins

X-ray diffraction techniques have been used to study the structures of lipid bilayers containing basic proteins. Highly ordered multilayer specimens have been formed by using the Langmuir-Blodgett method in which a solid support is passed through a lipid monolayer held at constant surface pressure at an air/water interface. If the lipid monolayer contains acidic lipids then basic proteins in the aqueous subphase are transferred with the monolayer and incorporated into the multi-membrane stack. X-ray diffraction patterns have been recorded from multilayers of cerebroside sulphate and 40% (molar) cholesterol both with and without polylysine, cytochrome c and the basic protein from central nervous system myelin. Electron density profiles across the membranes have been derived at between 6 A and 12 A resolution. All of the membrane profiles have been placed on an absolute scale of electron density by the isomorphous exchange of cholesterol with a brominated cholesterol analog. The distributions and conformations of the various basic proteins incorporated within the cerebroside sulphate/cholesterol bilayer are very different. Polylysine attaches to the surface of the lipid bilayer as a fully extended chain while cytochrome c maintains its native structure and attaches to the bilayer surface with its short axis approximately perpendicular to the membrane plane. The myelin basic protein associates intimately with the lipid headgroups in the form of an extended molecule, yet its dimension perpendicular to the plane of the membrane of approx. 15 A is consistent with the considerable degree of secondary structure found in solution. In the membrane plane, the myelin basic protein extends to cover an area of about 2500 A2. There is no significant penetration of the protein into the hydrocarbon region of the bilayer or, indeed, beyond the position of the sulphate group of the cerebroside sulphate molecule.     

Structure-function relationships in a winter flounder antifreeze polypeptide. I. Stabilization of an alpha-helical antifreeze polypeptide by charged-group and hydrophobic interactions

The major antifreeze polypeptide (AFP) from winter flounder (37 amino acid residues) is a single alpha-helix. Aspartic acid and arginine are found, respectively, at the amino and carboxyl-termini. These charged amino acids are ideally located for stabilizing the alpha-helical conformation of this AFP by means of charge-dipole interaction (Shoemaker, K. R., Kim, P.S., York, E.J., Stewart, J. M., and Baldwin, R. L. (1987) Nature 326, 563-567). In order to understand these and other molecular interactions that maintain the AFP structure, we have carried out the chemical synthesis of AFP analogs and evaluated their conformations by circular dichroism spectroscopy. We synthesized the entire AFP molecule (37-mer) and six COOH-terminal peptide fragments (36-, 33-, 27-, 26-, 16-, and 15-mers). Peptides containing acidic NH2-terminal residues displayed greater helix formation and thermal stability compared to those peptides of similar size, but with neutral NH2-terminal residues. Helix formation was maximum above pH 9.2. The peptide conformations also displayed a pH-dependent sensitivity to changes in ionic strength. Helix formation was reduced in the presence of acetonitrile. We conclude that the AFP helix is most likely stabilized by: charge-dipole interactions between charged terminal amino acids and the helix dipole, a charge interaction between Lys18 and Glu22 (either a salt bridge or a hydrogen bond), and hydrophobic interactions.     

Poisson-Boltzmann Theory for Membranes with Mobile Charged Lipids and the pH-Dependent Interaction of a DNA Molecule with a Membrane

We consider a planar stiff model membrane consisting of mobile surface groups whose state of charge depends on the pH and the ionic composition of the adjacent electrolyte solution. To calculate the mean-field interaction potential between a charged object and such a model membrane, one needs to solve a Poisson-Boltzmann boundary value problem. We here derive and discuss the boundary condition at the membrane surface, a condition that is generally appropriate for biological membranes where two charge-regulating mechanisms are present at the same time: the pH-dependent chemical charge regulation and a regulation through the in-plane mobility of the surface groups. As an application of this general formalism, we consider the specific example of a single DNA molecule, approximated by a cylinder with smeared-out surface charges, interacting with such a model membrane. We study the effect that the two competing charge-regulating mechanisms have on the DNA/membrane interaction and the distribution of surface ions in the plane of the membrane. We find that, at short DNA-membrane distances, membrane fluidity can have a considerable impact on the DNA adsorption behavior and can lead to such counterintuitive phenomena as the adsorption of a negatively charged DNA onto a (on average) negatively charged membrane.     

The effect of lipid demixing on the electrostatic interaction of planar membranes across a salt solution

We study the effect of lipid demixing on the electrostatic interaction of two oppositely-charged membranes in solution, modeled here as an incompressible two-dimensional fluid mixture of neutral and charged mobile lipids. We calculate, within linear and nonlinear Poisson-Boltzmann theory, the membrane separation at which the net electrostatic force between the membranes vanishes, for a variety of different system parameters. According to Parsegian and Gingell, contact between oppositely-charged surfaces in an electrolyte is possible only if the two surfaces have exactly the same charge density (sigma(1) = -sigma(2)). If this condition is not fulfilled, the surfaces can repel each other, even though they are oppositely charged. In our model of a membrane, the lipidic charge distribution on the membrane surface is not homogeneous and frozen, but the lipids are allowed to freely move within the plane of the membrane. We show that lipid demixing allows contact between membranes even if there is a certain charge mismatch, /sigma(1)/ not equal /sigma(2)/, and that in certain limiting cases, contact is always possible, regardless of the value of sigma(1)/sigma(2) (if sigma(1)/sigma(2) < 0). We furthermore find that of the two interacting membranes, only one membrane shows a major rearrangement of lipids, whereas the other remains in exactly the same state it has in isolation and that, at zero-disjoining pressure, the electrostatic mean-field potential between the membranes follows a Gouy-Chapman potential from the more strongly charged membrane up to the point of the other, more weakly charged membrane.     

The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase

Alkaline phosphatase (AP) from the cold-adapted Vibrio strain G15-21 is among the AP variants with the highest known k(cat) value. Here the structure of the enzyme at 1.4 A resolution is reported and compared to APs from E. coli, human placenta, shrimp and the Antarctic bacterium strain TAB5. The Vibrio AP is a dimer although its monomers are without the long N-terminal helix that embraces the other subunit in many other APs. The long insertion loop, previously noted as a special feature of the Vibrio AP, serves a similar function. The surface does not have the high negative charge density as observed in shrimp AP, but a positively charged patch is observed around the active site that may be favourable for substrate binding. The dimer interface has a similar number of non-covalent interactions as other APs and the "crown"-domain is the largest observed in known APs. Part of it slopes over the catalytic site suggesting that the substrates may be small molecules. The catalytic serines are refined with multiple conformations in both monomers. One of the ligands to the catalytic zinc ion in binding site M1 is directly connected to the crown-domain and is closest to the dimer interface. Subtle movements in metal ligands may help in the release of the product and/or facilitate prior dephosphorylation of the covalent intermediate. Intersubunit interactions may be a major factor for promoting active site geometries that lead to the high catalytic activity of Vibrio AP at low temperatures.     

The role of surface charge on the accelerating action of heparin on the antithrombin III-inhibited activity of alpha-thrombin

We have compared surface charge and the surface charge density on the polyanions heparin and potassium polyvinyl sulfate (KPVS), as well as on hydrolyzed heparin and KPVS, with their accelerating effect on the inhibitory action of antithrombin III on thrombin. Polyelectrolyte titration of thrombin with KPVS or heparin at pH 7.4 clearly indicates an electrostatic interaction. In contrast, at the same pH no electrostatic interaction is observed between polyanions and antithrombin III. KPVS accelerates the inhibitory action of antithrombin III to the same extent as heparin on the basis of charge equivalence. Heparin and KPVS with a mean distance between two charged centers of less than 0.75 and 0.95 nm, respectively, accelerate strongly whereas hydrolysates with lower charge densities are far less active. The following observations are indicated. Intramolecular neutralization of oppositely charged residues occurs within thrombin, antithrombin III, and partially hydrolyzed heparin. Heparin acts on the antithrombin III-thrombin reaction through cooperative electrostatic binding to thrombin and nonelectrostatic interaction with antithrombin III. This indicates a quasi-catalytic action of the polyelectrolyte. Hydrolysis of only a few N-sulfate residues within the heparin molecule decreases the linear surface charge density to such an extent that the accelerating action is drastically reduced. The loss of accelerating capacity agrees with the sudden loss of counterion condensation due to the decrease of the linear surface charge density beyond limits postulated by Manning in a theory of polyelectrolytes.     

Transport of charged macromolecules across a biological charged membrane

The glomerular capillary wall of the kidney behaves as an electronegatively charged structure consisting of three layers, the lamina densa and the two laminae rarae, which are differently charged. Thus, a three layer model is proposed to analyse the transport of charged macromolecules across this wall. A modified Nernst-Planck equation describes the macromolecule flux across the wall and a Donnan equilibrium is assumed at each interface. For a given value of the fixed charge concentration in each layer, the local sieving coefficient of the macromolecule, i.e. the ratio between the concentrations in the filtrate and in the plasma, is calculated. A sieving curve which relates the sieving coefficient to the Einstein-Stokes radius of the macrosolute is obtained. The fixed charge concentrations in each layer are iteratively modified until simultaneous adjustment is achieved between calculated and experimental curves, for positively and negatively charged tracers and their neutral equivalent.