Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces.

Rather than acting by modifying van der Waals or electrostatic double layer interactions or by directly bridging neighboring molecules, polyvalent ligands bound to DNA double helices appear to act by reconfiguring the water between macromolecular surfaces to create attractive long range hydration forces. We have reached this conclusion by directly measuring the repulsive forces between parallel B-form DNA double helices pushed together from the separations at which they have self organized into hexagonal arrays of parallel rods. For all of the wide variety of "condensing agents" from divalent Mn to polymeric protamines, the resulting intermolecular force varies exponentially with a decay rate of 1.4-1.5 A, exactly one-half that seen previously for hydration repulsion. Such behavior qualitatively contradicts the predictions of all electrostatic double layer and van der Waals force potentials previously suggested. It fits remarkably well with the idea, developed and tested here, that multivalent counterion adsorption reorganizes the water at discrete sites complementary to unadsorbed sites on the apposing surface. The measured strength and range of these attractive forces together with their apparent specificity suggest the presence of a previously unexpected force in molecular organization.     

Solute—Water interactions: Do polyhydroxy compounds alter the properties of water?

The interactions between PHCs and water, like those between water molecules, are governed by hydrogen bonding. The details of these interactions are very sensitive to spacings and orientations of the OH groups on the solute molecules. Where different conformers can coexist in solution, the aqueous solvent acts so as to favor the conformer with the largest number of equatorial OH groups, because of their spatial compatibility with water.Because of this compatibility, aqueous solutions of PHCs have the tendency to supersaturation and incomplete freezing, manifestations of the phenomenon known as bound water which is, however, a misnomer. The range of water structure perturbation is probably governed by hydration forces which appear to dominate at solute-solute distances of < 3 nm and which decay exponentially. Although on a single hydrogen bond basis the hydration effects are marginal, they nevertheless are responsible for many macroscopic phenomena, e.g., gel formation, liquid crystals, and protection against dehydration.     

Measuring electrostatic, van der Waals, and hydration forces in electrolyte solutions with an atomic force microscope

In atomic force microscopy, the tip experiences electrostatic, van der Waals, and hydration forces when imaging in electrolyte solution above a charged surface. To study the electrostatic interaction force vs distance, curves were recorded at different salt concentrations and pH values. This was done with tips bearing surface charges of different sign and magnitude (silicon nitride, Al₂O₃, glass, and diamond) on negatively charged surfaces (mica and glass). In addition to the van der Waals attraction, neutral and negatively charged tips experienced a repulsive force. This repulsive force depended on the salt concentration. It decayed exponentially with distance having a decay length similar to the Debye length. Typical forces were about 0.1 nN strong. With positively charged tips, purely attractive forces were observed. Comparing these results with calculations showed the electrostatic origin of this force.

In the presence of high concentrations (> 3 M) of divalent cations, where the electrostatic force can be completely ignored, another repulsive force was observed with silicon nitride tips on mica. This force decayed roughly exponentially with a decay length of 3 nm and was ~0.07-nN strong. This repulsion is attributed to the hydration force.

     

Helix-specific interactions induce condensation of guanosine four-stranded helices in concentrated salt solutions.

Deoxyguanosine-5'-monophosphate in water self-associates into stable structures, which include liquid-crystalline hexagonal and cholesteric phases. The structural unit is a four-stranded helix, composed of stacked Hoogsteen-bonded guanosine quartets. By using the osmotic stress method, we recently measured the force between helices in KCl solutions up to 2 M. In addition to the long-range electrostatic force, a short-range hydration repulsive contribution was recognized. The hydration repulsion is exponential, and shows a decay length independent from the ionic strength of the solution. Here, we report that more concentrated KCl solutions cause condensation of the guanosine helix in a hexagonal phase with constant equilibrium separation of approximately 7 A between helix surfaces. Long-range attraction, which induces the self-assembly, and short-range repulsion, which prevents the contact between the helices, are implied. By using osmotic stress, the force needed to push helices closer from the spontaneously assumed position has been measured. The attractive force was then estimated as a difference between the net force and the repulsive contribution, revealing an exponential decay length about two times larger than that of the short-range repulsion. The agreement with the helix interaction theory introduced recently by Kornyshev and Leikin (Kornyshev, A. A., and S. Leikin, 1997. Theory of interaction between helical molecules. J. Phys. Chem. 107:3656-3674) suggests that the repulsive and attractive forces originate from helix-specific interactions.     

Differences between non-specific and bio-specific, and between equilibrium and non-equilibrium, interactions in biological systems

The interaction forces between biological molecules and surfaces are much more complex than those between non-biological molecules or surfaces, such as colloidal particle surfaces. This complexity is due to a number of factors: (i) the simultaneous involvement of many different molecules and different non-covalent forces - van der Waals, electrostatic, solvation (hydration, hydrophobic), steric, entropic and 'specific', and (ii) the flexibility of biological macromolecules and fluidity of membranes. Biological interactions are better thought of as 'processes' that evolve in space and time and, under physiological conditions, involve a continuous input of energy. Such systems are, therefore, not at thermodynamic equilibrium, or even tending towards equilibrium. Recent surface forces apparatus (SFA) and atomic force microscopy (AFM) measurements on supported model membrane systems (protein-containing lipid bilayers) illustrate these effects. It is suggested that the major theoretical challenge is to establish manageable theories or models that can describe the spatial and time evolution of systems consisting of different molecules subject to certain starting conditions or energy inputs.     

Structure and hydration of BamHI DNA recognition site: a molecular dynamics investigation

The results of a 3-ns molecular dynamics simulation of the dodecamer duplex d(TATGGATCCATA)(2) recognized by the BamHI endonuclease are presented here. The DNA has been simulated as a flexible molecule using an AMBER force field and the Ewald summation method, which eliminates the undesired effects of truncation and permits evaluation of the full effects of electrostatic forces. The starting B conformation evolves toward a configuration quite close to that observed through x-ray diffraction in its complex with BamHI. This configuration is fairly stable and the Watson-Crick hydrogen bonds are well maintained over the simulation trajectory. Hydration analysis indicates a preferential hydration for the phosphate rather than for the ester oxygens. Hydration shells in both the major and minor groove were observed. In both grooves the C-G pairs were found to be more hydrated than A-T pairs. The "spine of hydration" in the minor groove was clear. Water residence times are longer in the minor groove than in the major groove, although relatively short in both cases. No special long values are observed for sites where water molecules were observed by x-ray diffraction, indicating that water molecules having a high probability of being located in a specific site are also fast-exchanging.     

Variation in hydration forces between neutral phospholipid bilayers: evidence for hydration attraction

It is now generally recognized that hydration forces dominate close interactions of lipid hydrophilic surfaces. The commonality of their characteristics has been reasonably established. However, differences in measured net repulsion, particularly evident when phosphatidylethanolamine (PE) and phosphatidylcholine (PC) bilayers are compared, suggest there exists a variety of behavior wider than expected from earlier models of hydration and fluctuation repulsion balanced by van der Waals attraction. To find a basis for this diverse behavior, we have looked more closely at measured structural parameters, degrees of hydration, and interbilayer repulsive forces for the lamellar phases of the following lipids: 1-palmitoyl-2-oleoyl-PE (POPE), egg PE, transphosphatidylated egg PE (egg PE-T), mono- and dimethylated egg PE-T (MMPE and DMPE), 1-stearoyl-2-oleoyl-PC (SOPC), and mixtures of POPE and SOPC. POPE and SOPC bilayers differ not only in their maximum degrees of hydration but also in the empirical hydration force coefficients and decay lengths that characterize their interaction. When mixed with POPE, SOPC effects sudden and disproportionate increases in hydration. POPE, egg PE, and egg PE-T differ in their degree of hydration, molecular area, and hydration repulsion. A single methylation of egg PE-T almost completely converts its hydration and bilayer repulsive properties to those of egg PC; little progression of hydration is seen with successive methylations. In order to reconcile these observations with the conventional scheme of balancing interbilayer hydration and fluctuation-enhanced repulsion with van der Waals attraction, it is necessary to relinquish the fundamental idea that the decay of hydration forces is a constant determined by the properties of the aqueous medium. Alternatively, one can retain that fundamental idea if one recognizes the possibility that polar group hydration has an attractive component to it. In the latter view, that attractive component originates from interbilayer hydrogen-bonded water bridges between apposing bilayer surfaces, arising from correlation of zwitterionic or other complementary polar groups or from factors that affect polar group solubility. The same Marcelja and Radic formalism that accounts so well for the repulsive component also leads to an estimate of the attractive one. We suggest that the full range of degrees of hydration and of interbilayer spacings observed for different neutral bilayers results in part from variable contributions of the attractive and repulsive hydration components.(ABSTRACT TRUNCATED AT 400 WORDS)     

A comparison of DMPC- and DLPE-based lipid bilayers.

A 250 ps molecular dynamics simulation of the dimyristoylphosphatidylcholine (DMPC)-based lipid bilayer, including explicit water molecules, is reported. The solvent environment of the head groups and other structural properties of the bilayer have been analyzed and compared with experimental results as well as our previous simulation of the dilauroylphosphatidylethanolamine (DLPE)-based bilayer. From this comparison we find that the solvent structure around the DMPC head group (clathrate shell) is significantly different than that around the DLPE head group (typical hydrogen bonding interactions). We have modeled the probable relationship between the different solvent environments around the R-N(CH3)3+ (DMPC) and R-NH3+ (DLPE) head groups and the different interlammelar distances in these systems by performing potential of mean force (PMF) simulations on two N(CH3)4+ and NH4+ ions in water. From the PMF simulations it appears that the differences in the hydration of the DMPC and DLPE head groups is not responsible for the differences in the hydration force observed for these systems. We also find that the orientational polarization of DLPE and DMPC is similar, which suggests that solvent polarization is not responsible for the differences in the hydration repulsion behavior observed in these systems. We also examined the order parameters for DMPC and found them to be in reasonable agreement with experiment. Given the different characteristics of the DLPE and DMPC head groups, we suggest an explanation of the differences in the interlammellar spacings of bilayers composed of these like-charged lipids. From our DLPE simulations we find that the R-NH3+ head groups can interact with the nonesterified oxygens of the phosphate group in an intraleaflet or an interleaflet manner. For the latter a "cross link" between two leaflets can be formed, which causes a stabilization of the interlamellar spacings at fairly short distances. Moreover, due to the strong intraleaflet interaction we find that the DLPE interface is relatively "flat" (as opposed to DMPC-based bilayers), which results in a surface that has regions of positive and negative charge that reside in the same plane along the bilayer normal. Based on this we propose that the DLPE bilayer interface can correlate itself with another DLPE interface by alignment of the regions of positive (or negative) charge on one leaflet with the opposite charges on the opposing leaflet.     

Dipole–dipole interactions between tryptophan side chains and hydration water molecules dominate the observed dynamic stokes shift of lysozyme

The fluorescence intensity of tryptophan residues in hen egg-white lysozyme was measured up to 500 ps after the excitation by irradiation pulses at 290 nm. From the time-dependent variation of fluorescence intensity in a wavelength range of 320–370 nm, the energy relaxation in the dynamic Stokes shift was reconstructed as the temporal variation in wavenumber of the estimated fluorescence maximum. The relaxation was approximated by two exponential curves with decay constants of 1.2 and 26.7 ps. To interpret the relaxation, a molecular dynamics simulation of 75 ns was conducted for lysozyme immersed in a water box. From the simulation, the energy relaxation in the electrostatic interactions of each tryptophan residue was evaluated by using a scheme derived from the linear response theory. Dipole–dipole interactions between each of the Trp62 and Trp123 residues and hydration water molecules displayed an energy relaxation similar to that experimentally observed regarding time constants and magnitudes. The side chains of these residues were partly or fully exposed to the solvent. In addition, by inspecting the variation in dipole moments of the hydration water molecules around lysozyme, it was suggested that the observed relaxation could be attributed to the orientational relaxation of hydration water molecules participating in the hydrogen-bond network formed around each of the two tryptophan residues.     

Why forces between proteins follow different Hofmeister series for pH above and below pI

The relative effectiveness of different anions in crystallizing proteins follows a reversed Hofmeister sequence for pHpI. The phenomenon has been known almost since Hofmeister's original work but it has not been understood. It is here given a theoretical explanation. Classical electrolyte and double layer theory deals only with electrostatic forces acting between ions and proteins. Hydration and hydration interactions are dealt with usually only in terms of assumed hard core models. But there are, at and above biological salt concentrations, other non-electrostatic (NES) ion-specific forces acting that are ignored in such modeling. Such electrodynamic fluctuation forces are also responsible for ion-specific hydration. These missing forces are variously comprehended under familiar but generally unquantified terms, typically, hydration, hydrogen bonding, pi-electron-cation interactions, dipole-dipole, dipole-induced dipole and induced dipole-induced dipole forces and so on. The many important body electrodynamic fluctuation force contributions are accessible from extensions of Lifshitz theory from which, with relevant dielectric susceptibility data on solutions as a function of frequency, the forces can be extracted quantitatively, at least in principle. The classical theories of colloid science that miss such contributions do not account for a whole variety of ion-specific phenomena. Numerical results that include these non-electrostatic forces are given here for model calculations of the force between two model charge-regulated hen-egg-white protein surfaces. The surfaces are chosen to carry the same charge groups and charge density as the protein. What emerges is that for pHpI (where anions are co-ions) the forces increase in the order NaCl相似文献   

Structure, dynamics and hydration of the nogalamycin-d(ATGCAT)2Complex determined by NMR and molecular dynamics simulations in solution.

The structure of the 1:1 nogalamycin:d(ATGCAT)2 complex has been determined in solution from high-resolution NMR data and restrained molecular dynamics (rMD) simulations using an explicit solvation model. The antibiotic intercalates at the 5'-TpG step with the nogalose lying along the minor groove towards the centre of the duplex. Many drug-DNA nuclear Overhauser enhancements (NOEs) in the minor groove are indicative of hydrophobic interactions over the TGCA sequence. Steric occlusion prevents a second nogalamycin molecule from binding at the symmetry-related 5'-CpA site, leading to the conclusion that the observed binding orientation in this complex is the preferred orientation free of the complication of end-effects (drug molecules occupy terminal intercalation sites in all X-ray structures) or steric interactions between drug molecules (other NMR structures have two drug molecules bound in close proximity), as previously suggested. Fluctuations in key structural parameters such as rise, helical twist, slide, shift, buckle and sugar pucker have been examined from an analysis of the final 500 ps of a 1 ns rMD simulation, and reveal that many sequence-dependent structural features previously identified by comparison of different X-ray structures lie within the range of dynamic fluctuations observed in the MD simulations. Water density calculations on MD simulation data reveal a time-averaged pattern of hydration in both the major and minor groove, in good agreement with the extensive hydration observed in two related X-ray structures in which nogalamycin is bound at terminal 5'-TpG sites. However, the pattern of hydration determined from the sign and magnitude of NOE and ROE cross-peaks to water identified in 2D NOESY and ROESY experiments identifies only a few "bound" water molecules with long residence times. These solvate the charged bicycloaminoglucose sugar ring, suggesting an important role for water molecules in mediating drug-DNA electrostatic interactions within the major groove. The high density of water molecules found in the minor groove in X-ray structures and MD simulations is found to be associated with only weakly bound solvent in solution.     

The interactions of nucleic acids at elevated hydrostatic pressure

The application of elevated hydrostatic pressure on the order of a few thousand bar provides insight into the molecular forces responsible for stabilizing the conformations and non-covalent interactions of biological molecules in aqueous solution. In particular, the parameters derived from these studies have enabled researchers to glean information regarding the importance of hydration in the energetics and kinetics of these systems. This review presents data concerned with the application of hydrostatic pressure to study the thermodynamics, kinetics, and structure of nucleic acids and the interactions between nucleic acids and proteins, enzymes, and drugs. These complexes often form extremely stable non-covalent complexes in which electrostatic interactions play an important role. The sensitivity of these interactions to pressure offers a valuable experimental tool for investigating the energetics of the complexes.     

Preferential hydration of DNA: the magnitude and distance dependence of alcohol and polyol interactions

The physical forces that underlie the exclusion of solutes from macromolecular surfaces can be probed in a similar way as the measurement of forces between macromolecules in condensed arrays using the osmotic stress technique and x-ray scattering. We report here the dependence of alcohol exclusion or, equivalently, the preferential hydration of DNA on the spacing between helices in condensed arrays. The actual forces describing exclusion are quite different from the commonly assumed steric crowding coupled with weak binding. For a set of 12 nonpolar alcohols, exclusion is due to repulsive hydration interactions with the charged DNA surface. Exclusion amplitudes do not depend simply on size, but rather on the balance between alkyl carbons and hydroxyl oxygens. Polyols are included at very close spacings. The distance dependence of polyol inclusion, however, is quite different from nonpolar alcohol exclusion, suggesting the underlying mechanism of interaction is different.     

Measurement and modification of forces between lecithin bilayers.

We probe in two different ways the competing attractive and repulsive forces that create lamellar arrays of the phospholipid lecithin when in equilibrium with pure water. The first probe involves the addition of low molecular weight solutes, glucose and sucrose, to a system where the phospholipid is immersed in a large excess of water. Small solutes can enter the aqueous region between bilayers. Their effect is first to increase and then to decrease the separation between bilayers as sugar concentration increases. We interpret this waxing and waning of the lattice spacing in terms of the successive weakening and strengthening of the attractive van der Waals forces originally responsible for creation of a stable lattice. The second probe is an "osmotic stress method," in which very high molecular weight neutral polymer is added to the pure water phase but is unable to enter the multilayers. The polymer competes for water with the lamellar lattice, and thereby compresses it. From the resulting spacing (determined by X-ray diffraction) and the directly measured osmotic pressure, we find a force vs. distance curve for compressing the lattice (or, equivalently, the free energy of transfer to bulk water of water between bilayers. This method reveals a very strong, exponentially varying "hydration force" with a decay distance of about 2 A.     

The interaction and fusion of bilayers formed from unsaturated lipids

The interactions between unsaturated phospholipid bilayers deposited on mica were measured in aqueous solution using a surface forces apparatus. The bilayers were made of L--dioleoylphosphatidylcholine (DOPC), L--dioleoylphosphatidyl ethanolamine (DOPE), and mixtures of the two, and were formed on mica by Langmuir-Blodgett deposition after the lipids were spread on an aqueous substrate from a chloroform solution. The forces are interpreted as electrostatic double-layer and van der Waals forces with long range, and a strong repulsion (hydration or steric force) at distances of several nm. Together they produce a region of weak attraction (a secondary minimum) at 5 nm (DOPE) and 6 nm (DOPC). Fusion of two bilayers into one was observed when the local force per unit area was 2–3 MPa. Other researchers report that phosphatidylethanolamine in vesicles enhances fusion. In this study using deposited bilayers, the presence of DOPE in a DOPC bilayer did not promote fusion, nor did DOPE bilayers fuse more easily than DOPC. The value of the force per unit area at which the two bilayers fuse into one was however decreased by several orders of magnitude when the bilayers were formed from lipids kept in chloroform solution for several days or more. Chromatography showed traces of lipid degradation products in such chloroform solutions.Abbreviations DO dioleoyl- - PE phosphatidyl ethanolamine - PC phosphatidylcholine - FECO fringes of equal chromatic order Of fprint requests to: J. Wolfe     

Effects of charged amino acids at b and c heptad positions on specificity and stability of four-chain coiled coils

An understanding of the balance of chemical forces responsible for protein stability and specificity of structure is essential for the success of efforts in protein design. Specifically, electrostatic interactions between charged amino acids have been explored extensively to understand the contribution of this force to protein stability. Much research on the importance of electrostatic interactions as specificity and stability determinants in two-stranded coiled coils has been done, but there remains significant controversy about the magnitude of the attractive forces using such systems. We have developed a four-stranded coiled-coil system with charged residues incorporated at b and c heptad positions to explore the role of charge interactions. Here, we test quantitatively the effects of varying sidechain length on the magnitude of such electrostatic interactions. We synthesized peptides containing either aspartate or ornithine at both b and c heptad positions and tested their ability to self-associate and to hetero-associate with one another and with peptides containing glutamate or lysine at the same positions. We find that interactions between glutamate and either lysine or ornithine are more favorable than the corresponding interactions involving aspartate. In each case, charged interactions provide additional stability to coiled coils, although helix propensity effects may play a significant role in determining the overall stability of these structures.     

Theory for the formation of intercellular junctions based on intramembranous particle patterns observed in the freeze fracture technique

A heterogeneous continuum theory of biological membrane interactions is presented which takes account of the spatial inhomogeneity of intramembranous particle patterns observed in ultrastructural studies of junctional complexes using the freeze-cleaved technique. The theory attempts to explain (i) how electrostatic and electrodynamic forces between particles of different biochemical composition in the same and opposing membranes might give rise to the specialized particle configurations characteristic of tight and gap junctions, (ii) how the spatial non-uniformity of the membrane proteins quantitatively modifies the local long range molecular level force field between adjacent membrane bilayers and (iii) how membrane elastic stresses and the modified molecular level forces combine to determine the equilibrium configurations of the various junctional complexes. The mathematical problem is highly non-linear since the molecular forces are a rapidly varying function of the local membrane spacing which is a priori unknown. The simplified dimensionless boundary value problem to determine the junction geometry has been reduced to a fourth order quasi one-dimensional equation with split end point conditions. The equation is singular in the vicinity of the junction complex and special solution techniques had to be employed. The numerical results are in reasonable quantitative agreement with electron microscopic observations of tight, gap and venous junctions.     

Possible Specificity of Cellular Interactions Due to Electrostatic Forces

It is known that the cells from a mixed population in a culture medium will finally segregate. This “social behavior” of the cells is a direct consequence of both physical and chemical interactions between cells. The physical forces involved in cell-cell interactions are considered to be the electrostatic, van der Waals, and very-short-range hydration forces.

It has been believed until now that the electrostatic forces acting between identical cells were always repulsive and nonspecific. In the present work, we try to suggest that even the electrostatic forces could manifest a slightly specific character, so that a completely random Brownian motion of the cells could be influenced, corrected, and transformed into a “docking maneuver,” which could favor the specific interactions between cells suspended in a culture medium. The main point of our approach is that the peculiar patterns of electric charge distribution on the cell surfaces act like specific electrostatic fingerprints that could be responsible for the preferential interactions which precede cellular segregation (1).     

Protein-protein and protein-salt interactions in aqueous protein solutions containing concentrated electrolytes

Protein-protein and protein-salt interactions have been obtained for ovalbumin in solutions of ammonium sulfate and for lysozyme in solutions of ammonium sulfate, sodium chloride, potassium isothiocyanate, and potassium chloride. The two-body interactions between ovalbumin molecules in concentrated ammonium-sulfate solutions can be described by the DLVO potentials plus a potential that accounts for the decrease in free volume available to the protein due to the presence of the salt ions. The interaction between ovalbumin and ammonium sulfate is unfavorable, reflecting the kosmotropic nature of sulfate anions. Lysozyme-lysozyme interactions cannot be described by the above potentials because anion binding to lysozyme alters these interactions. Lysozyme-isothiocyanate complexes are strongly attractive due to electrostatic interactions resulting from bridging by the isothiocyanate ion. Lysozyme-lysozyme interactions in sulfate solutions are more repulsive than expected, possibly resulting from a larger excluded volume of a lysozyme-sulfate bound complex or perhaps, hydration forces between the lysozyme-sulfate complexes.     

Investigation on the mechanism of crystallization of soluble protein in the presence of nonionic surfactant

The mechanism of crystallization of soluble, globular protein (lysozyme) in the presence of nonionic surfactant C8E4 (tetraoxyethylene glycol monooctyl ether) was examined using both static and dynamic light scattering. The interprotein interaction was found to be attractive in solution conditions that yielded crystals and repulsive in the noncrystallizing solution conditions. The validity of the second virial coefficient as a criterion for predicting protein crystallization could be established even in the presence of nonionic surfactants. Our experiments indicate that the origin of the change in interactions can be attributed to the adsorption of nonionic surfactant monomers on soluble proteins, which is generally assumed to be the case with only membrane proteins. This adsorption screens the hydrophobic attractive force and enhances the hydration and electrostatic repulsive forces between protein molecules. Thus at low surfactant concentration, the effective protein-protein interaction remains repulsive. Large surfactant concentrations promote protein crystallization, possibly due to the attractive depletion force caused by the intervening free surfactant micelles.