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.     

Temperature-induced complementarity as a mechanism for biomolecular assembly

Recent advances in the measurement and theory of “hydration” interactions between biomolecules provide a basis on which to formulate mechanisms of biomolecular recognition. In this paper we have developed a mathematical formalism for analyzing specificity encoded in dynamic distributions of surface polar groups, a formalism that incorporates newly recognized properties of directly measured “hydration” forces. As expected, attraction between surfaces requires complementary patterns of surface polar groups. In contrast to usual expectations, thermal motion can create these complementary surface configurations. We have demonstrated that assembly can occur with an increase in conformational entropy of polar residues. Elevated temperature then facilitates recognition rather than hinders it. This mechanism might underlie some temperature-favored assembly reactions common in biological systems that are usually associated with the “hydrophobic effect” only. © 1994 Wiley-Liss, Inc.     

Determination of the second virial coefficient of bovine serum albumin under varying pH and ionic strength by composition-gradient multi-angle static light scattering

Composition-gradient multi-angle static light scattering (CG-MALS) is an emerging technique for the determination of intermolecular interactions via the second virial coefficient B₂₂. With CG-MALS, detailed studies of the second virial coefficient can be carried out more accurately and effectively than with traditional methods. In addition, automated mixing, delivery and measurement enable high speed, continuous, fluctuation-free sample delivery and accurate results. Using CG-MALS we measure the second virial coefficient of bovine serum albumin (BSA) in aqueous solutions at various values of pH and ionic strength of a univalent salt (NaCl). The systematic variation of the second virial coefficient as a function of pH and NaCl strength reveals the net charge change and the isoelectric point of BSA under different solution conditions. The magnitude of the second virial coefficient decreases to 1.13 x 10⁻⁵ ml*mol/g² near the isoelectric point of pH 4.6 and 25 mM NaCl. These results illuminate the role of fundamental long-range electrostatic and van der Waals forces in protein-protein interactions, specifically their dependence on pH and ionic strength. Electronic supplementary material The online version of this article (doi:10.1007/s10867-014-9367-7) contains supplementary material, which is available to authorized users.     

A state and transition model for the eastern Monte Phytogeographycal Province in Rio Negro

We developed a functional model for a shrub steppe vegetation of the eastern Monte Phytogeographical Province in Río Negro (Argentina) with six stable states and 12 transitions, based on the woody encroachment degree, characteristics of the herbaceous layer and the soil surface, and biological crust cover. Information was obtained from letters of naturalists and travelers along the region since the late eighteenth century, reports of old settlers, and our own research work. On the Monte, different functional groups can be distinguished. Our work focused on the three most conspicuous to analyze the dynamics of the system: shrubs, grasses and biological crust. The shrub layer is only affected by large-scale disturbances (fire, mechanical clearing) which maintain the balance between grasses and shrubs in the system. Mechanical clearing with soil removal also causes a decrease in grass cover and vegetation diversity. This layer, however, is most frequently affected by intensive and continuous grazing, which reduces the occurrence of fires and shifts the equilibrium toward the shrubs. All disturbances in general deteriorate the biological crust that covers the soil, which offers situations of facilitation for the regeneration of the herbaceous layer. Grazing and mechanical clearing reduce soil cover and promote the development of soil compaction, which reduce water infiltration and germination and/or seedling establishment, and this creates deteriorated states difficult to reverse. Those states can also be produced by tillage for agriculture and stubble grazing. Some of the transitions that we describe can be favored through grassland management strategies, in order to reach higher states of pastoral value and reverse deteriorating situations.     

Detection of two loci involved in (1-->3)-beta-glucan (curdlan) biosynthesis by Agrobacterium sp. ATCC31749, and comparative sequence analysis of the putative curdlan synthase gene

Genes essential for the production of a linear, bacterial (1-->3)-beta- glucan, curdlan, have been cloned for the first time from Agrobacterium sp. ATCC31749. The genes occurred in two, nonoverlapping, genomic fragments that complemented different sets of curdlan( crd )-deficient transposon-insertion mutations. These were detected as colonies that failed to stain with aniline blue, a (1-->3)-beta-glucan specific dye. One fragment carried a biosynthetic gene cluster (locus I) containing the putative curdlan synthase gene, crdS, and at least two other crd genes. The second fragment may contain only a single crd gene (locus II). Determination of the DNA sequence adjacent to several locus I mutations revealed homology to known sequences only in the cases of crdS mutations. Complete sequencing of the 1623 bp crdS gene revealed highest similarities between the predicted CrdS protein (540 amino acids) and glycosyl transferases with repetitive action patterns. These include bacterial cellulose synthases (and their homologs), which form (1-->4)-beta-glucans. No similarity was detected with putative (1-->3)- beta-glucan synthases from yeasts and filamentous fungi. Whatever the determinants of the linkage specificity of these beta-glucan synthases might be, these results raise the possibility that (1-->3)-beta-glucans and (1-->4)-beta-glucans are formed by related catalytic polypeptides.      

Parametrization of direct and soft steric-undulatory forces between DNA double helical polyelectrolytes in solutions of several different anions and cations.

Directly measured forces between DNA helices in ordered arrays have been reduced to simple force coefficients and mathematical expressions for the interactions between pairs of molecules. The tabulated force parameters and mathematical expressions can be applied to parallel molecules or, by transformation, to skewed molecules of variable separation and mutual angle. This "toolbox" of intermolecular forces is intended for use in modelling molecular interactions, assembly, and conformation. The coefficients characterizing both the exponential hydration and the electrostatic interactions depend strongly on the univalent counterion species in solution, but are only weakly sensitive to anion type and temperature (from 5 to 50 degrees C). Interaction coefficients for the exponentially varying hydration force seen at spacings less than 10 to 15 A between surfaces are extracted directly from pressure versus interaxial distance curves. Electrostatic interactions are only observed at larger spacings and are always coupled with configurational fluctuation forces that result in observed exponential decay lengths that are twice the expected Debye-Huckel length. The extraction of electrostatic force parameters relies on a theoretical expression describing steric forces of molecules "colliding" through soft exponentially varying direct interactions.     

Water movement during channel opening and closing

By applying the osmotic stress of a nonpenetrating polymer, we have measured the change v in polymer-inaccessible internal water volume of a voltagegated ionic channel. The voltage-dependent anion channel (VDAC) from mitochondrial outer membranes shows a v comparable in magnitude to the full channel volume estimated from solute penetrability, single-channel conductance, or image reconstruction. It thus appears that channel gating involves significant structure reorganization and water movement rather than the minimal changes caused by a local constriction or blockade. Hydration of the inner channel surface may be an important factor in channel gating as is the hydration of molecular surfaces in controlling macromolecular interaction in solution.     

Binding of divalent cations of dipalmitoylphosphatidylcholine bilayers and its effect on bilayer interaction

We have confirmed that CaCl2 swells the multilayer lattice formed by dipalmitolyphosphatidylcholine (DPPC) in an aqueous solution. Specifically, at room temperature 1 mM CaCl2 causes these lipid bilayers to increase their separation, dw, from 19 A in pure water to greater than 90 A. CaCl2 concentrations greater than 4 mM cause less swelling. We have measured the net repulsive force between the bilayers in 30 mM CaCl2 at T = 25 degrees C (below the acyl chain freezing temperature). For interbilayer separations between 30 and 90 A, the dominant repulsion between bilayers is probably electrostatic; Ca2+ binds to DPPc lecithin bilayers, imparting a charge to them. The addition of NaCl to CaCl2 solutions decreases this repulsion. For dw less than 20 A, the bilayer repulsion appears to be dominated by the "hydration forces" observed previously between both neutral and charged phospholipids. From the electrostatic repulsive force, we estimate the extent of Ca2+ binding to the bilayer surface. The desorption and bound Ca2+, apparent when bilayers are pushed together, is more rapid than one would expect if an association constant governed Ca2+ binding. The association affinity does not appear to be a fixed quantity but rather a sensitive function of ionic strength and bilayer separation.     

Probability of alamethicin conductance states varies with nonlamellar tendency of bilayer phospholipids.

With few exceptions, membrane lipids are usually regarded as a kind of filler or passive solvent for membrane proteins. Yet, cells exquisitely control membrane composition. Many phospholipids found in plasma membrane bilayers favor packing into inverted hexagonal bulk phases. It was suggested that the strain of forcing such lipids into a bilayer may affect membrane protein function, such as the operation of transmembrane channels. To investigate this, we have inserted the peptide alamethicin into bilayer membranes composed of lipids of empirically determined inverted hexagonal phase "spontaneous radii" Ro, which will have expectably different degrees of strain when forced into bilayer form. We observe a correlation between measured Ro and the relative probabilities of different conductance states. States of higher conductance are more probable in dioleoylphosphatidylethanolamine, the lipid of highest curvature, 1/Ro, than in dioleoylphosphatidylcholine, the lipid of lowest curvature.