Properties of Double-Stranded DNA as a Polyelectrolyte

The stability of the structure of double-stranded DNA in the salt-free solution is discussed on the basis of the polyelectrolyte theory. Assuming that DNA is an infinitely long rod, and the formation of double strands is divided into combining process and folding process, the free energy changes required in these processes are calculated by the use of the exact solutions of two-dimensional Poisson-Boltzmann equation for the one rod and the two rod systems.

By strong depression of electrostatic interaction due to counter-ion condensation phenomena, the free energy change is remarkably decreased so that the double-stranded structure of DNA can be stabilized by energy of hydrogen bonds between base pairs. The increase of the activity coefficient of a counterion upon heat denaturation of DNA is also explained.

     

An elastic rod model to evaluate effects of ionic concentration on equilibrium configuration of DNA in salt solution

As a coarse-gained model, a super-thin elastic rod subjected to interfacial interactions is used to investigate the condensation of DNA in a multivalent salt solution. The interfacial traction between the rod and the solution environment is determined in terms of the Young–Laplace equation. Kirchhoff’s theory of elastic rod is used to analyze the equilibrium configuration of a DNA chain under the action of the interfacial traction. Two models are established to characterize the change of the interfacial traction and elastic modulus of DNA with the ionic concentration of the salt solution, respectively. The influences of the ionic concentration on the equilibrium configuration of DNA are discussed. The results show that the condensation of DNA is mainly determined by competition between the interfacial energy and elastic strain energy of the DNA itself, and the interfacial traction is one of forces that drive DNA condensation. With the change of concentration, the DNA segments will undergo a series of alteration from the original configuration to the condensed configuration, and the spiral-shape appearing in the condensed configuration of DNA is independent of the original configuration.     

Dielectric increment and dielectric dispersion of solutions containing simple charged linear macromolecules. I. Theory

A theory is derived for the static and frequency dependent value of the electric permittivity for model systems representing a solution of a macromolecule bearing a large number of identical charges. The polyion is represented either as a charged rigid rod (A) or as a sequence of charged rodlike subunits in an arbitrary but fixed configuration (B) and it is assumed that a certain fraction of the counterions is closely associated to the macromolecule. The dielectric properties are described in terms of fluctuations in the distribution of the associated counterions along the polyion. These fluctuations can occur locally between potential barriers marking the ends of the subunits (if considered) but can also extend over the whole molecule. Neglecting correlations between different associated counterions expressions for the static value of the dielectric increment are obtained which reveal its dependence on the fraction of bound ions, on the charge of the counterions and on the length of the molecule for model A or the radius of gyration for model B. The dynamic behaviour of A is distinguishable from that of B as the former will present one single dispersion curve of the frequency dependent electric permittivity while the latter may give rise to two different dispersion regions. This will be the case if both the exchange between bound and free ions and the rotation of the complete molecule are relatively slow in comparison to the local bound counterion density fluctuations and if these fluctuations occur on a much shorter time scale than the ion density fluctuations extending over the complete macromolecule.     

Description of hydration free energy density as a function of molecular physical properties

A method to calculate the solvation free energy density (SFED) at any point in the cavity surface or solvent volume surrounding a solute is proposed. In the special case in which the solvent is water, the SFED is referred to as the hydration free energy density (HFED). The HFED is described as a function of some physical properties of the molecules. These properties are represented by simple basis functions. The hydration free energy of a solute was obtained by integrating the HFED over the solvent volume surrounding the solute, using a grid model. Of 34 basis functions that were introduced to describe the HFED, only six contribute significantly to the HFED. These functions are representations of the surface area and volume of the solute, of the polarization and dispersion of the solute, and of two types of electrostatic interactions between the solute and its environment. The HFED is described as a linear combination of these basis functions, evaluated by summing the interaction energy between each atom of the solute with a grid point in the solvent, where each grid point is a representation of a finite volume of the solvent. The linear combination coefficients were determined by minimizing the error between the calculated and experimental hydration free energies of 81 neutral organic molecules that have a variety of functional groups. The calculated hydration free energies agree well with the experimental results. The hydration free energy of any other solute molecule can then be calculated by summing the product of the linear combination coefficients and the basis functions for the solute.     

Sulla organizzazione dello strato granulare esterno e della membrana limitante esterna nella retina di coniglio

Summary The organisation of the outer nuclear layer and the structure of the outer limiting membrane of rabbit retina have been studied. In specimens stained by the Golgi method it was observed that in the outer nuclear layer each Müller cell envelops with its thin lamellar expansions ten to fifteen rod and cone cell bodies.The only cytoplasmic organelles in rod and cone cell bodies are a few free ribosomes and smooth surfaced vesicles. Neurotubules are prominent in the outer and inner fibres of the rods and cones.The processes of the Müller cells are distinctive because of the presence of many glycogen granules and glial filaments. Also present but only found near the outer limiting membrane are mitochondria, occasional centrioles and cilia that lack inner fibres. Long microvilli originate from the Müller cell processes on the scleral side of the outer limiting membrane.The photoreceptor cells on the vitreal side of the outer limiting membrane are completely isolated from each other by glial processes. On the scleral side of the membrane, the inner segments of the photoreceptor cells are not completely isolated by glial processes and so are frequently found in mutual contact. In the outer nuclear layer the granule of each photoreceptor is surrounded by more than one glial process while the fibres are often deeply embedded in a single glial process and provided with a mesofibre.At the level of the outer limiting membrane the visual cells and the glial expansions enveloping them are joined together by a junctional complex formed by a zonula adhaerens interposed between two very short zonulae occludentes. The same junctional complex joins to each other the contiguous expansions of the Müller cells and the mesofibres of the visual elements.     

Identification of free fatty acids in maize protein bodies and purified alpha zeins by (13)C and (1)H nuclear magnetic resonance

Zeins, the maize storage proteins, are the most abundant proteins in the corn endosperm, and are synthesized on the rough endoplasmatic reticulum and deposited in discrete organelles called protein bodies. Several authors, using circular dichroism and optical rotatory dispersion, have concluded that these proteins have a high alpha-helical content in alcoholic solution. In this work we have studied these proteins, within the protein bodies themselves and after extraction from the corn grains with 70% ethanol, using NMR (nuclear magnetic resonance) spectroscopy. We conclusively demonstrate the presence of free fatty acids within both the protein bodies and also in the alcohol extracted alpha zeins. We present evidence for a direct interaction between the free fatty acids and the alpha zein proteins within the protein body and suggest possible mechanisms by which such an association has arisen during the evolution of the maize endosperm.     

Long range intermolecular forces between macroscopic bodies: macroscopic and microscopic approaches.

Van der Waals energies of interaction are calculated by two methods, the macroscopic method of Lifshitz and the microscopic method of London-Casimir and Polder-Hamaker for the case of two semi-infinite slabs separated by a thin film. When retardation effects may be neglected, the London-Hamaker approach yields values of dispersion interactions which almost coincide with those of the Lifshitz approach, the magnitude of the former values being larger by approximately 10–25%, which is attributed to the effect of the molecular environment in condensed media. At 50–100 Å film thicknesses where retardation effects are small, dispersion terms are generally the major part of van der Waals forces in the Lifshitz formulation. Hence, for 50–100 Å film thicknesses the Hamaker approach, which only includes dispersion interactions is generally adequate. By accounting for retardation effects, which significantly reduce the magnitude of dispersion interactions at several hundred Å, there is a reasonable agreement between the values obtained by the macroscopic and microscopic approaches. When polar substances are present and for film thicknesses of several hundred Å, where dispersion interactions are significantly reduced, the major contribution to van der Waals forces may arise from orientation and induction terms. For such cases the Hamaker approach may lead to critical underestimates of the calculated magnitude of van der Waals forces. An ad hoc way to overcome this difficulty which is applicable to any geometry is proposed. This study presents a simple procedure for the determination of free energies of interaction between macroscopic bodies of various shapes. The procedure, which is applicable when the molecules of bodies and surrounding medium are isotropic, yields results which closely approximate those obtained with the Lifshitz theory.     

A simple and efficient dispersion correction to the Hartree–Fock theory

One of the most challenging problems in computational chemistry and in drug discovery is the accurate prediction of the binding energy between a ligand and a protein receptor. It is well known that the binding energy calculated with the Hartree–Fock molecular orbital theory (HF) lacks the dispersion interaction energy that significantly affects the accuracy of the total binding energy of a large molecular system. We propose a simple and efficient dispersion energy correction to the HF theory (HF-D_tq). The performance of HF-D_tq was compared with those of several recently proposed dispersion corrected density functional theory methods (DFT-Ds) as to the binding energies of 68 small non-covalent complexes. The overall performance of HF-D_tq was found to be nearly equivalent to that of more sophisticated B3LYP-D₃. HF-D_tq will thus be a useful and powerful method for accurately predicting the binding energy between a ligand and a protein, albeit it is a simple correction procedure based on HF.     

Flagellar apparatus duplication and partition, flagellar transformation during division in Entosiphon sulcatum.

Electron microscopic examination of serial sections of developmental stages of the flagellar apparatus during the cell cycle indicates that the basal bodies replicate in a semi-conservative manner and that there is a flagellar transformation over two cell cycles in euglenoids as in other algal flagellate groups. Two new pairs of basal bodies are formed, each pair comprising one parental and one newly developed basal body. There is a transformation of the parental dorsal flagellum containing a thin paraxonemal rod into a ventral flagellum bearing a large paraxonemal rod. Observation of the roots associated with the basal bodies shows that the dorsal root transforms into an intermediate root over two cell cycles following the transformation of the dorsal basal body/flagellum to a ventral one. Also the two ventral roots are newly formed in relation to the formation of two new phagotrophic apparatuses during the division. After the breakage of the connection between the parental basal bodies the two new pairs move apart and are guided/drawn by transverse microfibrillar bundles which connect them to opposite sides of the pellicle. The axis of the separation/migration of the pairs of basal bodies is parallel to the axis of elongation of the dividing nucleus.     

Modulating DNA configuration by interfacial traction: an elastic rod model to characterize DNA folding and unfolding

As a continuum model of DNA, a thin elastic rod subjected to interfacial interactions is used to investigate the equilibrium configuration of DNA in intracellular solution. The interfacial traction between the rod and the solution environment is derived in detail. Kirchhoff’s theory of elastic rods is used to analyze the equilibrium configuration of a DNA segment under the action of the interfacial traction. The influences of the interfacial energy factor and bending stiffness on the toroidal spool formation of the DNA segment are discussed. The results show that the equilibrium configuration of DNA is mainly determined by competition between the interfacial energy and elastic strain energy of the DNA itself, and the interfacial traction is one of the forces that drives DNA folding and unfolding.     

Assembly of retinal rod or cone Na(+)/Ca(2+)-K(+) exchanger oligomers with cGMP-gated channel subunits as probed with heterologously expressed cDNAs

Proper control of intracellular free Ca(2+) is thought to involve subsets of proteins that co-localize to mediate coordinated Ca(2+) entry and Ca(2+) extrusion. The outer segments of vertebrate rod and cone photoreceptors present one example: Ca(2+) influx is exclusively mediated via cGMP-gated channels (CNG), whereas the Na(+)/Ca(2+)-K(+) exchanger (NCKX) is the only Ca(2+) extrusion protein present. In situ, a rod NCKX homodimer and a CNG heterotetramer are thought to be part of a single protein complex. However, NCKX-NCKX and NCKX-CNG interactions have been described so far only in bovine rod outer segment membranes. We have used thiol-specific cross-linking and co-immunoprecipitation to examine NCKX self-assembly and CNG-NCKX co-assembly after heterologous expression of either the rod or cone NCKX/CNG isoforms. Co-immunoprecipitation clearly demonstrated both NCKX homooligomerization and interactions between NCKX and CNG. The NCKX-NCKX and NCKX-CNG interactions were observed for both the rod and the cone isoforms. Thiol-specific cross-linking led to rod NCKX1 dimers and to cone NCKX2 adducts of an apparent molecular weight higher than that predicted for a NCKX2 dimer. The mass of the cross-link product critically depended on the location of the particular cysteine residue used by the cross-linker, and we cannot exclude that NCKX forms a higher oligomer. The NCKX-NCKX and NCKX-CNG interactions were not isoform-specific (i.e., rod NCKX could interact with cone NCKX, rod NCKX could interact with cone CNGA, and vice versa). Deletion of the two large hydrophilic loops from the NCKX protein did not abolish the NCKX oligomerization, suggesting that it is mediated by the highly conserved transmembrane spanning segments.     

Molecular regions controlling the activity of CNG channels

The alpha subunits of CNG channels of retinal photoreceptors (rod) and olfactory neurons (olf) are proteins that consist of a cytoplasmic NH(2) terminus, a transmembrane core region (including the segments S1-S6), and a cytoplasmic COOH terminus. The COOH terminus contains a cyclic nucleotide monophosphate binding domain NBD) that is linked by the C-linker (CL) to the core region. The binding of cyclic nucleotides to the NBD promotes channel opening by an allosteric mechanism. We examined why the sensitivity to cGMP is 22 times higher in olf than in rod by constructing chimeric channels and determining the [cGMP] causing half maximum channel activity (EC(50)). The characteristic difference in the EC(50) value between rod and olf was introduced by the NH(2) terminus and the core-CL region, whereas the NBD showed a paradoxical effect. The difference of the free energy difference Delta(DeltaG) was determined for each of these three regions with all possible combinations of the other two regions. For rod regions with respect to corresponding olf regions, the open channel conformation was destabilized by the NH(2) terminus (Delta(DeltaG) = -1.0 to -2.0 RT) and the core-CL region (Delta(DeltaG) = -2.0 to -2.9 RT), whereas it was stabilized by the NBD (Delta(DeltaG) = 0.3 to 1.1 RT). The NH(2) terminus deletion mutants of rod and olf differed by Delta(DeltaG) of only 0.9 RT, whereas the wild-type channels differed by the much larger value of 3.1 RT. The results show that in rod and olf, the NH(2) terminus, the core-CL region, and the NBD differ by characteristic Delta(DeltaG) values that do not depend on the specific composition of the other two regions and that the NH(2) terminus generates the main portion of Delta(DeltaG) between the wild-type channels.     

Physicochemical characterization of Escherichia coli. A comparison with gram-positive bacteria.

Eight Escherichia coli strains were characterized by determining their adhesion to xylene, surface free energy, zeta potential, relative surface charge, and their chemical composition. The latter was done by applying X-ray photoelectron spectroscopy (XPS) and infrared spectroscopy (IR). No relationship between the adhesion to xylene and the water contact angles of these strains was found. Three strains had significantly lower surface free energies than the other strains. Surface free energies were either obtained from polar and dispersion parts or from Lifshitz-van der Waals and acid/base parts of the surface free energy. A correlation (r = 0.97) between the polar parts and the electron-donor contributions to the acid/base part of the surface free energy was found. The zeta potentials of all strains, measured as a function of pH (2-11), were negative. Depending on the zeta potential as a function of pH, three groups were recognized among the strains tested. A relationship (r = 0.84) was found between the acid/base component of the surface free energy and the zeta potential measured at pH = 7.4. There was no correlation between results of XPS and IR studies. Data from the literature of XPS and IR studies of the gram-positive staphylococci and streptococci were compared with data from the gram-negative E. coli used in this study. It appeared that in these three groups of bacteria, the polysaccharide content detected by IR corresponded well with the oxygen-to-carbon ratio detected by XPS.     

Possible role of helix-coil transitions in the microscopic mechanism of muscle contraction.

Local helix-coil transitions in the coiled coil portion of myosin have long been implicated as a possible origin of tension generation in muscle. From a statistical mechanical theory of conformational transitions in coiled coils, the free energy required to form a randomly coiled bubble in the hinge region of myosin of the type conjectured by Harrington (Harrington, W. F., 1979, Proc. Natl. Acad. Sci. USA, 76:5066-5070) is estimated to be approximately 25 kcal/mol. Unfortunately this is far more than the free energy available from ATP hydrolysis if the crossbridges operate independently. Thus, in solution such bubbles are predicted to be absent, and the theory requires that the rod portion of myosin be a hingeless, continuously deforming rod. While such bubble formation in vivo cannot be entirely ruled out, it appears to be unlikely. We further conjecture that in solution the swivel located between myosin subfragments 1 and 2 (S-2 and S-1) is due to a locally random conformation of the chains caused by the presence of a proline residue at the point that physically separates the coiled coil from the globular portion of myosin. On attachment of S-1 to actin in the strong binding state, the configurational entropy of the random coil in the swivel region is greatly reduced relative to the case where the ends are free. This produces a spontaneous coil-to-helix transition in the swivel region that causes rotation of S-1 and the translation of actin. Thus, the model predicts that the actin filaments are pushed rather than pulled past the thick filaments by the crossbridges. The specific mechanism of force generation is examined in detail, and a simple statistical mechanical realization of the model is proposed. We find that the model gives a substantial number of qualitative and at times quantitative predictions in accord with experiment, and is particularly appealing in that it provides a simple means of free energy transduction--the well known fact that topological constraints shift the equilibrium between helical and random coil states.     

Studying excited states of proteins by NMR spectroscopy.

Protein structure is inherently dynamic, with function often predicated on excursions from low to higher energy conformations. For example, X-ray studies of a cavity mutant of T4 lysozyme, L99A, show that the cavity is sterically inaccessible to ligand, yet the protein is able to bind substituted benzenes rapidly. We have used novel relaxation dispersion NMR techniques to kinetically and thermodynamically characterize a transition between a highly populated (97%, 25 degrees C) ground state conformation and an excited state that is 2.0 kcal mol(-1) higher in free energy. A temperature-dependent study of the rates of interconversion between ground and excited states allows the separation of the free energy change into enthalpic (Delta H = 7.1 kcal mol(-1)) and entropic (T Delta S = 5.1 kcal mol(-1), 25 degrees C) components. The residues involved cluster about the cavity, providing evidence that the excited state facilitates ligand entry.     

Standardizing the free energy change of transmembrane helix-helix interactions

Side-to-side associations of transmembrane alpha-helices are integral components of the structure and function of helical membrane proteins. A fundamental unknown in the understanding of the chemical principles driving the lateral interactions between transmembrane alpha-helices is the balance of forces arising from the polypeptide sequence versus the hydrophobic solvent. To begin to address this question, a consideration of basic thermodynamic principles has been applied to assess the experimental free energy change associated with transmembrane helix dimerization in micelles. This analysis demonstrates the ability to partition the apparent free energy of transmembrane helix-helix association into two components. The first component is a statistical energy term, which arises from the fact that there are an unequal number of reactants and products. The second component is a standard state free energy change, which informs on the molecular details of the transmembrane helix self-association reaction. The advantage of separating these two energy terms arises from the fact that extrapolation to the standard state free energy change normalizes the statistical energy term so that it applies equivalently in all experimental systems. Accompanying experimental results for the glycophorin A transmembrane alpha-helix dimer measured in micelles are well described by these theoretical components assuming an ideal-dilute solution.     

Physicochemical characterization ofEscherichia coli

EightEscherichia coli strains were characterized by determining their adhesion to xylene, surface free energy, zeta potential, relative surface charge, and their chemical composition. The latter was done by applying X-ray photoelectron spectroscopy (XPS) and infrared spectroscopy (IR). No relationship between the adhesion to xylene and the water contact angles of these strains was found. Three strains had significantly lower surface free energies than the other strains. Surface free energies were either obtained from polar and dispersion parts or from Lifshitz-van der Waals and acid/base parts of the surface free energy. A correlation (r=0.97) between the polar parts and the electron-donor contributions to the acid/base part of the surface free energy was found. The zeta potentials of all strains, measured as a function of pH (2–11), were negative. Depending on the zeta potential as a function of pH, three groups were recognized among the strains tested. A relationship (r=0.84) was found between the acid/base component of the surface free energy and the zeta potential measured at pH=7.4. There was no correlation between results of XPS and IR studies. Data from the literature of XPS and IR studies of the gram-positive staphylococci and streptococci were compared with data from the gram-negativeE. coli used in this study. It appeared that in these three groups of bacteria, the polysaccharide content detected by IR corresponded well with the oxygen-to-carbon ratio detected by XPS.     

Image reconstruction of the flagellar basal body of Salmonella typhimurium

The basal body is thought to be a part of the rotary motor of the bacterial flagellum. It consists of a central rod coaxial with a set of four rings, which are associated with the cell envelope. We used single-particle averaging methods to analyze images of negatively stained basal bodies of Salmonella typhimurium. Several averages were computed, so that the reliability of features could be assessed. We carried out the same analysis on electron micrographs of isolated, negatively stained L-P rings. In order to interpret the averages in terms of a three-dimensional structure, we carried out image reconstruction on them. The resulting three-dimensional map corresponds to the cylindrically averaged structure of the basal body. To show that the reconstruction procedure is legitimate, we demonstrate it on model data. The results of the modelling show that features very near to the axis of the reconstruction are not reliable but that broader, off-axis features are represented faithfully. The L ring is L-shaped, with the long arm of the L parallel to the axis of the rod, and the short arm pointing away from the rod. The P ring, on the other hand, appears to be a ring or disk. The position of the L-P ring complex on the rod seems to vary somewhat, consistent with its putative role as a bushing. The cross-sectional shape of the S ring is that of a frustum rather than a disk. The M ring, which is oval in cross section, sits atop the S ring, making contact with it at an outer radius. The S ring appears to make contact with the rod, whereas the M ring does not. This situation, if true, is difficult to reconcile with the common notion that the S ring is stationary and the M ring rotates. It seems more likely that the S ring and rod rotate as a unit.