bluuebunny/crossref_metadata_2025 huggingface dataset:
Apparent persistence lengths and diffusion behavior of high molecular weight hyaluronate
Authors: Ghosh Snehasish , Li Xiao , Reed Christopher E. , Reed Wayne F.
Published: December 2004

High purity, high molecular weight hyaluronate from bacteria and rooster comb exhibited clear polyelectrolyte properties, as observed by static and dynamic light scattering. The scattered intensity of hyaluronate solutions increased markedly with ionic strength, while the radii of gyration decreased. Apparent persistence lengths within the wormlike chain model in the coil limit were estimated as a function of ionic strength. The total apparent persistence length varied from about 87 Å in the high ionic strength limit to nearly 400 Å at 1 mM added NaCl. The apparent electrostatic persistence length varied approximately as the inverse square root of the ionic strength. Deviations from the theoretically predicted inverse ionic strength dependence were investigated in terms of excluded volume effects. Dynamic light scattering yielded “ordinary phase” diffusion coefficients whose dependence on polymer and salt concentration agreed reasonably well with hydrodynamic coupled mode theory in the linear limit. Extrapolations to infinite polymer dilution at fixed salts yielded, surprisingly, a constant diffusion coefficient. Thus, there was no evidence of either polyion expansion or electrolyte friction effects in the infinite dilution diffusion coefficients. Since clear evidence for polyion expansion was seen in the static scattering, it is thought that the relative stiffness and consequent openness of the hyaluronate coils lead to partial free draining behavior. There was no evidence for an “extraordinary phase” under no added salt and low added salt conditions. The overall results are contrasted with the very different behavior previously reported for medium purity hyaluronate from animal sources.
A general secular equation for cooperative binding of n‐mer ligands to a one‐dimensional lattice
Authors: Chen Yi‐Der
Published: December 2004

The binding of n‐mer ligands to a one‐dimensional lattice involving many ligand species and complex multiple‐binding mechanisms is studied. We show that, when derived using the sequence‐generating function method of Lifson, the secular equation of any binding system with a finite number of “elementary units” can be expressed in a matrix determinant form that is very symmetric and easy to construct. In other words, for any binding system whose elementary units are known, the secular equation of the system can be obtained readily without going through the formal derivation of the equation. We also show that the “determinant” secular equation obtained using the present procedure can be employed directly to the calculation of binding isotherms.
Determination of the conformation of Lewis blood group oligosaccharides by simulation of two‐dimensional nuclear overhauser data
Authors: Cagas Perseveranda , Bush C. Allen
Published: December 2004

Through control of both the nmr probe temperature and of the solvent viscosity, phase‐sensitive two‐dimensional 1H nuclear Overhauser data (NOESY) at 300 and 500 MHz are obtained with excellent signal‐to‐noise ratios for Lewis blood group penta‐ and hexasaccharides isolated from human milk. Relatively long mixing times are required to produce measurable NOE intensities in these oligosaccharides, which makes a full relaxation maxtrix analysis necessary. By measurements of selective T1 for a few isolated 1H resonances, it was possible to generate a simulation of the complete NOESY spectrum at arbitrary mixing time for comparison with the experimental data. From an exhaustive search of the conformational space, it was found that only a small range of glycosidic dihedral angles for the nonreducing terminal Lewis blood group determinant fragments of the milk oligosaccharides LNF‐2 and LND‐1 produce simulated spectra agreeing within experimental error to the data. Conformational energy calculations reveal that each of these conformations is also one of minimum energy. It is concluded that the Lewisa and Lewisb oligosaccharides adopt relatively compact rigid structures in solution, as shown by the observation of cross peaks between protons in nonadjacent residues. Like the blood group A and H oligosaccharides, there exists only a small dependence of the conformation for Lewisa and Lewisb oligosaccharides on solvent. The apparent lack of dependence of conformation of these oligosaccharides on DMSO in D2O suggests that modification of solvent viscosity with mixtures of DMSO : D2O may provide a useful general strategy of NOESY studies of oligosaccharides.
The reliability of wormlike polysaccharide chain dimensions estimated from electron micrographs
Authors: Stokke Bjørn T. , Brant David A.
Published: December 2004

Electron micrographs of alginate, xylinan, xanthan, and scleroglucan were prepared by vacuum‐drying aqueous glycerol‐containing solutions, and then heavy‐metal, low‐angle rotary replicated. Quantitative methods for excluding streamlining effects and deformation artifacts were developed and applied to the digitized polymer contours prior to analysis of stiffness. The apparent macromolecular dimensionalities were not obtainable on the basis of the change in the scaling coefficient a relating the rms end‐to‐end distance and the contour length, 〈r2〉1/2 ∼ Lα, for chains subject to the excluded volume effect in two and three dimensions. Using a two‐dimensional model, the persistence length of these molecules was estimated to be (9 ± 1) nm (alginate), (25 ± 4) nm (xylinan), (30 ± 4) nm (single‐stranded xanthan), (68 ± 7) nm (double‐stranded xanthan), and (80 ± 10) nm (scleroglucan). Monte Carlo calculations for wormlike chains close to an interacting surface or confined to the region between two surfaces showed that (1) strongly adsorbed molecules are essentially two‐dimensional and (2) molecules restricted to the space between two surfaces separated by a distance less than 20% of the persistence length are two‐dimensional in their directional correlation. The somewhat low estimates of the persistence lengths obtained from the electron micrographs compared with those reported from solution measurements can be accounted for by the adoption of a strictly two‐dimensional model in the analysis, whereas the adsorbed polymers are most likely intermediate between the two‐and three‐dimensional cases. The model calculations and the analysis of the electron micrographs suggest that stiffness parameters are obtainable from the electron micrographs when the proper theoretical description are used in the analysis.
On the kinetics of oligomer binding
Authors: Poland Douglas
Published: December 2004

The kinetics of oligomer binding to a polymer are treated in the approximation that the internal states of the oligomer–polymer complex equilibrate rapidly compared with the rate of binding. In that case one can use equilibrium statistical mechanics to give the density of appropriate binding sites required in the kinetic equation. In this manner one can obtain a general differential equation in one variable (the net density of oligomer bound) for the case of cooperative binding. Several simple, but accurate, approximate solutions to the binding kinetics are presented.
Quantitative IR spectrophotometry of peptide compounds in water (H2O) solutions. I. Spectral parameters of amino acid residue absorption bands
Authors: Venyaminov S. Yu. , Kalnin N. N.
Published: December 2004

Infrared spectra of the amino acid residues in H2O solution have been obtained in the 1800–1400‐cm−1 region. It has been established that amino acid residues of arginine, asparagine, glutamine, aspartic and glutamic acids, lysine, tyrosine, histidine, and phenylalanine have intensive absorption in this spectral region. Infrared spectra for a set of model compounds have been measured. On the basis of these data, spectral parameters of amino acid residue absorption bands have been determined.
Variation of the permeability of bacteriophage T4: Analysis by use of a protein‐specific probe for the T4 interior
Authors: Griess Gary A. , Khan Saeed A. , Serwer Philip
Published: December 2004

The permeability of bacteriophage T4 and the change in T4 permeability caused by mutation to osmotic shock resistance are investigated here by quantification of the kinetics with which both a DNA‐specific probe (ethidium) and a protein‐specific probe [1,1′‐bi(4‐anilino) naphthalene‐5,5′‐di‐sulfonic acid, or bis‐ANS] bind to T4. In the case of an osmotic shock‐resistant mutant, T40s41, both ethidium and bis‐ANS bind with first order kinetics. The first‐order rate constant (k*) for both bis‐ANS and ethidium is a function of anion type and concentration. Adenosine triphosphate, phosphate, bisulfite, sulfate, and acetate anions all reduce k* below the k* observed when chloride is the only anion. When chloride is the only anion at 25°C, k* values for binding to T40s41 are orders of magnitude above k* values for binding to wild‐type T4 (T4wt). At 25°C, k* forT4wt is too small to measure, but k* for T4wt increases at 50–55°C to values approaching those measured for T40s41, without inactivating T4wt, when chloride is the only anion; during heating, T4wt is stabilized by both ethidium and bis‐ANS. Binding to T4wt is reversible at 50‐55°C, but not at 25°C. Equilibrium binding of bis‐ANS to T40s41 reveals 112 ± 24 sites per T4 capsid. Equilibrium binding of ethidium to T40s41 reveals both high‐ and low‐affinity sites previously observed in the packaged DNA of other bacteriophages. The ATP‐induced decrease in k* is not accompanied by a decrease in equilibrium binding. The following hypotheses are presented to explain the above data: (a) All detected bis‐ANS binding sites on T4 are interior to the outer surface of T4. (b) The value of k* for both bis‐ANS and ethidium is controlled at the port(s) of passage through the outer shell of the T4 capsid. (c) The anions present control k* values at the port(s) of entry, probably by controlling the size of this port. The effects on k* of phosphate explain the otherwise paradoxical observation [P. J. McCall and V. A. Bloomfield (1976) Biopolymers 15, 2323–2336] that in a phosphate buffer the permeabilities of T4wt and T40s41 are the same.
L‐Alanyl‐L‐alanyl‐L‐alanine: Parallel pleated sheet arrangement in unhydrated crystal structure, and comparisons with the antiparallel sheet structure
Authors: Hempel A. , Camerman N. , Camerman A.
Published: December 2004

The tripeptide L‐alanyl‐L‐alanyl‐L‐alanine has been crystallized from a water/dimethyl‐formamide solution in an unhydrated form, with cell dimensions a = 11.849, b = 10.004, c = 9.862 Å, β = 101.30°, monoclinic space group P21, with 4 molecules per cell (2 independent molecules in the asymmetric unit). The Structure was determined by direct methods and refined to a discrepancy index R = 0.057. The tri‐L‐alanine molecules are packed in a parallel pleated sheet arrangement with unusually long amide nitrogen‐carbonyl oxygen contacts within sheets. Comparisons are made with the antiparallel pleated sheet structure of tri‐L‐alanine hemihydrate, previously crystallized from the same solvent system.
Thermodynamics of drug–DNA interactions: Entropy‐driven intercalation and enthalpy‐driven outside binding in the ellipticine series
Authors: Schwaller Marc‐Antoine , Dodin Guy , Aubard Jean
Published: December 2004

Viscosimetric and kinetic results allow one to characterize three modes of DNA binding in the ellipticine series: (1) Ellipticine and its 9 methoxy derivative, which present maximal DNA lengthening properties and bind DNA through a single step mechanism, can be considered as pure intercalators. (2) Ellipticinium derivatives and short‐chain substituted oxazolopyridocarbazoles, which present intermediate DNA lengthening properties, bind DNA through a two‐step mechanism, one being intercalation. (3) Long‐chain substituted oxazolopyridocarbazole derivatives, which display the smallest DNA lengthening properties, bind DNA through a single‐step mechanism, probably resulting from an outside binding mode.

The viscosimetric and kinetic results are compared with the thermodynamic results obtained from the temperature dependence of the binding constants. It appears that drugs binding on the outside of the DNA double helix tend to have large enthalpy and small entropy contributions, whereas pure intercalating drugs have contributions from both enthalpy and entropy, with entropy dominating by about 2 : 1. Drugs showing two binding modes exhibit a continuum between the aforementioned extremes, with no breaks in behavior.

From this comparison, a correlation between thermodynamic data and DNA binding modes is proposed. Possible molecular implications of both enthalpy and entropy to DNA binding free energy are discussed.
Structure and antigenic activity of rubella E1 glycoprotein synthetic peptides
Authors: Neri P. , Corti M. , Lozzi L. , Valensin P. E.
Published: December 2004

Minimal sequences of rubella E1 glycoprotein epitopes were previously identified as the tripeptide 250PER252 for the EP2 epitope, the tetrapeptide 260ADDP263 for the EP3 epitope, and the tripeptide 273EVW275 plus the octapeptide 278PVIGSQAR285 for the EP1 epitope.

In order to establish for each epitope the shortest sequence that was able to give the maximum binding with human antirubella immunoglobulins, synthetic peptides with increasing number of residues flanking these essential parts of rubella E1 glycoprotein epitopes were synthesized and examined for their antigenic activity.

Usually higher activity was observed with progressively longer homologues, whereas the additions of Pro‐271, Pro‐278 to 272GEVWVT277 peptide, and additions of Ala‐248 to 249TPERP253and 249TPERPR254, led to an abrupt decrease in binding. Taken together, our results indicated that the antigenic activity of the whole antigen could be dissected and reproduced using synthetic peptides of appropriate structure for each epitope.
Preferred conformation of peptides from Cα,α‐symmetrically disubstituted glycines: Aromatic residues
Authors: Crisma M. , Valle G. , Bonora G. M. , Toniolo C. , Lelj F. , Barone V. , Fraternall F. , Hardy P. M. , Maia H. L. S.
Published: December 2004

The conformational preference of Cα,α‐diphenylglycinc (Døg) and Cα,α‐dibenzylglycine (Dbz) residues was assessed in selected derivatives and small peptides by conformational energy computations, ir absorption, 1H‐nmr, and x‐ray diffraction. Conformational energy computations on the two monopeptides strongly support the view that these Cα,α‐symmetrically disubstituted glycines are conformationally restricted and that their minimum energy conformation falls in the fully extended (C5) region. The results of the theoretical analyses appear to be in agreement with the solution and crystal‐state structural propensities of three derivatives and seven di‐and tripeptides.
The kinetics of chain exchange in two‐chain coiled coils: αα‐ and ββ‐tropomyosin
Authors: Ozeki Sumio , Kato Tadashi , Holtzer Marilyn Emerson , Holtzer Alfred
Published: December 2004

Measurements are presented on the time course of chain exchange among two‐chain α‐helical coiled coils of rabbit tropomyosin. All experiments are in a regime (temperature, protein concentration) in which coiled‐coil dimers are the predominant species. Self‐exchange in αα‐tropomyosin was investigated by mixing αα species with α*α*, the asterisk designating an α‐chain whose lone sulfhydryl (C190) has been blocked by carboxyamidomethylation. The overall process αα + α*α* ⇄ 2αα* is followed by measurement of the fraction (h ) of αα* species as a function of time. Similarly, self‐exchange in ββ‐tropomyosin is examined by measurements of the overall process: ββ + β*β* ⇄ 2ββ*, in which β* signifies a β‐chain blocked at both sulfhydryls (C36 and C190). The observed time course for both chains is well fit by the first‐order equation: h (t ) = h (∞)(1 − e), with h (∞) ≃ 0.5. This long‐time limit is as expected for self‐exchange, and agrees with experiments that attain equilibrium after slow cooling of thermally dissociated and unfolded chains. The simplest consonant mechanism is chain exchange by rate‐limiting dissociation of dimers followed by random reassociation. Kinetic analysis shows k 1 to be the rate constant for the chain dissociation step, a quantity not previously measured for any coiled coil. This rate constant for ββ species is about an order of magnitude greater than for αα. In both, the activation enthalpy and entropy are very large, suggesting that activation to an extensively (>50%) unfolded species necessarily precedes dissociation. Experiments are also reported for overall processes: αα + β*β* ⇄ 2αβ* and α*α* + ββ ⇄ 2α*β. Results are independent of which chain is blocked. Again h (∞) ≃ 0.5, in agreement with equilibrium experiments, and the time course is first order. The rate constants and activation parameters are intermediate between those for self‐exchange.
The hydration response of poly(L‐lysine) dynamics measured by 13C‐nmr spectroscopy
Authors: Swanson Scott D. , Bryant Robert G.
Published: December 2004

13C‐nmr measurements are reported for samples of poly (L‐lysine) both static and spinning at the magic angle in the β‐sheet form as a function of water content. The addition of water decreases the side‐chain line widths considerably. Measurements of the cross‐polarization time constants indicate that hydration by either H2O or D2O increases the time constant. Measurements of spin–lattice relaxation times in the laboratory frame and the rotating frame indicate that hydration does not change the dynamics of the backbone carbon atoms in the β‐sheet structure appreciably, but the side‐chain atoms experience considerable increase in local mobility with increasing hydration. Deuteration of the exchangeable protons or the water has only small effects on the carbon relaxation times indicating that relaxation is driven by intramolecular dipole–dipole interactions.
Solvent reorganization contribution to the transfer thermodynamics of small nonpolar molecules
Authors: Lee B.
Published: December 2004

The experimental thermodynamic data for the dissolution of five simple hydrocarbon molecules in water were combined with the solute–solvent interaction energy from a computer simulation study to yield data on the enthalpy change of solvent reorganization. Similar data were generated for dissolving these same solute molecules in their respective neat solvents using the equilibrium vapor pressure and the heat of vaporization data for the pure liquid. The enthalpy and the free energy changes upon cavity formation were also estimated using the temperature dependence of the solute–solvent interaction energy. Both the enthalpy and TΔS for cavity formation rapidly increase with temperature in both solvent types, and the free energy of cavity formation can be reproduced accurately by the scaled particle theory over the entire temperature range in all cases. These results indicate that the characteristic structure formation around an inert solute molecule in water produces compensating changes in enthalpy and entropy, and that the hydrophobicity arises mainly from the difference in the excluded volume effect.
Interaction of La(III) and Tb(III) ions with purine nucleotides: Evidence for metal chelation (N‐7‐M‐PO3) and the effect of macrochelate formation on the nucleotide sugar conformation
Authors: Tajmir‐Riahi Heidar‐Ali
Published: December 2004

The interaction of the La(III) and Tb(III) ions with adenosine‐5′‐monophosphate (5′‐AMP), guanosine‐5′‐monophosphate (5′‐GMP), and 2′‐deoxyguanosine‐5′‐monophosphate (5′‐dGMP) anions with metal/nucleotide ratios of 1 and 2 has been studied in aqueous solution in acidic and neutral pHs. The solid complexes were isolated and characterized by Fourier transform ir and 1H‐nmr spectroscopy.

The lanthanide(III)–nucleotide complexes are polymeric in nature both in the solid and aqueous solutions. In the metal‐nucleotide complexes isolated from acidic solution, the nucleotide binding is via the phosphate group (inner sphere) and an indirect metal‐N‐7 interaction (outer‐sphere) with the adenine N‐1 site protonated. In the complexes obtained from neutral solution, metal chelation through the N‐7 and the PO group is prevailing. In aqueous solution, an equilibrium between the inner and outer sphere metal‐nucleotide interaction has been observed. The ribose moiety shows C2′‐endo/anti pucker in the free AMP anion and in the lanthanide(III)–AMP complexes, whereas the GMP anion with C2′‐endo/anti sugar conformation exhibits a mixture of the C2′‐endo/anti and C3′‐endo/anti sugar puckers in the lanthanide(III)–GMP salts. The deoxyribose has O4′‐endo/anti sugar pucker in the free dGMP anion and a C3′‐endo/anti, in the lanthanide (III)–dGMP complexes.
Experimental and theoretical studies of DNA separations by capillary electrophoresis in entangled polymer solutions
Authors: Grossman Paul D. , Soane David S.
Published: December 2004

Studies of electrophoretic separations of DNA restriction fragments by capillary electrophoresis in solutions of (hydroxyethyl) cellulose (HEC) were performed. Rheological studies were used to confirm that the entanglement threshold (Φ*) for the HEC solutions used is approximately 0.004 g/mL, in good agreement with theoretical predictions. A mesh size an order of magnitude smaller than that found in agarose gels (on a per weight basis) was calculated using polymer‐entanglement theory and was confirmed by electrophoretic measurements. Electrophoretic migration was shown to follow the Ogston regime under most conditions. An approach for obtaining smaller mesh sizes is presented.
Structural properties of polydisperse biopolymer solutions: A light scattering study of bovine α‐crystallin
Authors: Schurtenberger P. , Augusteyn R. C.
Published: December 2004

We have measured 〈RH〉z, 〈R〉, and 〈M〉w for individual fractions of the protein α‐crystallin obtained by gel filtration of bovine lens nuclear extracts. A strong and monotonic decrease of 〈RH〉z and 〈M〉w with increasing elution volume could be observed, indicating a broad size distribution. The experimental results are quantitatively consistent with a polymerization of monomeric units into linear chains, which may have a certain degree of flexibility. Using theoretical expressions for 〈R〉 and RH originally derived for semiflexible polymers in solution, we can self‐consistently analyse the data from static and dynamic light scattering, and from electron microscopy experiments. We thus obtain detailed information on the molecular weight distribution and the quaternary structure of α‐crystallin in these solutions.
Probe diffusion in solutions of filamentous actin formed in the presence of gelsolin
Authors: Newman Jay , Gukelberger Gerlinde , Schick Kenneth L. , Zaner Ken S.
Published: December 2004

Dynamic light scattering was used to characterize the diffusion of monodisperse polystyrene latex spheres (PLS) of different sizes (55‐, 105‐, and 265‐nm radii) in column‐purified 0.65 mg/mL actin solutions polymerized with 100 mM KCl in the absence and presence of various amounts of the actin‐binding protein gelsolin. The gelsolin and its interaction with actin was initially studied to ensure that the gelsolin could be used to produce filament populations with well‐defined mean lengths. Measurements with PLS diffusion probes present showed, in the absence of gelsolin, that the effective local microviscosity in the actin solutions was 5–20 times that of water and that a large fraction of the PLS are trapped within the pores of the actin filament network, as found previously [J. Newman, K. L. Schick, & K. S. Zaner, (1989) Biopolymers 28, 1969–1980]. As the molar ratio of gelsolin to actin was increased, the diffusion coefficients of the PLS approached those in pure water while the degree of PLS trapping went to zero. Measurements of the dependence of the PLS diffusion coefficients on the ratio of actin concentration to the semidilute overlap concentration showed, for the smaller PLS, a transition occurring near the mean global overlap concentration. These results reflect the dissolution of the actin network as the gelsolin concentration is increased and illustrate the role of gelsolin/actin interactions in the control of macromolecular transport within the periphery of cells.
Birefringence of actin
Authors: Kakar Sharwan K. , Bettelheim Frederick A.
Published: December 2004

The total strain birefringence of F‐actin isolated from chicken gizzards was measured as a function of elongation in thin transparent films. Each film held at a certain elongation in a jig was allowed to swell in a penetrating but nondissolving liquid. Seven liquids with different refractive indices were employed. The thickness of the film in each swelling liquid was obtained once equilibrium was established. At each elongation, from 0 to 16%, a Wiener curve was obtained. The minima of the Wiener curves yielded the intrinsic birefringence of F‐actin as a function of elongation. The intrinsic birefringence increases with elongation up to 16%, above which the thin films break. The form birefringence at a set refractive index also increases with elongation. The implication of the strain birefringence of F‐actin is discussed as it affects the optical properties, mainly light scattering, of tissues such as the fiber cells of lens of the eye.
Unfolding of an α‐helix in water
Authors: Soman Kizhake V. , Karimi Afshin , Case David A.
Published: December 2004

We describe a 1 ns molecular dynamics simulation of an 18‐residue peptide (corresponding to a portion pf the H helix of myoglobin) in water. The initial helical conformation progressively frays to a more disordered structure, with the loss of internal secondary structure generally proceeding from the C‐terminus toward the N‐terminus. Although a variety of mechanisms are involved in the breaking of helical hydrogen bonds, the formation of transient turn structures, with i → i + 3 hydrogen bonds, and bifurcated hydrogen‐bond structures intermediate between α and turn or 310 structures is a common motif. In some cases a single water molecule is inserted into an internal hydrogen bond, but it is also common to have several water molecules involved in transient intermediates. Overall, the results provide new information about the detailed mechanisms by which helices are made and broken in aqueous solution.
Solution conformation of laminaribioside and (1 → 3)‐β‐D‐glucan from optical rotation
Authors: Duda Christopher A. , Stevens Eugene S.
Published: December 2004

A chiroptical method of conformational analysis is applied to linear (1 → 3)‐β‐D‐glucans and the dimeric analogues β‐ and α‐laminaribioside. The method is based on a recently developed semiempirical calculational model for saccharide optical activity. We conclude that disaccharide conformational energy maps in the literature represent the effective potential energy surface in aqueous solution well. The positive optical rotation observed with long chains in dilute alkaline solution is not characteristic of any single–chain conformation, and must reflect chain association.
Vibrational CD of the amide II band in some model polypeptides and proteins
Authors: Gupta Vijai P. , Keiderling Timothy A.
Published: December 2004

The amide II vibrational CD (VCD) spectra of poly(L‐glutamic acid) and poly(L‐lysine) in various conformational forms and those of several proteins in H2O have been measured. Characteristic VCD patterns have been observed in the amide II region due to helix, β‐sheet, and coil conformations in polypeptides. Based on their x‐ray crystal structures, the proteins studied have been assigned to six categories. Proteins in the same category give rise to similar amide II VCD. While the protein conformational type is indicated using the amide II VCD, discrimination between types is less characteristic than with the previously studied amide I' VCD in D2O.
Multivalent ions are necessary for poly[d(AC) · d(GT)] to assume the Z form: A CD study
Authors: Riazance‐Lawrences Jeannine H. , Johnson W. Curtis
Published: December 2004

In previous work, it was shown that poly [d(AC) · d(GT)] could be forced into the Z form by strong dehydrating conditions, provided EDTA was not present. Presumably multivalent impurities were also necessary for the transition. In order to gain control over the B to Z transition for this DNA, we carefully removed all divalent contaminants from the sample and asked the obvious question: What ions are necessary for the transition under dehydrating conditions? We systematically investigated the effect of various multivalent ions. The common contaminants Ca2+, Mg2+, and Fe3+ will not cause the transition, but Co2+ and Ni2+ facilitate the transition, undoubtedly because of their well‐known propensity to bind to purine N7. Since the transition also depends on the synergistic dehydrating action of sodium perchlorate and ethanol, we include CD spectra for the independent variations of these two factors. In addition, vacuum‐uv CD spectra for the A form and various B forms of poly [d (AC) · d (GT)] are presented for the first time.
Stoichiometry of calcium binding to a synthetic heterodimeric troponin‐C domain
Authors: Shaw Gary S. , Hodges Robert S. , Sykes Brian D.
Published: December 2004

In this work we describe calcium binding to two synthetic 34‐residue peptides, determined by 1H‐nmr spectroscopy. The peptides investigated, SCIII and SCIV, encompass the calcium‐binding sites III and IV, respectively, of troponin‐C. In the absence of calcium it has previously been shown that each of these peptides possesses little regular secondary structure. Further, the 1H‐nmr spectra of an equimolar mixture of both of these apo‐peptides (apo‐SCIII/SCIV) shows that little interaction occurs between peptides. Upon calcium binding the spectral changes that occur to SCIII/SCIV are consistent with global conformational changes in both peptides. We have shown previously that these conformational changes are a product of calcium binding to SCIII and SCIV to form a two‐site heterodimer Ca2‐SCIII/SCIV. It is proposed that this calcium‐induced folding proceeds via calcium binding to SCIII to form Ca‐SCIII, peptide association with apo‐SCIV to form the heterodimer Ca‐SCIII/SCIV, and calcium binding to form Ca2‐SCIII/SCIV. The dissociation constants involved in this pathway, K1, Kd, and K2, respectively, have been determined by stoichiometric calcium titration of SCIII/SCIV, monitored by 1H‐nmr spectroscopy. Using this procedure it has been determined that K1 = 3 μM, Kd = 10 μM, and K2 = 2 μM.
A molecular mechanical study of the structure of poly(α‐aminoisobutyric acid)
Authors: Alemán Carlos , Subirana Juan A. , Perez Juan J.
Published: December 2004

A molecular mechanical study has been carried out to determine the most favorable conformation of poly(Aib) both in solution and in the solid state. An energetic approach to the packing has been carried out by studying the stability of pairs of poly(Aib) chains. The study reveals a higher stability of a 310‐helix when forming part of a dimer whereas in isolated molecules the α‐helix structure seems to be more stable depending on the length of the chain and dielectric constant of the environment.
Crystal structure of a helical oligopeptide model of polyglycine II and of other polyamides: Acetyl‐(glycyl‐β‐alanyl)2‐NH propyl
Authors: Tormo José , Puiggali Jordi , Vives Joan , Fita Ignasi , Lloveras Joaquim , Bella Jordi , Aymamí Joan , Subirana Juan A.
Published: December 2004

We synthesized and solved the crystalline structure of the oligopeptide acetyl‐ (glycyl‐β‐alanyl)2‐NH propyl. The crystal is formed by layers of helical molecules with the same chirality; however, right‐handed layers alternate with left‐handed ones. Inside every layer, the packing of helices is pseudohexagonal with hydrogen bonds between neighbor molecules. The structure found affords direct support for the model proposed by Crick and Rich for polyglycine II and also provides an interpretation for the structure of a newly found family of polyamides that do not form sheets as observed in most nylon structures.
Kinetics of folding of αα‐tropomyosin subsequences
Authors: Mo Jianming , Holtzer Marilyn Emerson , Holtzer Alfred
Published: December 2004

The kinetics of folding random coils of αα‐tropomyosin (Tm) subsequences to two‐chain coiled coils was studied by stopped‐flow CD. Subsequences studied were those comprising residues 11–127 (11Tm127), 142–281 (142Tm281), 1–189 (1Tm189), and 190–284 (190Tm284) of the parent 284‐residue α‐tropomyosin chain. Unlike the parent, subsequences 1Tm189 and 11Tm127 fold within the dead time of the instrument (< 0.04 s). Like the parent, subsequences 142Tm281 and 19Tm284 fold in two phases. In the fast phase, 45% and 32%, respectively, of the equilibrium helical content form. In the time‐resolvable, first‐order slow phase (k−l = 2.7 s at 20°C for 142Tm281 and k−l = 2.0 s at 15°C for 190Tm284), the remaining structure forms. Neither reduced 142Tm281 nor 190Tm284 show any dependence of the rate on concentration, so chain association occurs in the fast phase. Like the parent, 142Tm281 forms more helical content in the fast phase when cross‐linked at C‐190, and the remaining structure forms slowly with rate parameters similar to those of the reduced species. Comparison of the folding behavior of C‐ and N‐terminal subsequences with that of the parent protein suggests that the slow phase in the parent is caused by a folding bottleneck somewhere nearer the C‐terminus. However, rapid association and partial folding near the N‐terminus is not necessary for prompt folding, since even 190Tm284 chains associate and partially fold very rapidly (<0.04 s), and then complete the folding in seconds.
Spectroscopic study of the interaction between poly‐(9‐vinyladenine) and single or multistrand RNA
Authors: Yashima Eiji , Tajima Teruyo , Miyauchi Noriyuki , Akashi Mitsuru
Published: December 2004

The interaction between poly(9‐vinyladenine) (PVAd) and poly[r (U)] was investigated by means of uv, CD, 1H‐, and 31P‐nmr spectroscopies. The interaction was dependent on the molecular weight of PVAd determined by uv and CD spectroscopies. Based on imino proton nmr, it was clearly found that PVAd formed the complex with poly [r(U)] by complementary hydrogen bonding. The interaction of PVAd with double‐ and triple‐stranded helices of RNA was also investigated by uv melting behavior and 31P‐nmr spectroscopy. The results suggested that PVAd could not interact with the double‐stranded poly [r (A)] · poly[r(U)] but did with the triple‐stranded RNA.
Conformational and ion binding properties of a cyclic octapeptide, cyclo(Ala‐Leu‐Pro‐Gly)2
Authors: Jois D. S. Seetharama , Easwaran K. R. K. , Bednarek Maria , Blout E. R.
Published: December 2004

The conformation and ion‐binding characteristics of a cyclic octapeptide, cyclo(Ala‐Leu‐Pro‐Gly)2, in a liphophilic solvent, acetonitrile, have been studied using CD and nmr spectroscopy. The peptide binds preferentially to divalent cations such as calcium, magnesium, and barium. The conformations of the free cyclic peptide and its calcium complex are very similar with well‐defined β‐ and γ‐turns. The cyclic peptide readily forms equimolar and possibly 2 : 1 (peptide:cation) complexes with divalent cations.
Hydrophobicity scale for proteins based on inverse temperature transitions
Authors: Urry Dan W. , Gowda D. Channe , Parker Timothy M. , Luan Chi‐Hao , Reid Michael C. , Harris Cynthia M. , Pattanaik Asima , Harris R. Dean
Published: December 2004

In general, proteins fold with hydrophobia residues buried, away from water. Reversible protein folding due to hydrophobia interactions results from inverse temperature transitions where folding occurs on raising the temperature. Because homoiothermic animals constitute an infinite heat reservoir, it is the transition temperature, Tt, not the endothermic heat of the transition, that determines the hydrophobically folded state of polypeptides at body temperature. Reported here is a new hydrophobicity scale based on the values of Tt for each amino acid residue as a guest in a natural repeating peptide sequence, the high polymers of which exhibit reversible inverse temperature transitions. Significantly, a number of ways have been demonstrated for changing Tt such that reversibly lowering Tt, from above to below physiological temperature becomes a means of isothermally and reversibly driving hydrophobic folding. Accordingly, controlling Tt, becomes a mechanism whereby proteins can be induced to carry out isothermal free energy transduction. © 1992 John Wiley & Sons, Inc.
The spectroscopic properties of the lipodepsipeptide, syringomycin E
Authors: Vaillo Eva , Ballo Alessandro , Luisi Pier‐Luigi , Thomas Richard M.
Published: December 2004

The Spectroscopic properties of syringomycin E, an antibiotic lipodepsinonapeptide associated with pathological states in plants, have been investigated by uv absorbance and CD spectroscopies, and by the synthesis of relevant model compounds. Initial studies [E. Vaillo, A. Ballio, P. L. Luisi, and R. M. Thomas (1990) in Peptides 1990, Giralt, E. & Andreu, D., Eds., Escom Scientific, Leiden, Netherlands] suggested that a significant contribution to the spectra was due to the presence of a zdehydroaminobutyric acid residue in the amino acid sequence. The model peptides N‐Boc‐L‐Phe‐ΔZAbu‐OMe and its analogue, N‐Boc‐L‐Phe‐L‐Thr‐OMe, lacking the unsaturated bond, were synthesized using standard solution chemistry, and a detailed investigation was made in which the spectra of the models and that of syringotoxin (an antibiotic closely related to syringomycin E but without a Phe residue) were compared with those of syringomycin E under a variety of solvent conditions. The uv absorbance spectra of both N‐Boc‐L‐Phe‐ΔZAbu‐OMe and syringomycin E clearly showed the presence of the unsaturated residue while the CD spectra were complex, environmentally sensitive, and contained contributions from both the ΔzAbu and Phe residues. In the course of these studies extinction coefficients were obtained for syringomycin E and its dipeptide model. The origins of the uv and CD spectra are discussed in detail, and a comparison is made with the spectra of other, similar lipopeptide antibiotics. Finally, a structural model for syringomycin is proposed in which the changes induced in the spectrum by alterations in the solvent environment are accommodated. © 1992 John Wiley & Sons, Inc.
Interpretation of 25Mg spin relaxation in Mg‐DNA solutions: Temperature variation and chemical exchange effects
Authors: Berggren Elisabet , Nordenskiöld Lars , Braunlin William H.
Published: December 2004

The temperature dependencies of line shapes and spin lattice relaxation times Tl have been measured for 25Mg in dilute solutions of Na‐DNA/NaCl containing varying amounts of added magnesium(II) ions. The 25Mg spectrum is clearly non‐Lorentzian, due to the presence of motions modulating the quadrupolar interaction that are slow compared to the inverse of the Larmor frequency. The weakly temperature dependent line shapes and relaxation rates appear to be influenced by the relatively slow exchange of the Mg2+ ions between the DNA surface and the aqueous bulk phase. The observed temperature dependencies depend on the ratio of total magnesium to DNA phosphate, Mg/P. The line shape as well as the temperature dependence of the line width at half height can be qualitatively reproduced with a two‐site discrete exchange model for the quadrupolar relaxation of a spin \documentclass{article}\pagestyle{empty}\begin{document}$ \frac{5}{2} $\end{document} nucleus in isotropic solution. The calculations give a value of the lifetime for magnesium bound to DNA of 4 ms at room temperature. Previously reported temperature dependent 43Ca relaxation measurements in DNA solution can be reproduced under the assumption of a mean lifetime of bound calcium that is not, larger than 2 ms but not smaller than 50 μs at room temperature. The temperature variation of T1 for 25Mg has been calculated, giving some qualitative agreement with the data. The correlation time for bound 25Mg has been found to be about 40 ns at room temperature. © 1992 John Wiley & Sons, Inc.
Excluded volume effects on the partition of single‐ and double‐stranded oligodeoxynucleotides between two liquid phases
Authors: Zimmerman Steven B. , Murphy Lizabeth D.
Published: December 2004

The distribution coefficients of single‐ and double‐stranded Oligodeoxynucleotides in a PEG 8000/phosphate two‐phase system are a function of their chain length. Values of the distribution coefficients are in general agreement with a simple extension of a model for excluded volume effects (the “available volume model”) which was applied previously to the distribution of proteins in this system. The current results therefore provide a second set of examples for molecules of very different geometry where the distribution of added molecules is controlled by excluded volume interactions between those molecules and the PEG 8000 of the two‐phase system. © 1992 John Wiley & Sons, Inc.
Fourier transform IR study of enzymatically isolated tomato fruit cuticular membrane
Authors: Ramirez F. J. , Luque P. , Heredia A. , Bukovac M. J.
Published: December 2004

Fourier transform ir study on enzymatically isolated tomato fruit cuticle has been performed. Assignments of the observed frequencies to functional groups present in the cuticular membrane yield information on the polyester cross‐links and the interactions among the different components that form this plant protective barrier. © 1992 John Wiley & Sons, Inc.
Quasielastic light scattering study of thermal excitations of F‐actin solutions and of growth kinetics of actin filaments
Authors: Piekenbrock Th. , Sackmann E.
Published: December 2004

In the first part of this work we report quasielastic light scattering (QELS) studies of the internal dynamics of transient actin networks over a time range of 10−6–10−2 s, scattering angles between ζ = 20° and 150°, and a concentration range of 0.015 (0.3) to 0.7 mg/mL (15 μM). We confirm our previous result that (1) the dynamic structure factor g(q, t) is determined by the thermally excited undulations of the actin filaments and (2) that the initial decay of g(q, t) scales as g(q, t)∝ exp(qαt) while the long time decay scales as g(q, t) ∝ exp[‐(Aqαt)2/3] with α = 2.75. The deviation of α from the theoretical value of α = 3 predicted for Rouse‐Zimm chains is similar to that found for high molecular weight macromolecular solutions by QELS. A refined analysis of the dynamic structure factor showed that it can be interpreted in terms of three relaxation processes (besides the contribution of the residual monomer diffusion): (1) the dominant Rouse‐Zimm dynamics, which comprises between 65 (at high concentrations) and 85% of the signal; (2) a fast relaxation process with a decay constant of Γ = 9 × 103 s−1, which contributes at all concentrations with the same amplitude; and (3) a nonexponential ultraslow contribution of the form gus ∝ exp[(– Γust)] 1/4. The third contribution appears only at high concen‐trations and increases strongly with decreasing scattering angles. It is thus attributed to fluctuations of the mesh size of the transient actin network.

In the second part we show that high sensitivity QELS may be applied to follow the actin polymerization process at low temperatures (10°C). The apparent diffusion coefficient and the static scattering intensity of the actin filaments were determined as functions of polymerization time tpol. We show that the process consists of the rapid growth of a few filaments that become very long (≈10 μm; even at actin concentrations of 0.04 μg/mL) near the critical growth concentration of 0.012 μg/mL, as is expected for a growth process determined by nucleation.

Finally, we studied actin networks polymerized in the presence of complexes of gelsolin with actin. By application of the CONTIN program we could determine the length distribution of the filaments. The very broad length distribution is nearly exponential, quite analogous to the distribution predicted for polymers grown by the polycondensation process; that is the association of monomers and oligomers. © 1992 John Wiley & Sons, Inc.
Monte carlo calculations of ion distributions surrounding the oligonucleotide d(ATATATATAT)2 in the B, A, and wrinkled D conformations
Authors: Mills Pamela A. , Rashid Ali , James Thomas L.
Published: December 2004

We calculated the uni‐univalent ion distributions around‐ the oligonucleotide d(AT)5 · d(AT)5 in the A, B and wrinkled D conformation using the Metropolis Monte Carlo method. All atoms were included in the oligonucleotide model with partial charges and hard sphere radii assigned to each atom. The univalent counter‐ and coions were modeled as hard spheres with radius 0.3 nm. The solvent was assigned a dielectric constant of 80, corresponding to a temperature of 298K. The counterion distribution surrounding each of the conformers and the distribution surrounding an impenetrable cylinder, were calculated for four salt concentrations. We found significant counterion density in the major groove of the A DNA while fewer counterions occupied the grooves of B DNA. In the wrinkled D DNA, where groove occupancy is sterically hindered, the ion distributions were identical to the distributions surrounding the impenetrable, cylindrical model. This suggests that excluded volume effects significantly influence the details of the ion distributions near the oligomer, while the detailed charge distributions of the oligomer affects the ion distributions only minimally. Although substantial variation in counterion density was observed near the oligomers of differing conformations, the total number of counterions located within a cylinder surrounding the oligomer bounded radially by 2.4 nm was independent of the conformation of the oligomer. Therefore, for this model system, the local univalent counterion distributions are extremely sensitive to the geometry of the oligonucleotide whereas the extent of neutralization of the oligoanion is insensitive to the conformation of the oligomer. © 1992 John Wiley & Sons, Inc.
Conformational perturbation of the anticancer nucleoside arabinosylcytosine on Z‐DNA: Molecular structure of (araC‐dG)3 at 1.3 Å resolution
Authors: Zhang Hong , Van Der Marel Gijs A. , Van Boom Jacques H. , Wang Andrew H.‐J.
Published: December 2004

The left‐handed Z‐DNA structure of an araC‐containing (where araC stands for arabinosylcytosine) hexamer, (araC‐dG)3, has been solved by x‐ray diffraction analysis at 1.3 A resolution. This hexamer was crystallized in the hexagonal P6522 (a = b = 17.96 Å, c = 43.22 Å) space group in which the hexamers have statistically disordered packing arrangement along the 65 screw axis, yet the crystals diffract x‐rays to high resolution. Its structure has been refined by the constrained least square refinement to a final R factor of 0.287 using 737 [> 3.0 σ(F)] observed reflections. The asymmetric unit of the unit cell contains only a dinucleotide, 5′‐p(araC)p(dG). The overall conformation resembles that of the canonical Z‐DNA, but with some differences in details. The O2′ hydroxyl groups of the araC residues form intramolecular hydrogen bonds with N2 of the 5′‐guanine residues. In the deep groove of Z‐DNA, these hydroxy groups replace the bridging water molecules that stabilize the guanine in the syn conformation. The results reinforce the earlier observation made by the structural analysis of another hexamer, d(CG[araC]GCG), with a mono‐substitution of araC [M.‐K. Teng, Y.‐C. Liaw, G. A. van der Marel, J. H. van Boom, and A. H.‐J. Wang (1989) Biochemistry, vol. 28, pp. 4923–4928]. These two structures show that araC residue can be incorporated readily into the Z structure and probably facilitates the B to Z transition, as supported by uv absorption spectroscopic studies in a number of araC‐containing oligonucleotides. The potential biological roles of the araC‐modified Z‐DNA are discussed. © 1992 John Wiley & Sons, Inc.