bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular configuration of amylose and its complexes in aqueous solutions. Part III. Investigation of the DP distribution of helical segments in amylose–iodine complexes
Authors: Szejtli J. , Augustat S. , Richter M.
Published: December 2004

The equilibrium normality [If] of free iodine in amylose‐iodine complex formation is a function of the length of the polyiodine chains. This length depends on the DP of helical segments of amylose (sDPn). Values of [If] and of the concentration of the bound iodine [Ib] were determined by the continuous photometric titration with automatic recording. Plots of [Ib] versus [If] give an integral distribution curve. Since the relation between [If] and sDPn is known, the graphic differentiation of the [Ib] versus [lf] curve furnishes the differential distribution curve, representing the mass distribution of the helical segments according to their DP. The peak of this curve is characteristic of the percentage and DP of those helical segments, which occur in the largest amount. On the basis of the differential distribution curve the polymolecularity of the investigated sample may be judged. The titration of amylose samples degraded by various methods gives different distribution curves. Titrating mixtures of samples with widely differing average DP values results in differential curves having more than one maximum.
Theory and practice of the analytical centrifugation of an active substrate–enzyme complex
Authors: Cohen R. , Giraud B. , Messiah A.
Published: December 2004

The active enzyme centrifugal‐ion (AEC) method presented here permits the hydrodynamic study of active enzyme–substrate(s) complexes in solutions containing micro‐gram amounts of the studied enzyme, even if the enzyme preparation is very impure. The AEC method can he used only when the specific enzymatie reaction can be measured directly in a spectrophotometer. The general equations relevant to the method and their solutions are presented in detail. Their use requires some numerical calculations. A practical summary of the AEC method is given, and the precision of the measured values of the sedimentation and diffusion coefficients is discussed.
General method for calculating helical parameters of polymer chains from bond lengths, bond angles, and internal‐rotation angles
Authors: Sugeta Hiromu , Miyazawa Tatsuo
Published: December 2004

Helical conformations of infinite polymer chains may be described by the helical parameters, d and θ (the translation along the helix axis and the angle of rotation about the axis per repeat unit), pi (the distance of the ith atom from the axis), dij, and dij (the translation along the axis and the angle of rotation, respectively, on passing from the ith atom to the jth). A general method has been worked out for calculating all those helical parameters from the bond lengths, bond angles, and internal‐rotation angles. The positions of the main chain and side chain atoms with respect to the axis may also be calculated. All the equations are applicable to any helical polymer chain and are readily programmed for electronic computers. A method is also presented for calculating the partial derivatives of helical parameters with respect to molecular parameters.
Numerical solutions of the Lamm equation. III. Velocity centrifugation
Authors: Dishon Menachem , Weiss George H. , Yphantis David A.
Published: December 2004

We have generated solutions to the Lamm equation to examine the effects of concentration dependence on velocity experiments. Two forms of c dependence are considered: s/s0 = 1 – kc and s/s0 = (1 + kc)−1. Features of these solutions are discussed. The magnitude of the errors resulting from the usual procedure of measuring the rate of movement of schlieren maxima or of the position at which the concentration is one half the plateau value have been examined. These errors are usually negligible after sufficient centrifugation time. The errors in using the half‐plateau concentration are less than those using the movement of the peak. We have also examined a technique due to Fujita for determining D from boundary spreading when s/s0 = (1+kc)−1. This method is satisfactory when s/s0 is actually of this form, or under certain limitations when s/s0 = (1 + kc)−1. Creeth has shown that under certain conditions the concentration gradient, curve remains virtually unchanged in shape after separating from the meniscus. When this occurs it is possible to estimate s/D from the data. The condition for such a steady state is that kc0 be sufficiently large. Numerical confirmation of this method is presented in the final section.
Electron microscope examination of fibroin precipitated from silk fibroin solutions
Authors: Happey F. , Hyde A. J. , Manogue B.
Published: December 2004

The structure of gels formed from solutions of silk fibroin has been observed by electron microscopy. The gels consist of fibrils, and possible methods of formation of these fibrils are suggested.
Dielectric properties and oxygenation of hemoglobin
Authors: Hanss Maxime , Banerjee Ramalprasad
Published: December 2004

Dielectric properties of human and horse hemoglobin were studied at frequencies ranging from 20 kc./sec. to 7 Mc./sec. The relative errors in the measurements were usually less than 10−3 even for mildly conducting solutions (10−3M KCl). The experimental setup allowed us variation and measurement of the degree of oxygenation of the protein and to determine its dielectric parameters. Our main conclusion is that it was not possible to find any variation of the dielectric increment for hemoglobin oxygenation levels of 25, 50, 75, and 100%, approximately. This result is at variance with some previous reports. We cannot give the reason for this discrepancy but discuss some possible explanations. The specific dielectric increment, Δεs/c, of human hemoglobin was shown to be significantly smaller than that of horse hemoglobin (0.28 against 0.32). This physical property is lowered with increasing ionic strength I: Δεs/c = 0.28 and 0.20 for I = 10−4 and 10−3, respectively (human protein).
Electrostatic effects on polynucleotide transitions. II. Behavior of titrated systems
Authors: Record M. Thomas
Published: December 2004

The theory developed in the previous paper to discuss changes in electrostatic free energies in polynucleotide order–disorder transitions is extended to cases where one or more of the participating species is titrated to some degree α. It is shown that, for any class of transition, the melting temperature Tm at constant pH is a linear function of the logarithm of the monovalent counterion concentration M, that at high salt the logarithm of the depression of the melting temperature by pH titration is proportional to the pH change, and that the stability of the ordered form as measured by its melting temperature at neutral pH, is a monotonic function of the quantity pHm – pK, where pHm and pK are the pH of melting and the monomer base pK, both measured under similar conditions of temperature and ionic strength. For the transition from double helix to coil, the dependences of Tm and dTm/d log M on pH are determined experimentally and compared with the qualitative predictions of the theory. It is found that dTm/dlog M, a measure of – ΔF̄el (the negative of the electrostatic free energy change in the transition), decreases with increasing pH. In acid solution, where the coil is more extensively prolonated than the helix, the change in electrostatic free energy in the transition is larger than at neutral pH. Conversely, in alkali the electrostatic five energy change is smaller than at neutral pH. Hence (dTm/d log M)acid > (dTm/d log M neutral) > (dTm/d log M)alkali. At Suffeciently high pH, dTm/d log M is observed to become negative, indicating that the electrostatic free energy change is positive in the transition of this region. Date from the literature on the ionic strength dependence of the melting temperature for the acid helices of poly rA, poly rC, and poly dC are also considered from the standpoint of the theory.
Molecular configuration of amylose and its complexes in aqueous solutions. Part IV. Determination of DP of amylose by measuring the concentration of free iodine in solution of amylose–iodine complex
Authors: Szejtli J. , Richter M. , Augustat S.
Published: December 2004

In aqueous solutions of the amylase–iodine complex the concentration of free iodine [If]v after reaching equilibrium (or closely approximating it) is determined by the following factors: temperature, pH, concentration of iodide ions and amylose, and DP of amylose. In the present paper the role of temperature, amylose concentration, and DP has been investigated. At half‐saturation of amylose by iodine, the reciprocal value of free iodine defines the equilibrium constant: 1/[If]v = K. The relation between [If]v, in normality and temperature is the following: 5 + log [If]v = −(2.132/T) + 8.52, for DPn = 1290, 0.4 mg. amylose in 100 ml. 0.1N HCl. The value of the energy of activation Ea between 2 and 52°C. is 9.72 kcal./mole. The influence of amylose concentration [Am] on photometrically determined [If]v, at 20°C, in the range of 0.1–1.2 mg./100 ml. 0.1 N HCl for DPn = 1290 is: 5 + log [If]v = 0.209 − 0.047 log [Am]. At [Am] = 0.6 mg. amylose/ 100 ml. 0.1 N HCl and 20°C, the value of [If]v depends on DPn as follows: 5 + log [If]v = 0.085 = + 0.222 log (104/DPn). These above equations are summarized by the relation: [If]v = exp {16.865 − (Ea/RT)}[Am]0.047(104/DPn)0.222 ×10−5
Considering that the determination of [If]v by automatic photometric titration can be performed quickly and with appropriate reproducibility, this method is convenient for a rapid empirical and approximate determination of DP of amylose on a microscale. The iodine‐binding capacity [IBC] as well as the value of λmax, have been also investigated as functions of DPn, by photometric and by amperometric titration.
On the complex formation of acridine dyes with DNA. VII. Dependence of the binding on the dye structure
Authors: Löber G. , Achtert G.
Published: December 2004

The binding constants for the complex formation of more than twenty ring nitrogen‐and amino‐substituted acridine derivatives with calf thymas DNA were measured by a fluorescence method. DNA quenches the fluorescence of the aminoacridine dyes so long as both amino hydrogens are not substituted. These dyes show an enhancement of their fluorescence intensity in the presence of DNA. Typical representatives of both are proflavine and acridine orange derivatives, respectively. A discussion of steric and electronic influences of various substituents attached to the ring nitrogen and amino groups on the binding led to the concept of different conformations for intercalated acridines without amino groups and the aminoacridines. The electrostatic binding site of the former seems to be the positively charged ring nitrogen, while the binding sites in the aminoacridines are so located that the amino groups are directed towards the negatively charged DNA phosphates.
Dielectric properties of hemoglobin and myoglobin II. Dipole moment of sperm whale myoglobin
Authors: Schlecht Peter
Published: December 2004

This paper is concerned with the molecular origin of the dipole moment of sperm whale myoglobin as it can be calculated from the dielectric dispersion at 1 Mcps on the basis of a mechanism of orientational polarization. It was possible to compare the dielectric increment of native myoglobin and its change during the reaction with bromo acetate with dipole moments calculated according to the known coordinates of the charged groups of the molecule. The agreement between the two shows that in myoglobin only the permanent dipole moment due to these charged groups is important, and that contributions from other possible sources remain within the limits of experimental error.
Fluorescence polarization study of DNA–proflavine complexes
Authors: Ellerton Nerida F. , Isenberg Irvin
Published: December 2004

The binding of proflavine to DNA has been studied by measuring the polarization and intensity of emission of DNA–dye complexes. Such measurements also permit the determination of the fluorescence of the bound dye as a function of the degree of binding. Techniques of emission spectroscopy permit the study of complexing at high phosphate to dye ratios, and we have examined complexes formed at up to 12,300:1 phosphates to dye. At high phosphate to dye ratios, we find that equilibrium plots of the binding data show only one type of binding. Reports in the literature of multiple binding constants are shown to be due to the incorrect assumption that the fluorescence of the bound dye is independent of the amount bound. The emission properties can be qualitatively accounted for by assuming that nearest‐neighbor interaction between bound dyes quenches the fluorescence. We report that, within experimental error, the binding constant is insensitive to the base content of the DNA. The DNA‐dye complexes show a temperature dependent depolarization, the cause of which is, as yet, unknown. Heat denaturation of the DNA–dye complex may be followed on a Perrin plot.
Thermal conformational transformation of tropocollagen. I. Calorimetric study
Authors: Privalov P. L. , Tiktopulo E. I.
Published: December 2004

Effects of heat in heated solution of tropocollagens of different origins were calorimetrically studied. It was found that denaturation enthalpy and entropy of different tropocollagens increase with increasing imino acid content and thermostability. It is shown that the value and dependence of denaturational enthalpy and entropy on the denaturation temperature for tropocollagens with different imino acid contents are inconsistent with the assumption that the native structure of tropocollagen is stabilized only by intramolecular hydrogen bonds. A supposition is made that the regular water structure near the macromolecule plays an essential role in stabilizing the structure. From the character of tropocollagen melting curves in salt‐free solution it is found that the tropocollagen macromolecule is linearly heterogeneous. It is shown that the complex pattern of thermal absorption observed in tropocollagen salt, solution is connected with pre‐denaturational conformational transformation when approaching conditions close to the physiological.
Polymerization of amino acid derivatives by polymer catalysts. V. Polymerization of DL‐β‐phenylalanine N‐carboxyanhydride by several poly(N‐alkylamino acid) diethylamides
Authors: Sisido Masahiko , Imanishi Yukio , Okamura Seizo
Published: December 2004

The polymerization of DL‐β‐phenylalanine N‐carboxyanhydride (NCA) initiated by poly(N‐benzylglycine)diethylamide (DEA) and poly(N‐methyl‐DL‐alanine)DEA has been investigated. As previously reported, polysarcosine DEA, poly‐N‐ethylglycine DEA, and poly‐N‐n‐propylglycine DEA showed marked accelerations in the polymerization of DL‐β‐phenylalanine NCA as compared with the polymerization initiated by low molecular weight, amines having similar base strength. However, this phenomenon (the chain effect) was not observed with the two polymer catalysts studied in the present investigation With poly‐N‐methyl‐DL‐alanine DEA, adsorption of DL‐β‐phenylalanine NCA onto the polymer chain takes place, though not so effectively as with other polypeptides, so the absence of chain effect was ascribed to a reduced flexibility of the polymer chain. With poly(N‐benzylglycine)DEA, the reactivity of terminal base group was found to be much lower than that of other polymer catalysts. However, the absence of the chain effect would be attributed to the rigidity of polymer chain of poly‐N‐benzylglycine DEA due to the bulkiness of the N‐benzyl group.
Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleolides
Authors: Cantor Charles R. , Warshaw Myron M. , Shapiro Herman
Published: December 2004

The circular dichroism (CD) spectra of the four usual deoxymononucleosides, all sixteen deoxydinucleotides, and a number of trinucleotides have been measured. The dimer spectra are quite different from the sum of the spectra of their constituent monomers. This indicates the presence of base‐stacked conformations analogous to those found for ribonucleoside diphosphates. The CD spectra of several deoxytrinucleotide diphosphates and single‐strand f 1 DNA can be calculated fairly well by using a semi‐empirical nearest‐neighbor approach. There is little or no effect of terminal phosphate or of salt concentration on the optical properties of most deoxy oligomers. The possibility of simultaneous analysis of mixtures of deoxypurine or deoxypyrimidine sequence isomers has been examined. This seems to be a viable approach for the analysis of purine runs but cannot promise much success for pyrimidine runs.
Electric and hydrodynamic properties of polypeptides in solution. II. Conformation of poly(L‐glutamic acid) in various organic solvents
Authors: Matsumoto Mitsuhiro , Watanabe Hiroshi , Yoshioka Koshiro
Published: December 2004

The electric birefringence of poly(L‐glutamic acid) (PLGA) in methanol, dimethyl sulfoxide, dimethylformamide, N‐methylacetamide, trifluoroacetic acid, dioxane–water mixtures (3:1 and 4:1 by volume), and dioxane–formamide mixture (1:1 by volume) has been measured by the use of the rectangular pulse technique at 30 °C. The intrinsic viscosity has also been measured at the same temperature. The magnitude of the specific Kerr constant and the intrinsic viscosity suggests that PLGA is helical and has a large dipole moment in methanol, dimethyl sulfoxide, dimelhylformamide, N‐methylacetamide, and dioxane–water mixtures. In this case we have obtained the length distribution curve and the mean length of PLGA molecules from the decay of the electric birefringence, by applying the method recently developed for helical polypeptides. Furthermore, we have proposed and applied a method of obtaining the mean dipole moment and the optical anisotropy factor from the field strength dependence of the electric birefringence for polydisperse systems on the basis of the knowledge on the length distribution. The results show that PLGA may have a different helical conformation in dimethyl sulfoxide. The specific Kerr constant of PLGA in trifluoroacetic acid is very small, which suggests that PLGA is a random coil in this solvent.
Sedimentation and viscosity of bacteriophage T7 DNA in presence of CH3HgOH
Authors: Gruenwedel Dieter W. , Brown Susan E.
Published: December 2004

The effects of increasing concentartions of methylmercuric hydroxide (CH3HgOH) on the rate of sedimentation, S0, and intrinsic viscosity, [η], of T7 DNA have been studied at 20°C in 0.005, 0.05, and 0.5M Na2SO4, respectively, whereby each salt solvent conatined, in addition, 0.005M sodium borate, pH 9.18, as a buffer. Both S0 and [η] are independent of organomercurial concentration as long as DNA remains native. Denaturation, brought about by the complexing of CH3HgOH with the polymer, produces large changes in S0 as wll as [η]. The sedimentation coefficient increases strongly with increasing oragnomercurial concentration once strand separation has occured. Experimental difficulties prevented measuring of [η] in the posttransition region. The data on S0 have been used, in combination with available information on the so‐called density increment (∂ρ/∂c2), to obtain information on the frictional properties of single‐stranded and methylmercurated T7 DNA. The frictional coefficient, defined as f′2 = M2(∂p/∂c2)/S0ηNA, where M2 is the molecular wieght of T7 DNA, c2 is the concentration of DNA in g/ml of solution, ηr the realtive viscosity of the salt solvents, and NA is Avogadro's number, was evaluated for all three salt media as a function of organomercurial concentration. f′2 of native T7 DNA was found not to be sensitive to changes in ionic strngth; but f′2 of single‐stranded and methylmercurated T7 DNA varied strongly with salt concentration. Since f′2 of single‐stranded T7 DNA was barely affected by organomercurial concentration at a given ionic strength, it is concluded that the dramatic variations of S0 with pM (pM ≡ ‐log[CH3HgOH]) observed in the posttransition zone reflect only changes in the thermodynamic interactions (“preferential interactions”) existing between DNA and the vatious other solution components, but not changes in the coil dimensions of the polymer.
Adsorption of molecular oxygen by polymer covalently bonded co(II) porhyrin complex in toluene
Authors: Hasegawa Etsuo , Kanayama Tatsuya , Tsuchida Eishun
Published: December 2004

Reaction betwenn molecular oxygen and polystyrene covalently bonded Co(II) protoporphyrin IX complex, which was prepaired by the incorporation of a cobaltous ion into the metal‐free porphyrin polymer, was studied in the presence of N‐ethylimidazole by measuring visible absorption and electron spin resonance spectra. It was found that the complex forms a monomeric oxygen adduct reversibly at low temperature dependent on oxygen pressure. In the presence of molecular oxygen, a new electron spin resonance signal due to the oxygen complex at giso=2.02 shows no superhyperfine splitting structure in fluid toluene solution even at −80 °C, but it was observed in frozen toulene glass solution at −120°C, The oxygen adducts of the complexes between C0(II) protoporphyrin IX dimethyl ester and N‐ethylimidazole and copoly(styrene‐N‐vinylimidazole) showed eight resolved superhyperfine splitting at −40 and −60°C, respectively. The polymer covalently bonded Co(II) complex with N‐ethylimidazole was oxidized at room temperature under oxygen atmosphere. It was suggested that a Co(II) porphyrin–oxygen adduct with an axial ligand may be oxidised monomolecularly at high temperature.
Protonated polynucleotide structures. IX. Disproportionation of poly (G)·poly (C) in acid medium
Authors: Thiele Danielle , Guschlbauer Wilhelm
Published: December 2004

The interaction between poly (G) and poly (C) was investigated in neutral and acid medium by optical methods. Three main points arise from this investigation. (1) The formation of poly (G)·poly (C) was complete only above an ionic strength of about 0.6M [Na+]. Lowering the ionic strength increased the amounts of free poly (G) and free poly (C) that could be detected. (2) When titrating towards acid pH values a transition took place which was characterized by potentiometry, mixing curves, and circular dichroism: a three‐stranded poly (G)·poly (C)·poly (C+) complex was formed analogous to the transition observed for the acid titration of poly (I)·poly (C). (3) Even when the poly (G)·poly (C) complex was incompletely formed (at low ionic strength) in neutral medium all poly (C) entered the triple‐stranded complex.
Acridine orange–poly (α‐L‐glutamic acid) complexes. I. Stoichiometry and stacking coefficients
Authors: Myhr Brian C. , Foss John G.
Published: December 2004

By means of fluorescence, absorption, and acid‐base titrations, it has been shows that there is a one‐to‐one correspondence between free carboxylates and bound acridine orange in the dye‐polyacid complex. Contrary to expections, stacking coefficients for the dye were found to be virtually the same on binding to the helical or coiled polyacid, indicating a strong similarity in the binding sites for both forms of the polyelectrolyte.
Statistical thermodynamics of nucleic acid melting transitions with coupled binding equilibria
Authors: Crothers Donald M.
Published: December 2004

Equations are developed to describe the shift in the temperature of the helix–coil transition when small molecules bind to nucleic acids. Included are high polymers, oligonucleotides, and oligomer–polymer interactions. The equations prescribe simple ways of plotting experimental data to evaluate transition and binding parameters.
Volume and sound velocity changes accompanying the α‐helix to β‐form and coil to α‐helix transitions in aqueous solution
Authors: Noguchi Hajime , Yang Jen Tsi
Published: December 2004

The volume increment per amino acid residue for the α‐helix to β‐form transition of uncharged poly‐L‐lysine in aqueous solution was 3.8 ml in water and 4.3 ml in 0.2M and 1M NaBr solutions at 26°C, respectively. The sound velocity of the polymer solution was greater with the β‐helix than with the β‐form, but the difference was less in dilute salt solutions and disappeared in 1 or 2M NaBr solution. Thus, the β poly‐L‐lysine solution was slightly more compressible than the α‐polymer solution, but this difference was diminished with increasing salt concentration. Both the volume change and the change in adiabatic compressibility of the polymer solution suggest that hydrophobic interactions among the lysyl groups in the β‐form reduce the amount of “icebergs” surrounding the polymer molecules as compared with the amount originally present with the α‐helix. The coil‐to‐helix transition of poly‐L‐glutamic acid in aqueous solution was also accompanied by a decrease in sound velocity. This can be attributed to the reduction of the water of hydration which is less compressible than free water.
Normal mode spectrum of the parallel‐chain β‐sheet
Authors: Bandekar Jagdeesh , Krimm S.
Published: December 2004

Normal mode calculations have been carried out for parallel‐chain β‐sheet structures. These include the parallel‐chain pleated sheet of poly(L‐alanine) and the parallel‐chain rippled sheet of polyglycine. Dipole derivative coupling has been included for amide I and II modes, and the effects of parallel‐sheet and antiparallel‐sheet arrangements of varying separation have been examined for the poly(L‐alanine) case. Some amide and nonamide modes are distinctly different from their antiparallel‐chain counterparts, thus providing a basis for distinguishing between such structures from their ir and Raman spectra. As in our previous studies, these results emphasize the need for both kinds of spectral data in order to draw definitive conclusions about conformation.
Thermodynamics of the various forms of the dodecamer d(ATTACCGGTAAT) and of its constituent hexamers from proton nmr chemical shifts and UV melting curves: Three‐state and four‐state thermodynamic models
Authors: Pieters Jane M. L. , Mellema Jan‐Remt , Van Den Elst Hans , Van Der Marel Gijs A. , Van Boom Jacques H. , Altona Cornelis
Published: December 2004

Chemical shifts of base and H1′ protons of the single‐stranded hexamers d(ATTACC) and d(GGTAAT), of the 1 : 1 mixtures of these complementary hexamers, and of the self‐complementary dodecamer d(ATTACCGGTAAT) were measured at various temperatures in aqueous solution. Four different sample concentrations were used in the case of the dodecamer and of the mixture of the complementary hexamers; the individual hexamers were measured at two different DNA concentrations. Absorbance temperature profiles at five different NaCl concentrations were measured for the dodecamer in order to quantify the effect of the ionic strength on the duplex formation.

Under suitable conditions of nucleotide concentration, temperature, and ionic strength, the dodecamer adopts either a B‐DNA duplex or a hairpin‐loop structure. Chemical shift vs temperature profiles, constructed for all samples, were used to obtain thermodynamic parameters either for the various stacking interactions in the single strands or for the duplex or the hairpin‐loop formation. In the analysis of the duplex formation of the hexamers, a two‐state approach appeared too simple, because systematic deviations were revealed. Therefore, a new three‐state model (DUPSTAK) was developed. In order to investigate the magnitude of error arising from the use of the two‐state approach in cases where the DUPSTAK model appears more appropriate, a series of test calculations was made. The magnitude of error in the enthalpy and in the entropy of duplex melting is found to depend linearly upon the actual melting temperature and not upon the individual ΔHand ΔSvalues.

Thermodynamic analysis of the chemical shift vs temperature profiles in D2O solution (no added salt) yields an averageTmdvalue of 341 K (1MDNA) and ΔHof −121 kJ · mol−1for the dimer/random‐coil transition of the hexamer duplex d(ATTACC) · d(GGTAAT). For the duplex ⇄ random‐coil transition of the 12‐mer d(ATTACCGGTAAT) an averageTmdvalue of 336 K (1MDNA) and ΔHof −372 kJ · mol−1are found. The hairpin/random‐coil transition of d(ATTACCGGTAAT) is characterized by a rather large ΔHvalue, −130 kJ · mol−1, and an averageTmhvalue of 304 K.
Elongational flow studies on type IV collagen: Comparison with type I
Authors: Barnard K. , Atkins E. D. T. , Taylor M. A. , Gathercole L. J.
Published: December 2004

Elongational flow techniques have been used to investigate the birefringent response of monodisperse type IV collagen in dilute solution and the results compared with type I. collagen. A four‐roll mill apparatus was used to characterize the solutions at low strain rates, \documentclass{article}\pagestyle{empty}\begin{document}$\dot{\varepsilon}$\end{document} ⩾ 300 s−1. The birefringence is nonlocalized and rises gradually to a plateau value, in accordance with rigid‐rod behavior. The gradients of the tangent to the curves at zero strain rate are estimated for types IV and I collagen. The concentrations of the solutions used were in the dilute to semidilute regimes. Using a value of 300 nm for the length of type I collagen, values of 364–408 nm were calculated for the length of the type IV collagen molecule, depending on the concentration regime chosen, which is consistent with biochemical predictions based on a rigid molecule. The results imply that the behavior of type IV collagen molecules in solution is similar to type I collagen, despite the presence of several sequence interruptions in the type IV helix. © 1993 John Wiley & Sons, Inc.
Crystal structures of two cyclic pseudopentapeptides containing ψ[CH2S] and ψ[CH2SO] backbone surrogates
Authors: Ma Sougen , Richardson John F. , Spatola Arno F.
Published: December 2004

The solid state conformations of cyclo[Gly–Proψ[CH2S]Gly–D–Phe–Pro] and cyclo[Gly–Proψ[CH2–(S)–SO]Gly–D–Phe–Pro] have been characterized by X‐ray diffraction analysis. Crystals of the sulfide trihydrate are orthorhombic, P212121, witha= 10.156(3) Å,b= 11.704(3) Å,c= 21.913(4) Å, andZ= 4. Crystals of the sulfoxide are monoclinic, P21, witha= 10.662(1) Å,b= 8.552(3) Å,c= 12.947(2) Å, β = 94.28(2), andZ= 2. Unlike their all‐amide parent, which adopts an all‐transbackbone conformation and a type II β‐turn encompassing Gly‐Pro‐Gly‐D‐Phe, both of these peptides contain acisGly1‐Pro2bond and form a novel turn structure, i.e., a type II′ β‐turn consisting of Gly–D–Phe–Pro–Gly. The turn structure in each of these peptides is stabilized by an intramolecular H bond between the carbonyl oxygen of Gly1and the amide proton ofD‐Phe4. In the cyclic sulfoxide, the sulfinyl group is not involved in H bonding despite its strong potential as a hydrogen‐bond acceptor. The crystal structure made it possible to establish the absolute configuration of the sulfinyl group in this peptide. The two crystal structures also helped identify a type II′ β‐turn in the DMSO‐d6solution conformers of these peptides. © 1993 John Wiley & Sons, Inc.
Vibrational Raman optical activity of alanyl peptide oligomers: A new perspective on aqueous solution conformation
Authors: Ford Steven J. , Wen Zai Q. , Hecht Lutz , Barron Laurence D.
Published: December 2004

The vibrational Raman optical activity (ROA) spectra of di‐ and tri‐L‐alanine in the range 650–1750 cm−1 have been measured in H2O and D2O solution at high, neutral, and low pH and pD. Corresponding ROA spectra for tetra‐ and penta‐L‐alanine have also been obtained, but over a more restricted set of pH and pD conditions. There are similarities with the ROA spectrum of L‐alanine below ∼ 1200 cm−1, but the spectra are very different above this wavenumber due to the influence of the vibrational coordinates of the peptide group. The similar overall appearance of the di‐, tri‐, and tetrapeptide ROA under selected conditions of pH and pD, and of all four peptide ROA spectra in DCl and HCl solutions, in the backbone skeletal stretch region ∼ 1050–1200 cm−1 and the extended amide III region ∼ 1250–1350 cm−1, suggests that the backbone conformation is approximately the same in all four structures. One difference, however, is a shift of a large positive ROA band in H2O at ∼ 1341 cm−1 in the dipeptide, assigned to Cα–H and in‐plane N–H deformations, down to ∼ 1331 cm −1 in the tripeptide and to ∼ 1315 cm−1 in the tetrapeptide and pentapeptide (the last in HCl due to insufficient solubility in H2O), which indicates increasing delocalization of the corresponding normal mode with increasing chain length. Our results do not support the suggestion that stabilizing interactions of the zwitterionic end groups in tri‐L‐alanine at neutral pH leads to a different solution structure to that at high pH. © 1994 John Wiley & Sons, Inc.
Analyzing the normal mode dynamics of macromolecules by the component synthesis method: Residue clustering and multiple‐component approach
Authors: Hao Ming‐Hong , Scheraga Harold A.
Published: December 2004

A study of the component synthesis method (CSM) for analyzing the normal mode dynamics of macromolecules is reported. The procedure involves a reduction of the dimensions of the normal mode problems for large molecular systems and the accurate extraction of the low‐frequency modes. A macromolecule is divided into small components based on a hierarchical clustering of the residues in the structure. Interactions between coupled components are treated by the method of static correlation. The normal modes of the components are obtained first, and a fraction of the low‐frequency normal modes of the components under mutual correlations are then used as a reduced basis for solving for the normal modes of the whole molecule. Multiple components are introduced for large macromolecules so that the dimensions of the eigenvalue problems at the component level are small. The method is applied to the protein crambin. In test calculations in which the dimensions of the eigenvalue equations are reduced to 1/6 of their natural size, the errors in the normal mode frequencies calculated by the CSM procedure are only about 1–2% when compared with the exact values. The rms fluctuations of all atoms in crambin calculated by the CSM procedure are basically identical to the exact results. The CSM procedure is shown to be accurate for calculating the normal modes of large macromolecules with a significant reduction of the size of the problem. © 1994 John Wiley & Sons, Inc.
Lagrangian molecular dynamics using selected conformational degrees of freedom, with application to the pseudorotation dynamics of furanose rings
Authors: Rudnicki Witold R. , Lesyng Bogdan , Harvey Stephen C.
Published: December 2004

Using internal conformational degrees of freedom for biopolymers as natural variables, and introducing a Lagrangian dynamics approach, one can simulate time‐dependent processes over a much longer time scale than in classical Newtonian molecular dynamics (MD) techniques. Two factors contribute to this: a substantial reduction in the number of degrees of freedom and a very large increase in the size of the time step. We present the Lagrangian equations of motion for repuckering transitions in model furanose (F), ribose (R), and 2′‐deoxyribose (dR) ring systems using the pseudorotation phase angle as the single dynamic variable. As in most Lagrangian analyses, the effective masses for the R and dRmodels are dependent on conformation, and we test the behavior of this variable mass (VM) model. Since the variation in effective mass is small, the VM model is compared with a simplified constant mass (CM) model, which is shown to be an excellent approximation. The equations of motion for the CM and VM models are integrated with the leapfrog and the iterative leapfrog algorithms, respectively. The Lagrangian dynamics approach reduces the number of degrees of freedom from about 40 to 1, and allows the use of time steps on the order of 20 fs, about an order of magnitude greater than is used in conventional MD simulations. © 1994 John Wiley & Sons, Inc.
Crystal structure and nmr conformation of a cyclic pseudotetrapeptide containing urethane backbone linkages
Authors: Parkinson Gary N. , Wu Youling , Fan Pei , Kohn Joachim , Baum Jean , Berman Helen M.
Published: December 2004

Urethane bonds, derived from the hydroxyl group of the tyrosine side chain, have been investigated as a new type of amide bond mimetic in the design of pseudopeptides. The structure of a representative cyclic pseudotetrapeptide that consists of an — Ala — Tyr(urethane) Ala — Tyr (urethane) sequence fused into a rigid ring has been studied in the solid state by x‐ray crystallography and in solution by two‐dimensional nmr techniques. The cyclic pseudotetrapeptide has an oblong shape. The backbone urethane bonds assume a trans–trans conformation. The carbonyl groups in the ring have an alternating pattern of down, up, down, up with respect to the average ring plane. Solution nmr studies give observed nuclear Overhauser effects and coupling constants largely in agreement with the crystal structure. However, in solution the observed structure is likely to be conformationally averaged, and in the averaged structure, the urethane bond is perpendicular to the plane of the aromatic ring of the tyrosine, while in the crystal it is close to this plane. These differences may be explained by intermolecular hydrogen‐bonding interactions. Four aspects of the conformation of the cyclic pseudotetrapeptide were investigated in detail: the tyrosine residue with the attached side‐chain urethane bond (the tyrosine‐urethane unit), the conformation of the two urethane backbone linkages, the conformation of the two conventional peptide bonds within this unusual ring structure, and the tight turns within the cyclic pseudotetrapeptide. The conformation of the tight turns present in the cyclic pseudotetrapeptide is very similar to that of a β‐bend of type II. Intermolecular hydrogen bonding, joining adjacent layers of the cyclic pseudotetrapeptide in the solid state, resemble a parallel β‐pleated sheet. The presence of these structural motifs in the cyclic pseudotetrapeptide indicates that the tyrosine urethane unit may find applications in peptide and protein engineering. © 1994 John Wiley & Sons, Inc.
Kinetics of DNA supercoiling studied by Brownian dynamics simulation
Authors: Chirico Giuseppe , Langowski Jörg
Published: December 2004

We have developed a model for the simulation of the structure and dynamics of covalently closed circular DNA. It is based on the generalization of the original Brownian dynamics algorithm [D. L. Ermak & J. A. McCammon (1978) Journal of Chemical Physics, Vol. 69, pp. 1352–1359; M. Fixman (1978) Journal of Chemical Physics, Vol. 69, pp. 1527–1537] developed for bead‐chain models of linear DNA to a second order numerical integration [ A. Iniesta & J. Garcia de la Torre (1990) Journal of Chemical Physics.Vol. 92, pp. 2015–2018], which we extended here to accommodate the torsional potential. The topological constraints and torsional‐bending coupling in superhelical DNA are explicitly taken into account in this work by adapting a model for torsional‐bending motion of linear DNA developed by Allison et al. [S. A. Allison, R. Austin, & M. Hogan (1989) Journal of Chemical Physics, Vol. 90, pp. 3843–3854].

The dynamics of closed DNAs of 1124 base pairs (380 nm in length) were simulated up to ≅ 40 μs for linking number differences ΔLk between 0 and −6. Each bead in the model corresponded to 37 base pairs.

For −2 ≅ ΔLk −6, the writhing number appears to decay to a limiting negative value with a single exponential law, and the relaxation time of this decay, starting from a planar closed molecule, is 3–6 μs. For the trajectories studied here, the formation of the superhelix proceeds through an initial phase of 1–2 μs where a toroidal‐like structure is formed, which then converts into an interwound structure starting from a random nucleation site. For one simulation at ΔLk = −6, a branched structure was observed that did not convert into the linear interwound form for the time course of the simulation (31 μs).

A verification of the simulation was performed by computing the diffusion coefficient of the 1124 base pair circle through known hydrodynamic formulas or through the center of mass displacement, and comparing these theoretical values with diffusion coefficients previously measured by dynamic light scattering. © 1994 John Wiley & Sons, Inc.
Evidence of hemoglobin dissociation
Authors: Lunelli Lorenzo , Zuliani Paola , Baldini Giancarlo
Published: December 2004

Bovine carbonmonoxy hemoglobin investigated with light scattering studies is found to dissociate from its native tetramer structure into dimers and monomers. The values of the hydrated tetramer radius, RT = 32.1 Å, and the fractional dissociation vs pH, have been obtained at different ionic strengths from the autocorrelation function of the scattered light.

The results suggest that a relevant contribution to Hb dissociation is due to electrostatic effects and, by means of a model derived by Tanford, it has been possible to predict the behavior of dissociation. Among the findings of this approach, we recall the estimates of the electrostatic energy contributions to Hb dissociation, up to ≃ GRT, and the predicted charge of tetrameric Hb vs pH, which agrees very well with the experimental data. © 1994 John Wiley & Sons, Inc.
Physicochemical properties of aqueous xanthan solutions: Static light scattering
Authors: Gamini Amelia , Mandel Michel
Published: December 2004

The secondary structure of xanthan in solutions of relatively low salt concentration and at room temperature has been investigated using static light scattering experiments. Additional evidence has been found for a dimeric structure at 25°C in 0.01M NaCl. From the experimental z‐average mean square (ms) radius of gyration, a value for the persistence length p has been estimated, taking explicitly into account the polydispersity of the three samples used, which has been established by gel permeation chromatography (GPC) measurements. The experimental particle scattering functions of the three samples are consistent with theoretical estimates for polydisperse systems with the same value of p = 65 ± 10 nm and the molar mass per unit length for a dimeric structure.

This secondary structure remains unaffected by the ionic strength in the 0.005–0.0lM range. Partial aggregation seems to occur at higher NaCl concentrations.

Light scattering and GPC data show that heating the xanthan 0.01M NaCl solutions to about 70°C considerably reduces the Mw of the low molar mass sample (2.3 × 105‐g·mol−1), contrary to what is observed for the high molar mass sample (1.8 × 106‐g·mol−1). These experimental findings can be accounted for by a partial temperature‐induced dissociation of the xanthan dimers according to an all‐or‐none mechanism. © 1994 John Wiley & Sons, Inc.
Circularization of small DNAs in the presence of ethidium: A theoretical analysis
Authors: Clendenning James B. , Schurr J. Michael
Published: December 2004

A rigorous theory is developed for ethidium binding to linear and circular DNAs and for the ratios of topoisomers produced upon ligation of an equilibrium population of noncovalently closed circles in the presence of ethidium. Assuming an unwinding angle ϕE = 26° for intercalated ethidium, optimum values of the intrinsic binding constant, KE = 7.16 × 104 M−1, the intrinsic twist, l0 = 23.746 turns, and twist energy parameter, Et = 5250, are obtained by fitting the present theory to the data of Shore and Baldwin [(1993) Journal of Molecular Biology, Vol. 170, pp. 983–1007] for a 247 base pair DNA. A very good fit is achieved with these optimum values, but a poor fit results when the parameters estimated by Shore and Baldwin are employed in the same theory. Three assumptions employed in the analysis of Shore and Baldwin are found to be not strictly valid. Adoption of the present substantially larger Et value as representative of their short DNAs would allow the Et vs N data of Shore and Baldwin to conform to the shape predicted by Shimada Yamakawa [(1985) Journal of Molecular Biology, Vol. 184, pp. 319–329] and Frank‐Kamenetskii et al. [(1985) Journal of Biomolecular Structure and Dynamics, Vol. 2, pp. 1005–1012], and would imply that all of their DNAs exist in a substantially stiffer than normal state. © 1994 John Wiley & Sons, Inc.
Nanometric design of extraordinary hydrophobic‐induced pKa shifts for aspartic acid: Relevance to protein mechanisms
Authors: Urry Dan W. , Gowda D. Channe , Peng Shaoqing , Parker Timothy M. , Jing Naijie , Harris R. Dean
Published: December 2004

Commonly a key element enabling proteins to function is an amino acid residue or residues with functional side chains having shifted pKa values. This article reports the results on a set of protein‐based polymers (model proteins) that exhibit hydrophobic folding and assembly transitions, and that have been designed for the purpose of achieving large hydrophobic‐induced pKa shifts by selectively replacing Val residues by Phe residues. The high molecular weight polypentapeptides, actually poly (tricosapeptides) with six varied pentamers in fixed sequence, were designed and synthesized to have the same amino acid compositions but different proximities between a single aspartic acid residue and 5 Phe residues per 30 residues. With the 5 Phe residues distal from the Asp residue, the observed pKa shift was 2.9 when compared to the Val‐containing reference. With the 5 Phe residues within 1 nm of the Asp residue, the pKa shift was 6.2. This represents a free energy of interaction of 8 kcal/moles. To our knowledge, this is the largest pKa shift documented for an Asp residue in a polypeptide– or protein–water system.

Data are reviewed that do not support the usual electrostatic arguments for pKa shifts of charge–charge repulsion and/or unfavorable ion self‐energies arising from displacement of water by hydrophobic moieties, but rather the data are interpreted to indicate the presence of an apolar–polar repulsive free energy of hydration, which results from a potentially highly cooperative competition between apolar and polar species for hydration. © 1994 John Wiley & Sons, Inc.