bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis and characterization of four sequential glycyl/glutamate polypeptides
Authors: Rippon W. B. , Lowbridge J. , Walton A. G.
Published: May 2005

Poly(Glu(OBzl)‐Gly)n, poly(Glu‐Gly)n, poly(Gly)‐(Glu(OBzl)‐Gly), and poly(Gly‐Glu‐Gly) were synthesized from the pentachlorophenyl esters of the sequential monomer. Both of the polymers containing free glumatic‐acid residues are soluble in water, as is the lower molecular weight fraction of the polytripeptides with the benzyl ester in place. Circular dichroism studies and infrared dichroism studies suggest that the 21 helix is favored for the polydipeptide with removal of the benzyl ester reducing the conformational integrity. The polytripeptide showed evidence of 31 helix in addition to the 21 form, depending on solvent. A rationale for the conformations observed is developed based on the bulkiness of the side‐chain residues and conformational stabilization, in certain cases, by hydrophobic interactions between the benzyl ester groups.
Elastin as a rubber
Authors: Dorrington K. L. , McCrum N. G.
Published: May 2005

The thermoelastic behavior of water solvated elastin has been investigated in simple tension, in the temperature range 0–70°C. Specimens purified from both the ox ligamentum nuchae and pig thoracic aorta have been studied. Force data obtained by cycling the temperature for various constant specimen lengths display a separated variable dependence of the form f = A(T)B(α), where T is absolute temperature and α the extension ratio. For ligament elastin B(α) is a linear function whereas for aortic elastin it is a nonlinear function. The applicability of the rubber elasticity theory to elastin has been tested by setting A(T) equal to the temperature‐dependent front factor for simple tension of a homogeneous rubber whilst B(α) is left undefined. In this way it has been possible to take into account the fibrous nonhomogeneity of the polymer, and also to avoid any inconsistency within the theory of attributing a dependence of the variable fe/f upon extension ratio. The behavior of both ligament and aortic elastin agrees well with the conclusion that the dominant deformation mechanism is entropy elastic, fe/f ≪ 1. The linearity of the load isotherm for ligament elastin permits a particularly simple experimental procedure using a single force‐temperature plot for one value of interclamp length. Using this procedure high precision has been obtainble, and the data shows a close adherence to the theory with fe/f = 0.1. The relationship between this result and current controversy over the molecular conformation of elastin is discussed.
The viscometric behavior of native and relaxed closed circular PM2 DNAs at intermediate and high ethidium bromide concentrations
Authors: Watson Robert , Bauer William R.
Published: May 2005

We have measured the specific viscosity of closed circular PM2 DNA in the presence of concentrations of ethidium bromide ranging up to 5 mg/ml. Both native viral PM2 DNA I and enzymatically prepared relaxed, closed circular PM2 DNA I0 exhibit a complex dependence of the specific viscosity upon the extent of supercoiling. As the number of superhelical turns is increased in the positive sense from zero, the viscosity first decreases to a minimum, then passes through a secondary maximum, and eventually again increases as the dye‐induced duplex unwinding proceeds. In the case of DNA I, a corresponding behavior is mirrored in the negative sense as dye is removed from the principal viscometric maximum (complete relaxation of the DNA by dye). The shape of the curve relating specific viscosity to extent to supercoiling is similar for superhelical DNAs of either handedness, a result which we interpret to mean that the influence of any regions of special secondary structure (such as denatured loops) upon the viscosity is minimal. At very high dye concentrations the specific viscosity decreases dramatically. This effect might arise either from intermolecular aggregation or from a dye‐induced collapse in the DNA secondary structure.
Interactions of highly charged colloidal cylinders with applications to double‐stranded DNA
Authors: Stigter Dirk
Published: May 2005

This paper presents new applications of the McMillan‐Mayer solution theory to dispersions of highly charged colloidal cylinders in monovalent salt solutions. The thermodynamic solution properties are given in terms of the virial expansions relating to a Donnan membrane equilibrium. General expressions are derived for the second Donnan pressure virial coefficient B2 and for the first two salt distribution coefficients A1 and A2. The effect of electric interactions is represented as an increased effective diameter dB or dA of the colloidal cylinder. This yields the simple excluded volume expressions B2 = πdBL2/4 and A1 = πdA2L/4 for hard cylinders of length L and diameter dB and dA, respectively. The coefficient A2 is derived from the dependence of B2 on the salt concentration.

Computations are made for double‐stranded DNA in sodium chloride solutions with the DNA model developed in the preceding paper: a uniformly charged cylinder, with size and charge consistent with transport experiments, and surrounded by a Gouy double layer. In 1–0.005M sodium chloride solutions dB is found to vary from 29 Å to about 220 Å, and dA from 30 Å to about 170 Å, with little sensitivity to the uncertainties in the kinetic diameter d ≈ 24 Å and the experimental ζ potentials of DNA. Corresponding results predicted by the classical Donnan theory are 6–167 times too high for B2.

Values of A2 are relatively small, in line with the expected rapid convergence of the virial expansion for the salt distribution. This is consistent with a phase transition from random to parallel orientation of the cylinders predicted first by Onsager for hard cylinders on the basis of B2, but not yet observed for DNA in simple salt solutions.
The interaction of 8‐anilino‐1‐naphthalenesulfonate with polylysine and polyarginine
Authors: Ichimura Sachiko , Zama Mitsuo
Published: May 2005

Comparative studies on the interaction of 8‐anilino‐1‐naphthalenesulfonate (ANS) with polylysine and polyarginine have been made by equilibrium dialysis and fluorescence or circular dichroism measurements, to investigate the structural characteristics of the polypeptides. The results are summarized as follows: (i) ANS binds to either of the polypeptides primarily by electrostatic interaction while hydrophobic interaction partially facilitates the dye binding; both interactions are stronger in the polyarginine‐dye binding than the polylysine‐dye binding. (ii) The fluorescence of ANS is more intensified when the dye binds to polyarginine than to polylysine regardless of the value of r (number of bound dye per amino‐acid residue) of polypeptide‐dye complexes, although the intensification depends on the r value and becomes maximum at r = 0.25–0.35 for both cases. (iii) The binding of ANS to each polypeptide is cooperative at r < 0.4. (iv) The circular dichroism is more efficiently induced in the spectral region of ANS by binding to polyarginine than to polylysine.

From these results, it was concluded that, compared to polylysine, polyarginine suffers some structural change by ANS binding into a more compact molecular configuration having some regularity with a lower dielectric environment.
Measurement of diffusion coefficient and electrophoretic mobility with a quasielastic light‐scattering–band‐electrophoresis apparatus
Authors: Lim Tong K. , Baran George J. , Bloomfield Victor A.
Published: May 2005

We have constructed an apparatus for the simultaneous measurement of electrophoretic mobility, μ, and diffusion coefficient, D, of macromolecules and cells. It combines band electrophoresis in a vertical, sucrose‐gradient stabilized column, with quasielastic laser light‐scattering determination of the diffusion coefficient of the species within the band. The entire electrophoresis cell is scanned through the laser beam of the quasielastic laser light‐scattering apparatus by a vertical translation stage. Total intensity light‐scattering measurement at each point in the cell gives the macromolecular concentration at that point. Solvent viscosity and electrical potential are measured at each point in the cell. Application of this apparatus to resealed red blood cell ghosts and to bovine hemoglobin indicates that measurements of field, viscosity, and migration distance are reliable, and that electroosmosis is insignificant. Application to T4D bacteriophage gives μ20,w = (−1.05 ± 0.05) × 10−4 cm2/V sec and D20,w = (3.35 ± 0.10) × 10−8 cm2/sec for fiberless particles, and μ20,w = −(0.59 ± 0.03) × 10−4 cm2/V sec and D20,w = (2.86 ± 0.09) × 10−8 cm2/sec for whole phage with 6 fibers. Approximate analysis of these results with the Henry electrophoresis theory for spheres in dicates that each fiber contributes about 193 positive charges to the phage particle, compared with 327 from amino‐acid analysis. The advantages and disadvantages of this apparatus, relative to conventional electrophoresis and to electrophoretic light scattering, are discussed.
Helix‐coil stability constants for the naturally occurring amino acids in water. XII. Asparagine parameters from random poly(hydroxybutylglutamine‐co‐L‐asparagine)
Authors: Matheson R. R. , Nemenoff R. A. , Cardinaux F. , Scheraga H. A.
Published: May 2005

The synthesis and characterization of water‐soluble random copolymers containing L‐asparagine with N5‐(4‐hydroxybutyl)‐L‐glutamine, and the thermally induced helix‐coil transitions of these copolymers in water, are described. The incorporation of L‐asparagine was found to decrease the helix content of the polymers in water at all temperatures. The Zimm‐Bragg parameters σ and s for the helix‐coil transition in poly(L‐asparagine) in water were deduced from an analysis of the copolymer melting curves in the manner described in earlier papers. The computed values of s indicate that asparagine destabilizes helical sequences at all temperatures in the range 0–60°C.
Helix‐coil stability constants for the naturally occurring amino acids in water. XIII. The presence of by‐products in amino‐acid analysis of copolymers and their effect on the guest parameters; recomputed values of σ and s for L‐serine
Authors: Van Nispen J. W. , Hill D. J. , Scheraga H. A.
Published: May 2005

Previously used procedures for processing the amino acids from 6N hydrochloric acid hydrolysis of poly[N5‐(4‐hydroxybutyl)‐L‐glutamine], poly[N5‐(3‐hydroxypropyl)‐L‐glutamine], and several random copolymers derived from these, led to the formation of spurious products. These have been isolated and characterized as the γ‐ester of glutamic acid and the hydroxyalkyl amine, and chloro‐alkyl amine hydrochloride. The former reduces the observed values for glutamic acid, but the latter has no effect on them. A method is used to avoid formation of these artifacts in the amino‐acid analysis. Of all the copolymers studied previously in this series, the compositions of only those containing L‐serine are in error as a result of the formation of the γ‐ester. A redetermination of the amino‐acid compositions of the copolymer fractions studied earlier leads to slightly revised values for the Zimm‐Bragg parameters σ and s of serine.
Hydrodynamics of macromolecular complexes. II. Rotation
Authors: De La Torre Jose Garcia , Bloomfield Victor A.
Published: May 2005

We have used the modified Oseen hydrodynamic interaction tensor along with iterative numerical solution of the coupled hydrodynamic interaction equations to calculate the rotational diffusion coefficients of macromolecular complexes composed of nonidentical spherical subunits. For the one structure, a prolate ellipsoid of revolution, for which exact solutions are available, a subunit model with the same length and volume gives asymptotic agreement with the Perrin equations. Other structures considered include plane polygonal rings, lollipops, and dumbbells.
The mechanism of nucleation for in vitro collagen fibril formation
Authors: Comper W. D. , Veis A.
Published: May 2005

The formation of collagen fibrils from soluble monomers and aggregates by thermal gelation at neutral pH can be divided into two distinct stages: a nucleation phase and a growth phase. Turbidity studies of the kinetics of the precipitation reaction show that the lag‐phase time or nucleation reaction time, t′l, is markedly temperature dependent while the growth reaction time is temperature independent. The activation energy of the nucleation reaction is essentially constant over the temperature range studied. In monitoring the nucleation‐phase reaction by various physicochemical techniques, including viscosity, sedimentation equilibrium, and light scattering, no evidence for the formation of aggregates was observed. Enrichment of the initial collagen solution with aggregates accelerates nucleation, but de novo nuclei formation is still required even in highly aggregated collagen preparations. Removal of pepsin and pronase susceptible peptides lengthens the nucleation reaction time and increases the sensitivity of the rate of nuclei formation to changes in ionic strength. Electron microscope studies show the fibrils formed from the protease‐treated collagen to be less well organized. With pepsin‐treated collagen, subfibrils and obliquely striated fibrils are seen, showing that while microfibrils are formed interactions between them are modulated by the enzyme susceptible peptides in the same way that these regions modulate nuclei assembly. It appears that pepsin and pronase susceptible peptide regions of collagen play a more prominent role in the in vitro assembly of collagen molecules to form D‐stagger nuclei and fibrils than do ionic interactions between helical molecular regions. A mechanism of nucleation of collagen fibrillogenesis is discussed.
Characterization of nuclei in in vitro collagen fibril formation
Authors: Comper W. D. , Veis A.
Published: May 2005

Heat precipitation fibril formation in collagen solutions depends upon the prior thermal history of the solution. Collagen solutions were heat precipitated to various extents at 30°C, cooled, and then brought to a second precipitation. Kinetic analysis of the secondary precipitation demonstrated that only the nucleation phase of the precipitation was affected, not the fibril growth phase. Thermal history, or memory, is thus related to the formation of low‐temperature‐stable nuclei. A range of nuclei sizes is evident, supporting the concept of a homogeneous nucleation process. Schiffs base formation and establishment of cross‐linkages play no role in the in vitro nucleation: thiosemicarbazide treated collagen behaves identically to untreated collagen in kinetics of assembly to fibrils. Low‐temperature‐stable nuclei formed at neutral pH are dissociated in the cold in acetic acid at pH 4. Pronase and pepsin susceptible molecular end regions are important in establishing the low‐temperature‐stable nuclei. Pronase treatment completely abolishes the acquisition of memory of prior thermal history in collagen solutions. We speculate that biological control mechanisms for fibril formation in vivo relate to specific interactions between non‐helical, enzyme susceptible regions on collagen molecules.
The dichroic tensor of flexible helices
Authors: Wilson Robert W. , Schellman John A.
Published: May 2005

A statistical theory of the linear dichroism of DNA‐like chains is presented for two models which are discrete versions of the wormlike coil. In the final form the linear dichroism of the entire chain is related directly to the dichroic properties of a chain segment (base pair). Though the derivations are somewhat complicated, the result [Eq. (28)] is simple and the required statistical parameters can be easily calculated for either model from measured values of the persistence length. In fact, for molecules as stiff as double‐stranded DNA, the results can be reduced with good accuracy to the form

showing that the “optical persistence” given on the left is directly proportional to the structural persistence, P∞/l. As in previous theories the results are restricted to chains in their Gaussian limit.
Histidine‐containing cyclic dipeptides as catalysts in the hydrolysis of carbonic acid p‐nitrophenyl esters
Authors: Imanishi Yukio , Tanihara Masao , Sugihara Toshiharu , Higashimura Toshinobu
Published: May 2005

A histidine‐containing cyclic dipeptide, cyclo(D‐Leu‐L‐His), was almost 20 times as efficient a catalyst as imidazole in the hydrolysis of p‐nitrophenyl laurate. The effect of dioxane on the hydrolysis showed that hydrophobic interaction between the cyclic dipeptide and the ester is very important. This reaction obeyed the Michaelis‐Menten kinetics, and the Michaelis constant Km was as low as 9.98 × 10−5M. Since the linear dipeptide having D‐Leu‐L‐His sequence was nearly inactive in the hydrolysis, the functional groups of cyclo(D‐Leu‐L‐His) in a specific arrangement held by the rigid backbone must have cooperated in the fast hydrolysis. Very weak catalysis by the diasteremeric cyclic dipeptide, cyclo(L‐Leu‐L‐His), in the hydrolysis supported the above view.
Solution conformation and hydrolytic activity of cyclo(D‐leu‐L‐His)
Authors: Tanihara Masao , Imanishi Yukio , Higashimura Toshinobu
Published: May 2005

It has been reported previously that a cyclic dipeptide, cyclo(D‐Leu‐L‐His), showed a high hydrolytic activity toward a hydrophobic ester, p‐nitrophenyl laurate. In order to determine the reason for the high catalytic activity, the conformation of cyclo(D‐Leu‐L‐His) in aqueous solution was investigated by nuclear magnetic resonance and circular dichroism spectroscopy and compared with the conformation of cyclo(L‐Leu‐L‐His), which was nearly inactive in otherwise the same conditions for the hydrolysis. It was demonstrated that the spatial arrangement of the hydrophobic isobutyl group of the D‐leucyl residue and of the nucleophilic imidazolyl group of the L‐histidyl residue in cyclo(D‐Leu‐L‐His) matches very well with the long acyl chain and the active ester function of p‐nitrophenyl laurate. On the other hand, in cyclo(L‐Leu‐L‐His) the hydrophobic and the nucleophilic pendant groups are too close with each other to cooperate intramolecularly for the hydrolysis. It was concluded that the different steric structures of the diastereomers can explain the large difference of the catalytic activities.
Poly(L‐histidyl‐L‐alanyl‐α‐L‐glutamic acid). I. Synthesis
Authors: Goren H. Joseph , Katchalski‐Katzir Ephraim , Fridkin Mati
Published: May 2005

Poly(L‐histidyl‐L‐alanyl‐α‐L‐glutamic acid) has been prepared in order to test the acid–base catalytic ability of a carboxyl‐imidazole hydrogen‐bonded system. Two different blocked histidyl‐alanyl‐glutamic acid monomers were used in the polymerization step. The imidazole ring was blocked with either a dinitrophenyl or a t‐butyloxycarbonyl group. The γ‐carboxyl of glutamic acid was protected as the benzyl ester. Both the coupling reactions and the polymerization step were via the N‐hydroxysuccinimide active ester method. Thiolysis removed the dinitrophenyl group, while hydrogen bromide removed the t‐butyloxycarbonyl and the benzyl groups. The water‐soluble unblocked polymers obtained were fractionated on Sephadex G‐50 or Bio‐Gel P30. Fractions within a range of average molecular weights of 2,000 to 25,000 were isolated. Enzymatic oxidation of the acid hydrolyzate of the polymers revealed that no detectable racemization had occurred.
A theory for polarized fluorescence microscopy of chromosome structures
Authors: Basu Samarendra
Published: May 2005

A theory for the determination of DNA arrangements in DNA‐containing specimens, using planar aromatic dye molecules as probes for plane polarization of fluorescence, has been described. At low dye‐to‐DNA concentrations, the dye molecules are sandwiched between the stacked bases of DNA; hence, the fluorescence from the dye bound to a local region of DNA helix is plane‐polarized with the polarization direction perpendicular to the local axis of DNA. The degree of such polarization from an aligned DNA‐specimen complexed with dye is determined both by the DNA orientation and the conformational state (e.g., base tilt) of DNA into that specimen. Analysis has been made of the relationship between the degree of polarization and the orientation of the emitting dipoles of dye. The dye complexes may be aligned in a mechanical shear or electric field. However, any change in the orientation distribution of the emitting dipoles due to force fields should be taken into account. With some assumptions and approximations, the magnitude and the direction of maximum polarization can be related to different orders of DNA coiling and to their various combinations. Since the measured polarization is averaged over all DNA regions of the specimen, if the magnitude of polarization is appreciable and the polarization occurs in the specific direction of the specimen, the theory helps to eliminate several probable arrangements of DNA. The predominant molecular features of the actual DNA arrangement can be determined through this process of elimination, as explained in two subsequent papers with T‐even bacteriophage and chromosome systems.
Conformation study on poly(L‐tyrosine) in dimethyl formamide by small‐angle X‐ray scattering
Authors: Hamada Fumiyuki , Ishimuro Yoshitaka , Hayashi Toshio , Nakajima Akio
Published: May 2005

The size and shape parameters of poly(L‐tyrosine) in dimethyl formamide were investigated with fractionated samples of different molecular weight by small‐angle X‐ray scattering. The molecular weight, the radius of gyration of the molecule as a whole, the radius of gyration of the cross section, the mass per unit length, and the length of helix molecule were determined. The molecular conformations proposed by Applequist and Pao for poly(L‐tyrosine) were compared with the experimental results obtained. It was concluded that poly(L‐tyrosine) exists in a form of the right‐handed α‐helix in dimethyl formamide.
Structural studies on aqueous and hydroalcoholic solutions of a polyene antibiotic: Amphotericin B
Authors: Rinnert Hubert , Thirion Christian , Dupont Gaston , Lematre Jean
Published: May 2005

Circular dichroism and absorption and light scattering have been used to study the effect of ethyl alcohol on an aqueous solution of Amphotericin B (“Fungizone”), which is an antifungal heptene. In aqueous solution, light‐scattering studies show that Amphotericin B exists in an aggregated form. The estimated mass of these aggregates is about 2 × 106 daltons, representing about 2000 molecules. Since the aggregated form is high molecular weight and scattering, the CD involves probably the differential scattering of right and left polarized light. In aqueous solution, Amphotericin B exhibits a strong dissymetric couplet in CD at the wavelength of the absorption maximum (328 nm). This latter maximum presents a blue shift when compared with the normal absorption in polar organic solvents. In hydroalcoholic solutions, for alcohol concentrations below 35%, the molecular weight of the aggregates is unchanged, while the absorption and CD spectra are modified. For alcohol concentrations greater than 35%, the aggregates mass decreases quickly and becomes undetectable at 50% ethyl alcohol concentration. For these solutions, the CD and absorption spectra are practically constant and characteristic of unaggregated Amphotericin B form.
On the amino‐acid‐sequence distribution in benzylglutamate‐methionine copolymers prepared from N‐carboxyanhydrides
Authors: Hill D. J. T. , Cardinaux F. , Scheraga H. A.
Published: May 2005

The amino‐acid‐sequence distribution in poly(γ‐benzyl‐L‐glutamate, L‐methionine) prepared by polymerization of the respective N‐carboxyanhydrides has been investigated. This copolymer was converted first to poly(L‐glutamic acid, L‐methionine), which was subsequently cleaved by treatment with cyanogen bromide. The resulting material was fractionated into oligomers of (glutamic acid)n‐homoserine whose relative molar amounts were determined quantitatively. The results have been compared with those for a random incorporation of the methionine in a γ‐benzylglutamate host polymer. Fairly close agreement has been found.
Nearest‐neighbor and next‐nearest‐neighbor effects in the proton NMR spectra of the oligoribonucleotides ApXpG, CpXpG, CpApXpUpG, ApGpXpC, and ApGpXpCpU
Authors: Bell Russell A. , Everett Jeremy R. , Hughes Donald W. , Alkema Dirk , Hader Paul , Neilson Thomas , Romaniuk Paul J.
Published: May 2005

The proton nmr spectra of the oligoribonucleotides in the series CpXpG, ApXpG, CpApXpUpG, and ApGpXpC (X = A, G, C, and U), together with the reference compounds CpG, ApG, CpApUpG, and ApGpC, have been measured. A complete analysis of all the nonexchangeable base protons and the ribose H‐1′ protons was made. The insertion of a nucleotide X into a oligoribonucleotide led to shift changes at both nearest‐neighbor and next‐nearest‐neighbor positions, which were rationalized in terms of the shielding abilities of the various bases. The derived shielding trends in the ApGpXpC series of compounds were successfully used to predict the chemical shifts of resonances in the related ApGpXpCpU series.
Ultrastructure of chitosan and some gel‐forming, branched‐chain chitosan derivatives
Authors: Hall Laurance D. , Yalpani Mansur , Yalpani Nasser
Published: May 2005

Chitosan flakes from shrimp shells and xerogels derived from branched 1‐deoxyglycit‐1‐yl chitosan derivatives were examined by scanning electron microscopy; the former displayed relatively large, dome‐shaped orifices and the latter were found to exhibit a wide variety of ultrastructures, ranging from smooth, nonporous to microporous and microfibrillar. Some correlation between the chemical structure of the side chains of the chitosan derivatives and their microarchitecture could be established.
Conformational properties of central nervous system myelin basic protein, β‐endorphin, and β‐lipotropin in water and in the presence of anionic lipids
Authors: Mattice Wayne L. , Robinson Randall M.
Published: May 2005

Conformational properties have been examined for three proteins which are disordered when dissolved in water but become partially ordered in the presence of anionic lipids. The three proteins, which play important roles in the central nervous system, are myelin basic protein, β‐endorphin, and β‐lipotropin. When evaluated using matrix methods, the helical content of each protein is predicted to be vanishingly small in water, in agreement with experiment. Unperturbed root‐mean‐square radii of gyration are also evaluated for these proteins in water using generator matrices, which have seen wide application to synthetic polymers. Agreement between computed and measured dimensions is found to be excellent. Having successfully described the conformations of myelin basic protein, β‐endorphin, and β‐lipotropin in water, attention is then directed to the changes induced upon interaction with anionic lipids or detergents. Computations predict an increase in helical content, with numerical results being in quite good agreement with experimental observations using several anionic lipids. Examination of the helix‐propagation‐probability profiles reveals an interesting feature of regions where this probability is high. When folded into a α‐helix, these regions show one surface where the only side chains are hydrophobic. Charged side chains (with positive charges predominating) are found on the other surface of the helical segment. The arrangement of side chains on these helices is thus well suited to promote favorable interactions with a membrane containing anionic lipids. Examples of the occurrence of these helices are provided by amino acid residues 13–25 and 130–157 in myelin basic protein and residues 17–29 in β‐endorphin.
One hundred‐fold acceleration of DNA renaturation rates in solution
Authors: Wieder Robert , Wetmur James G.
Published: May 2005

Solvents which accelerate DNA renaturation rates have been investigated. Addition of NaCl or LiCl to DNA in 2.4M Et4NCl initially increases renaturation rates at 45°C and then leads to a loss of second‐order behavior. The greatest accelerations are seen with LiCl and dilute DNA. Volume exclusion by dextran sulfate is the most effective method of accelerating DNA renaturation with concentrated DNA. Addition of dextran sulfate beyond 10–12% in 2.4M Et4NCl fails to increase the acceleration beyond approximately 10‐fold. Accelerations of 100‐fold may be achieved with 35–40% dextran sulfate in 1M NaCl at 70°C. No other mixed solvent system was found to be more effective, although acceleration may be achieved in solvents containing formamide or other denaturants. The acceleration in 2M NaCl occurs without loss of the normal concentration and temperature dependence of DNA renaturation and is also independent of dextran sulfate concentration if sufficient dextran sulfate is used. Dextran sulfate may be selectively precipitated by use of 1M CsCl.
Structure of amphotericin B aggregates as revealed by UV and CD spectroscopies
Authors: Ernst C. , Grange J. , Rinnert H. , Dupont G. , Lematre J.
Published: May 2005

The aqueous and hydroalcoholic solutions of the heptenic macrolide amphotericin B display strong and variable signals in CD and absorption spectroscopies in the range of the π* ← π transition. An interpretation of the spectroscopic changes is proposed based on the equilibrium between two forms of the intermolecular organization: the aggregated one (A) with strong excitonic interaction and the nonaggregative one (B) whose spectra are like those of linear conjugated polyenes in true solution with a well‐developed vibrational structure. The intermediate spectra are fitted by linear combination of the A‐ and B‐form spectra. A two‐level organization of the aggregates is proposed for the A‐form: (1) a close packing of few molecules, which is the origin of the absorption maxima hypsochromic shift; and (2) interaction between the preceding small units inside the aggregates, which is spectroscopically expressed by the intense CD couplet.
Properties of P‐form DNA as revealed by circular dichroism
Authors: Zehfus Micheal H. , Johnson W. Curtis
Published: May 2005

Investigations of DNA using CD spectroscopy show that the P‐form is available in a wide variety of methanol–ethanol mixtures when the water content is low. Increasing the temperature or the ethanol content of a 95% methanol solution causes DNA to undergo a cooperative transition to the P‐form. However, this transition cannot be reversed on cooling, or on adding methanol. Thus P‐form DNA appears to be stable at high methanol concentrations, but it is usually not observed because the DNA is trapped by a kinetic barrier. P‐form DNA will instantaneously assume the native B‐form on addition of water, confirming earlier reports that P‐form DNA is not strand separated [E. Kay (1976) Biochemistry 15, 5241]. CD spectra extended to 190 nm show that there is no base–base interaction in the P‐form. However, the P‐form is extremely stable to heat denaturation in solvents which promote hydrogen bonding between the base pairs. A number of models that can account for the properties of P‐form DNA are discussed.
Use of potentiometric titration for determination of α‐ and ω‐peptide bonds in poly(aspartic acid) and poly(glutamic acid)
Authors: Saudek V.
Published: May 2005

Polypeptides of dicarboxylic amino acids having the monomer units linked in α‐ and ω‐peptide bonds contain two kinds of carboxyls of different acidity. How well potentiometric titration can distinguish these two carboxyls and so characterize the nature of the peptide bonds is evaluated critically. An analysis of the equation describing the dependence of pH on the degree of neutralization based on neglecting the polymer effect and a discussion of the dissociation behavior of polyanions show that the method of evaluating experimental data found in the literature is incorrect. Nevertheless, if a conformational transition does not interfere, some useful and reliable information may be gained by this method; namely, an indication of the presence of two different peptide bonds, their mole ratio, and an approximate pK value for the carboxyl of the amino acid linked in the ω‐peptide bond. The presence of two types of carboxyls complicates the evaluation of the titration curves in the conformation studies.
Why peptide synthesis continues to remain a formidable challenge
Authors: Meienhofer Johannes
Published: May 2005

Striking advances have been made in the synthesis of biologically active peptides. The synthesis of fully active crystalline bovine ribonuclease A by Yajima and Fujii [(1981) Biopolymers 20, 1855–1863] represents an exciting milestone. The main factors contributing to this success include sequential coupling of many small segments and a sophisticated multistage protocol for the final acidolytic cleavage of all protecting groups. However, syntheses of large peptides and proteins and even of many medium‐sized peptides continue to present formidable challenges. In peptide coupling the challenge is to join large peptide segments efficiently and in good yields. For solid‐phase synthesis the challenge is application of polar supports and alternative Nα‐protection. With protecting groups the challenge is to achieve quantitive cleavage at the end of synthesis. Concerning racemization the challenge is to develop sensitive and rapid procedures for measuring racemization during coupling. For purification the challenge is to improve the existing procedures and to search for novel alternative separation principles.
β‐Turn preference of tetrapeptide sequences as analyzed by CD spectra of their Dnp‐pNA derivatives
Authors: Sato K. , Kawai M. , Nagai U.
Published: May 2005

The Dnp‐pNA derivatives of more than 30 tetrapeptides were synthesized and subjected to CD measurements in MeOH. The CD spectra were analyzed on the basis of exciton chirality theory and were found to be useful for estimating β‐turn preference of the parent tetrapeptides based on the following facts: (1) when a compound of the series takes the βturn conformation, a pair of strong CD bands with opposite sign are observed at 305 and 350 nm, and (2) when it is in a random or nonfolded conformation, no significant bands are observed at the wavelengths. The intensity of the 350‐nm band reflects especially well the βturn preference. The CD spectra can be classified into two groups according to the sign of the band at 350 nm, and the groups seem to correspond to the type of βturn. By summarizing the results obtained, some generalizations concerning the sequence–conformation relationship are proposed.
Nmr studies on linear homo‐oligopeptides: A perspective view
Authors: Goodman Murray , Saltman Robert P.
Published: May 2005

The use of high‐resolution nmr to determine the structure of linear homo‐oligopeptides in solution is described. Complete assignments of NH and α‐CH resonances were elucidated based upon a guest–host series of compounds and selective α‐deuteration of residues in the chain. The conformations for oligomethionines and oligoglutamates in dimethylsulfoxide, chloroform, and trifluoroethanol are discussed, and molecular models are described. Recent studies of L‐glutamate peptides attached to polyoxyethylene are also included. These peptide–polyoxyethylene conjugates are soluble in a broad range of solvents, such as dimethyl‐sulfoxide, chloroform, trifluoroethanol, and water. Preliminary conclusions are drawn concerning the effects of amine terminal end groups and the nature of the solvent on the conformations of these peptide derivatives.
Some aspects of the relationship between the structure of a bitter diketopiperazine and its receptor
Authors: Shiba Tetsuo , Uratani Hiroshi , Kubota Ichiro , Sumi Yoshihiko
Published: May 2005

A conformation of a diketopiperazine, cyclo(L‐leucyl‐L‐tryptophyl), was determined by nmr and x‐ray analysis. The receptor for this bitter diketopiperazine neither recognizes chirality nor requires a strict conformation of the substrate. A good correlation was found between the bitterness of diketopiperazine and its hydrophobicity. Experiments using liposome as a model of the receptor membrane suggested that a lecithin‐like lipid is a candidate for a binding site of the bitter diketopiperazine. Furthermore, affinity chromatography using cyclo(L‐leucyl‐L‐phenylalanyl) as a bitter ligand indicated that phosphoglycerides of the lipids tested showed a particular affinity to the bitter diketopiperazine.
Tobacco mosaic virus as a carrier for small molecules: Artificial receptor antibodies and superhormones
Authors: Schwyzer Robert , Kriwaczek Verena Marly
Published: May 2005

Peptide agonists covalently attached to tobacco mosaic virus exhibit such unusual properties as superpotency, superaffinity, enhanced resistance towards enzymic degradation, and prolonged action at the target cell. These properties can be exploited for the isolation by density‐gradient centrifugation of membrane vesicles bearing specific receptors for the peptides and for radioactive and fluorescent labeling of cell‐surface receptors. Our observations can be explained by cooperative–affinity phenomena caused by the deployment in space of the agonist molecules.
Helix–coil transition of poly‐γ‐N‐carbobenzoxy‐L‐α,γ‐diaminobutyrate and poly‐δ‐N‐carbobenzoxy‐L‐ornithine
Authors: Gaskin Felicia , Yang Jen Tsi
Published: May 2005

The helix–coil transition of poly‐γ‐N‐carbobenzoxy‐L‐α,γ‐diaminobutyrate (PCLB) and poly‐δ‐N‐carbobenzoxy‐L‐ornithine (PCLO) in chloroform–dichloroacetic acid mixtures was followed by optical rotatory dispersion. PCLB displays a “normal” temperature‐induced transition, but PCLO an “inverse” one. The thermodynamic parameters for helix formation of the two polymers were determined using the Zimm‐Bragg theory. The enthalpy for adding an amide residue to a helical region, ΔH, and the initiation factor σ were ΔH = −180 cal/mole and σ = 9.2 × 10−5 for PCLB and ΔH = +490 cal/mole and σ = 1.9 × 10−5 for PCLO.
Permeability of synthetic polypeptide membranes. I. Poly‐D,L‐leucine‐co‐D,L‐methionine
Authors: Klein E. , May P. D. , Smith J. K. , Leger N.
Published: May 2005

D,L‐Leucine‐NCA and D,L‐methionine‐NCA were copolymerized in varying mole fractions by using primary base initiation. The methionine segments were oxidized to both sulfoxide and sulfone functions by using peroxide oxidation. The compositions of the resulting polymers were established with the aid of 60 MHz NMR. The transport properties of aqueous solutes through membranes formed from these polymers were studied by means of a diffusive dialysis measurement. The transport of NaCl, urea, creatinine, uric acid, and bacitracin were found to be strongly dependent on the degree of hydration of the polymers. The relative rates of transport of these solutes were affected by interaction with the polymers, when the degree of hydration was not excessive. The degree of hydration was a function of the extent of methionine oxidation.
Optical rotary dispersion of mucopolysaccharides III. Ultraviolet circular dichroism and conformation al specificity in amide groups
Authors: Stone Audrey L.
Published: May 2005

The circular dichroism of glycosaminoglycans and ganglioside in distilled water are described, showing two bands in the region of amide and carboxyl transitions. The first, negative hand is common to all polymers and the amino sugar derivatives. The characteristics of the second band depend upon polymer structure. Those containing 4–1‐linked amino sugars show a second, positive, resolved band about 190 mμ, while those with 3–1‐linked amino sugars show a second, negative band less resolved from the first usually ≤185mμ, but clearly centered at 188mμ for dermatan sulfate. Ultraviolet optical absorption from 300 to ∼183 mμ showed inflection regions around 190 mμ for most compounds.
Stereoselective polymerization of γ‐Benzyl Glutamate NCA
Authors: Williams Fred D. , Eshaque M. , Brown Ronald D.
Published: May 2005

The polymerization of γ‐benzyl glutamate NCAs has been investigated. The results indicate that a coil‐to‐helix transformation is not responsible for the kinetic data. The results were rationalized by assuming formation of polymer aggregates coupled with the stereoselective adsorption of monomer onto growing polymer prior to reaction. From kinetic data a ratio of equilibrium constants for adsorption was determined. Independent data confirmed the assumption that adsorption of monomer onto polymer occurred. Equilibrium constants were evaluated, and their ratio was found to be comparable with that obtained from the kinetic data.
Solute binding curves for (two polymer + solute)–complex systems I. “one‐solute‐stack” systems
Authors: Schmitz Kenneth S.
Published: May 2005

The matrix method is used for calculating the grand partition function for the reaction: 2 polymer + solute = complex. The homogeneous polymers are assumed to have two types of sites within each nucleotide unit: sites for the polymer–polymer association, i.e., (p‐p) sites; sites for polymer–solute association i.e., (p‐s) sites. The respective binding parameters, P and F, and nearest‐neighbor interaction parameters, W and S, are assumed independent. Complications due to ring entropy are avoided by rest riding the model to one‐solute‐stack systems, which are physically realizable when the reciprocal of the solute cooperativity parameter is much larger than the number of nucleotides in the polymer. The 4 × 4 generating matrix is shown to be a tensor product of two 2 × 2 matrices, each the generating matrix of a particular type of site. The scalar product of the 4 × 4 matrix is shown to be equivalent to the scalar product of a 2 × 2 matrix in the weak interaction limit, W ≈ 0. Calculations are presented for the general case which restricts the (p‐s) association to occur only with (p‐p) associated nucleotide units. The nature of the binding curve in relation to partitioning the total interaction energy (F + P + S + W) among the parameters is discussed. Also presented is a criterion for neglecting possible states in the calculation of the grand partition function.
Hydration of DNA: A neutron scattering study of oriented NaDNA
Authors: Dahlborg U. , Rupprecht A.
Published: May 2005

A preliminary neutron‐scattering study of wet‐spun oriented NaDNA samples with various contents of H2O or D2O has been performed to obtain information about the hydration of NaDNA. The preferred orientation was in the direction of the crystallographic c axis. Perpendicular to this direction the samples could be regarded as poly‐crystalline. It has been found that the preferred crystallite orientation was also reflected in the water structure. This fact, taken together with the small energy widths of the measured near‐elastic peaks indicates that water molecules in the sample are relatively strongly bound to the DNA helix either directly or via other water molecules. Angular distribution measurements of elastically scattered neutrons were performed with the momentum transfer vector directed along and perpendicular to the DNA helix axis. Different Debye‐Waller factors were obtained, indicating different water dynamics in the two directions. Comparison between the H2O and D2O measurements suggests that the difference is caused by motions of rotational nature. The shape of the frequency distribution function for the H2O molecules in the NaDNA sample was somewhat similar to that which has been measured in ice.
Dichroism of TMV in pulsed electric fields
Authors: Allen F. S. , Van Holde K. E.
Published: May 2005

The linear dichroism induced in a solution of electrically anisotropic molecules by a pulsed electric field has been studied. Equations have been obtained which express the dichroism as a function of dipole moment, excess polarizability, field strength, and the angle α between the dipole moment and the transition moment for the absorption band. These expressions have been related to the experimentally observed difference signal in such a way that when the dichroism is measured as a function of field strength the permanent moment, excess polarizability and angle a can be determined.

Experiments have been carried out on tobacco mosaic virus (TMV), which is similar in its properties to the theoretical model. The polarizability anisotropy and rotary diffusion constant for the monomer and dimer of TMV have been obtained from these experiments. In addition to the molecular parameters mentioned above, the saturated electric dichroism of the virus was measured as a function of wave length and the presence of an n–π* transition in the tryptophan spectrum was indicated.

Further experiments measuring dichroism as a function of pH demonstrated the general denaturation of the virus at high pH (10–11) but also the existence of a stable fraction which is not fragmented even at the high pH involved.
Statistical length of DNA from light scattering
Authors: Schmid Carl W. , Rinehart Frank P. , Hearst John E.
Published: May 2005

An analysis of hydrodynamic data of DNA by use of the wormlike coil model gave a statistical length of 1300 Å, in the absence of excluded volume corrections. The worm‐like coil model and this hydrodynamically observed statistical length adequately describe the light scattering properties of DNA.
Kinetic studies of interaction between acridine orange and DNA
Authors: Sakoda Mitsuaki , Hiromi Keitaro , Akasaka Kazuyuki
Published: May 2005

The interaction between acridine orange (AO) and deoxyribonucleic acid (DNA) was studied by the stopped‐flow method. The spectral change of AO due to interaction with DNA was followed over the wavelength range 350–600 nm at various concentration ratios of DNA phosphate to dye. The spectral change observed by the stopped‐flow method was found distinctly different from that, during the dead‐time, leading to a conclusion that the binding of AO to the outside of DNA occurs much faster than the intercalation into base pairs of DNA. The dependence of the rate of reaction on the reactant concentration and on the salt, concentration of the solution was also studied. The results are consistent with the mechanism that the intercalation proceeds via the outside bound state.
Circular dichroism of superhelical DNA
Authors: Maestre Marcos F. , Wang James C.
Published: May 2005

The circular dichroism (CD) spectra of a number of superhelical DNA's have been measured. The introduction of negative superhelical turns causes an increase in magnitude of the positive band around 280 mμ, while the trough around 250mμ is little affected. For two samples of λb2b5c DNA (20 Mdalton) containing different number of negative superhelical turns, the magnitude of the positive band relative to that of the nicked control increases with increasing number of superhelical turns. In 2M NaCl, the small (1.45 Mdalton) superhelical DNA from E. coli 15 shows an unusually large difference in CD compared with that of the same DNA with a few single‐chain scissions per molecule. This large difference is not observed in a medium containing p. 0.11M NaCl. These results indicate that the double helix in a superhelical DNA is perturbed somewhat due to the bending and torsional forces in such a molecule. The magnitude of such structural alteration seems to depend on the number of superhelical turns per unit length, the size of the DNA molecule, as well as the ionic medium.
Morphological and structural studies of poly(gly‐gly‐ala)
Authors: Andries J. C. , Anderson J. M. , Walton A. G.
Published: May 2005

The ultrastructural morphology and x‐ray and electron diffraction of poly (Gly‐Gly‐Ala) have been studied. The polymer has two forms; the first, form I possesses a super‐folded cross‐β structure, long fibers of which show some twisting and intertwining. Form II precipitates in a less distinct fibrous form from aqueous solution. The x‐ray diffraction and oriented electron diffraction data suggest that form II is a polyglycine II helix situated in a monoclinic cell with dimensions a = 8.86 Å, b = 22.0 Å, c = 9.42 Å, and β = 90°. Combined with the morphological evidence it appears likely that form II is also in an antiparallel superfolded array.