bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrodynamics of macromolecular complexes. II. Rotation
Authors: De La Torre Jose Garcia , Bloomfield Victor A. 
Published: May 2005

AbstractWe 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

AbstractThe 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

AbstractHeat 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

AbstractA 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

AbstractA 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

AbstractIt 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

AbstractPoly(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

AbstractA 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

AbstractThe 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

AbstractCircular 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

AbstractThe 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

AbstractThe 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

AbstractChitosan 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

AbstractConformational 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

AbstractSolvents 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

AbstractThe 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

AbstractInvestigations 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

AbstractPolypeptides 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

AbstractStriking 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

AbstractThe 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.