bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self‐association of N‐protected α‐amino acids. Optically active and racemic N‐tert‐butyloxycarbonyl‐alanine
Authors: Benedetti Ettore , Di Blasio Benedetto , Pavone Vincenzo , Pedone Carlo , Toniolo Claudio , Bonora Gian Maria 
Published: May 2005

AbstractThe ir absorption and x‐ray diffraction analysis of N‐tert‐butyloxycarbonyl‐DL‐alanine (t‐Boc‐DL‐Ala‐OH) in the solid state has revealed a new mode of self‐association for a N‐urethanyl‐α‐amino acid, i.e., ribbons of hydrogen‐bonded cyclic dimers formed through the —COOH groups. In contrast to the recemate, a water molecule, incorporated into the crystal of the chiral t‐Boc‐D‐Ala‐OH, alters in part that hydrogen‐bonding scheme. In the two independent molecules of the unit cell of the optically active alanine derivative, as in that of the racemic derivative: (i) the conformation of the —CONH group is trans, also a new observation for a N‐urethanyl‐α‐amino acid, and (ii) the overall conformation is quasi‐extended. These findings exclude the occurrence of an oxy‐C7 peptide conformation. In solvents of high polarity, strongly solvated species predominate, as shown by ir absorption spectroscopy. In deuterochloroform nonassociated and associated species occur simultaneously. No differences were observed between the optically active and racemic derivatives. The type of self‐association near saturation seems to differ, at least in part, from that found in the anhydrous racemic compound in the crystal state.
Kinetics of nucleic acid–large ligand interactions: Multiplet‐closure approximations and matrix‐iteration techniques
Authors: Dateo Christopher , Epstein Irving R. 
Published: May 2005

AbstractApproximate methods are developed and evaluated for treating the rate of binding ligands that cover several contiguous sites to a homogeneous one‐dimensional lattice, which represents a nucleic acid or other linear biopolymer. The model requires as input only the number of lattice sites necessary for binding, the total number (possibly infinite) of lattice sites, and elementary rate constants for the cooperative and noncooperative association and dissociation of the ligand on the lattice. The computational methods employed are an extension of the triplet closure approximation from the helix–coil (single‐site ligand) problem to the large ligand binding problem. It is found that consideration of clusters ofn+ 2 lattice sites, where each ligand coversnsites, gives a surprisingly accurate description of the kinetics. The approximation is implemented by an extension of the matrix‐iteration approach proposed by Craig and Crothers. The effects of the finite lattice length, as well as the capability to treat ligand motion along the lattice, are incorporated. When all symmetries are taken into consideration, the time required for the matrix iteration calculation rises only linearly with the ligand lengthnand is considerably less than that of the Monte Carlo method, which is used as a standard for comparison.
Proton magnetic resonance study of nucleosides, nucleotides, and dideoxynucleoside monophosphates containing a syn pyrimidine base
Authors: Niemczura Walter P. , Hruska Frank E. , Sadana Krishna L. , Loewen Peter C. 
Published: May 2005

AbstractProton magnetic resonance data have been obtained for 6‐methyl‐2′‐deoxyuridine (dT*), its 3′‐ and 5′‐monophosphates, and its 3′,5′‐diphosphate, as well as for the corresponding thymine derivatives. The synthesis of the dideoxynucleoside monophosphates—d(TpT), d(T*pT), d(TpT*), and d(T*pT*)—was accomplished, and spectral data were obtained for these four dimers. The data show that the 6‐methyluracil base prefers the syn conformation about the N‐glycosyl bond at the monomer and dimer levels. The presence of the syn base leads to increases in the cis couplings of the sugar ring, J1′2″ and J2′3′, which indicate a trend towards eclipsing of the substituents on the C1′‐C2′ and C2′‐C3′ fragments. This trend is discussed in terms of changes in the pseudorotational parameters which describe the pucker of the ring. The syn base destabilizes the g+ conformer about the C4′‐C5′ bond, leading to a preference for the t conformer in all dT* residues at the monomer and dimer levels. Preliminary work on the formation of cyclobutane‐type photodimers in d(T*pT) and d(T*pT*) is discussed and presented as evidence for the capability of the syn 6‐methyluracil base to form base‐stacked complexes.
Conformational and structural constraints in double‐helical polynucleotides
Authors: De Santis P. , Morosetti S. , Palleschi A. , Savino M. 
Published: May 2005

AbstractConformational analysis of antiparallel double‐helical polynucleotides with Watson‐Crick base pairing was reduced to a four‐dimensional problem using original mathematical methods. In the four‐dimensional conformational space the family of structures, characterized by the base‐pair stacking with the most stable conformations in water solution as well as in the solid state, was localized. For the C′2‐endo sugar pucker, both right‐handed and left‐handed structures were found; right‐handed structures only, however, seem to be allowed for the C′3‐endo pucker, the only possible one for ribonucleotides with base stacking.
Conformational analysis of double‐stranded B‐type DNA structures
Authors: De Santis P. , Morosetti S. , Palleschi A. , Savino M. 
Published: May 2005

AbstractA complete conformational analysis of B‐type DNA was carried out in the independent two‐dimensional surface of the hexa‐dimensional conformational space of the helical structures. A theoretical double‐helical model was derived by locating the deepest minimum of the conformational energy. It is similar to that obtained by x‐ray refining methods; significant differences seem to be supported by relevant experimental data. Examination of the energy map allows a direct estimate of the flexibility limits of B‐DNA, which are found to be consistent with a smoothly supercoiled DNA in chromatin. The structure of the hypothetical left‐handed B‐type DNA was predicted to be as stable as the standard right‐handed model at high ionic strength. Left‐ and right‐handed helices are, however, not interconvertible without separation of the strands, and mixing of opposite screw sense fragments is unlikely to give coaxial helices, which would prevent their packing in fibers.
Synthesis of biologically active cyclic peptides
Authors: Izumiya Nobuo , Kato Tetsuo , Waki Michinori 
Published: May 2005

Abstract1. The extent of racemization and the coupling yield in peptide synthesis were studied under high dilution conditions. The azide method yielded the best results. 2. Five linear penta‐peptide precursors related to gramicidin S were subjected to cyclization in order to study how the difference in the sequence influences the yield and the ratio of cyclic dimer to monomer. The azide with the sequence of ‐L‐Pro‐L‐Val‐L‐Orn(Z)‐L‐Leu‐D‐Phe‐ afforded diZ‐gramicidin S in a high yield of 63%. 3. Alternaria mali toxin III, a cyclotetradepsipeptide phytotoxin, was synthesized. The activated linear tetradepsipeptide containing a D‐Dap(Z) (N3‐Z‐D‐2,3‐diaminopropionic acid) residue at the N‐terminus afforded the cyclic precursor (53%). The Dap residue in the precursor was converted into a ΔAla residue by Hofmann degradation to give the desired product.
The amine capture strategy for peptide bond formation—an outline of progress
Authors: Kemp D. S. 
Published: May 2005

AbstractA review is presented of the general features of amide bond formation by prior capture of the amine‐bearing peptide fragment. Capture by formation of a bond to the N‐terminal nitrogen is shown in eight model systems to result in slow intramolecular acyl transfer, accompanied by anomalously large Gly/Ala and Gly/Val rate ratios. Two examples are given of rapid intramolecular acyl transfer via rings of 9 and 12 members. The transfer efficiency as estimated by the effective molarity of reactive amine at the acyl carbon in the latter case is 18M. Capture at the thiol function of an N‐terminal cysteine residue is shown to be feasible in mercurithio and disulfide systems. In the latter case, effective concentrations of 3M and intramolecular transfer half‐times of 10 min are demonstrated.
Protection during peptide synthesis: Some new directions
Authors: Young Geoffrey T. 
Published: May 2005

AbstractMethods available for the protection of the functional groups of amino acids during peptide synthesis are discussed, and attention is drawn to the advantages of side‐chain protection of the 4‐pyridylmethyl type, having increased acid stability and cleaved by mild reductive procedures in the presence of sulfur. The use of S‐diphenyl‐4‐pyridylmethyl‐cysteine and Nim‐diphenyl‐4‐pyridylmethyl‐histidine is described.
Studies on 2‐aziridinecarboxylic acid peptides: Their reaction and uses
Authors: Okawa K. , Nakajima K. 
Published: May 2005

AbstractThe reaction of 2‐aziridinecarboxylic acid derivatives with several protic reagents was used to synthesize depsipeptides, dehydroamino acid derivatives, diaminopropionic acid derivatives, and phospho peptide derivatives. The reaction of N‐aminoacyl‐2‐aziridinecarboxylic acid benzyl ester with amino acid ester induced stereoselective transacylation.
Strategy for the synthesis of large peptides: An application to the total synthesis of human parathyroid hormone [hPTH(1–84)]
Authors: Kimura T. , Takai M. , Masui Y. , Morikawa T. , Sakakibara S. 
Published: May 2005

AbstractA strategy suitable for the synthesis of larger peptides is proposed. It involves the following four considerations: (1) all of the side‐chain functional groups are protected by benzyl‐type protective groups; (2) a water‐soluble carbodiimide, 1‐ethyl‐3‐(3‐dimethylaminopropyl)‐carbodiimide, is used for the fragment‐condensation reactions together with 1‐hydroxybenzotriazole as the additive; (3) all the protective groups are cleaved simultaneously by the HF method in the final stage of the synthesis; and (4) side products formed are detected and removed by an efficient high‐performance liquid chromatography procedure. The usefulness of these procedures is demonstrated taking the synthesis of human parathyroid hormone [hPTH(1–84)] as an example.
Solid‐phase synthesis of larger peptides by a new strategy of detachment from the resin
Authors: Niu Ching‐I , Yang Shi‐Zhen , Ma An‐Qing , Chen Yun‐Neng , Jiang Yong‐Qing , Huang Wei‐Teh 
Published: May 2005

AbstractAttachment of the side‐chain carboxyl of the protected aspartic or glutamic acid ester to the resin support has been established for the solid‐phase synthesis of the asparagine or glutamine peptide. After further elongation of the α‐amino deprotected resin‐bound peptide ester with protected peptide fragments and the final detachment from the resin support by ammonolysis, the larger peptides containing, or preferably C‐terminated with, asparagine or glutamine could be obtained. Thus, the C‐peptide of human proinsulin was prepared by coupling to the resin‐bound dipeptide derivative, Leu‐Glu(OCH2Ph®)·OtBu, with six fragments consecutively. It was obtained in an overall yield of 36% after detaching from the resin with alcoholic ammonia, followed by mild acidolysis, DEAE cellulose chromatography, and gel filtration. This procedure has now been applied to the synthesis of the C‐terminal fragment of the insulin A chain ending in asparagine, and also to the synthesis of the threonine or serine peptide, where the anchorage to the resin was designed by the reaction of the sidechain hydroxyl with succinic anhydride in the presence of 4‐dimethylaminopyridine to form the hemiester of succinic acid, which in turn was condensed to the aminomethyl resin by the DCC‐HOBt procedure. Model experiments on the synthesis of the Z‐Thr(CO‐CH2CH2CONHCH2Ph®)·OtBu and Bpoc‐Lys(Boc)‐Thr(COCH2CH2CONHCH2Ph®)·OtBu, as well as their detachment from the resin by amminolysis or hydrazinolysis, have shown the potential for a milder process in the solid‐phase synthesis of larger peptides.
Semisynthesis and properties of some insulin analogs
Authors: Inouye Ken , Watanabe Kunio , Tochino Yoshihiro , Kobayashi Masashi , Shigeta Yukio 
Published: May 2005

AbstractThe trypsin‐catalyzed coupling of bovine (Boc)2‐desoctapeptide (B23‐B30)‐insulin with synthetic octapeptides, H‐Gly‐X2‐X3‐X4‐Thr‐Pro‐Lys(Boc)‐Thr‐OH (X2 = Phe or Ala, X3 = Phe or Ala, X4 = Tyr or Ala), followed by deprotection and purification produced the [AlaB24, ThrB30]‐, [AlaB25, ThrB30]‐, and [AlaB26, ThrB30]‐analogs of bovine insulin in yields of 32, 35, and 32%, respectively. The biological activity of these analogs decreased in the order, normal insulin ([ThrB30]‐bovine insulin) = AlaB26‐insulin > AlaB25‐insulin > AlaB24‐insulin, as assayed for receptor binding and some other biological effects, in contrast with the corresponding Leu‐analogs of human insulin, in which the activity decreased in the order, normal insulin > LeuB24‐insulin > LeuB25‐insulin. The affinity to insulin antibodies greatly diminished in both AlaB24‐insulin and LeuB24‐insulin but not in the B25‐substituted analogs. The CD spectra of the Leu‐ and the Ala‐analogs were compared with those of normal insulins to show that no apparent correlation seems to exist between the decrease in biological activity and the conformational changes observed in solution. The effects of organic solvents on the peptide‐bond equilibrium and on the stability of trypsin are also discussed.
A new method for the determination of optical purity of synthetic peptides
Authors: Kusumoto Shoichi , Matsukura Masayuki , Shiba Tetsuo 
Published: May 2005

AbstractA novel and very accurate method was established for the determination of the optical purity of a peptide by use of the following procedure: (1) hydrolysis of the peptide in deuterium chloride, (2) gas chromatographic separation of each amino acid enantiomer on a chiral phase, and (3) determination of the D/L ratio by mass fragmentography. In this manner, one can estimate the true chiral purity of each amino acid residue with an accuracy of ∼0.2%. The recemization effected during hydrolysis could be eliminated in principle, since the artificially formed DL‐amino acids are necessarily labeled at the α‐position with deuterium and can thus be distinguished mass spectrometrically from the D‐ and L‐isomer originally present in the peptide. The versatility of the method was proven by analysis of model peptides, as well as by a racemization test in fragment condensation.
Mutations and protein stability
Authors: Schellman John A. , Lindorfer Margaret , Hawkes Richard , Grutter Markus 
Published: May 2005

AbstractThe comparative study of proteins which differ in primary structure by point mutations permits one to use thermodynamic experiments to obtain information about the role of specific amino acids in determining protein structure and stability. We have now determined the thermodynamic changes induced in six mutants of T4 lysozyme and have compared the results with the wildtype enzyme. Our work is in collaboration with B. Matthews and his colleagues, who have determined the crystal structure of T4 lysozyme and have obtained difference Fourier maps for four of the mutants. The ultimate aim is to correlate changes in protein stability with changes in the detailed structure of the protein. This paper discusses the thermodynamic results obtained from the mutants studied. All the mutants have a lower Tm than the wild‐type enzyme and changes in the enthalpy of denaturation are sometimes extraordinarily large. Changes in ΔH of denaturation are usually accompanied by compensating changes in ΔS. The general question of protein stability and the manner in which it varies with temperature and mutations is discussed.
Comparison of helix stabilities of poly‐L‐lysine, poly‐L‐ornithine, and poly(L‐diaminobutyric acid)
Authors: Grourke Martin J. , Gibbs Julian H. 
Published: May 2005

AbstractThe helix–coil transitions of aqueous solutions of poly‐α‐L‐lysine (PLL), poly‐α‐L‐ornithine (PLO), and poly(α,γ‐L‐diaminobutyric acid) (PLDBA) have been investigated as functions of pH at 25°C and of temperature at pH 11.75, where these polymers are uncharged; in the cases of the latter two polyamino acids, the transitions have also been studied as functions of apparent pH in methanol‐water solution (50/50 by volume). The helix stability of the polypeptides is shown to be a direct function of the number of methylene groups on the side chain. From an analysis of potentiometric titration data, we find that the difference between the helix stability of PLL and that of PLO is due to a difference of about 1 e.u. in the ΔS° of the transition. Combining the “melting curves” obtained from optical rotatory dispersion studies with the potentiometric titration data permits evaluation of the initiation parameter Z (or 1/σ½) of the statistical mechanical theories for these transitions. The value obtained for Z in the case of uncharged aqueous PLO is ca. 35.
Decay processes of electric birefringence in chemically reacting system
Authors: Kobayasi Syoyu 
Published: May 2005

AbstractAnalytical and numerical calculations of the decay processes of the electric birefringence in an isomerizing system have been performed. Two modes of isomerization are considered: in the first mode, the direction of the axis (of the optical anisotropy) of a molecule is conserved during isomerization; in the second mode, it is not. In the first mode, if GAis not equal to GB, and that, if kAopA2 is not equal to kBopB2 (when the orienting electric field is weak), in which GA, GB and pA, pb are the optical anisotropy and permanent electric dipole moments, of the molecule in two states A and B of the isomerization, and kAo and kBo are the rate constants for the transitions A → B and B → A, respectively, and if diffusion rates are very much slower than the chemical rates, the relaxation due to the chemical reaction can be detected in the decay of the electric birefringence. In the second mode, if diffusion rates are somewhat slower than the chemical rates, the relaxation due to the chemical reaction appears in the decay, even though there are no differences in optical anisotropy and electric moments in the two states. When the rotary diffusion coefficients are different in the two states, the decay process becomes almost one‐component, bringing the chemical rate about ten times higher to diffusion coefficients in both modes.
Conformational aspects of polypeptide structure. XXXIII. Infrared spectra and molecular conformations of γ‐ethyl L‐glutamate oligopeptides
Authors: Goodman Murray , Masuda Yukio , Verdini Axtonio S. 
Published: May 2005

AbstractInfrared spectra of homo‐ and co‐oligopeptides containing glutamate residues were studied in both solution and solid state. Conformational analyses of these oligomers were carried out by using amide I and II band frequencies. Trimethyl phosphate supports the folded structure of oligomers above the heptamer. In chloroform solution, these oligomers assume the β‐extended structures above the pentamer.
The chain length dependence of the conformation for oligomers of L‐lysine in aqueous solution: Optical rotatory dispersion studies
Authors: Yaron A. , Katchalski E. , Berger A. , Fasman G. D. , Sober H. A. 
Published: May 2005

AbstractThe optical rotatory dispersion of L‐lysine oligopeptides (Lysn, n = 2–22) in solution was measured in water and in 50% methanol. A gradual change with increasing chain length in the ORD curves of the oligomers was observed at pH 4. 3. Not even a chain of 22 residues had ORD identical with that of high molecular weight poly‐L‐lysine. A plot of the average molar residue rotation at 233 nm versus 1/n (where n is the chain length) resulted in a straight line with an intercept of −1900, representing the internal residue rotation of a lysine residue in the random conformation, and a slope of +6200 representing the large end effect. At pH 11.9 a stright line is obtained up to n = 12 after which it deviates from the initial slope indicating onset of helicity. Extrapolation of the initially straight line to tire higher n's provided the necessary zero‐helicity values for calculation of helicity. The highest oligolysine (n = 22) showed at pH 11. 9 13% helicity, which on adding methanol to 50% increased to about 50% helicity. It is shown that helix‐coil data which are usually obtained from the temperature dependence of helicity can be obtained from the dependence of helicity on chain length applying the statistical theory. For the methanol‐water system the cooperativity parameter v was calculated to be in the range 0.024–0.060, with corresponding equilibrium constants w of 1.32–1.43. The helical structure was calculated to be less stable in water than in methanol‐water by about 250 calories per residue.
Estimation of the relative stiffness of the molecular chain in polyelectrolytes from measurements of viscosity at different ionic strengths
Authors: Smidsrød Olav , Haug Arne 
Published: May 2005

AbstractA method was developed that allowed comparison of the stiffness of the chain in different polyelectrolyte from measurements of the intrinsic viscosity at different concentrations of added monovalent (sodium) salt. The response to salt was quantitatively expressed as the slope of straight lines relating the intrinsic viscosity to the reciprocal of the square‐root of the ionic strength. This slope increased considerably with increasing molecular weight of the polyelectrolyte, and could serve to characterize the response to salt of different substances only when comparison was made at a constant molecular weight. An empirical parameter, B, which is the slope corresponding to an intrinsic viscosity of 1.0 at an ionic strength of 0.1 M could be correlated to the unperturbed dimensions of the molecules. A method of extrapolation, enabling the determination of B from measurements of viscosity on only one sample of unknown molecular weight, was evaluated. The empirically found correlation between Band some well established parameters of stiffness did not contrast predictions from the “fuzzy‐sphere model” of Fixman, provided that reasonable assumptions regarding ion‐binding and the interaction between polymer and solvent were made.
Quenching of the emission of tryptophan, tyrosine, and serum albumins by cupric ion
Authors: Luk Chun Ka 
Published: May 2005

AbstractThe effect of cupric ion on the emission of tryptophan, tyrosine, and serum albumins is studied by emission spectroscopy and lifetime measurements. It is found that whenever cupric ion is bound to tryptophan or tyrosine, their emissions are quenched completely. The quenching may be due to an electron transfer mechanism. The fluorescence of complexes of cupric ions with serum albumins is partially quenched; this is because energy is transferred from tryptophan to the complexed cupric ions by a dipolar energy transfer mechanism. It is deduced from the present study that the tryptophan in the human serum albumin molecule is between 11 and 16 Å from the nearest eupric ion binding sites (assumed to be at the surface of the protein) and that one of the tryptophan in the bovine serum albumin molecule is very close to the cupric ion binding sites and the other is near the center of the bovine serum albumin molecule. It is also found that the deuterium solvent effect on serum albumin fluorescence is very small, and that the quenching of bovine serum albumin fluorescence at the N‐F transition is the result of quenching of the fluorescence of both tryptophans. The phosphorescence lifetime apparatus, capable of measuring decay times of signals with intensities changing over a few orders of magnitude, and the ratio spectrofluorometer, both of which were constructed in this laboratory, are also described.