bluuebunny/crossref_metadata_2025 huggingface dataset:
Dinucleoside monophosphates. II. Nearest neighbor interactions
Authors: Topal Michael D. , Warshaw Myron M.
Published: May 2005

A method has been developed which enables calculation and unambiguous comparison of the thermodynamics for the stacking process of dinucleoside monophosphates (dimers) from a study of their titration properties. This method has been applied to dimers containing adenosine and/or cytidine with the result that the dimers studied can be ordered with respect to their tendency to stack as ApA > ApC > CpA ≃ C – containing homodimers. This dependence of the relative magnitude of ΔFstacking on composition is consistent with hydrophobic interactions, as manifested by the solubility of the bases, being the main driving force toward stacking. The sequence dependence of ΔFstacking as well as of the optical properties of the dimers is related to van der Waals interaction between the bases. The lack of variation in ΔFstacking of the C‐containing isomers indicates that the role of the 2′‐OH in RNA versus DNA structure is not H‐bonding.
Synthesis of sequential oligopeptides and polypeptide having the sequence of L‐alanyl‐L‐leucylglycine
Authors: Katakai Ryoichi
Published: May 2005

A series of sequential oligopeptides having simple nonpolar side chains, Nps‐(L‐Ala‐L‐Leu‐Gly)n‐ OEt has been prepared by a stepwise fragment‐condensation method using Nps‐L‐alanyl‐L‐leucylglycine N‐hydroxysuccinimide ester, which was prepared by the Nps‐N‐carboxy α‐amino‐acid‐anhydride method. The success of the synthesis of the peptide having a high‐molecular weight, such as octadecapeptide, results from the highest solubility of the tripeptide unit, L‐alanyl‐L‐leucylglycine. The sequential polypeptide having the same tripeptide sequence was also prepared by polycondensation of the tripeptide N‐hydroxy‐succinimide ester.
Conformational studies of peptides. The crystal structures of N‐acetyl‐L‐prolinamide and N‐acetyl‐(S)‐thiazolidine‐4‐carboxamide
Authors: Benedetti E. , Christensen A. , Gilon C. , Fuller W. , Goodman M.
Published: May 2005

The crystal structure of N′‐acetyl‐L‐prolinamide and its isomorphous alalog N′‐acetyl‐(S)‐thiazolidine‐4‐carboxamide was determined using highly accurate parameters obtained by room‐ and low‐temperature data‐collecting systems. Both crystals are orthorhombic, space group P212121, with four molecules per unit cell held together by a hydrogen‐bond system that extends in all directions.

Both molecules exhibit the following conformational features: the acetyl group is in the trans configuration in respect to the tertiary amide. The primary amide is almost at right angles with respect to the mean plane of the ring and the –NH2 group is over the ring. The pyrrolidine and thiazolidine rings were found to be rather flexible with Cβ puckering in the former and sulfur in the latter.
Mass–length ratio of fibrin fibers from gel permeation and light scattering
Authors: Carr Marcus E. , Shen Linus L. , Hermans Jan
Published: May 2005

Mass–length ratios of fibers in fibrin gels were obtained from measurements of the angular dependence of the intensity of light scattered by dilute gels and from the permeability of more concentrated gels. The permeability was determined by measuring the forced flow of buffer through a short column of gel held in a glass tube. The results obtained with the two methods are consistent. At high pH and high ionic strength the mass–length ratio is found to be that calculated for a protofibril, i.e., a double strand of fibrin molecules laid end to end at a separation of 450 Å. This same value is found under conditions where the polymerized fibrin is not gelled (pH 10.25) and where it is just gelled (pH 10.0). At pH 7.4, ionic strength 0.35, the fibers are found to have a higher mass–length ratio, the average fiber consisting of some three protofibrils associated laterally. At pH 7.4 and low ionic strength (0.10 M) the fibers are up to a hundred times more massive.
Circular dichroism of the complex between N‐N′‐diethylpseudoisocyanine and sodium poly(L‐glutamate) in aqueous solutions
Authors: Pal M. K. , Mandel M.
Published: May 2005

In the presence of sodium poly(L‐glutamate) at pH = 7.5 the dye pseudoisocyanine in dilute aqueous solution (Cd = 1.10 × 10−5 M) and low P/D values exhibits an absorption spectrum with a very sharp red‐shifted J‐band. Under the same conditions circular dichroism (CD) in the visible region is observed with an extremely sharp peak at the position of the J‐band. At pH = 4.6, where the polypeptide is in the α‐helix conformation, no such J‐band is observed and no CD spectrum can be detected at the same P/D values. CD spectra in the uv range demonstrate that the occurrence of the dye–polypeptide complex which gives rise to the J‐band at slightly alkaline pH is not accompanied by a conformational transition of the polypeptide towards the α‐helical form.
Effect of the fluctuations in electron density within a globular protein on the excess small‐angle X‐ray scattering
Authors: Mattice Wayne L. , Carpenter Dewey K.
Published: May 2005

Excess small angle X‐ray scattering in solvents of differing electron density has been calculated from the crystal structures obtained for rubredoxin, trypsin inhibitor, myogen, ferricytochrome c2, ribonuclease S, lysozyme, nuclease, myoglobin, α‐chymotrypsin, elastase, subtilisin, carboxypeptidase A, thermolysin, methemoglobin, deoxyhemoglobin, and a single polypeptide chain of M4 lactate dehydrogenase. The scattering curves for each protein can be reproduced by the sum of three curves, with the weighting of the three curves depending on the electron density of the solvent. The radius of gyration obtained from the small angle X‐ray scattering by globular proteins in aqueous solution will usually exceed the values defined by the shape of the macromolecule. Deviations for certain of the proteins cited are calculated to be as large as 6%. These deviations arise from the tendency for the amino acid residues with low electron density to be situated closer to the center of the protein than the amino acid residues of high electron density. An upper limit of 19% is obtained for the discrepancy between the radius of gyration defined by the shape of a spherical globular protein of typical amino acid composition and the apparent radius of gyration measured for that protein in water by small angle X‐ray scattering.
Ion complexation in nonactin, monactin, and dinactin: A Raman spectroscopic study
Authors: Asher Irvin M. , Phillies George D. J. , Kim B. J. , Stanley H. E.
Published: May 2005

The ability of the macrotetrolide nactins to complex selectivity with a wide variety of cations makes these ionophorous antibiotics important model systems for the study of biologic ionic transport. We report a Raman spectroscopic investigation of the Na+, K+, Rb+, Cs+, Tl+, NH4+, NH3OH+, C(NH2)3+, and Ba++ complexes of nonactin, monactin, and dinactin in 4:1 (v/v) CH3OH/CHCl3 and in the solid state. The nactins display characteristic spectral changes upon complexation, some of which are specific for a given cation. In the K+, Rb+, Cs+, NH3OH+, and C(NH2)3+ complexes, which are apparently isosteric, the ester carbonyl stretch frequency is found to be linearly proportional to the cation–carbonyl electrostatic interaction energy, as calculated from a simplified model. Deviations for the Na+, NH4+, Tl+, and Ba++ complexes are interpreted as arising from additional nonelectrostatic interactions. Additional information is obtained from other spectral regions and from measurements of depolarization ratios. Spectra of the nactin complexes differ from each other more in the solid state than in solution, reflecting the effects of crystalline contact forces.
Polymerization of N‐carboxyanhydrides of various α‐amino acids using secondary amines as initiator
Authors: Imanishi Yukio , Aoyama Akimasa , Hashimoto Yutaka , Higashimura Toshinobu
Published: May 2005

In the polymerizations of alanine, γ‐ethyl glutamate, and leucine N‐carboxyanhydrides (NCA's) initiated by tertiary amines and some secondary amines such as N‐methyl‐L‐alanine dialkylamide, a stereoselectivity was observed: the polymerization rates of L‐ and D‐NCA's were identical to each other and larger than that of DL‐NCA. However, this selectivity was not observed in the polymerizations of valine and isoleucine NCA's initiated by N‐methyl‐L‐alanine dialkylamide. The stereoselective polymerizations of valine and isoleucine NCA's were induced only with tetriary amines such as tri‐n‐butylamine. N‐Methyl‐L‐alanine di‐alkylamide has been shown to initiate the polymerization of usual α‐amino acid NCA according to the activated‐NCA mechanism, but it initiated the polymerizations of valine and isoleucine NCA's according to the primary amine‐type mechanism. This is because in the latter NCA's the N–H group is masked by the adjacent Cβ‐branched alkyl substituent against the approach of the secondary amine. Poly(DL‐alanine)s produced in the stereoselective polymerization had higher viscosities and were more stereoblock‐like than those produced without the stereoselectivity. These experimental results indicate that the stereoselective polymerization is possible only when the polymerization proceeds through the activated‐NCA mechanism.
ESR investigation of the binding of some neutral polyamino acids to synthetic apatite
Authors: Peckauskas R. A. , Pullman I. , Termine J. D.
Published: May 2005

Interaction between synthetic crystalline apatitic calcium phosphate and neutral polypeptides [poly(DL‐alanine), poly(L‐proline), poly(L‐hydroxyproline)] was investigated by elecron‐spin‐resonance spectroscopy of mineral‐macromolecule complexes doped with vanadyl ion (VO++) as a paramagnetic probe. Changes in magnetic parameters were interpreted in terms of polypeptide‐induced axial interactions with VO++ ions that have mineral surface phosphate oxygens as their primary ligands. This implies very close proximity between mineral surface and macromolecular peptide bond dipolar substituents.
Characterization of meningococcal polysaccharides by optical mixing spectroscopy. II. Effects of temperature, EDTA, and ionic strength on aggregation of group C polysaccharides in solution
Authors: Fujime S. , Chen F. C. , Chu B. , Liu T. Y.
Published: May 2005

We have studied the effects of temperature, EDTA, and ionic strength on C‐polysaccharides in solution by examining the details of the time‐correlation function using a 96‐channel single‐clipped photon correlation spectrometer. Our linewidth results have shown that the C‐polysaccharides in buffer solution form aggregates of very broad distributions. Thus, fractionation by gel‐filtration chromatography is only mildly effective. Although the aggregate sizes seem to remain relatively constant from 4 to 25°C, a fraction of those aggregates break up to form smaller fragments or monomers at higher temperatures. However, the dissolution‐association process is quite slow and takes days even at room temperatures before the equilibrium is reached. We have also shown that by adding an excess amoutn of EDTA, the aggregates can be broken up. Again the dramatic changes occur only at short delay times suggesting that a protion of the larger aggregates remains. Finally, the amount and size of aggregates depend upon the ionic strength which exhibit a maximum ΓT/sin2 (θ/2) around 0.1–0.2 M KCl.

If the activities of polysaccharides in solution depend upon molecular size, the standard techniques such as gel‐permeation chromatography and ultracentrifugation cannot properly characterize the detailed size distribution. Quasielastic laser light scattering can provide us with a qualitative model. The quantitative details must necessarily await more extensive investigations using a combination of the techniques and better fractionation procedures in an appropriate buffer solution.
The interaction of carboxymethylamylose and diethylaminoethylamylose with iodine
Authors: Cesàro Attilio , Brant David A.
Published: May 2005

Spectrophotometric titrations of slightly substituted carboxymethylamylose (CM‐Amy) and diethylaminoethylamylose (DEAE‐Amy) with iodine in the presence of iodide (I2/I−) were carried out as a function of iodide concentration, temperature, and polymeric charge. Binding isotherms for the polymer‐I2/I− complex are reported in terms of an apparent binding constant (Ka) plotted versus degree of saturation of the complex (θ). The dependence of Ka upon polymeric charge is interpreted as evidence for the negatively charged character of the bound species. The cooperative nature of the binding process is evident in the positive slope of Ka vs (θ). Whereas the apparent binding constants and binding cooperativities for the derivatives are smaller than for the amylose‐I2/I− complex, the binding enthalpies deduced from the temperature dependence of Ka at θ = 0.5 appear to be the same for amylose and CM‐Amy. A viscometric titration of fully charged CM‐Amy with I2/I−, conducted at dialysis equilibrium between the CM‐Amy‐I2/I− solution and the polymer‐free solvent phase, disclosed a maximum in the plot of intrinsic viscosity ([η]) vs θ. The increase in [η] at small θ was interpreted as a reflection of polyelectrolyte expansion provoked by absorption of the negatively charged bound species; the subsequent decline in [η] is attributed to stabilization by I2/I− of compact helical sequences or to the formation at higher θ of intermolecular aggregates.
Evidence for electrically induced partial strand separation of DNA
Authors: Pollak M. , Glick H. A.
Published: May 2005

We measured electrically induced changes of some optical properties of DNA solutions. These were the absorption coefficient and the reduced dichroism. The electric fields were applied in the form of 50–300‐μsec‐long pulses of varying field strength, up to 20 kV/cm. Changes of the optical properties were studied during the pulse. Solutions of varying DNA and salt concentrations were used. The qualitative predictions expected from the theory of electrically induced partial denaturation of the DNA were all observed. These are: (1) a decrease of the reduced dichroism at high fields; (2) a concurrent increase in the absorption coefficient; (3) a critical field above which effect (1) and (2) begin to occur; (4) a decrease of the magnitude of the above effects with increasing salt concentration; (5) a return to the status quo ante after short pulses.
The effect of ions on the enzymatic properties of beef‐liver glutamate dehydrogenase
Authors: Blauer G. , Sund H.
Published: May 2005

The effect of various salts on the enzymatic activity of beef‐liver glutamate dehydrogenase, on the binary enzyme‐reduced coenzyme (NADH or NADPH) comples, as well as on the ternary complex with glutamate was investigated in aqueous solution (0.067M phosphate buffer, pH 7.6). Binding studies in the analytical ultracentrifuge and circular dichroism measurements indicated dissociation of the coenzyme from the enzyme‐coenzyme complex by the action of various salts. The efficiency of this change was largely dependent on the type of anion present and generally followed the series: acetate < Br− < I− < SCN−. Acetate ions and guanidinium thiocyanate showed exceptional behaviour in some cases, while K+ and Na+ gave similar results. The reversibility of the ion effects on the enzymatic activity was demonstrated by dilution tests. Upon addition of salts, the inhibitory effect of GTP was slightly changed in most cases, while the activating effects of ADP and L‐leucine were practically abolished and with ADP, the halides caused an additional inhibition. Assuming an equilibrium involving dissociation of the enzyme‐coenzyme complex by the action of salts, an exponent of 1.3 for NaBr and of 2.0 for KSCN was calculated for the respective concentrations. The apparent equilibrium constants were evaluated to be about 20 times greater for KSCN than for NaBr.
The organization and repair of DNA in the mammalian chromosome. II. A gradient‐shape‐induced speed dependence affecting DNAs larger than T4 DNA
Authors: Lange Christopher S. , Martin Patricia , Ferguson Pamm , Resnick Michael A.
Published: May 2005

The addition of a lytic layer to a preformed linear sucrose gradient induces a temporary (up to half a day) initial gradient of considerable steepness which retards the sedimentation of large (>T4) DNAs. Centrifugation at sufficiently slow angular velocities permits the temporary initial gradient to disappear and therefore the sedimentation distance increases, yielding a rotor speed dependent effect on sedimentation distance. Gradients which are free of this effect are described and shown to permit mouse leukemia cell DNA to sediment independently of rotor speed (5–30 krpm).
Correlation between percentage guanine‐cytosine content and melting temperature of deoxyribonucleic acid
Authors: Tong B. Y. , Leung M. L. C.
Published: May 2005

An explicit relation between the percentage (G + C)‐content XGC, and the melting temperature (Tm) of a natural DNA, is derived froma a statistical mechanics calculation with due consideration given to the base pair bonding and stacking interactions. The well‐known Marmur‐Doty empirical formula, linearly relating these two quantities, can now be understood in terms of the fundamental processes. We also propose a simpler experimental procedure for the determination of XGC. It is similar to the melting temperature method, but we take only one reading at a prescribed temperature of any natural DNA in addition to the two normalization readings. It should be more sensitive for DNAs having XGC ranging from 35 to 65%.
Application of modified ising model to the helix‐coil transition of DNA molecules
Authors: Leung M. , Choo F. C. , Tong B. Y.
Published: May 2005

Equilibrium properties of heterogeneous DNA near the melting temperature Tm are investigated using the grand partition function. The present approach gives exact and analytical solutions. The algebraic expressions enhance a more thorough understanding of the correlation among many observed equilibrium phenomena. The following quantities have been examined: melting temperature Tm, transition width W, partial melting curves θAT and θGC, mean length of a helical segment h, and correlation length γ.
Deamination of protein lysyl ε‐amino groups by peroxidase in vitro
Authors: Stahmann M. A. , Spencer A. K.
Published: May 2005

Peroxidase, catechol, and hydrogen peroxide were shown to react with proteins, causing a decrease in lysine detectable after acid hydrolysis. The loss of lysine did not occur in the presence of benzenesulfinic acid which suggested that the quinones formed by peroxidase had oxidized some lysyl residues to lysyl aldehyde that formed a cyclic ninhydrin negative Shiff's base. When peroxidase treated protein was oxidized with performic acid prior to hydrolysis a new ninhydrin positive compound was found, which was shown by cochromatography and mass spectroscopy to be α‐aminoadipic acid. The α‐aminoadipic acid recovered accounted for (20–40)% of the lysine lost.
Conformational changes induced in ionized poly(L‐arginine) and poly(L‐histidine) by sodium dodecyl sulfate
Authors: McCord Robert W. , Blakeney Ernest W. , Mattice Wayne L.
Published: May 2005

Circular dichroism spectra have been obtained for cationic poly(L‐arginine) and poly(L‐histidine) in aqueous solutions containing varying amounts of sodium dodecyl sulfate. The detergent induces a disorder‐order transition in both polypeptides. In each case the transition is cooperative and occurs when the ratio of detergent to amino acid residue is near unity. The ordered structure formed by poly(L‐arginine) is readily identifiable as an α helix. Poly(L‐histidine) appears to form a β structure in which the 211‐nm electronic absorption band of the imidazole group exhibits significant rotatory strength.
Synthesis and carbon‐13 nuclear magnetic resonance spectra of Cyclo(D‐leucyl‐L‐leucine) and Cyclo(L‐leucyl‐L‐leucine)
Authors: Exner Mary M. , Kostelnik Robert J.
Published: May 2005

Cyclo(D‐Leu‐L‐Leu) and cyclo(L‐Leu‐L‐Leu) were synthesized, and their carbon‐13 nmr spectra at 65 MHz were examined in dimethylsulfoxide and trifluoroacetic acid solutions. The chemical shift data are consistent with a boat or “twisted” boat conformation of the diketopiperazine ring in both solvents. There was no indication of protonation of the cyclic dipeptides by trifluoroacetic acid. Attempts at polymerizing the cyclic dipeptides were unsuccessful.
Electrical double layer, zeta potential, and electrophoretic charge of double‐stranded DNA
Authors: Schellman John A. , Stigter Dirk
Published: May 2005

The principal aim of this work is the proper interpretation of electrophoresis as an important tool for determining the immediate ionic environment of polyelectrolyte molecules like DNA. We also explore the relation with other experiments. We define an electrostatic model of double‐stranded DNA in monovalent salt solutions. The electrical double layer is divided in an inner Stern layer, inside the surface of hydrodynamic shear of DNA, and a Gouy‐Chapman type diffuse ionic atmosphere with cylindrical symmetry outside the shear surface. We discuss the assumptions made in applying to DNA the charge‐potential relation and the electrical free‐energy expression of the charged cylinder with a Gouy double layer. The conclusion is that reliable free‐energy data, better than 1kT per phosphate group, require a detailed model of the Stern layer. On the other hand, the Gouy model of a charged cylinder should be fairly good for the interpretation of the electrophoretic mobility of DNA. We introduce several modifications of the linear electrophoresis theory of the cylinder (Henry‐Gorin), related to the averaging over the orientations of DNA in the external electrical field, the relaxation effect, the nonlinear charge‐potential relation, and to geometrical aspects of the DNA model. Applied to published mobility data the modified theory yields roughly the same ζ potentials as before, but DNA charges which are about twice as high as derived earlier from the linear Henry‐Gorin theory. The charge calculation is quite sensitive to the assumed geometrical model of DNA. Our electrophoresis results are somewhat higher than the charges derived from Donnan equilibria of DNA in monovalent salt solutions measured by Strauss et al. The required self‐consistency of electrophoretic charge and ζ potential of DNA as a function of the salt concentration is treated on the basis of adsorption of counterions to the DNA phosphate groups (site binding). It is predicted that at low ionic strength the electrophoretic charge of DNA should be independent of the salt concentration.
Poly(L‐lysyl‐L‐alanyl‐α‐L‐glutamic acid)
Authors: Goren H. Joseph , Fletcher T. , Epand R. M.
Published: May 2005

Poly(Lys(Cbz)‐Ala‐Glu(OBzl)) was prepared by the self‐condensation of Lys(Cbz)‐Ala‐Glu(OBzl)‐ONSu in dimethylformamide. After deprotection of the side chains, the product was subjected to Sephadex G‐50 chromatography. The molecular weight of unfractionated and fractionated poly(Lys‐Ala‐Glu) was calculated from a calibrated Sephadex G‐50 column, spectrophotometrically from Dnp‐(Lys‐Ala‐Glu), equilibrium centrifugation, and viscosity measurements. Approximately 21% of the unfractionated material was polymeric with the remaining 79% being cyclic and monomeric material. Treatment of polymer hydrolysate with L‐amino acid and D‐amino acid oxidase indicated poly(Lys‐Ala‐Glu) to be optically pure. The apparent pKa's of the two ionizable groups were 4.1 and 9.7.
15N nmr spectroscopy. I. Polysarcosine and related sequence polypeptides
Authors: Kricheldorf Hans R. , Hull William E. , Formacek Viktor
Published: May 2005

The natural abundance 15N nmr spectra of linear polysarcosine (DP = 35) has been recorded in Me2SO and H2O solution. Because of cis/trans isomerization at the peptide bond, a broad signal with several splittings was observed. These splittings appear to reflect the influence of three peptide bonds on a single N atom. The 15N signals from the sequence polypeptides (β‐Ala‐Sar‐Gly)n and (β‐Ala‐Sar‐D,L‐Ala)n also show a cis/trans splitting, as well as chemical shifts which are dependent on the peptide sequence. The tertiary nitrogen of the sarcosyl residue has a T1 relaxation time which is longer than the T1 for secondary nitrogens of the other amino acids. The nuclear Overhauser effect is also discussed.
d‐CpCpGpG and d‐GpGpCpC self‐complementary duplexes: Nmr studies of the helix‐coil transition
Authors: Patel Dinshaw J.
Published: May 2005

We have monitored the helix‐coil transition of the self‐complementary d‐CpCpGpG and d‐GpGpCpC sequences (20mM strand concentration) at the base pairs, sugar rings, and backbone phosphates by 360‐MHz proton and 145.7‐MHz phosphorus nmr spectroscopy in 0.1M phosphate solution between 5 and 95°C. The guanine 1‐imino Watson‐Crick hydrogen‐bonded protons, characteristic of the duplex state, are observed below 10°C, with solvent exchange occurring by transient opening of the tetranucleotide duplexes. The cytosine 4‐amino Watson‐Crick hydrogen‐bonded protons resonate 1.5 ppm downfield from the exposed protons at the same position in the tetranucleotide duplexes, with slow exchange indicative of restricted rotation about the C‐N bond below 15°C. The guanine 2‐amino exchangeable protons in the tetranucleotide sequence exhibit very broad resonances at low temperatures and narrow average resonances above 20°C, corresponding to intermediate and fast rotation about the C‐N bond, respectively. Solvent exchange is slower at the amino protons compared to the imino protons since the latter broaden out above 10°C. The well‐resolved nonexchangeable base proton chemical shifts exhibit helix‐coil transition midpoints between 37 and 42°C. The transition midpoints and the temperature dependence of the chemical shifts at low temperatures were utilized to differentiate between resonances located at the terminal and internal base pairs while the H‐5 and H‐6 doublets of individual cytosines were related by spin decoupling studies. For each tetranucleotide duplex, the cytosine H‐5 resonances exhibit the largest chemical shift change associated with the helix‐coil transition, a result predicted from calculations based on nearest‐neighbor atomic diamagnetic anisotropy and ring current contributions for a B‐DNA duplex. There is reasonable agreement between experimental and calculated chemical shift changes for the helix‐coil transition at the internal base pairs but the experimental shifts exceed the calculated values at the terminal base pairs due to end‐to‐end aggregation at low temperatures. Since the guanine H‐8 resonances of the CpCpGpG and d‐CpCpGpG sequences exhibit upfield shifts of 0.6–0.8 and <0.1 ppm, respectively, on duplex formation, these RNA and DNA tetranucleotides with the same sequence must adopt different base‐pair overlap geometries. The large chemical shift changes associated with duplex formation at the sugar H‐1′ triplets are not detected at the other sugar protons and emphasize the contribution of the attached base at the 1′ position. The coupling sum between the H‐1′ and the H‐2′ and H‐2″ protons equals 15–17 Hz at all four sugar rings for the d‐CpCpGpG and d‐GpGpCpC duplexes (25°C), consistent with a C‐3′ exo sugar ring pucker for the deoxytetranucleotides in solution. The temperature dependent phosphate chemical shifts monitor changes in the ω,ω′ angles about the O‐P backbone bonds, in contrast to the base‐pair proton chemical shifts, which monitor stacking interactions.
Kinetics of complex formation between fluorescein mercuric acetate and DNA
Authors: Takeuchi Shintaro , Maeda Akio
Published: May 2005

The kinetics of complex formation between fluorescein mercuric acetate and heat‐denatured DNA were studied by measuring the fluorescence quenching of this reagent. This quenching process involved no immeasurably rapid phase and it was shown that this reaction follows simple second‐order kinetics. The rate constant at 25°C was estimated to be 2.9 × 104M−1 sec−1 for calf‐thymus DNA (42% G + C) and 1.1 × 104M−1 sec−1 for Micrococcus lysodeikticus DNA (72% G + C). Activation parameters for this reaction were calculated from the temperature dependence of the reaction rate, and the activation entropy was found to be highly negative (−27.5 cal/mol deg for calf‐thymus DNA and −25.5 cal/mol deg for M. lysodeikticus DNA). The binding of fluorescein mercuric acetate to native DNA, which requires the opening of the double‐helical structure, was also followed by measuring the absorbance change of this reagent. There was a lag phase in this binding process, and the enthalpy change for the opening step corresponded roughly to that for the opening of one base pair. These findings are discussed in relation to the results of a similar study with formaldehyde.
Circular dichroism of the nucleic acid monomers
Authors: Sprecher Cindy A. , Johnson W. Curtis
Published: May 2005

Circular dichroism spectra of the nucleic acid monomers have been measured in aqueous solution and extended into the vacuum ultraviolet region to about 166 nm. Measurements were made on ribo and deoxyribo derivatives of adenine, guanine, hypoxanthine, cytosine, thymine, and uracil derivatives both with and without the 5′‐phosphate (with the exception of ribosyl thymine 5′‐phosphate). Absorption spectra of the deoxyribonucleotides measured to about 175 nm are also presented. The results demonstrate that both the circular dichroism and absorption spectra observed below 200 nm are no more complicated than the spectra normally recorded above 200 nm. In most cases, the circular dichroism spectra of the various derivatives of a given base are similar, indicating that the conformations are similar. On the other hand, the differences among the circular dichroism spectra of the various derivatives of a given base are sufficient to identify a particular derivative. The average circular dichroism for the deoxyribonucleotides is compared with the circular dichroism of native E. coli DNA. The comparison reveals that the circular dichroism of DNA below 200 nm is due principally to the interaction between the bases rather than the intrinsic circular dichroism of the monomers. The monomer transitions are discussed in relationship to the absorption and circular dichroism spectra presented.
Molecular arrangement of DNA in bacteriophage T4
Authors: Basu Samarendra
Published: May 2005

The degree of preferred orientation and the coiling of the deoxyribonucleic acid within phage T4 was studied by two independent techniques, namely, polarization of fluorescence and uv linear dichroism. A correlation between the two kinds of data was obtained, which indicated that a significant proportion (about 30%) of total phage DNA is aligned preferentially along the long axis of phage heads. Analyses of the data suggest that all of the phage DNA cannot be in a highly supercoiled helical configuration. A few models of the DNA arrangement in T4 have been discussed in which linear sidewise packings of DNA would be predominant and may explain the observed longitudinal orientation of intraphage DNA.
Helix‐coil stability constants for the naturally occuring amino acids in water. XIV. Methionine parameters from random poly(hydroxypropylglutamine,L‐Methionine)
Authors: Hill D. J. T. , Cardinaux F. , Scheraga H. A.
Published: May 2005

Water‐soluble, random copolymers containing L‐methionine and N5‐(3‐hydroxypropyl)‐L‐glutamine have been prepared, fractionated, and characterized. The thermally induced helix‐coil transitions of these copolymers in water have been investigated, and it has been found that incorporation of L‐methionine increases the helix content of the polymers at all temperatures in the range of 0–60°C. The Zimm‐Bragg parameters σ and s for the helix‐coil transition in poly(L‐methionine) in water were deduced from an analysis of the melting curves of the copolymers using the methods described in earlier papers.
A new procedure for refining force constants in normal coordinate calculations on large molecules
Authors: Van Zandt L. L. , Lu K.‐C. , Prohofsky E. W.
Published: May 2005

We develop a force‐constant refinement procedure which we believe capable of being used in problems of large molecules and biopolymers. The procedure is based on a Green‐function expression which relates changes in frequency to changes in force constants. The method does not require that assignments be made before refinment (although they may be). An expansion of this expression gives rise to a set of linear algebraic equations for the force‐constant corrections, rather than an equation involving residuals to minimize. The resulting calculations are considerably simpler. This approximate is iterated to find the final refined force‐constants. We discuss several methods of improving the convergence of the procedure which take into account the experimental information which may be available. Of particular interest is a scheme to select the force constants to be refined by imposing a criterion for selecting those which will fit the experimental data with the smallest changes of the force constants from their expected values. We discuss some limitations which occur for all methods of refinement applied to large molecules.
Sequential polypeptides by matrix‐controlled thermal polymerization. Synthesis and racemization studies
Authors: Sakarellos‐Daitsiotis Maria , Gilon Chaim , Sakarellos Constantinos , Goodman Murray
Published: May 2005

A new method for the synthesis of sequential polypeptides is described. The approach consists of the thermal condensation in vacuo of the trifluoroacetate salts of tripeptide pentachlorophenyl esters deposited on a micron‐size celite matrix. The synthesis and polymerization of the trifluoroacetate salts of L‐valy‐L‐valyl‐L‐alanine pentachlorophenyl ester, glycyl‐L‐valyl‐L‐alanine pentachlorophenyl ester, and L‐valyl‐L‐alanylglycine pentachlorophenyl ester are described. High‐molecular‐weight polymers are obtained rapidly in high yield by this method. Comparison of the extents of racemization in the last two polymers constitutes a general approach for assessing racemization during the synthesis of sequential polypeptides since both yield the same polymer, but only the C‐terminal alanine may recemize in the former case.
n‐Mer binding on a one‐dimensional lattice of two‐state m‐site cells: Heavy meromyosin on regulated actin as an example
Authors: Tsuchiya Takashi , Hill Terrell L.
Published: May 2005

Heavy meromyosin binding to F‐actin saturated with tropomyosin is studied theoretically. The problem is formulated as a special case of n‐mer adsorption to a one‐dimensional Ising lattice which is divided into m‐site‐long blocks.
Vacuum‐ultraviolet circular dichroism of chondroitins and their complexes with poly(L‐arginine)
Authors: Stipanovic Arthur J. , Stevens E. S.
Published: May 2005

The vacuum‐ultraviolet circular dichroism (VUCD) of chondroitin and chontroitin‐6‐sulfate has been measured to 160 nm for films and to 170 nm for D2O solutions. The pD‐dependent dichroic behavior of these glycosaminoglycans in D2O is similar above 200 nm and is in agreement with previous studies. Near 190 nm, the CD band sign is also dependent on pD. VUCD spectra were recorded for films and solutions of poly(L‐arginine). In trifluoroethanol the polypeptide is α‐helical, while in D2O it exists as a random coil. The well‐characterized coil–helix transition of poly(L‐arginine) during complexation with chondroitin‐6‐sulfate was observed by VUCD, including the previously inaccessible entire π → π* band. By construction of difference spectra it was also possible to monitor the VUCD of the polysaccharide component during complexation.
Nmr study of poly(aspartic acid). I. α‐ and β‐Peptide bonds in poly(aspartic acid) prepared by thermal polycondensation
Authors: Pivcová H. , Saudek V. , Drobník J. , Vlasák J.
Published: May 2005

The structure of poly(aspartic acid) prepared by thermal polycondensation has been studied by means of nmr spectroscopy. The analysis of the 13C‐nmr spectra of the polymer at various pH values and comparison with the spectrum of poly(α‐L‐aspartic acid) revealed that the polymer contained aspartic acid linked in α‐ and β‐peptide bonds. The mole fraction of the β‐peptide bonds has been found to be 0.8 ± 0.1. The significance of the results for the evolutionary theory of S. W. Fox is mentioned.
Nmr study of poly(aspartic acid). II. α‐ and β‐Peptide bonds in poly(aspartic acid) prepared by common methods
Authors: Saudek V. , Pivcová H. , Drobník J.
Published: May 2005

The nature of peptide bonds in poly(aspartic acid) prepared by debenzylation of poly(β‐benzyl‐L‐aspartate) under various conditions has been studied by means of nmr spectroscopy. It was established that the majority of the polymers prepared, as well as the commercially obtained polymer, contained aspartic acid linked in both α‐ and β‐peptide bonds. The purest polymer, having practically undetectable amounts of β‐bond, was prepared by debenzylation by HBr in trifluoroacetic acid. It was established that the β‐bonds are formed via succinimides.
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

The 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

Approximate 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

Proton 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

Conformational 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

A 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

1. 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

A 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

Methods 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

The 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

A 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.