bluuebunny/crossref_metadata_2025 huggingface dataset:
Intrachain hydrolysis in sarcosine–γ‐p‐nitrophenyl‐L‐glutamate copolymers
Authors: Sisido Masahiko , Imanishi Yukio , Higashimura Toshinobu
Published: May 2005

Random copolymers of sarcosine and small amounts of γ‐p‐nitrophenyl‐L‐glutamate (poly(Sar,pNPGlu)) were synthesized and their hydrolyses were investigated in buffer solutions. The reaction courses of their spontaneous hydrolyses consisted of two parts; the initial fast reaction and the subsequent slow reaction. Since the former became shorter as the chain length of copolymer increased, it was attributed to a faster hydrolysis of ester groups near the chain ends.

The hydrolysis was considerably accelerated by the introduction of a pyridyl group to a chain end of the copolymer. This was explained by the intrachain catalysis, since the contribution of interchain catalysis was found to be very small. The extent of acceleration was much smaller than in the reaction along the polyacrylamide chain reported by Morawetz et al. The lesser flexibility of polysarcosine chain may account for the difference. Also in the intrachain hydrolysis a large deviation from the first‐order kinetics was observed, which indicated the different reactivities of each ester group positioned at the different separation along the chain from the terminal pyridyl group. Kinetic calculations were carried out using rate constant ki, for the hydrolysis of an ester group attached to the ith residue by the terminal puridyl group. It was found that the dependence of ki on i, Which is the distance between an ester group and the terminal pyridyl group, was more specific than that of intrachain rate constants for the chain effect polymerization of DL‐phenylalanine NCA previously investigated.
Electrical conduction in hydrated collagen. I. Conductivity mechanisms
Authors: Bardelmeyer G. H.
Published: May 2005

The electrical conductivity of bovine Achilles tendon with various amounts of adsorbed water was measuredas a function of temperature. The conduction appeared to be fully determined by the water of hydration. The current is probably primarily carried by protons at water contents up to 45% and by small ions at water contents beyond 65%. In both ranges of water content, a linear relation between activation energy and water and content was found. As to the lower range, this is explained by the action of Coulombic forces during the separation of proton–hydroxyl ion pairs. In two regions of water content a linear relation between the logarithm of the pre‐exponential factor and the activation energy was found. There are, however, indications that at certain water contents the dissociation constant of the adsorbed water is several orders of magnitude higher than in liquid water.
Electrical conduction in collagen. II. Some aspects of hydration
Authors: Bardelmeyer G. H.
Published: May 2005

Determinations of the amount of bound water in hydrated proteins yield strongly diverging values. The cause of this is the continuity of the transition from bound to free water, and the diffeernt sensitivities to water structure of the measuring techniques. Only the methods that aim at the determination of the amount of water, whose phase remians unchanged duing freezing, yield similar values. The value for collagen as deduced from conductivity data is about 50% water of the dry weight. It is believed that this water interacts with adsorptive groups on the macromolecules, whereas the freezable water occurs in capillaries.
The effects of salts on the nmr spectra of D2O in collagen fibers
Authors: Dehl R. E.
Published: May 2005

The effects of two salts, MgCl2 and MgSO4 on the wide‐line nmr spectrum of D2O in oriented, undernatured collagen fibers have been examined at four different D2O contents. MgCl2 was found to decrease the nmr doublet splitting, as compared with equal quantities of pure D2O while the major effect of MgSO4 was to inhibit the adsorption of D2O without significantly affecting its nmr spectrum. The results, together with a few observations of KCl and LiCl solutions, indicate that even fairly high concentrations of salt have only small effects on the nmr spectrum of D2O in fibrous collagen. It is considered unlikely that either “two‐state” or “structured‐water” models can satisfactorily account for the D2O‐nmr doublet spectrum or the effects of salts on it, over the entire range of observed D2O content.
Temperature dependence of partial volumes of proteins
Authors: Bull Henry B. , Breese Keith
Published: May 2005

The change of the apparent partial specific volumes of egg albumin, bovine serum albumin, bovine methemoglobin, β‐lactoglobulin, and lysozyme with temperature through the thermal transitions of the proteins have been measured with dilatometers. Four regions in the plot of the apparent partial specific volumes against temperature can be recognized: (1) linear sections extending from 25°C up to 45–50°C: (2) a decrease in slope between 50°C and 60°C; (3) a sharp increase in slope with increasing temperature coinciding with the appearance of heat coagulation of the protein and followed by (4) a decrease in the slope. The return of the protein samples to 25°C yields linear relations between the apparent partial specific volumes of the heat‐denatured proteins and the decreasing temperature.
Determination of the molecular conformation of β‐D‐O2,2′‐cyclouridine in aqueous solution by proton magnetic resonance spectroscopy
Authors: Cross Bradford P. , Schleich Thomas
Published: May 2005

The solution conformation of β‐D‐O2,2′‐cyclouridine has been determined at 27 and 88°C in D2O by proton magnetic resonance spectroscopy. The conformation is described in terms of a fixed syn‐like sugar‐base torsional angle, a type S furanose ring conformation (similar to 2′‐endo), and a temperature‐dependent exocyclic C(4)′–C(5′) rotamer population containing approximately 50% of the gauche‐gauche form at 27°C. β‐D‐O2,2′‐Cyclouridine 5′‐phosphate likewise possesses a type S furanose ring conformation.
Intramolecular distances determined by energy transfer. Dependence on orientational freedom of donor and acceptor
Authors: Dale Robert E. , Eisinger Josef
Published: May 2005

The dependence of Förster long‐range resonance energy transfer efficiency on the orientational freedom of donor D and acceptor A molecules attached to a macromolecular substrate is examined. The usefulness of polarized emission measurements in determining the mutual orientation as well as the degree of orientational freedom of D and A and thereby deriving maximum and minimum values for the D–A separation from the transfer efficieny is demonstrated.
The calculated circular dichroism of polyproline ii in the polarizability approximation
Authors: Ronish E. W. , Krimm S.
Published: May 2005

The circular dichroism (CD) spectrum of polyproline II (PPII) has heretofore been moderately well calculated from exciton theory only at the expense of assuming unreasonable chain conformations and accepting a conservative spectrum in the 180–250‐nm region (which is not observed). We have incorporated far uv transitions in the polarizability approximation and, together with the π2π* transition, have calculated the resulting correction to the exciton model. This has been accompanied by a modified assignment of the ππ* transition in PPII, and a simultaneous calculation of the absorption and CD spectra of the α‐helix, β structure, PPI, and PPII. We obtain good agreement with the observed CD spectrum of PPII in the 180–250‐nm region for acceptable chain conformations. In addition, we predict a negative CD into the far uv, in agreement with recent experimental observations. Our calculations also reproduce features of the far uv CD spectrum of the α‐helix, and are in agreement with the CD spectra of the β chain and PPI. The calculated CD of the unordered polypeptide chain is not significantly influenced by far uv contributions, indicating that our previous calculation is valid for such a system. These results demonstrate the importance of incorporating far uv transitions in order to achieve an adequate theoretical explanation of the CD spectra of polypeptides.
Helix–coil transition in nucleoprotein. Effect of ionic strength on thermal denaturation of polylysine–DNA complexes
Authors: Li Hsueh Jei , Brand Benjamin , Rotter Arnold , Chang Catherine , Weiskope Manuel
Published: May 2005

Thermal denaturation of direct‐mixed and reconstituted polylysine–DNA complexes in 2.5 × 10−4 M EDTA, pH 8.0 and various concentrations of NaCl has been studied. For both complexes, increasing ionic strength of the solution raises Tm, the melting temperature of free base pairs. The linear dependence of Tm on log Na+ indicates that the concept of electrostatic shielding on phosphate lattice of an infinitely long pure DNA by Na+ can be applied to short free DNA segments in a nucleoprotein. For a direct‐mixed polylysine–DNA complex, the melting temperature of bound base pairs Tm′ remains constant at various ionic strengths. On the other hand, the Tm′ in a reconstituted polylysine–DNA complex is shifted to lower temperature at higher ionic strength. This phenomenon occurs for reconstituted complex with long polylysine of one thousand residues or short polylysine of one hundred residues. It is shown that such a decrease of Tm′ is not due to a reduction of coupling melting between free and bound regions in a complex when the ionic strength is raised. It is also not due to intermolecular or intramolecular change from a reconstituted to a direct‐mixed complex. It is suggested that this phenomenon is due to structural change on polylysine‐bound regions by ionic strength. It is suggested further that Na+ may replace water molecules and bind polylysine‐bound regions in a reconstituted complex. Such a dehydration effect destabilizes these regions and lowers Tm′. This explanation is supported by circular dichroism (CD) results.
Theoretical investigation of semiconductive properties in proteins. I. Electrical conductivity, charge carrier mobilities, and free paths in β‐polyglycine
Authors: Suhai Sándor
Published: May 2005

Theoretical values are reported for the specific conductivity, charge carrier mobilities, and delocalized free paths in β‐polyglycine using the parallel‐chain pleated sheet conformation and the all‐valence electron energy band structure obtained previously. The mobilities are found to be much larger along the polypeptide backbones than in the direction of the hydrogen bonds. This indicates a mechanism of conduction in which the former path is favored for electronic delocalization. The preexponential factor of the specific conductivity obtained theoretically agrees well with experimental results.
Circular dichroism studies of complexes of the antibiotics daunomycin, nogalamycin, chromomycin, and mithramycin with DNA
Authors: Dalgleish D. G. , Fey G. , Kersten W.
Published: May 2005

The circular dichroism spectra of complexes of the antibiotics daunomycin, nogalamycin, chromomycin, and mithramycin with calf thymus DNA have been measured over a range of drug/DNA ratios. The similarity of the CD spectra of bound chromomycin and mithramycin suggests that they have very similar binding sites, which produce strong effects on the CD spectra of the bound drugs, and remove the differences arising from local stereochemistry in the free drugs. It was found that it was not possible to predict whether the antibiotics intercalated, from studies of the CD spectra alone, even when comparisons were made with the CD spectra of aminoacridine–DNA complexes with intercalating or nonintercalating ligands.
Theory of dipolar relaxation in aqueous macromolecular solutions
Authors: South G. P. , Grant E. H.
Published: May 2005

Recent advances in dielectric theory are applied to two models representing an aqueous solution of dipolar macromolecules. In one model the water is treated as a dielectric continuum and the macromolecule as a finite‐sized sphere; in the other both components are represented as point dipoles suspended in a background dielectric. The predicted frequency dependences of the complex permittivity in these two cases agree and the validity of the dielectric technique for estimating macromolecular size and shape is established. The model in which water is treated as a dielectric continuum predicts a larger dielectric dispersion in the radio frequency region, which is consistent with the experimental data available for myoglobin. The validity of the Debye formula for relaxation time and the effect of “dielectric friction” in macromolecular solutions are also discussed.
Molecular visualization of pectin and DNA by ruthenium red
Authors: Hanke D. E. , Northcote D. H.
Published: May 2005

Apple fruit pectin was visualized in the electron microscope by the Kleinschmidt technique with Pt/Pd rotary shadowing, and also on benzalkonium‐treated, especially thin carbon films using ruthenium red stain. Apple pectin molecules formed reticulate associations, which were partly dispersed after increasing the charge density of the molecules by enzymatic demethylation. Sycamore callus pectin molecules were visualized by the benzalkonium‐ruthenium red technique as short rows of intensely electrondense dots, 3 nm across. Using the same technique, short sections of the ϕX174 RF DNA double helix were visualized and the existence of the B conformation in solution directly confirmed. These observations confirm the nature of chromotropism as indicated by physical studies and provide new evidence on the staining reactions of ruthenium red.
Self‐association of β‐lactoglobulin A in acid solution. I. Translational diffusion coefficients
Authors: Chu B. , Yeh A. , Chen F. C. , Weiner B.
Published: May 2005

We report measurements of the diffusion coefficient of β‐lactoglobulin A (βLG‐A) at pH = 5.60 and 4.58 in 0.10 ionic strength acetate buffer by the techniques of analog photocurrent signal correlation and digital single‐clipped photon correlation. At a concentration of 21 mg/ml and a pH of 4.58, the self‐association of β‐lactoglobulin can be represented by a simple dimer–octamer equilibrium model. We determined the translational diffusion coefficient of the dimer and that of the octamer using the scattering results of Kumosinski and Timasheff in a dimer–octamer mixture. Our analysis shows that the dimer βLG‐A does not change its size if the pH is varied from 5.60 to 4.58 and both species remain constant in size for temperature changes from 3.5° to 25°C Hydrodynamically, the octamers behave like closed‐packed spheres with an effective radius of about 45 Å according to the Stokes‐Einstein relation.
Transient electric birefringence of T‐even bacteriophages. II. T4B in the Presence of tryptophan and T4D
Authors: Greve J. , Blok Joh.
Published: May 2005

Measurements of electric birefringence, sedimentation velocity, and biological adsorption rate are used to study the properties of bacteriophage T4B in the presence of excess tryptophan. The adsorption rate determined in borate buffer pH 9 (at 25°C) increases from 0.003 × 10−8 ml min−1 (0.025 M) to 0.130 × 10−8 ml min−1 (0.150 M). The Kerr coefficient, rotational diffusion coefficient, and the sedimentation coefficient of the phage are also dependent on buffer concentration and reach plateau values above 0.12 M given by Ksp = −(275 ± 18) × 10−9 OD−1 cm2 statvolt−2, D25,w = 133 ± 4 sec−1, and s20,w = 818 ± 11 S. From a comparison of electric birefringence measurements of T4B and T4D it is concluded that T4D and T4B (in the presence of excess tryptophan) exhibit a similar hydrodynamic behavior. The change in physical parameters is solely due to a shift in fiber configuration. At high buffer concentrations the fibers make an angle of approximately 3π/4 with the sheath and the permanent dipole moment is about 200,000 D. This dipole moment is roughly ten times as large as that of a phage particle with nonextended fibers. This difference may be due to a change in hydrodynamic center upon fiber extension or to the presence of positive charges on the fiber tips, or both. At intermediate buffer concentrations the phage population behaves as if it were monodisperse. Probably not all six fibers are extended under such conditions.
Optical activity of polypeptides in the infrared. Predicted CD of the amide I and amide II bands
Authors: Snir Joseph , Frankel Richard A. , Schellman John A.
Published: May 2005

The Miyazawa‐Blout‐Krimm (M‐B‐K) treatment of polypeptide absorption in the infrared is extended to the calculation of circular dichroism (CD), linear dichroism, and oriented CD for the amide I and amide II transitions. Matrix methods are applied to the α helix and β structures using measured values for the strengths and directions of the transition dipole moments and empirical values from M‐B‐K for the coupling constants.

Relatively small aggregates, a 36‐residue helix, and 8‐chain × 4‐residue β sheets, are large enough to show calculated absorption agreeing with M‐B‐K results, which are based on infinite lattices.

In all cases the predicted CD is an approximately conservative couple. The strongest CD should appear in the α helix, Δε/ε ≃± 10−3 for both transitions. The amide II transition should show moderate CD couples in both β structures, Δε/ε ≃ (+2 to −1) × 10−4. The amide I transitions in β structures should show weak CD couples, Δε/ε = (+3 to −2) × 10−5, except that the negative branch in the antiparallel structure may be detectable (Δε/ε ≃ −2 × 10−4) because absorption is very low at its wavelength peak.

CD on oriented samples should be enhanced over the unoriented cases, giving values as large as Δε/ε = 3 × 10−3 because particular directions of observation allow the light to avoid much of the absorption in the sample.

If all three structures are considered as helices, then the larger distance of the transition dipoles from the axis in the α helix, and the orientations of the transitions in the different structures, are the factors that, in terms of our previous theoretical work [Snir and Schellman (1973) J. Phys. Chem. 77, 1653] satisfactorily explain the calculated results. Simple dipole–dipole interaction is calculated to make a substantial contribution to the coupling between groups.
Ethidium bromide–dinucleotide complexes. Evidence for intercalation and sequence preferences in binding to double‐stranded nucleic acids
Authors: Krugh Thomas R. , Wittlin Frederick N. , Cramer Stephen P.
Published: May 2005

The solution complexes of ethidium bromide with nine different deoxydinucleotides and the four self‐complementary ribodinucleoside monophosphates as well as mixtures of complementary and noncomplementary deoxydinucleotides were studied as models for the binding of the drug to DNA and RNA. Ethidium bromide forms the strongest complexes with pdC‐dG and CpG and shows a definite preference for interaction with pyrimidine–purine sequence isomers. Cooperativity is observed in the binding curves of the self‐complementary deoxydinucleotides pdC‐dG and pdG‐dC as well as the ribodinucleoside monophosphates CpG and GpC, indicating the formation of a minihelix around ethidium bromide. The role of complementarity of the nucleotide bases was evident in the visible and circular dichroism spectra of mixtures of complementary and noncomplementary dinucleotides. Nuclear magnetic resonance measurements on an ethidium bromide complex with CpG provided evidence for the intercalation model for the binding of ethidium bromide to double‐stranded nucleic acids. The results also suggest that ethidium bromide may bind to various sequences on DNA and RNA with significantly different binding constants.
Circular dichroism of histone‐bound regions in chromatin
Authors: Li Hsueh Jei , Chang Catherine , Evagelinou Zoi , Weiskopf Manuel
Published: May 2005

Native, NaCl‐treated, trypsin‐treated, and polylysine‐bound nucleohistones were studied in 2.5 × 10−4 M EDTA, pH 8.0, using circular dichroism (CD) and thermal denaturation. Removal of histone I by 0.6 M NaCl has a much smaller effect on both Δε220 and Δε278 than the removal of other histones. This indicates that histone I has less helical content and less conformational effect on the DNA in nucleohistone. By extrapolating to 100% binding by histones other than I, the positive CD band near 275 nm is close to zero. Comparison is also made between the effects of binding by the more basic and the less basic halves of histones by trypsin‐digestion and polylysine‐binding experiments. Trypsin digestion of nucleohistone reduces melting band IV at 82°C much more than melting band III at 72°C. However, the CD changes of Δε278 and Δε220 induced by trypsin digestion are small, unless melting band III is also reduced by the use of a higher trypsin level. This implies that the less basic halves of histones, which stabilize DNA to 72°C (melting band III), have more helical structure and are more responsible for conformational change in DNA than are the more basic halves, which stabilize DNA to 82°C (melting band IV). Polylysine binding to nucleohistone diminishes melting band III but has no effect on melting band IV. This binding affects only slightly the Δε220 of nucleohistone, indicating that polylysine interferes very little with the structure of the less basic halves of bound histones. The implications of these studies with respect to chromatin structure are discussed.
The low‐temperature mechanical relaxation of elastin. I. The dry protein
Authors: Pezzin G. , Scandola M. , Gotte L.
Published: May 2005

The low‐temperature relaxation of native ox Ligamentum nuchae elastin and of two purified elastin samples has been investigated in the dry state by means of the Rheovibron DDV II viscoelastometer, at the fixed frequencies of 3.5, 11, 35, and 110 Hz. Besides the glass transition at about 200°C, a relatively strong secondary loss‐tangent peak, whose activation energy is about 13 kcal/mol, is found for all samples below room temperature. The peak maximum is at −71°C for the 3.5‐Hz frequency. On the basis of its location, intensity, and width, it is attributed to a main‐chain relaxation of the pure protein. When suitable reduced variables are used, the loss‐tangent‐temperature curves obtained at different frequencies can be satisfactorily superimposed to give a master curve. Comparison of the data with the prediction of a semiempirical viscoelastic model can also be considered satisfactory.
Preferential solvent binding and change in conformation of bovine serum albumin in 2‐chloroethanol–water mixed solvents
Authors: Maes Eddie
Published: May 2005

Solvent binding to bovine serum albumin in 2‐chloroethanol‐water mixed solvents of different composition, measured previously by Inoue and Timasheff (Biopolymers (1972) 11, 737–43) is applied to a hydrodynamic study of the solvated protein.

From sedimentation and diffusion data, the apparent molecular weight of the solvated protein particle can be calculated, provided an average partial specific volume, computed from the composition of the particle, is introduced in Svedberg's equation. The unsolvated molecular weight of the protein can than be calculated by subtraction of the bound solvent. Further data on the hydrodynamic particle (f/fmin and axial ratio of the equivalent ellipsoid) are readily calculated from these experiments, and reinforce the supposition that 2‐chloroethanol is a strong helix‐inducing solvent.
High‐resolution nmr study of yeast tRNA and the native and denatured conformers of yeast tRNA
Authors: Rordorf B. F. , Kearns D. R. , Hawkins Erin , Chang S. H.
Published: May 2005

The high‐resolution nmr spectrum of baker's yeast tRNA, a recently sequenced non‐denaturable tRNA, has been compared with the spectra of the native and denatured conformers of the closely related species tRNA. Because of the presence of many common base pairs in the different tRNA's, it is possible to assign most of the low‐field resonances to specific secondary‐structure base pairs. A comparison of the observed positions of the various resonances with those predicted by a semiempirical ring‐current shift theory shows a root‐mean‐square deviation of 0.14, 0.11, and 0.12 ppm for tRNA (native), and tRNA (denatured), respectively. These results support the ring‐current shift theory currently used to interpret the low‐field nmr spectra of the tRNA molecules. Differences between the predicted and observed positions of some resonances provide new evidence for higher order effects such as shifts from second nearest neighbors, anomalous shifts exerted by G·U base pairs, and tertiary‐structure effects. A model that was previously proposed for the denatured conformer of tRNA is also supported.
Circular dichroism studies of an elastin crosslinked peptide
Authors: Foster J. A. , Bruenger E. , Rubin L. , Imberman M. , Kagan H. , Mecham R. , Franzblau C.
Published: May 2005

Circular dichroic studies of a desmosine crosslinked peptide reveal a hitherto undescribed elastin spectrum possessing a weak negative band at 230–235 nm, a weak positive band at 215 nm, and a maximum negative band at 190 nm. The spectrum is sensitive to both pH and temperature displaying increased ellipticity of the 215‐nm band at acidic pH and low temperature. The general shape of the spectrum and its behaviour toward temperature changes suggest the presence of an extended helical conformation. Susceptibility of insoluble elastin to digestion with chymotrypsin is increased tenfold at low temperature (4°C), supporting the contention that the conformational change of the type described above occurs in insoluble elastin. Such changes in conformation would result in increased availability of aromatic amino‐acid resiudues to peptide bond cleavage.
Sedimentation of generalized systems of interacting particles. III. Concentration‐dependent sedimentation and extension to other transport methods
Authors: Claverie Jean‐Michel
Published: May 2005

The simulation method presented in the previous papers is related to the concentration‐dependent sedimentation–diffusion. It can be shown that the efficiency of the program described previously is maintained. A simulation of a system exhibiting the Johnston–Ogston effect is presented.

Through the similarity of their continuity equations with the Lamm equation, electrophoresis, molecular sieve, and chromatography are treated. A general simulation of transport for systems of many interacting components is thus presented, which is able to take into account kinetically controlled chemical reactions and nonideal phenomena.
Infinite dilution viscoelastic properties of poly(γ‐benzyl‐L‐glutamate) in m‐cresol
Authors: Ookubo Norio , Komatsubara Michiro , Nakajima Haruhiko , Wada Yasaku
Published: May 2005

The real and imaginary parts of complex viscosity, η′ and η″, are measured for dilute solutions of poly(γ‐benzyl‐L‐glutamate) in m‐cresol, a helicogenic solvent. The frequency range is 2.2–525 kHz; the concentration range 0.2–5 g/dl; the temperature 30°C, and the molecular weights Mr are 6.4 × 104–17 × 104. The dispersion curve of extrapolated intrinsic dynamic viscosity [η′] of samples with Mr > 105 is interpreted in terms of three mechanisms appearing from low to high frequencies: end‐over‐end rotation, flexural deformation, and side‐chain motion. For a sample with Mr < 105, the flexural relaxation disappears and a plateau of [η′] is distinctly observed between rotational and side‐chain relaxations. Rotational relaxation times of all the samples obey the Kirkwood–Auer theory. The strong concentration dependence of rotational relaxation time is explained by collisions of molecules rather than association. Flexural relaxation times calculated from a theory by assuming the persistence length as 1200 Å are consistent with observed dispersion curves of [η′].
Conformational energy calculations for dinucleotide molecules. A systematic study of dinucleotide conformation, with application to diadenosine pyrophosphate
Authors: Thornton Janet M. , Bayley Peter M.
Published: May 2005

A systematic study of the conformational states of the dinucleotide diadenosine 5′,5′‐pyrophosphate (AppA), an analog of the coenzyme NAD+, has been made using semi‐empirical energy calculations. Taking low‐energy mononucleotide structures as starting conformations, energy minimizations have been performed. The most stable structures exhibit stacking interactions between the adenine bases; there are many different stacked states of similar energy; their stability is derived from nonbonded interactions primarily between the bases but also from base–sugar interactions. The most common form of stacking in the most stable structures was found to be antiparallel A‐A helix. These findings are consistent with the experimental data, which suggest that AppA adopts predominantly a stacked state in solution, and this state incorporates a variety of stacked conformations.
Contribution of side‐chain chromophores to the optical activity of proteins: Model compound studies. IV. The indole chromophore of yohimbinic acid
Authors: Goux Warren J. , Kadesch Thomas R. , Hooker Thomas M
Published: May 2005

The optical properties of the indole chromophore of the indole alkaloid yohimbinic acid have been investigated as a function of molecular conformation. Theoretical rotatory strengths have been calculated and compared with experimental circular dichroism spectra. Optical data that may be suitable for calculating the chiroptical properties of the near ultraviolet electronic transitions of the indole chromophores, which occur in tryptophan residues of proteins, have been developed. The far ultraviolet transitions of yohimbinic acid have also been investigated.
N‐acetylchitosan gel: A polyhydrate of chitin
Authors: Hirano Shigehiro , Yamaguchi Ryuji
Published: May 2005

N‐Acetylchitosan gel, a polyhydrate of chitin, and partially O‐acetylated N‐acetylchitosan gel were produced by a facile acetylation of chitosan with acetic anhydride in 10% acetic acid and in aqueous acetic acid/methanol at room temperature. Under the same conditions, a series of N‐acylchitosan gels was produced in reaction with the other carboxylic anhydrides. The gels thus produced were colorless, transparent and rigid, and stable on heating. The gels were insoluble in cold and boiling water, formic acid, aqueous acids, and the other solvents examined. Significant changes in specific rotation occurred in the acylation of chitosan and its aggregation.
Studies of peptide conformation: Backbone folding of tetrapeptide derivatives in methanol and water
Authors: Kopple Kenneth D. , Go Anita
Published: May 2005

Derivatives of tetrapeptide sequences considered likely to form β‐turns were investigated by the study of their proton magnetic resonances in methanol and in water. Differential broadening of N—H resonances by an added nitroxyl was used to indicate the presence of the sequestered N—H proton expected in β‐turn conformations. Transfer of magnetic saturation from solvent water protons to N—H protons was also examined. The evidence is consistent with significant contributions by β‐turn‐like backbones to the conformational averages in methanol of the sequences Gly‐L‐Pro‐D‐Val‐Gly, D(or L)‐Val‐L‐Pro‐Gly‐Gly, and Gly‐L‐Pro‐L‐Asn‐Gly, but not the sequence Gly‐D‐Ala‐L‐Val‐Gly. It is suggested that a Type I turn, Likely in Gly‐L‐Pro‐L‐Asn‐Gly derivatives, is characterized by sequestered N—H protons of both the third and fourth residues. For all of the peptide derivatives, save possibly Ac‐L‐Val‐L‐Pro‐Gly‐Gly‐NHNH2, contributions from folded structures in water are not detectable by line‐broadening experiments. However, the transfer of saturation experiments may be interpreted as indicating some degree of chain folding in water.
Synthesis of a cross‐linked polypentapeptide of tropoelastin
Authors: Okamoto K. , Urry D. W.
Published: May 2005

The synthesis of a cross‐linked polypentapeptide (an insoluble product) by means of a cross‐linking reaction between a lysine‐containing (1%) polypentapeptide and a glutamic acid‐containing (2%) polypentapeptide is described, following description of the synthesis and polymerization of the corresponding pentapeptide p‐nitrophenyl esters. The pentapeptide p‐nitrophenylesters—H‐Val1‐Pro2‐Gly3‐Val4‐Gly5‐ONp, H‐Val1‐Pro2‐Gly3‐Lys4(ε‐Z)‐Gly5‐ONp, and H‐Val1‐Pro2‐Gly3‐Glu4‐Gly5‐ONp—prior to polymerizing and the polypentapeptides prior to cross‐linking were analyzed by proton and carbon‐13 magnetic resonance. The cross‐linking reaction was achieved in the coacervate state by intermolecular primary amide bond formation. The coupling reagent was a water‐soluble carbodiimide (1‐cyclohexyl‐3‐(2‐N‐methylmorpholinoethyl)‐carbodiimide‐p‐toluenesulfonate).
Transition temperature and enthalpy change dependence on stabilizing and destabilizing ions in the helix–coil transition in native tendon collagen
Authors: Lim Jong Jin
Published: May 2005

The transition temperatures tt and enthalpy changes ΔH in the helix–coil transition of solid tendon collagen soaked in a solution containing one of the following stabilizing or destabilizing agents, HCHO, NaF, NaCl, NaI, NaBr, NaOH, NH2CONH2, CaCl2, MgCl2, were measured as a function of molar concentration by a calorimetric method. The temperature and the enthalpy changes accompanying the transition behaved in a similar manner: when the tt was depressed by the presence of ions, similar behaviour was observed in ΔH. Both parameters (tt and ΔH) increased for HCHO, and decreased for NaF and NaCl at concentrations lower than 0.2 M. Above 0.2 M they increased for NaF and NaCl, and decreased in the presence of the other reagents listed above. The average tt and the ΔH observed in collagen soaked in water were 63.5°C and 12.3 cal/g, respectively. In addition to the parameters mentioned above, the molar effectiveness of the various reagents was obtained for the cases where there was a linear relationship between the tt and molar concentration of the reagent in the solution.

Since both the tt and the ΔH were observed to vary, the entropy change (ΔS) accompanying the transition was calculated using thermodynamic relations. In order to explain the ΔS observed as a function of ionic concentration, the thermodynamic relationships have been obtained from a partition function under suitable assumptions. Since the partition function is dependent on the number of hydrogen bonds responsible for collagen stability, the result obtained has been compared with the values predicted by the two most quoted models for collagen. The present study is in accordance with the Ramachandran model for collagen structure, which predicts more than one hydrogen bond per three residues.
A configurational interpretation of the axial phosphate spacing in polynucleotide helices and random coils
Authors: Olson Wilma K. , Manning Gerald S.
Published: May 2005

The structural implications arising from the observation (set forth in the preceding paper) that the charge density of a single‐stranded randomly coiling polynucleotide chain is approximately equal to that of one strand of the familiar double helix are here examined. A computational scheme is described to obtain (using bond lengths, valence bond angles, and internal rotation angles) the mean phosphate–phosphate spacing parameter b along the chain axes of any single‐stranded polynucleotide molecule. Attention is then focused upon the computed interphosphate spacing associated with both the theoretical randomly coiling polynucleotide that reproduces the observed experimental unperturbed dimensions and the familiar single‐stranded helix. The calculations clearly demonstrate that the parameter b only weakly reflects the spatial configuration of the chain. The approximate equivalence of the b values associated with the single‐stranded helix and the unperturbed randomly coiling polynucleotide is not indicative of strong configurational similarities between the two forms. The familiar helix is composed of a sequence of identically conformed compact structural residues while the random coil is characterized by a variety of chain‐repeating residues of which a large proportion are extended units.
Study of thermal denaturation of lysozyme and other globular proteins by light‐scattering spectroscopy
Authors: Nicoli D. F. , Benedek G. B.
Published: May 2005

The technique of intensity correlation light‐scattering spectroscopy has been used to accurately determine the extent of physical swelling of lysozyme, ribonuclease, and chymotrypsinogen produced by thermal denaturation. The change in hydrodynamic radius is deduced from direct measurements of the diffusion coefficient, carried out in the temperature range 20° to 70°C at various values of pH in the range 1.0 to 3.0 at ionic strengths of from 0.01 M to 0.2 M. An average radius increase of 18% is observed for lysozyme and ribonuclease, with an estimate of 26% for chymotrypsinogen. Analysis of the pH dependence of the transition temperature leads to the conclusion that the lysozyme charge increases by approximately +2e during unfolding. We have applied this value of the charge increase along with the 18% average radius increase to estimate the electrostatic contribution to the free‐energy change for denaturation of lysozyme. The results are consistent with the experimental observation that the transition temperature is nearly independent of ionic strength.
Vibrational analysis of peptides, polypeptides, and proteins. II. β‐Poly(L‐alanine) and β‐poly(L‐alanylglycine)
Authors: Moore W. H. , Krimm S.
Published: May 2005

The normal vibration frequencies of poly(L‐alanine) and poly(L‐alanylglycine) in the antiparallel chain‐pleated sheet structure have been calculated, using the force field for polyglycine I from the previous paper (Biopolymers 15, 2439–2464) plus additional force constants for the methyl group. The agreement with observed ir and Raman bands is very good. This substantiates the excellent transferability of the force field, since polyglycine I was shown to have a rippled‐sheet structure. The amide I and amide II mode splittings are very well accounted for by transition dipole coupling, showing that subtle structural differences are sensitively manifested through this mechanism.
Conformational energy calculations of enzyme‐substrate complexes of lysozyme. I. Energy minimization of monosaccharide and oligosaccharide inhibitors and substrates of lysozyme
Authors: Pincus Matthew R. , Burgess Antony W. , Scheraga Harold A.
Published: May 2005

Conformational energy calculations were performed on monosaccharide and oligosaccharide inhibitors and substrates of lysozyme to examine the preferred conformations of these molecules. A grid‐search method was used to locate all of the low‐energy conformational regions for N‐acetyl‐β‐D‐glycosamine (NAG), and energy minimization was then carried out in each of these regions. Three stable positions for the N‐acetyl group have ben located, in two of which the plane of the amide unit is normal to the mean plane of the pyranosyl ring. Nine local energy minima were located for the —CH2OH group. The positions of the two vicinal cis —OH groups are determined predominantly by interactions with either the —CH2OH or the N‐acetyl group. The most stable conformations of β‐N‐acetylmuramic acid (NAM) were determined from the study of the low‐energy conformations of NAG. In the two stable orientations for the D‐lactic acid side chain, the O—C—C′ plane (C′ being the carbon atom of the terminal carboxyl group) was found to be normal to the mean plane of the pyranosyl ring. The low‐energy positions for the COOH group of NAM are determined mainly by interactions with neighboring groups.

The conformational preferences of the α‐anomers of NAG and NAM were also explored. The calculated conformation of the N‐acetyl group for α‐NAG was quite close to that determined by X‐ray analysis. Two of the three lowest energy conformations of α‐NAM are similar to the corresponding conformations of the β‐anomer. A third low‐energy structure, which has a hydrogen bond from the NH of the N‐acetyl group to the CO of the lactic acid group, corresponds very closely to the X‐ray structure of this molecule.

The preferred conformations of the disaccharides NAG–NAG, NAM–NAG and NAG–NAM were also investigated. Two preferred orientations of the reducing pyranosyl ring relative to the nonreducing ring were found for all of these disaccharides, both of which are close to the extended conformation. In one of these conformations, a hydrogen bond can form between the OH group attached to C3 of the reducing sugar and the ring oxygen of the preceding residue. Each conformation can be stabilized further by a hydrogen bond between the CH2OH (donor) of residue i + 1 and the CO of residue i (acceptor). The interactions that determine conformations for all oligosaccharides containing both NAG and NAM are shown to be exclusively intraresidue and nearest neighbor interactions, so that it is possible to predict all stable conformations of oligosaccharides containing NAG and NAM in any sequence.
The random coil → β transition of copolymers of L‐lysine and L‐isoleucine: Potentiometric titration and circular dichroism studies
Authors: Walter Bert , Fasman Gerald D.
Published: May 2005

Copolymers of L‐lysine and L‐isoleucine [poly(L‐Lysf,L‐Val1 − f)] containing 4–15% isoleucine were investigated using potentiometric titration and circular dichroism (CD) spectroscopy. With increasing isoleucine content, β‐sheet formation is favored over α‐helix formation at high pH and room temperature. The fraction of β‐sheet present, as a function of pH, calculated from titrations of poly(L‐Lys85.2,L‐Ile14.8), agreed well with data obtained from CD studies for the same copolymer. Thermodynamic parameters were determined from titrations using the method of Zimm and Rice; the partial free energy (ΔG°C → β) at 25° for the coil‐to‐β‐sheet transition for isoleucine was estimated to be −515 cal/mol; from the temperature dependence of free energy, the partial entropy (ΔS°cβ), and the partial free enthalpy (ΔH°c → β) of the coil → β transition for isoleucine is estimated to be 2.6 e.u. and 260 cal/mol, respectively. The partial thermodynamic parameters obtained for lysine are in good agreement with literature values. It is concluded from these studies that isoleucine has a very high potential for a β‐sheet formation.
Influence of fluctuations in electron density on the excess small‐angle X‐ray scattering from dilute solutions of macromolecules
Authors: Carpenter Dewey K. , Mattice Wayne L.
Published: May 2005

The influence on the excess scattering function P(μ) of flutuations in the electron density ρ within a macromolecule is treated, to the approximation that the solvent is a structureless medium of constant electron density ρ0. The results for P(μ) and the apparent value of the mean square radius Rapp2, can be expressed as functions of the excess electron density Δρ: P(μ) = X(μ) + (Δρ)−1Y(μ) + (Δρ)−2Z(μ) and Rapp2 = Rx2 + (Δρ)−1Ry2 + (Δρ)−2Rz2, where X(μ) and Rx2 depend only on the shape of the macromolecule, while Y(μ) and Ry2 as well as Z(μ) and Rz2 depend on the shape and the fluctuations in ρ. By varying the electron density of the solvent, the contributions of the shape and the internal structure of the macromolecule can be resolved. The quantities Rx2, Ry2, and Rz2 are evaluated for seven models to illustrate the relative importance of these contributions for representative structures.
A Study of stepwise conformational changes in poly(β‐benzyl‐L‐aspartate) with the helix–coil transition by means of proton and carbon‐13 NMR
Authors: Sase Shigeru , Suzuki Yasuyuki , Inoue Yoshio , Chûjô Riichirô
Published: May 2005

The helix–coil transition for poly(β‐benzyl‐L‐aspartate) [poly(Asp[OBzl])] in solvent mixtures of trifluoroacetic acid/deuterated chloroform (F3AcOH/CDCl3) was studied by means of proton and carbon‐13 nmr. Conformational fixation of the side chain occurs before the coil–helix transition of the backbone, when neighboring phenyl rings face each other. Another type of conformational fixation occurs in the side chain after the coil–helix transition of the backbone. These conformational changes of the side chain are due to the changes of the strength of the interaction between the side‐chain ester group and the F3AcOH molecule. In the absence of F3AcOH (coil‐forming solvent), the polymer has a rather rigid structure in which the side chain may wrap around the backbone. These conformational changes of the polymer are closely related to the changes of the interaction between the polymer and F3AcOH molecules.
Intermolecular indole–imidazolium complexes. II. Interaction of a block copolymer (L‐tryptophan)n–(γ‐ethyl‐DL‐glutamate)m with imidazolium hydrochloride and poly(L‐histidine hydrochloride)
Authors: Palumbo Manlio , Cosani Alessandro , Terbojevich Maria , Peggion Evaristo
Published: May 2005

The charge‐transfer complexes of a poly(L‐tryptophan) sequence with imidazolium hydrochloride and poly(L‐histidine hydrochloride) have been investigated in 2,2,2‐trifluoroethanol by ultraviolet (uv), circular dichroism (CD), and fluorescence techniques. Both complexes exhibit absorption maxima centered at around 275 nm, whereas hypochromism with respect to the combined spectra of the constituents can be observed below 250 nm. All complexes show optical activity in the near uv and in the peptide absorption region, which is discussed in terms of the conformational properties of the donor. A marked decrease of the fluorescence intensity of the L‐tryptophan sequence is observed upon addition of imidazolium hydrochloride and poly(L‐histidine hydrochloride). From the fluorescence data the formation constant of the charge‐transfer complex between the L‐tryptophan sequence and imidazolium ions is also evaluated.
Statistical theory of chain scission and concurrent damage not associated with chain scission in linear polymers
Authors: Hawkins Roland B.
Published: May 2005

A statistical theory of the parallel accumulation of randomly placed breaks and damage not associated with breaks in linear polymers is presented. Expressions for the weight fraction of polymer in the form of chains that bear n or more sites of nonbreak damage (markers) are developed, and results of numerical computations with them presented. The effects of polydispersity in the undamaged sample are discussed. The relation of the computed quantities to experimental methods used in the study of damage to nucleic acids due to radiation and chemical exposure is discussed.
On the B to A conformation change of the double helix
Authors: Eyster James M. , Prohofsky E. W.
Published: May 2005

We have investigated the B to A conformation change of DNA double helices by a new method “soft‐mode analysis.” We find theoretically that a mode does soften when the vibration normal modes are perturbed by increasing the electrostatic interaction between the unbalanced charges on atoms in the double helix. The same mode also softens for enhanced van der Waals interactions. The mode softening indicates the onset of conformation change. The enhancing of the electrostatic and van der Waals interaction mimic the effect of decreasing the polar nature of the solvent or water of hydration associated with the B conformation DNA. We discuss qualitatively the concept of soft modes and their relation to conformation change as well as their applicability to macromolecules. We discuss previous work in which the normal vibrational modes have been calculated. We also discuss the displacement which comes from the soft mode and show that it correlates very well with that expected for the B to A conformation charge.
Helix coil transitions of d (A)n·d(T)n, d(A‐T)n·d(A‐T)n, and d(A‐A‐T)n·d(A‐T‐T)n; evaluation of parameters governing DNA stability
Authors: Oliver Adrian L. , Wartell Roger M. , Ratliff Robert L.
Published: May 2005

The thermally induced helix‐coil transitions of three A‐T DNAs, d(A)n·d(T)n, d(A‐T)n·d(A‐T)n, and d(A‐A‐T)n·d(A‐T‐T)n, were studied. Experimental transition curves of the DNAs were analyzed using the loop entropy model of DNA melting. The calculation of the melting curve of d(A‐A‐T)n·d(A‐T‐T)n is presented using the integral equation formalism of Goel and Montroll. The aim of this work was to evaluate thermodynamic parameters which govern DNA stability and to test the theoretical model employed in the analysis. Our results show (1) an excellent over‐all agreement between theory and experiment, (2) a loop entropy exponent k = 1.55 ± 0.05 provided the best fit to all the polymer transition curves, (3) the evaluated stacking free energies reflect the relative stability of the DNAs, and (4) the stacking energies of the ApA·TpT dimer evaluated from d(A)n·d(T)n and d(A‐A‐T)n·d(A‐T‐T)n differ. The last result is consistent with different conformations for the dimer in these two polymers.