bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermodynamic interaction between urea and the peptide group in aqueous solutions at 25°C
Authors: Schönert Hansjürgen , Stroth Leo
Published: December 2004

Isopiestic vapor pressure measurements of the ternary systems water + triglycine + urea and water + glycine‐L‐alanine + urea were made and used to calculate the Gibbs free energy of these systems. Together with recently published analogous results on systems, in which the first solute was glycine or alanine or diglycine, and measurements of the excess enthalpy of all these solutions, it is possible to calculate the Gibbs free energy of transfer and the enthalpy of transfer of the peptide group from water to aqueous urea solutions. The transfer can be described as a binding of urea to the peptide group with ΔG = −1.85 kJ mol−1 and ΔH = −18.7 kJ mol−1 at 298.1 K.
Transient‐phase energetics of the oxidative deamination of L‐glutamate by L‐glutamate dehydrogenase and NADP: A reaction with a large negative heat capacity of activation
Authors: Colen Alan H. , Medary Richard T. , Fisher Harvey F.
Published: December 2004

A study of the temperature dependence of the initial transient velocities of the oxidative deamination of L‐glutamate by glutamate dehydrogenase and NADP has permitted the determination of the enthalpies, entropies, and heat capacities of the phenomenological parameters for mechanistic steps up to and including the catalytic hydrogen‐transfer step. The most striking feature observed is the extremely large negative heat capacity of activation (−590 ± 150 cal K−1 mol−1) for the catalytic step itself. Possible sources of such heat capacities are considered, with particular focus on the effects of hidden equilibria among multiple thermodynamic states. Heat‐capacity changes of the sort observed here can be produced by shifts of such dynamic equilibria between multiple forms of the free enzyme induced by the formation of the catalytic transition state.
A circular dichroism study of valinomycin barium ion complex
Authors: Devarajan S. , Easwaran K. R. K.
Published: December 2004

Complex formation of valinomycin with Ba2+ ions was investigated by circular dichroism spectroscopy. The results indicated that Ba2+ forms entirely different types of complexes when compared with K+. The data with perchlorate salt showed evidence for the formation of less stable V2C (peptide sandwich), VC (1:1), and VC2 (ion sandwich) complexes followed by a stable final complex upon gradual addition of salt (V stands for valinomycin and C for the cation). This final complex possibly has a flat structure with no internal hydrogen bonds, similar to that of valinomycin in highly polar solvents. The possible complexation mechanism and the role played by anions and isopropyl side chains are highlighted.
Hetero‐α‐helical, two‐chain coiled‐coils. Clam–worm hybrid paramyosins
Authors: Crimmins Daniel L. , Holtzer Alfred
Published: December 2004

The specificity of the interaction between the α‐helices in two‐chain coiled‐coils is investigated by studying the formation of hybrid molecules in which one α‐helix is a clam paramyosin chain and the other a worm paramyosin chain. Hybrids are formed by mixing, denaturation, and subsequent renaturation. Comparison is made with a blank solution in which renaturation precedes mixing, thus precluding hybridization. Hybrids are detected by a ruse based on the presence of free sulfhydryl functions on calm chains. This allows molecules comprising two clam chains to be covalently crosslinked by oxidation with 5,5′‐dithiobis(2‐nitrobenzoate). Worm paramyosin chains have no sulfhydryl, so molecules comprising two worm chains or hybrid molecules comprising one chain of each type cannot crosslink. When run on sodium dodecyl sulfate polyacrylamide gel electrophoresis, therefore, the protein separates into two well‐resolved regions, one containing one‐chain species and the other two‐chain species. When the gels are scanned and quantitated, the hybrids show up as an increase in the fraction of material in the one‐chain band compared with the fraction in the blank solution. When renaturation is direct, we find that the fraction of renaturated molecules that are hybrids varies from ∼10% at 5°C to ∼5% at 25°C. These are judged to be nonequilibrium (quenched) values. When renaturation is by slow annealing, the equilibrium fraction hybrids are ∼4% and show a modest, but measurable, increase with increasing temperature. These data allow calculation of the equilibrium constant Kh and standard free energy for the hybridization reaction: (1/2)CC + (½)WW = CW, in which C(W) stands for an α‐helical clam (worm) polypeptide chain. The temperature dependence gives the standard enthalpy and entropy of the reaction. We find ΔH ≃ 1800 cal mol−1 and ΔH ≃ 1.4 cal mol−1 K−1, using molarity concentration units and the infinitely dilute solution in NaCl/phosphate buffer as reference state. The possible molecular significance of these values is discussed, and it is concluded that the observed standard entropy arises essentially entirely from the rotational dissymmetry of the hybrids.
Cu(II)–Protamine interaction. I. The formation and structure of Cu(II)–clupeine Z complexes
Authors: Garnier Arlette , Tosi Lucia , Mosoni Lucienne , Toniolo Claudio , Bonora Gian Maria , Paniago Euclear B.
Published: December 2004

The formation and structure of four different Cu(II)–clupeine Z complexes have been studied using potentiometric and spectroscopic (ir and visible absorption, and CD) measurements. The results thus obtained indicate the presence of up to 8 binding sites in the pH range from 6.5 to 10.5. The spectroscopic evidence suggests that the strongest site available contains the α‐amino terminal and the adjacent peptide nitrogen, which bind to copper from pH 5 to 6.5 to form the first complex. The stability constant of this first complex has a value of (9.5 ± 0.9) × 103 mol−1 1. From pH 6.5 to 8.5, two intervening guanidinium nitrogens of arginine residues occupy the two other corners of the coordination square, giving rise to the second complex. The other sites potentially available from pH 6.5 to 10.5 are formed by two amino nitrogens of arginine residues and two contiguous peptide nitrogens. The first intervene up to pH 8.5, forming the third complex, and the latter from this pH to 10.5, forming the fourth complex. Although the ligands intervening at sites 2–8 appear to be the same, the sites are by no means equivalent. The spectroscopic data enable one to distinguish three different types of binding sites.
Conformational studies on polynucleotide chains. V. A comparison between the quantum‐mechanical and the consistent force field approach
Authors: Tosi Camillo , Rasmussen Kjeld
Published: December 2004

Consistent force field (CFF) calculations were performed for the sugar–phosphate–sugar fragment, taken as a model of the polynucleotide backbone. The potential‐energy‐function is the sum of four contributions, accounting for bond and angle deformation, torsional motions, and nonbonded interactions. Both deoxyribose and ribose systems, with either C(2′)‐endo or C(3′)‐endo puckering in the starting geometry of ribose rings, were considered. A fair number of minima of the conformational‐energy hypersurface were found. Although the numerical method employed in the CFF context cannot solve the problem of finding the global minimum in a definite way, one of the final conformations has a total energy much more attractive than the others, and may be regarded as the most stable conformation attainable with our potential‐energy function. The energy‐minimization affects the puckering of the first ribose ring differently from that of the second: in general, for the C(2′)‐endo system the second ring retains its starting conformation (Ψ′ = 152°), while in the first the Ψ′ is modified by up to 70°; the opposite occurs for the C(3′)‐endo system. This is explained by the different positions of the two rings relative to the phosphate group.
X‐Pro peptides: Synthesis and solution conformation of benzyloxycarbonyl‐(Aib‐Pro)4methyl ester. Evidence for a novel helical structure
Authors: Venkatachalapathi Y. V. , Balaram P.
Published: December 2004

The synthesis of the octapeptide, benzyloxycarbonyl‐(α‐aminoisobutyryl‐L‐prolyl)4‐methyl ester [Z‐(Aib‐Pro)4‐OMe] and an analysis of its solution conformation is reported. The octapeptide is shown to possess three strong intramolecular hydrogen bonds on the basis of studies of the solvent and temperature dependence of NH chemical shifts and rates of hydrogen–deuterium exchange. 13C studies are consistent with a structure involving only trans Aib‐Pro bonds, while ir experiments support a hydrogen‐bonded conformation. The Aib 3, 5, and 7 NH groups are shown to participate in hydrogen bonding. A 310 helical conformation compatible with the spectroscopic data is suggested. The proposed conformation consists of three type III β‐turns with Aib and Pro at the corners and stabilized by 4 → 1 intramolecular hydrogen bonds.
Analysis of high‐resolution thermal dispersion profiles of DNA: Treatment as a collection of discrete subtransitions
Authors: Yen W. S. , Blake R. D.
Published: December 2004

The thermal dissociation of DNA by five distinct local processes as outlined by Azbel [(1980) Biopolymers 19, 61–80] is treated as a collection of two‐state substransitions. With the traditional expression for loop entropy and the assumption of a small, positive loop‐initiation enthalpy, explicit relationships between thermodynamic parameters are derived for all five processes. The effect of each process on subtransitional width, unit enthalpy, and melting temperature is estimated; the latter being in excellent agreement with that predicted by Azbel. Criteria proposed for the deconvolution of the oscillatory high‐resolution melting profiles exhibited by short, homogeneous DNAs [Yen & Blake (1980) Biopolymers 19, 681–700] have been applied to profiles of SV40 fragment [Gabbarro‐Arpa et al. (1979) Nature 280, 515–517] and ϕx174‐RF DNA at two ionic strengths [Vizard et al. (1978) 275, 250–251] and indicate that dissociation of the strands proceeds as a series of local two‐state subtransitions of domains 200–300 base pairs in length. Although the obvious overlap of some subtransitions raises questions about resolution, most sections are very well resolved with the minimum number of subtransitions and yield values for the apparent van't Hoff enthalpy in excellent agreement with those expected by calorimetric measurements. The flexibility of such an approach, where the enthalpy is recognized explicitly as an adjustable parameter, is especially suited for the analysis of profiles from unkown DNA sequences, and for the evaluation of extraordinary variations in free energy, such as that associated with loop formation or that resulting from variations in the linear charge density at low ionic strengths.
Solvent and side‐chain contributions to the two‐cis ⇄ all‐trans equilibria of cyclic hexapeptides, cyclo(Xxx‐Pro‐D‐Yyy)2
Authors: Kopple Kenneth D. , Sarkar Susanta K. , Giacometti Giovanni
Published: December 2004

Cyclic hexapeptides of the type cyclo(L‐Xxx‐L‐Pro‐D‐Yyy)2 or cyclo(L‐Xxx‐L‐Pro‐Gly)2 exist in solution predominantly in two forms of C2 average symmetry, one with all‐trans peptide bonds and generally well‐established conformation, and another with both Xxx‐Pro peptide bonds cis. We have been measuring the thermodynamic parameters of this equilibrium using carbon and proton nmr spectroscopy. Data have been obtained for peptides in which Yyy = Gly, D‐Ala, or D‐Phe, and Xxx = Gly, L‐Ala, L‐Leu, and L‐Val. In a given solvent, stability of the all‐trans form decreases (ΔG0 increases) as Xxx is changed through the series Gly, L‐Ala‐, L‐Leu, and L‐Val, consistent with expected increasing repulsion between the Xxx side chain and the proline δ methylene across the trnas Xxx‐Pro bond. Also, for a given set of side chains, the stability of the all‐trnas form increases as the polarity of the solvent decreases, consistent with models in which all CO and NH groups are accessible for solvation in the two‐cis form, but two CO and two NH groups are somewhat sequestered in the all‐trans form. With the available data it is not possible to identify pure intramolecular (solvent‐independent) or pure peptide‐bond solvation (side chain‐independent) terms in ΔH° or ΔS°, although trends are discernible.
Synthesis and conformational characterization in the solid state of peptides consisting of L‐phenylalanyl‐L‐phenylalanylglycyl and L‐phenylalanyl‐L‐leucylglycyl residues
Authors: Katakai Ryoichi , Nakayama Yoko
Published: December 2004

Two series of peptides containing L‐phenylalanine, Nps‐(L‐Phe‐L‐Phe‐Gly)n‐OEt (n = 1–6) and Nps‐(L‐Phe‐L‐Leu‐Gly)n‐OEt (n = 1–7), were prepared by the fragment‐condensation method using the tripeptide N‐hydroxysuccinimide esters. Conformational characterization of these peptides in the solid state was performed by ir spectroscopy and x‐ray powder diffraction measurement. The peptides Nps‐(L‐Phe‐L‐Phe‐Gly)n‐OEt take the β‐structure, but the pentadecapeptide and higher peptides of Nps‐(L‐Phe‐L‐Leu‐Gly)n‐OEt form the α‐helix, although the lower homologs take the β‐structure.
Quantitative test of Record's theory for proton‐induced lowering of DNA melting temperature
Authors: Mingot Francisco
Published: December 2004

This report presents a quantitative test of the ability of the counterion condensation theory to describe the proton‐induced lowering of DNA melting temperature. From a general approach of Record et al. [Record, M. T., Anderson, C. F. & Lohman, T. H. (1978) Q. Rev. Biophys. 11, 103–178], we have obtained an expression that may be computer‐fitted to the experimental data by numerical minimization of χ2. To do this, in addition to the assumptions made by Record et al., it was necessary to suppose that the interchange between protons and sodium is independent of pH and, due to the absence of data, take the enthalpies of protonation as thermally independent over the experimental temperature range. The dependences of the enthalpy of denaturation at neutral pH on sodium concentration and on G + C content were taken from literature. In the fitting process we have used 250 melting temperatures obtained at different pH and sodium concentrations for various natural DNAs. The theoretical expression gives a good quantitative description of the G + C and sodium concentration influences on the phenomenon but is only qualitative with respect to the dependence of dT/d log[Na+] on the pH. The adjusted pK values for the bases in denatured DNA agree with those for isolated deoxynucleosides. Interchange between sodium and protons is found to be less than 1:1. Calculated protonation enthalpies are ill‐defined because of their low numerical influence. In short, it appears that the theory gives a good description of most of the aspects of the phenomenon even if it has some shortcomings, perhaps due to the great number of assumptions.
Flow dichroism of T7 DNA as a function of salt concentration
Authors: Rizzo Vincenzo , Schellman John
Published: December 2004

Measurements have been made on the flow dichroism of T7 DNA as a function of NaCl concentration. In high salt, our results are compatible with an optical factor of −1.4 and a persistence length of 470 Å. The former is in agreement with expectations from the x‐ray diffraction structure of fibrous B–DNA, and the latter is in the midrange of recent determinations. As salt concentration is decreased, the persistence length increases. The relation of our study to other recent investigations and with current theories of the electrostatic contribution to persistence length is discussed. We note that the separation of the electrostatic expansion factor into long‐ and short‐range effects is somewhat arbitrary and might affect the interpretation of different experimental results in different ways. Finally, our hydrodynamic factors are consistent with a chain which is partially free‐draining. This goes against the traditional interpretation but is in agreement with two recent observations.
Theoretical π‐π* absorption and circular dichroic spectra of helical poly(L‐proline) forms I and II
Authors: Applequist Jon
Published: December 2004

Absorption and CD spectra of the π‐π* transition near 200 nm are calculated for helical (Pro)n I and II (n = 6, 10) using the dipole interaction model, including interactions among all atoms, with optical parameters obtained from previous studies of related molecules. Calculated spectra for (Ala)n and (Pro)n in the same conformation show marked differences. The spectra for (Pro)n are sensitive to side‐chain structure but are found to agree reasonably well with exeriment for forms I and II when the side‐chain CC bond length is set at 1.54 Å, with structural data otherwise obtained from x‐ray diffraction studies.
A general method for determination of nucleotide sequences in nucleic acids
Authors: Mandeles Stanley , Tinoco Ignacio
Published: December 2004

A method is proposed for the determiantion of nucleotide sequences in nucleic acids. Briefly, the procedure involves the formation of derivatives specific for either the 3′ or 5′ end of nucleic acid. This is followed by a partial enzymatic hydrolysis to yield specific fragments. The functions of the chemically modifying derivative are (a) to serve as a reference point which positions each base according to its distance from the modified end, (b) to provide a convenient means of separating oligomers with derivatives from those without derivatives, (c) to permit the use of additional parameters of fractionation of oligomers with derivative ends. The features of this method include: construction of long sequences from shorter fragments, unequivocal positioning of fragments, independence from quantitative procedures, economical use of nucleic acid polymer, determination of sequences from both ends simultaneously, application to DNA and RNA. Data are presented on the action of pancreatic ribonuclease on bis‐2,4 dinitrophenyl hydrazone derivatives of yeast ribonucleic acid and polyuridylic acid.
Effect of a helix‐coil transformation on magnesium binding to α‐poly‐L‐glutamic acid
Authors: Jacobson Ada L.
Published: December 2004

The effect of magnesium ion binding on the dissociation of side chain carboxyl group in α‐poly‐L‐glutamic acid has been measured by a modified titration technique involving pretitration of the polyacid with a strong base of a weakly bound counterion followed by addition of aliquots of the neutral salt of the more strongly bound counterion, magnesium chloride. The changes in the ionization of the carboxylic acid groups in the poly‐L‐glutamic acid side chains have been measured as a function of both the degree of preionization and of the concentration of magnesium chloride added. These changes have been related to changes in the polymer configuration (helix‐coil transition) as a function of degree of pre‐ionization. The effects of ionic strength and of ion binding have been determined by a comparison of tetramethyl ammonium chloride and of magnesium chloride at the same ionic strength. The plot proposed by Wada has been used to determine the pure helical region, the region of helix‐coil transition, and the pure coil region with both magnesium chloride and tetramethyl ammonium chloride as added salts. At the same ionic strength the effects produced by magnesium chloride addition are far greater than for tetramethyl ammonium chloride. Magnesium chloride at an ionic strength of 0.25 × 10−4 produces an effect equivalent to that of tetramethyl ammonium at an ionic strength of 15.0 × 10−4. This effect is also apparent when the concentration of carboxyl groups ionized by magnesium chloride addition is determined. The much larger effects produced by the magnesium ion are attributed to the enhanced binding of this ion. The results reported indicate binding is favored in the helical configuration. The binding in the random coil configuration is similar to that reported previously for other randomly coiled polyelectrolytes.
Some optical properties of poly‐1‐benzyl‐L‐histidine and poly‐L‐histidine
Authors: Norland K. S. , Fasman G. D. , Katchalski E. , Blout E. R.
Published: December 2004

Optical rotatory dispersion and infrared studies made on solutions of poly‐1‐benzyl‐L‐histidine (PBLH) in the solvent system chloroform–dichloroacetic acid (CHCl3DCA) indicate that this polymer exists in three different forms depending upon the solvent composition. These forms are reversibly interconvertible. Form I (PBLH‐I) exists in 100% CHCl3, form II (PBLH‐II) in CHCl3 containing one residue equivalent of DCA (the histidyl‐DCA salt) and form III (PBLH‐III) in CHCl3 with a large excess of DCA. It is suggested that PBLH‐I is an unionized random chain, PBLH‐II is an ionized “left‐handed” α‐helix, and PBLH‐III is an ionized random chain. Some optical rotatory dispersion and infrared measurements are reported for poly‐L‐histidine. A marked change in specific rotation of this polypeptide occurs in aqueous solution in the pH range 5–6.
Optical properties of the poly‐L‐proline and collagen helices
Authors: Gratzer W. B. , Rhodes W. , Fasman G. D.
Published: December 2004

Poly‐L‐proline I and II, polyphydroxy‐L‐proline II, polysarcosine, and collagen, as well as two model amides have been examined by far ultraviolet spectrophotometry. Absorption spectral data are presented. Neither in solution nor in oriented films of poly‐L‐proline I and II is there any indication of excition resonance splitting of the peptide absorption band. In collagen there is some, in the poly‐L‐prolines only minimal, hypochromicity. These observations, at least in poly‐L‐proline II, run counter to theory. Optical rotatory dispersion measurements in the ultraviolet indicate simple dispersion in collagen and poly‐L‐proline II down to at least 232 mμ. The Cotton effect (trough at 233 mμ) observed in α‐helical polypeptides and proteins is absent. The implications of these findings are discussed.
Electric properties of macromolecules. VIII. Kerr constants and rotational diffusion of some proteins in water and in glycerol—water solutions
Authors: Krause Sonja , O'Konski Chester T.
Published: December 2004

Kerr constants and birefringence relaxation times were measured on gamma‐globulin (I) in aqueous solution and on bovine serum albumin (II), beta‐lactoglobulin (III), ovalbumin, (IV), ribonuclease (V), lysozyme (VI), and chymotrypsin (VII) in glycerol–water solutions. Rotational diffusion constants were calculated from the data and were compared with those calculated from the protein dimensions obtained by other methods. The calculated and observed rotational diffusion constants were in excellent agreement for I, IV, V, and VII, and were within a factor of two for III. VI showed evidence of aggregation and II gave a low relaxation time in glycerol–water solution, apparently because of a structural change or a localized solvent viscosity effect. The earlier results for maximum dimensions based upon the dielectric relaxation time method were found to be in agreement with present findings in a number of instances, in spite of the possible complication of the dielectric method by ionic polarization effects.
Electric properties of macromolecules. X. Conduction and the question of ferroelectricity in solid sodium deoxyribonucleate
Authors: O'Konski C. T. , Shirai M.
Published: December 2004

Data are presented for electric conduction in solid sodium deoxyribonucleate as a function of water content and over a wide range of frequencies. We have also examined the loops seen in a ferroelectric hysteresis bridge. It is proposed that both the conductivity and the loops of samples with high water content are probably due to ion conduction and electrolysis. Dry samples appear to have the characteristics of an inhomogeneous semiconductor. Possible mechanisms of carrier generation are briefly discussed.
NMR study on molecular mobility of DNA molecules in solution
Authors: Lubas Barbara , Wilczok Tadeusz
Published: December 2004

The molecular mobility of calf thymus DNA molecules in solution has been discussed in terms of correlation time τ calculated from measurements of longitudinal T1 and transverse T2 magnetic relaxation times. The influence of DNA concentration and ionic strength of the solution upon freedom of movement of DNA molecules was studied for native and denatured DNA and also during thermal helix‐coil transition. The dependence of τ values on temperature was carried out by comparing the values of correlation times τtat given temperature with the correlation time τ20 at 20°C. The molecular rotation of DNA at 20°C and at higher ionic strength at 0.15 and 1.0.M NaCl is described by τ values of the order of 1.0–1.2 × 10−8 and was reduced slightly with increase of temperature below the helix‐coil transition. The molecular rotation of DNA in 0.02MNaCl was lower at 20°C as compared to DNA in solvents with higher NaCl concentrations and increases rapidly with increase of temperature in the range 20–60°C. The values of correlation time are characterized by fast increase at temperatures above the spectrophotometrically determined beginning of melting curve. The beginning of this increase is observed at about 65, 80, and 85°C for DNA in 0.02, 0.15, and 1.0MNaCl, respectively. Values of correlation time for denatured DNA are in all cases about 1.1–1.4 times that for native DNA. The obtained results are discussed in terms of conformation of DNA molecules in solution as well as in terms of water dipole binding in DNA hydration shells.
Pressure independence of the rotor speed‐induced aggregation of DNA
Authors: Poon Pak H. , Schumaker Verne N.
Published: December 2004

The rotor speed‐dependent aggregation of T4 DNA in the analytical ultracentrifuge is studied in the presence of high pressure generated by compressed nitrogen gas in the cell. The extents of aggregation at various speeds are found to be practically the same in the presence and absence of pressure.
The glucan–chitin complex in Saccharomyces cerevisiae. IV. The electron diffraction of crustacean and yeast cell wall chitin
Authors: Gemperle A. , Holan Z. , Pokorný V.
Published: December 2004

Crustacean and yeast cell wall chitin were analyzed by means of transmission electron microscopy and selected‐area diffraction. Single fibrils 8–25 nm wide have been observed in the micrographs of crustacean chitin. Analysis of a series of diffraction patterns obtained from thin crustacean chitin platelets yielded results which were in a better agreement with the theoretical structural model than those measured earlier. In this respect electron diffraction is shown to be superior to the more commonly used x‐ray diffraction. Yeast cell wall chitin had a less perfect structure than the crustacean chitin. Single fibrils were not observed on the micrographs and electron diffraction patterns did not show any preferred fiber orientation. The evaluation of electron‐diffraction patterns of both the primary septum and the adjacent circular zone of scar ring led to the conclusion that α‐chitin is present in both these parts of the mother bud scar.
Fluorescent‐labeled crosslinks in collagen: Pyrenebutyrylhydrazine
Authors: Shambaugh Nathaniel , Fujimori Eiji
Published: December 2004

The aldehydes present in acid‐soluble type I collagen react with pyrenebutyrylhydrazine to form various types of complexes under different reaction conditions. These complexes exhibit one or more of three different pyrene fluorescence bands: monomer, excimer, and aggregate fluorescence. Collagen, whose aldehydes have been reduced with NaBH4, does not react with this fluorescent hydrazine, confirming that the hydrazine reacts specifically with aldehyde groups to form hydrazones. The absence of a reaction with pepsin‐treated collagen also shows that the fluorescent labels are primarily in the nonhelical terminal telopeptides. Upon dialysis, the pyrene label bound to a saturated aldehyde in an α‐chain is lost; whereas that bound to an unsaturated aldehyde remains on the protein. The pyrene monomer fluorescence in the β‐chain of old collagen is stronger than that of young collagen. The formation of the pyrene excimer fluorescence implies the proximity of two pyrene molecules, probably attached to two adjacent aldehydes. Upon changing from acidic to neutral pH, both excimer and aggregate fluorescence bands disappear within a few seconds, revealing a very rapid alteration at the telopeptides.
Interactions of DNA with divalent metal ions. I. 31P‐nmr studies
Authors: Granot Joseph , Feigon Juli , Kearns David R.
Published: December 2004

31P‐nmr has been used to investigate the specific interaction of three divalent metal ions, Mg2+, Mn2+, and Co+2, with the phosphate groups of DNA. Mg2+ is found to have no significant effect on any of the 31P‐nmr parameters (chemical shift, line‐width, T1, T2, and NOE) over a concentration range extending from 20 to 160 mM. The two paramagnetic ions, Mn2+ and Co2+, on the other hand, significantly change the 31P relaxation rates even at very low levels. From an analysis of the paramagnetic contributions to the spin–lattice and spin–spin relaxation rates, the effective internuclear metal–phosphorus distances are found to be 4.5 ± 0.5 and 4.1 ± 0.5 Å for Mn2+ and Co2+, respectively, corresponding to only 15 ± 5% of the total bound Mn2+ and Co2+ being directly coordinated to the phosphate groups (inner‐sphere complexes). This result is independent of any assumptions regarding the location of the remaining metal ions which may be bound either as outer‐sphere complexes relative to the phosphate groups or elsewhere on the DNA, possibly to the bases. Studies of the temperature effects on the 31P relaxation rates of DNA in the absence and presence of Mn2+ and Co2+ yielded kinetic and thermodynamic parameters which characterize the association and dissociation of the metal ions from the phosphate groups. A two‐step model was used in the analysis of the kinetic data. The lifetimes of the inner‐sphere complexes are 3 × 10−7 and 1.4 × 10−5 s for Mn2+ and Co2+, respectively. The rates of formation of the inner‐sphere complexes with the phosphate are found to be about two orders of magnitude slower than the rate of the exchange of the water of hydration of the metal ions, suggesting that expulsion of water is not the rate‐determining step in the formation of the inner‐sphere complexes. Competition experiments demonstrate that the binding of Mg2+ ions is 3–4 times weaker than the binding of either Mn2+ or Co2+. Since the contribution from direct phosphate coordination to the total binding strength of these metal ion complexes is small (∼15%), the higher binding strength of Mn2+ and Co2+ may be attributed either to base binding or to formation of stronger outer‐sphere metal–phosphate complexes. At high levels of divalent metal ions, and when the metal ion concentration exceeds the DNA–phosphate concentration, the fraction of inner‐sphere phosphate binding increases. In the presence of very high levels of Mg2+ (e.g., 3.1M), the inner‐sphere ⇄ outer‐sphere equilibrium is shifted toward ∼100% inner‐sphere binding. A comparison of our DNA results and previous results obtained with tRNA indicates that tRNA and DNA have very similar divalent metal ion binding properties. A comparison of the present results with the predictions of polyelectrolyte theories is presented.
A swivel‐jointed formalism for segmentally flexible macromolecules and its application to the rotational behavior of myosin
Authors: Wegener William A.
Published: December 2004

A formalism is presented to represent the hydrodynamic and diffusion behavior of segmentally flexible macromolecules with a high degree of flexibility. The development specifically treats open assemblies of cylindrically symmetric segments joined at their end points by frictionless swivels. Three‐dimensional diffusion and frictional tensors that govern the rotations of each segment and the translations of some chosen swivel are established and related by a Stokes–Einstein relation. The dependence of these tensors on the choice of swivel is examined, and simplified expressions are obtained by omitting hydrodynamic interactions between segments. These simplified expressions are used to analyze the rotational behavior of a Y‐shaped body in detail. If there is complete flexibility, the rotational motions of each segment reduce, for all practical purposes, to those of a cylindrically symmetric rigid body. Estimates are provided to relate segment rotations to internal motions and restrictions on flexibility. A procedural framework for generating rotational diffusion coefficients for segments of more complicated bodies is applied to a four‐segment two‐swivel myosin model. Comparison of calculated and experimental relaxation times for myosin and its fragments indicates the head–tail junction is highly flexible, with at least a ±60° angular extent of free bending between heads allowed, while the tail is neither straight and rigid nor highly flexible.
Proline‐containing β‐turns in peptides and proteins. II. Physicochemical studies on tripeptides with the Pro‐Gly sequence
Authors: Brahmachari Samir K. , Rapaka Rao S. , Bhatnagar Rajendra S. , Ananthanarayanan V. S.
Published: December 2004

Amino acids are known to differ in their individual preferences for each of the four positions of the β‐turn conformation formed by tetrapeptide segments. Proline and glycine show relatively high preferences for positions 2 and 3, respectively, of the β‐turn. Using tripeptides of the type N‐acetyl‐Pro‐Gly‐X‐OH, where X = Gly, Ala, Leu, Ile, and Phe, we have sought to study the influence of the 4th residue X on the stability of the β‐turn conformation in these tripeptides. Our nmr and CD results show that the β‐turn stability is quite significantly governed by the nature of the amino acid residue at this position in the following order: Leu > Ala > Ile, Gly > Phe.
Backbone conformations in nucleic acids: The occurrence of g+g+ internucleotide phosphodiester conformation
Authors: Jayaraman S. , Yathindra N. , Sundaralingam M.
Published: December 2004

Semiempirical conformational energy calculations have been performed on dinucleoside triphosphate models with and without base interactions to investigate the conformational requirement for the stereochemical and energetic feasibility of (gauche+,gauche+) phosphodiester conformation in a polynucleotide chain. Results show that the trans conformation of the C4′C5′ bond on the 5′‐sugar (either C3′‐endo or C2′‐endo) of a dinucleoside triphosphate renders the g+g+ phosphodiester energetically favorable. The degree of energetic preference shows a dependence on the C3′O3′ bond torsions (ϕ′); higher g+g+ conformation populations are correlated with higher values of ϕ′ ≃ 270° due to increased van der Waals interactions between adjacent sugar residues. For similar reasons, the g+g+ phosphodiester displays an energetic dependence on the nature and sequence of bases and their orientations. Other conformational combinations that also stereochemically permit the g+g+ phosphodiester are discussed along with base effects.
Two classes of β‐pleated sheet conformation in poly(L‐tyrosine): Evidence from solvent perturbation difference spectroscopy
Authors: Auer Henry E. , Miller‐Auer Helene
Published: December 2004

We had earlier observed that the detailed nature of the β‐structure adopted by poly(L‐tyrosine) depends on molecular weight [Auer, H. E. & McKnight, R. P. (1978) Biochemistry 17, 2798–2805]. It was proposed that shorter molecules form an open, single‐layered sheet (class I) and that longer chains fold over to generate at least two layers (class II). In this work, solvent perturbation difference spectroscopy of the chromophoric side chain was applied to gain additional support for the model. Two sample‐reference pairs of media, sodium acetate vs sodium chloride and urea vs buffer, were studied. Great care was taken to achieve identical conditions in the sample and reference cells. The factors of importance in executing the experiments are the polypeptide concentration, the degree of side‐chain ionization, achievement of the same class of β‐conformation, and the absence of significant aggregation. Difference spectra obtained with both solvent pairs have similar features. Low‐molecular‐weight samples manifest difference bands arising from both ionized and neutral tyrosine side chains, while high‐molecular‐weight samples yield spectra with contributions primarily from ionized residues. The interpretation of these results is that the class I particle has both ionized and neutral residues exposed to the solvent medium, whereas the class II particle is folded, with neutral residues restricted to the interior of the fold and primarily ionized residues on the outer surfaces exposed to the solvent. Our results, therefore, corroborate the original model.
Microdomain dynamics in folding proteins
Authors: Weaver D. L.
Published: December 2004

The basic formulas for the incorporation into the diffusion–collision model of the stabilities of intermediate states on the folding pathway are derived and discussed. A hypothetical two‐step folding pathway is calculated in detail. A model for the production of incorrectly folded intermediates is suggested and some numerical estimates made. Implications and future directions in the evolution of the model are discussed. Three appendices deal with some mathematical aspects of the model.
Microwave absorption by folded DNA chains
Authors: Kohli M. , Van Zandt L. L.
Published: December 2004

Absorption of radiation by DNA polymer is calculated for the case of bent polymer chains. The molecule is assumed to be straight except for localized bends. The region between two bends is studied in particular. The vibrational properties of the bends are parameterized by a transmission and a reflection coefficient. A general Green function expression for absorption is studied for various values of the damping rate, as well as the transmission/reflection coefficients. Curves of absorption vs frequency are shown for a number of cases.
Properties of the complexes formed by 1‐anilinonaphthalene‐8‐sulfonate with phosphorylase kinase and calmodulin
Authors: Steiner R. F. , Sternberg H.
Published: December 2004

Phosphorylase kinase contains four approximately equivalent binding sites for 1‐anilinonaphthalene‐8‐sulfonate (1,8‐ANS). Measurements of the time decay of fluorescence anisotropy have failed to give any indication of internal degrees of rotational freedom involving a significant portion of the tertiary structure. In the presence of 1 mM Ca2+, calmodulin binds one molecule of 1,8‐ANS. No binding occurs in the absence of Ca2+. The binding is strongly temperature‐dependent, a decrease in binding occurring with increasing temperature. Determinations of the time decay of fluorescence anisotropy indicate the presence of internal rotations, which become more important with increasing temperature. Complex formation between phosphorylase kinase and calmodulin reduces the binding of 1,8‐ANS.
Proline ring conformations corresponding to a bistable jump model from 13C spin‐lattice relaxation times
Authors: Shekar S. C. , Easwaran K. R. K.
Published: December 2004

A formalism for extracting the conformations of a proline ring based on the bistable jump model of R. E. London [(1978) J. Am. Chem. Soc. 100, 2678–2685] from 13C spin‐lattice relaxation times (T1) is given. The method is such that the relaxation data are only partially used to generate the conformations; these conformations are constrained to satisfy the rest of the relaxation data and to yield acceptable ring geometry. An alternate equation for T1 of 13C nuclei to that of London is given. The formalism is illustrated through an example.
Conformational preferences of amino acid side chains in collagen
Authors: Némethy George , Scheraga Harold A.
Published: December 2004

Conformational energy computations were carried out on collagenlike triple‐stranded conformations of several poly(tripeptide)s with the general structure CH3CO(GlyXY)3NHCH3. The sequences considered had various amino acid residues in position X or Y of the central tripeptide, with either Pro or Ala as a neighbor, i.e., Gly‐X‐Pro, Gly‐X‐Ala, Gly‐Pro‐Y, and Gly‐Ala‐Y. Minimum‐energy conformations were computed for the side chains, and their distributions were compared for the four sequences. The residues used were Abu (= α‐aminobutyric acid), Leu, Phe, Ser, Asp, Asn, Val, Ile, and Thr. The conformational energy of a Ch2CH3 side chain in Abu was mapped as a function of the dihedral angle χ1. Intrastrand interactions with neighboring residues do not affect the conformations of a side chain in position Y, and they have a minor effect on it in the X‐Ala sequence, but they strongly restrict the conformational freedom of the side chain in the X‐Pro sequence. Conversely, interstrand interactions do not affect side chains in position X, but they strongly restrict the conformational freedom of a side chain in position Y if there is a nearby Pro residue in a neighboring strand. Hydrogen bonds with the backbone can be formed in some conformations of long polar side chains, such as Asp, Asn, or Gln. All amino acid residues can be accommodated in collagen. Because of the interactions mentioned above, steric and energetic constraints can be correlated with observed preferences of certain amino acids for positions X or Y in collagen. Hence, these preferences may be explained, in part, in terms of differences in the conformational freedom of the side chains in the triple‐stranded structure.
Stabilization of collagen structure: Dependence of collagen denaturation enthalpy on the imino acid content
Authors: Burjanadze T. V.
Published: December 2004

An analysis of the available data on the enthalpy (ΔHr) of denaturation (melting) of collagens with different imino acid content in solution and in the aggregated state has shown that ΔHr in solution increases with increasing denaturation temperature, whereas in the aggregated state there is an inverse dependence. ΔHr in solution correlates with the hydroxyproline content but not with that of proline. No correlation between the change of ΔHr and the imino acid content is observed for the aggregated state.
Monte Carlo simulation of photoselective cyclization of azobenzene‐containing oligosarcosines
Authors: Sisido Masahiko , Imanishi Yukio
Published: December 2004

Conformations of (Sar)nAzo(Sar)n oligomers [Sar = sarcosine (N‐methylglycine) unit. Azo = p‐aminoazobenzene unit] were computer‐simulated for trans and cis states of the azobenzene group. Each part of the oligosarcosine chain was assumed to behave independently and the ring‐closure probability, i.e., the probability that the end‐to‐end distance of the above oligomer is shorter than 4 Å, was evaluated from an overlap integral of the two three‐dimensional distribution functions for the left and right halves of the oligosarcosine chain. The ring‐closure probability for the cis azobenzene unit was larger than that for trans, indicating the preference of cyclization reaction to the corresponding intermolecular reactions. The prediction agrees qualitatively with the experimental observation reported by us in our companion paper, but the calculated ring‐closure probability for the cis state was substantially larger than the experimental value. The difference was explained as a result of intramolecular overlappings of the two halves of the oligosarcosine chain, which is facilitated when the azobenzene group is in the cis state.
Ionization behavior of proteins. II. Chymotrypsinogen and its group‐modified derivatives: Study of their ionization characteristics by potentiometric and calorimetric titration
Authors: Martin C. J. , Marini M. A.
Published: December 2004

Chymotrypsinogen, nitrated chymotrypsinogen (two of the four tyrosyls nitrated), acetylated chymotrypsinogen (all amino groups blocked), and nitrated‐acetylated chymotrypsinogen were titrated as f(pH) in an isoperibolic calorimeter at 20°C. After appropriate correction and reduction of both the potentiometric and thermal titration data, the parameters N (ionizable groups per group‐set), pK′, and ΔHi (heat of ionization) were evaluated using the iterative curve‐fitting algorithm of the MLAB computer program. The pK′ parameters so obtained for the two normally ionizing tyrosyl groups in chymotrypsinogen and the two nitrated tyrosyl groups in the nitrated proteins essentially agreed with the results of spectral titration. Excellent fits to all data could be obtained using evaluated parameter sets of N and pK′ for the potentiometric titration data (groups vs pH plots) and N, pK′, and ΔHi sets for the calorimetric data (total heat vs pH plots). The invocation of electrostatic interaction effects was not required to explain the data satisfactorily, despite the differences in charge number and type among the four proteins. Rather, the data can be represented by series expressions of the mass‐action law. Using all information, viz., the consequences of functional group modification, the downscale shift in tyrosyl group pK's on nitration, and the numerical values of the evaluated N, pK′, and ΔHi parameter sets for all proteins, the chemical identity of the various classes of group sets can be assigned with reasonable assurance.
Steady‐state and transient electric birefringence of solutions of bent‐rod macromolecules
Authors: Mellado Pelayo , De La Torre José García
Published: December 2004

We first calculate the steady‐state birefringence, expressed in the form of specific Kerr constant, Ksp, of rigid, bent‐rod macromolecules. Equations are derived for Ksp as a function of the geometric and electro‐optical parameters. We also consider flexibly hinged rods and evaluate Ksp for them by averaging over the angle between the two arms, ϕ. Next, we turn to the time decay of the electric birefringence. The decay function for rigid bent rods is a sum of three exponential terms, and a procedure for their calculation is indicated. We observe that single‐exponential decays can be found for ϕ > 90° or ϕ < 60°, in spite of the high electro‐optical and hydrodynamic anisotropy of the macromolecule. Special attention is paid to the case of rods with equal arms.
Interactions between poly(Gly‐Pro‐Pro) triple helices: A model for molecular packing in collagen
Authors: Némethy George
Published: December 2004

Potential‐energy calculations are reported on the interaction between two collagenlike triple‐stranded poly(Gly‐L‐Pro‐L‐Pro) helices. Short helices can pack in a variety of orientations, but there is a unique parallel packing arrangement of the two helices for longer polypeptide chains.
Preferred conformations of peptides containing α,α‐disubstituted α‐amino acids
Authors: Toniolo Claudio , Bonora Gian Maria , Bavoso Alfonso , Benedetti Ettore , di Blasio Benedetto , Pavone Vincenzo , Pedone Carlo
Published: December 2004

The conformational preferences of linear peptides containing α,α‐disubstituted α‐amino acids, derived from the crystal structures of 28 compounds, are reviewed. In particular, the sensitivity of peptide conformation to the geometry of these unusual amino acids is underlined. We also consider possible future directions of research, which, we hope, will result in a complete understanding of the structures adopted by peptaibol antibiotics.
Refinement of the structure of bovine seminal ribonuclease
Authors: Capasso Sante , Giordano Federico , Mattia Carlo A. , Mazzarella Lelio , Zagari Adriana
Published: December 2004

We report here the refinement at 2.5‐Å resolution of the x‐ray crystal structure of bovine seminal ribonuclease, a dimeric covalent enzyme. The protein, which crystallizes with one molecule in the asymmetric unit, consists of two subunits of identical chemical sequences, related by an almost exact binary axis. The tertiary structure of the subunits is similar to that of the pancreatic enzyme, which shows similar catalytic properties. The refinement was carried out using the restrained least‐squares procedure both in the reciprocal and real spaces. The assemblage of the subunits in the dimer is described and discussed.