bluuebunny/crossref_metadata_2025 huggingface dataset:
Electric birefringence of restriction enzyme fragments of DNA: Optical factor and electric polarizability as a function of molecular weight
Authors: Stellwagen Nancy C.
Published: December 2004

The electric birefringence of restriction enzyme fragments of DNA has been investigated as a function of DNA concentration, buffer concentration, and molecular weight, covering a molecular weight range from 80 to 4364 base pairs (bp) (6 × 104–3 × 106 daltons). The specific birefringence of the DNA fragments is independent of DNA concentration below 20 μg DNA/ml, but decreases with increasing buffer concentration, or conductivity, of the solvent. At sufficiently low field strengths, the Kerr law is obeyed for all fragments. The electric field at which the Kerr law ends is inversely proportional to molecular weight. In the Kerr law region the rise of the birefringence is accurately symmetrical with the decay for fragments ≤ 389 bp, indicating an induced dipole orientation mechanism. The optical factor calculated from a 1/E extrapolation of the high field birefringence data is −0.028, independent of molecular weight; if a 1/E2 extrapolation is used, the optical factor is −0.023. The induced polarizability, calculated from the Kerr constant and the optical factor, is proportional to the square of the length of the DNA fragments, and inversely proportional to temperature. Saturation curves for DNA fragments ≤ 161 bp can be described by theoretical saturation curves for induced dipole orientation. The saturation curves of larger fragments are broadened, because of a polarization term which is approximately linear in E, possibly related to the saturation of the induced dipole in high electric fields. This “saturated induced dipole” is found to be 6400 D, independent of molecular weight. The melting temperature of a 216‐bp sample is decreased 6°C in an electric field of 8 kV/cm, because the lower charge density of the coil form of DNA makes it more stable in an electric field than the helix form.
Structure of viral φ29 DNA condensed by simple triamines: A light‐scattering and electron‐microscopy study
Authors: Allison Stuart A. , Herr John C. , Schurr J. Michael
Published: December 2004

The structures of viral φ29 DNA condensed by triamines, principally spermidine, in 10−3M NaCl were investigated by static and dynamic light scattering and electron microscopy. All of the results for DNA condensed in 30 μM spermidine at neutral pH are quantitatively consistent with a toroidal structure with a mean outer diameter of 1850 Å. At pH 10.2, however, condensed structures of a completely different size and shape are observed for the first time. These structures are also more irregular in shape and more polydisperse than those at neutral pH. This conformational change is believed to result from a change in the mode of spermidine binding that is coupled to, or associated with, the (premature) titration of protons on the base‐ring nitrogens of guanine and thymine. Besides spermidine, certain homologs of spermidine, in which the butyl moiety of spermidine was replaced by longer pentyl through octyl moieties, were also studied. Though all of the triamines condensed the DNA at 30 μM, aggregation became a more prevalent occurrence as the length of the end chain increased. This suggests that crosslinking may play an important role in the condensation process. Finally, these aggregates are dissociated to a considerable extent at pH 10.2, and the resulting compact structures appear to be quite similar, independent of the triamine used to condense the DNA. The observed partial breakdown of aggregates is also consistent with the hypothesis of a change in mode of triamine binding at pH 10.2.
Acoustic modes and nonbonded interactions of the double helix
Authors: Mei W. N. , Kohli M. , Prohofsky E. W. , Van Zandt L. L.
Published: December 2004

Observations of acoustic velocities in DNA fibers have been used to refine nonbonded force constants for the DNA double helix. Long‐range forces are found to be needed for A conformation and are likely to dominate in B conformation as well. The acoustic dispersion curves are described and calculated. A correction due to the effects of water is calculated. The effect of nonbonded interaction on other vibrational modes is calculated.
Locations of frequently opening regions on natural DNAs and their relation to functional loci
Authors: Gotoh Osamu , Tagashira Yusaku
Published: December 2004

The probability of each base pair being in open state under premelting conditions was calculated and plotted against the base number for nine DNA genomes whose entire nucleotide sequences have been determined. The base‐pair opening profiles thus obtained were compared with the functional maps. Origins of DNA replication fall on frequently opening regions for five of six DNA genomes with known initiation sites of replication. Coincidence of frequently opening regions with promoters and terminators of transcription is most prominent for DNAs with block heterogeneity in sequence such as papovavirus DNAs, a Colicin El‐related plasmid pAO3, pBR322, and Transposon 3 (Tn 3) DNAs, while this coincidence is less apparent in DNAs with random sequence such as the replicative form of ϕX174 and G4 phage DNAs. In fd phage DNA, about half the promoters are located in frequently opening regions, although the strength of a promoter is not correlated with the frequency of opening of base pairs. Correlation of frequently opening regions and gene boundaries is not so obvious as claimed previously. As a whole, coincidence of functional loci and frequently opening regions defined in base‐pair opening profiles is far from perfect but much better than that previously inferred from the conventional running average of local A + T content, theoretical denaturation mapping, or electron microscopy of partially denatured DNA molecules.
Does perchlorate ion change A·U combining ratios?
Authors: Howard Frank B. , Roy Kunal B. , Frazier Joe , Miles H. Todd
Published: December 2004

Infrared spectroscopy and equilibrium binding studies have been used to determine the combining ratio of adenosine and poly(U) in 1M NaClO4 solution. In contrast to a recent report, we find exclusively 1:2 stoichiometry in this solvent. Ultraviolet and infrared spectroscopy have been employed to show that the stoichiometry of poly(A) interaction with poly(U) is unaffected by 1M NaClO4.
Kinetics of chemical modification of arginine and lysine residues in calf thymus histone H1
Authors: Mita Kazuei , Ichimura Sachiko , Zama Mitsuo , Hamana Koei
Published: December 2004

The arginine and lysine residues of calf thymus histone H1 were modified with large molar excesses of 2,3‐butanedione and O‐methylisourea, respectively. Kinetic study of the modification reaction of the arginine residue revealed that the reaction is divided into the two pseudo‐first‐order processes. About a third (1 Arg) of the total arginine residues of the H1 molecule was rapidly modified without causing any detectable structural change of the molecule, and the slow modification of the remaining arginine residues (2 Arg) led to a loss of the folded structure of H1. In the case of lysine residue modification, 93% (56 Lys) of the total lysine residues of the H1 was modified with the same rate constant, while 7% (4 Lys) of lysine residue remained unmodified. When the reaction was performed in the presence of 6M guanidine‐HCl, all of lysine residues were modified. It is concluded that the 2 arginine and 4 lysine residues resistant to modification are buried in interior regions of the H1 molecule and play an important role in the formation of the H1 globular structure, while the other 1 arginine and 56 lysine residues are exposed to solvent.
Ionic strength effects on macroion diffusion and excess light‐scattering intensities of short DNA rods
Authors: Fulmer Andrew W. , Benbasat Julyet A. , Bloomfield Victor A.
Published: December 2004

Quasielastic and static light‐scattering measurements were made on DNA isolated from chicken erythrocyte mononucleosomes as a function of ionic strength between 6 × 10−4 and 1.0M. A transition from single‐exponential autocorrelation functions to markedly non‐single‐exponential decays was observed around 10−2M ionic strength and was accompanied by a large decrease in the excess light‐scattering intensity. Autocorrelation functions recorded below 10−2M salt were well fit by the sum of two exponential relaxation which differed by as much as 100‐fold in time constants. Apparent diffusion coefficients for the fast and slow processes plateaued around 10−3M with numerical values approximately 10‐fold and 1/10, respectively, of the translational diffusion coefficient for mononucleosome DNA at high ionic strength. This behavior is similar to that observed with poly(L‐lysine), for which the slow decay has been associated with a transition to an extraordinary phase. The strong and complex salt dependence observed here illustrates potential difficulties in deriving structural information from scattering by polyions at low ionic strength.
Elastin as a random‐network elastomer: A mechanical and optical analysis of single elastin fibers
Authors: Aaron B. B. , Gosline J. M.
Published: December 2004

The physical properties of single, 5–8‐μm diameter, water‐swollen elastin fibers have been investigated on a microtest apparatus attached to a polarizing microscope. Analysis of the mechanical and optical properties at extensions below 100% indicate that the elastic modulus (G) has a value of 4.1 × 105 N m−2, the average molecular weight of chains between crosslinks is in the range of 6000–7100, and the stress optical coefficient (C′) is 1 × 10−9 m2 N−1 at 24°C. Analysis of the temperature dependence of the stress optical coefficient indicates that the polarizability of the random link decreases with increasing temperature, with an apparent activation energy for this process of the order of 1.6 kcal/mol. Analysis of the non‐Gaussian mechanical and optical properties at extensions above about 100% suggest that the chains between crosslinks contain approximately 10 “effective” random links, with each link consisting of 7–8 amino acid residues. These parameters for the random chains in the elastin network have been used to predict the dimensions of other random proteins. The close correlation of these predictions with published values for the dimensions of a series of proteins in solution in 6M guanidinium hydrochloride provides an independent test of the appropriateness of our analysis.
The possibility of intrinsic local curvature in DNA toroids
Authors: Manning Gerald S.
Published: December 2004

A variety of solution conditions are known to induce collapse of linear DNA into a compact configuration without dramatic change of local structure. When visualized, these compact forms frequently have a toroidal appearance. We ask whether the molecular basis of the toroidal shape can be a stable curvature of isolated rodlike DNA segments. Application of the classical Euler‐Lagrange theory for the buckling of elastic rods provides us with an affirmative answer. Specifically, we see that, in principle, sufficient addition of inert polymer to DNA solutions can induce buckling of DNA segments. However, no attempt is made to quantitate the Euler‐Lagrange condition for sufficiency in terms of added polymer concentration. We find also that complete neutralization of the phosphate charge is more than sufficient to induce buckling of DNA segments of length comparable to a Kuhn segment. The quantitative argument involves comparison of buckling forces provided by polyelectrolyte theory with the Euler‐Lagrange criterion. Knowledge of the ionic‐strength dependence of DNA bending stiffness (persistence length) is not required.
Conformational studies of the pentapeptides with weak adrenocorticotropin (ACTH) activities by means of nuclear magnetic resonance spectroscopy
Authors: Higuchi Naoki , Kyogoku Yoshimasa , Yajima Haruaki
Published: December 2004

The conformations of a pentapeptide L‐His‐L‐Arg‐L‐Trp‐Gly with weak adrenocorticotropin (ACTH) activity and its analogs, where each L‐amino acid residue is substituted by D‐residue, were investigated by means of proton and carbon‐13 nmr spectroscopy on their DMSO‐d6 solutions. The spectra indicated the presence of slowly exchangeable conformation isomers for D‐Phe and D‐Arg analogs, due to steric hindrance around the arginine residue. The activation energy of the hindered rotation of the arginine side chain was estimated to be more than 19 ∼ 20 kcal/mol. Spin‐lattice relaxation times of carbon‐13 nuclei also indicated slow segmental motion of the arginine side chain of the D analogs. An effect on proton chemical shifts by intermolecular electrostatic interaction between the arginine side chain and the C terminal carboxylic residue was observed. We did not observe, however, a direct correlation between pentapeptide activity and molecular conformation at this stage of the experiments.
Free‐sliding ligands: An alternative model of DNA–protein interactions
Authors: Woodbury Charles P.
Published: December 2004

We present an alternative to the common lattice model for nonspecific DNA–protein interactions by using ligands that translate freely along the polynucleotide instead of binding to distinct lattice sites along the polynucleotide chain. The general model we present corresponds to a one‐dimensional continuum gas and is referred to as the “continuum model” to distinguish it from the general lattice model. Explicit expressions are obtained for the binding isotherm equation for two version of the continuum model, including the effects of binding‐site exclusion and attractions between bound ligands. Theoretical results are compared to those obtained from the McGhee‐von Hippel (1974) analysis of the lattice model with cooperative interactions between ligands occupying more than one lattice site. Practical applications of the continuum model are illustrated by analyzing (i) the noncooperative binding to single‐stranded DNA by RNase (Jensen and von Hippel, 1976), and (ii) the highly cooperative binding to poly(rA) by a proteolyzed fragment of the gene 32 protein of phage T4 (Lonberg et al., 1981).
Analysis of the potentiometric titration of reduced horse heart cytochrome c
Authors: Marini M. A. , Martin C. J. , Forlani L.
Published: December 2004

Curve fitting for the ionization constants found in the potentiometric titration curve of reduced horse heart cytochrome c in 0.15M KCl at 20°C yields values which can precisely reconstruct the experimental curve. The parameters were evaluated assuming that there were 13 group sets with individual ionization constants, that these groups were subject to electrostatic interaction (ω), and that both pK′ and (ω) were necessary to describe the curve. On the basis of an analysis of the residuals, both the simple sum of mass‐law expressions and the electrostatic model could be invoked, although the evaluated ω was both positive and negative. When the standard errors of the parameter values are considered, only the model which assumed no electrostatic interaction is acceptable. The experimental curve is completely described by eight group sets and no electrostatic interaction.
Theoretical evidence for the coupling of winding to compression in the solution conformation of duplex DNA
Authors: Manning Gerald S.
Published: December 2004

Published data indicate linear variation of the duplex winding of DNA with logarithm of the ionic strength. We show that this observation is a natural prediction of a current poly‐electrolyte theory if structural coupling between duplex rotation angle (rotation per base pair) and step height (axial translation per base pair) is assumed. We show also that the coupling must then be negative: the positive winding on augmentation of the ionic strength must be accompanied by a decrement of step height, or axial compression. Cation species specificity of winding, CD spectra, and cation binding affinity are discussed in terms of local variation of dielectric shielding, using current accurate data for dielectric constants of aqueous salt solutions. One need not invoke specific complexation of cations, for which there is no present evidence (in aqueous solution), to explain any of these effects. The analysis is limited to low and moderate ionic strengths. Experimental observations at very high ionic strengths are puzzling and possibly conflicting. It is concluded that a need exists for systematic extension of available duplex winding data throughout the region of moderate to very high ionic strengths. It would be useful to extend the region at the low end as well, in order to distinguish clearly the behavior predicted by our model from that predicted by a referee on the basis of an alternate model described herein.
pH‐Dependent Raman spectra and thermal melting profiles for polycytidylic acid
Authors: O'Connor Timothy , Scovell William M.
Published: December 2004

The Raman spectrum of polycytidylic acid was investigated in the pH range of 6.6–4.1. The thermal melting temperatures and the nature of the thermal melting profiles change in this range as monitored by the three Raman band envelopes, which include the 780‐, 805‐cm−1 bands, the 1190‐, 1285‐cm−1 bands, and the 1527‐cm−1 band. By coupling these data with the theory of Raman scattering intensity and quantitative pH profiles for cytidine, it is shown that the band envelopes studied exhibit specific, yet different information regarding the thermal melting process. The band envelopes at 1170–1310 and 1527 cm−1, which are a sensitive function of both the extent of protonation and base stacking (hypochromic), reveal Tm values which agree with values derived from uv melting profiles. The 760–830‐cm−1 envelope, which is not directly sensitive to cytosine residue protonation, but includes information associated with base stacking (the 780‐cm−1 band) and the nature of the phosphodiester backbone (the frequency‐dependent 805‐cm−1 component), exhibits Tm values which deviate from the values obtained from the other bands. The observed differences are pH‐dependent and correlate well with the extent of deprotonation that takes place in the denaturation process. Details of the spectrum of neutral and protonated poly(C) from pH 7 to 4.1 are discussed and related to the nature of the thermal denaturation process.
DNA and RNA oligomer thermodynamics: The effect of mismatched bases on double‐helix stability
Authors: Nelson Jeffrey W. , Martin Francis H. , Tinoco Ignacio
Published: December 2004

The thermodynamic parameters for the double‐strand formation of the molecules rCAmG + rCUnG, m,n = 5–7, and dCAmG + dCTnG, m,n = 5,6, were measured from optical melting curves. Normal helices are formed when m = n. The deoxyoligomers are more stable than the ribo‐oligomers, due to a more favorable enthalpy. Double helices with mismatched bases can be formed by mixing oligomers with m ≠ n. Such helices may form several possible structures. A structure with a dangling base is favored over a structure with a bulged base. The destabilization of the double strands by the formation of a bulged base was determined to be greater than 1.6 kcal/mol at 10°C. The extent of aggregation in the oligomer double strand rCA7G·rCU7G was determined using ultracentrifugation equilibrium. The possible effects of aggregation on the determination of the thermodynamic parameters for double‐strand formation are discussed.
Structure of micelles formed by monodisperse hexa‐(γ‐benzyl‐L‐glutamate) in solution
Authors: Imae Toyoko , Okahashi Kenji , Ikeda Shoichi
Published: December 2004

The angular dependence of light scattering and the concentration dependence of the relative viscosity have been measured in solutions of o‐nitrophenylthio‐hexa‐(γ‐benzyl‐L‐glutamate) ethylamide in ethylene dichloride. Both the reduced intensity of scattered light and the reduced viscosity of the solution suddenly increase above a certain critical concentration, below which both of them remain low and constant. The Debye plot of light scattering indicates that primary micelles having an aggregation number 48 are formed at the critical micelle concentration and that secondary micelles, each consisting of 294 molecules, then appear in increasing amounts with increasing concentration beyond the critical micelle concentration. The secondary micelle is rodlike and has a length of 1170 Å, if it is rigid. An analysis of the reduced viscosity leads to the intrinsic viscosity for the primary micelle, 0.360 dL g−1, and to that of the secondary micelle, 1.28 dL g−1. If the secondary micelle is represented by a prolate ellipsoid, it should have an axial ratio of 47. If the polypeptide chains are extended in the micelle, the observed aggregation number and axial ratio of the secondary micelle can well accommodate the intermolecularly hydrogen‐bonded in‐register β‐structure of anti‐parallel chains. In the primary micelle, some folded polypeptide chains are involved, and an intermolecularly hydrogen‐bonded out‐of‐register structure would form a rather open network.
Nmr studies of the rates of proline cis–trans isomerization in oligopeptides
Authors: Grathwohl Christoph , Wüthrich Kurt
Published: December 2004

1H‐Nmr was used to measure the rate of cis–trans interconversion of X‐Pro bonds in linear and cyclic oligopeptides. k(cis → trans) = 2.5 × 10−3 s−1 at 25°C was found for the zwitterionic form of H‐Ala‐Pro‐OH, in good agreement with earlier measurements. Replacement of Ala by Phe, Tyr, or Trp resulted in a 10‐fold slower interconversion rate, whereas after substitution of Ala by His or Glu, the rate decreased only slightly. Independent of the residues X, the interconversion rate was increased by a factor of ca. 20 when the peptide chain was elongated by addition of Ala to the C‐terminal Pro. An additional increase by a factor of 6 was observed when going from the protected linear peptide CF3CO‐Gly‐Gly‐Pro‐Ala‐OCH3 to the closely related cyclic compound c[‐Gly‐Gly‐Pro‐Gly‐Ala‐]. These data are evaluated with regard to their possible use in future studies on the role of X‐Pro cis–trans isomerization in the kinetics of protein folding.
Free water in hair keratin? a depolarization thermal‐current study
Authors: Leveque J. L. , Garson J. C. , Pissis P. , Boudouris G.
Published: December 2004

In the keratin structure, the presence of water having the usual properties of “bulk water” has been discussed for many years. Results of experiments designed to study this question are conflicting and thus do not allow a precise idea of the state of water molecules in keratin at high hydration. A recent depolarization thermal‐current (DTC) study gave good evidence for the presence of a well‐defined DTC peak in the depolarization spectrum of ice. Initially, we verified the exact characteristics of this particular peak under our own experimental conditions. Subsequently, we looked for and found this ice peak in keratin samples. It appears when the water content is 19% or greater. The meaning of this result is discussed in relation to the other experimental results reported in the literature dealing with this question.
High‐field magnetic birefringence study of the structure of rodlike phages Pf1 and fd in solution
Authors: Torbet J. , Maret G.
Published: December 2004

The magnetic orientation of the rodlike bacterial viruses Pf1 and fd in dilute aqueous solution was detected by high‐resolution birefringence measurements. Partial alignment takes place parallel to the magnetic field chiefly due to the diagmagnetic anisotropy of the highly ordered α‐helices in the coat protein. It follows from the analysis of the experimental diamagnetic anisotropy that in both phages the α‐helices and aromatic amino acids are oriented relatively parallel to the phage axis. In Pf1 these become, on average, more nearly parallel as the temperature is reduced from about 25 to 5°C. These results demonstrate that high‐resolution magnetically induced birefringence measurements can be used to investigate some general structural features of complicated biological particles in solution.
Viscometric and static light scattering studies on an exopolysaccharide produced by Lactobacillus delbrueckii subspecies bulgaricus NCFB 2483
Authors: Goh Kelvin Kim Tha , Hemar Yacine , Singh Harjinder
Published: December 2004

The rheological properties and molecular parameters of a purified exopolysaccharide (EPS) produced by a ropy strain of Lactobacillus delbrueckii subsp. bulgaricus NCFB 2483 were investigated. Using capillary viscometry, an intrinsic viscosity of 2,013 mL/g was obtained. The flow curves were fitted by both the Carreau and the Cross equations for shear‐thinning fluids, with the Carreau equation giving a better fit. The Cross equation fitted fairly well the plot of reduced viscosity as a function of reduced shear rate with an exponent value (1 − n) of ∼ 0.76, typical of random coil polymers. Furthermore, the concentration dependence of the viscosity plot showed a gradient of approximately 1.1 in the dilute regime and 3.3 in the semidilute regime. Molecular parameters were obtained using a multiangle laser light scattering technique. The 2483 EPS molecules had a weight‐average molar mass of approximately 2 × 106 Da and a z‐average root mean square radius (RMS) of approximately 151 nm. From the light scattering data, the bacterial EPS was also found to have a low polydispersity index (∼ 1.15) and adopt a random coil conformation. © 2004 Wiley Periodicals, Inc. Biopolymers, 2005
Engineering disulfide bonds of the novel human β‐defensins hBD‐27 and hBD‐28: Differences in disulfide formation and biological activity among human β‐defensins
Authors: Schulz Axel , Klüver Enno , Schulz‐Maronde Sandra , Adermann Knut
Published: December 2004

Human β‐defensins comprise a large number of peptides that play a functional role in the innate and adaptive immune system. Recently, clusters of new β‐defensin genes with predominant expression in testicular tissue have been discovered on different chromosomes by bioinformatics. β‐Defensins share a common pattern of three disulfides that are essential for their biological effects. Here we report for the first time the chemical synthesis of the new fully disulfide‐bonded β‐defensins hBD‐27 and hBD‐28, and compare the results with synthetic procedures to obtain the known hBD‐2 and hBD‐3. While hBD‐27 was readily converted into a product with the desired disulfide pattern by oxidative folding, hBD‐28 required a selective protective group strategy to introduce the three disulfide bonds. The established synthetic processes were applied to the synthesis of hBD‐2, which, like hBD‐27, was accessible by oxidative folding, whereas hBD‐3 required a selective strategy comparable to hBD‐28. Experimental work demonstrated that trityl, acetamidomethyl, and t‐butyl are superior to other protection strategies. However, the suitable pairwise arrangement of the protective groups can be different, as shown here for hBD‐3 and hBD‐28. Determination of the minimum inhibitory concentration against different bacteria revealed that hBD‐27, in contrast to other β‐defensins tested, has virtually no antimicrobial activity. Compared to the other peptides tested, hBD‐27 showed almost no cytotoxic activity, measured by hemoglobin release of erythrocytes. This might be due to the low positive net charge, which is significantly higher for hBD‐2, hBD‐3, and hBD‐28. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2005
High molecular weight poly‐L‐proline: Synthesis and physical‐chemical studies
Authors: Fasman G. D. , Blout E. R.
Published: December 2004

Poly‐L‐proline in the molecular weight range 50,000–90,000 has been synthesized from L‐proline‐N‐carboxyanhydride. The molecular weight obtained is dependent on the initiator concentration. The rate constants for the polymerization have been determined by measuring the CO2 evolution. By observation of rotation during the polymerization, it is possible to deduce the conformation of the polymer in the polymerization solution. It is concluded that the immediate product of the polymerization is neither pure form I nor pure form II. The differences between form I and form II of poly‐L‐proline have been further characterized by measurements of their ultraviolet rotatory dispersion and their ultraviolet spectra.
Copolymers of L‐proline and sarcosine: Synthesis and physical‐chemical studies
Authors: Fasman G. D. , Blout E. R.
Published: December 2004

A series of high molecular weight copolypeptides of L‐proline and sarcosine have been synthesized. Experimental evidence is presented which indicates that the products are true copolymers rather than mixtures of homopolymers. In contrast to poly‐L‐proline I, a copolymer of L‐proline‐sarcosine I containing approximately 50% sarcosine is soluble in water. Two molecular conformations of the copolymers, similar to those found for polyproline, have been characterized by means of infrared spectroscopy and optical rotatory dispersion. The residue rotation of L‐proline has been obtained from the copolymers and is −250°.
Dielectric dispersion of polyglutamic acid solution
Authors: Takashima Shiro
Published: December 2004

The dielectric dispersion of polyglutamic acid (PGA) was studied in the pH range of 4–9.8. Three different dispersion curves were obtained. Above pH 6.0, where PGA has a random coil configuration, the dielectric dispersion is characterized by a large dielectric increment (ca. 450) and a relaxation time of 10–12.7 × 10−6 sec. Between pH 6.0 and 5.0, where PGA is in a transitional state with small viscosity, a dispersion curve with very small dielectric increment and also small relaxation time was observed. Below pH 5.0, where PGA has a helical configuration, the dispersion is characterized by a relaxation time of 10–12 × 10−6 sec. and a dielectric increment of about 120. The dipole moment of coil and helical forms of PGA were calculated by using Allgen's equation, and qualitative discussions of these dielectric properties are presented.
Dilatometric and refractometric studies of the helix—coil transition of poly‐L‐glutamic acid in aqueous solution
Authors: Noguchi Hajime , Yang Jen Tsi
Published: December 2004

The helix—coil transition of poly‐L‐glutamic acid (PGA) in aqueous solutions was followed by volume changes, ΔV, and also differential refractive indices, Δn. The increase in ΔV or decrease in Δn upon mixing the sodium salt of PGA with dilute HCl gave three straight lines between pH 7 and 4, the two breaks corresponding to the transition zone observed by other physical methods. For the reaction: COO− + H+ → CO‐OH, ΔV per mole of H+ bound was 11.4 and 11.1 ml. in 0.01 and 0.2M NaCl solutions, respectively. An additional conformational change of about 0.5–1 ml. per amino acid residue was observed for the reaction: coil → helix, after taking electrostatic interaction into consideration. This was probably due to the release of the water of hydration at the amide linkages when the polypeptide coil is converted into the α‐helix, or even the occurrence of voids in the polypeptide chain as a result of imperfect packing of the atoms, although the origin of this volume change is still not fully understood at the present time. The volume changes as calculated from Δn by assuming a constant polarizability of the polymer was found to be higher for the association reaction than those mentioned above. On the other hand, the calculated ΔV for the transition was in fair agreement with those by direct measurements.
Effect of hydrophobic bonding on the stability of poly‐L‐alanine helices in water
Authors: Bixon Mordechai , Scheraga Harold A. , Lifson Shneior
Published: December 2004

The Lifson‐Roig theory for the helix‐random coil transition in polyglycine has been modified to take side‐chain interactions into account. The modified theory is developed specifically for poly‐L‐alanine which probably contains a β1‐α4 hydrophobic bond. A conditional probability, expressing the strength of such a hydrophobic bond, is evaluated from the Nemethy‐Scheraga data for the free energy of formation of the bond. This, together with the conditional probabilities for the states of the backbone chain, permit an evaluation of the partition function and properties of the helix‐random coil transition. It is seen that the hydrophobic bond renders the poly‐L‐alanine helix much more stable than the corresponding polyglycine one, in agreement with data obtained by Gratzer and Doty.
β‐Conformation in γ‐globulin
Authors: Imahori Kazutoma
Published: December 2004

An oriented film of γ‐globulin fibrils obtained by precipitating human γ‐globulin with anti‐human γ‐globulin horse serum was examined with polarized infrared light. When the film was examined with light polarized parallel to the fibril axis, the amide I band was observed at 1635 cm.−1, indicating the cross‐β structure in γ‐globulin fibrils. The reasonableness of this structure for γ‐globulin is discussed by comparing its optical rotatory dispersion constants with those of poly‐O‐acetyl‐L‐serine, which had previously been shown to be the intrachain cross‐β structure.
Energy transfer between tryptophans and aromatic ligands in apomyoglobin
Authors: Luk Chun Ka
Published: December 2004

The binding of three aromatic molecules to apomyoglobin has been investigated. In each case equilibrium dialysis studies and tryptophan fluorescence quenching studies indicate that a one to one complex has been formed. The fluorescence quenching studies further suggest that the binding of the aromatic molecules is at the heme site with possible involvement of the arginine CD3. Xenon, which is known to quench the fluorescence of aromatic hydrocarbons, is found to be bound to apomyoglobin‐aromatic molecule complexes and quenches the emission of the aromatic molecule in the complexes. Oxygen quenches pyrene fluorescence in water solution but does not quench the pyrene fluorescence from the apomyoglobin‐pyrene complex. This is explained by a slower rate of diffusion of oxygen to pyrene in the apomyoglobin‐pyrene complex.
Effects of salts on the nonequivalent stability of the α‐helices of isomeric block copolypeptides
Authors: Ihara Shoji , Ooi Tatsuo , Takahashi Sho
Published: December 2004

The stability of the α‐helices of isomeric block copolypeptides is nonequivalent, as reported previously. In order to explore the origin of the nonequivalence, the stability of α‐helix of two block copolypeptides, (L‐Ala)20‐(L‐Glu)20‐(L‐Phe) (designated as AEF) and (L‐Glu)20‐(L‐Ala)20‐(L‐Phe) (EAF), in aqueous solution was investigated as a function of pH, temperature, and salt concentration by the measurement of the α‐helical content using CD at 223 nm. The transition temperature, Tm, as a measure of the stability of the α‐helix, decreased with increasing the salt concentration for EAF, while Tm increased for AEF. The results indicate that electrostatic interactions affect the nonequivalence of such helical stability. Thermodynamic quantities, ΔG, ΔH, and ΔS, of the thermal transition from random coil to α‐helix were obtained by applying the curve‐fitting method to the data. The major contribution to the effects of salts seems to be the entropic term, not the enthalpy term. This is unexpected, since the salt ions would weaken electrostatic interactions between ionized groups and the dipole along the helical axis, which affect the enthalpy term. In addition, the dependence of the electrostatic effect on the salt concentration is different for EAF and AEF. There fore, the nonequivalence cannot be accounted for by only the electrostatic effect, suggesting that it originates from some intrinsic property of the α‐helix.
Hyaluronate diffusion in semidilute solutions
Authors: Wik K.‐O. , Comper W. D.
Published: December 2004

Analysis of the mutual diffusion coefficient of hyaluronate reveals that it rapidly increases with increasing concentration or decreasing ionic strength. The mutual diffusion coefficients analyzed by boundary relaxation in the analytical ultracentrifuge by either Raleigh interference optics or absorption optics (through the use of fluorescein‐labeled hyaluronate) yielded similar values. The theoretical treatment of the mutual diffusion coefficient has been analyzed in terms of experimentally measured intradiffusion coefficients and thermodynamic virial coefficients. Only approximate agreement between theory and experiment was found. The concept of formation of transient statistical network structures in semidilute solutions of hyaluronate was applied to evaluate a critical concentration at which network formation occurs. This has been discussed in relation to the marked decrease in the intradiffusion coefficient of hyaluronate with concentration. The formation of network structures in hyaluronate was found not to preclude the hyaluronate undergoing extremely rapid rates of mutual diffusion (with diffusion coefficients ∼30 × 10−11 m2 s1) under conditions of relatively large initial chemical potential gradients. Measurements of the unidirectional flux of hyaluronate for nonzero gradients demonstrated their marked sensitivity to the magnitude of the concentration difference across the boundary. An experimental feature of the unidrectional diffusion coefficients of hyaluronate is that they may be analyzed purely in terms of mutual and intradiffusion processes. The backflux diffusion coefficient (describing the flux against the imposed concentration gradient) appeared identical with the intradiffusion coefficient. The analysis of the various sources of errors made in this study suggests that the magnitude of the diffusion coefficients measured may be regarded only as approximate.
Kinetics of thermal denaturation of met‐hemoglobin in perturbed solvent: Relevance of bulk‐electrostatic and hydrophobic interactions
Authors: Cupane Antonio , Giacomazza Daniela , Cordone Lorenzo
Published: December 2004

We studied the kinetics of the heat denaturation (at 50°C) of met‐hemoglobin in the presence of various monohydric alcohols. The denaturation rate was slowed by the presence of small concentrations of methanol and ethanol; in all the other cases, i.e., at high concentrations of methanol and ethanol, and in the whole concentration range studied for iso‐ and n‐propanol, an increase in the denaturation rate was observed. Following a procedure already applied to the study of the effects of the same alcohols on the reaction of hemoglobin with oxygen, we separated the overall observed effects into contributions related to the variation of the bulk dielectric constant of the medium (bulk‐electrostatic contributions) and contributions not related to variations in this parameter (nonbulk‐electrostatic contributions). For all the alcohols, we found a unique correlation law connecting the above nonbulk‐electrostatic contributions with the analogous ones previously reported for the T → R transition of hemoglobin. This fact strongly supports the validity of the procedure used and suggests that nonbulk‐electrostatic contributions, relative to these two different processes, have a common background and are univocally determined by the extent of the “solvent perturbation” imposed by the presence of the perturbing cosolvents.
The poly(rU) coil: A minimum‐energy model that matches experimental observations
Authors: Hingerty Brian E. , Broyde Suse B. , Olson Wilma K.
Published: December 2004

A model of the randomly coiling form of poly(rU) based on minimum‐energy conformers of UpU is described. The blend of conformers is chosen to fit the CC rotational populations derived in nmr studies of UpU and poly(rU) and to match the experimental unperturbed dimensions of the poly(rU) chain. In addition, estimates of loop closure based on the model are comparable to the sizes of loops most frequently seen in model oligonucleotides. Approximately 60% of the conformers constituting the model are characterized by stacked, extended C2′‐endo ω′ωψ = tg−g+ rotations. The remainder of the chain is described by equal numbers of C3′‐endo A (ω′ωψ = g−g−g+) and Watson‐Crick (ω′ωψ = g−tt) helical arrangements.
Steady‐state opticohydrodynamic properties of DNA: Molecular weight dependence and the internal viscosity problem
Authors: Reeg Charles F. , Harrington Rodney E.
Published: December 2004

Extinction angles, flow birefringence, and intrinsic viscosities are compared for linear, bihelical DNAs from viral and other sources that span a range in molecular weight from ∼105 to 1.3 × 108. This range effectively spans the region over which transition from rigid‐rod to expanded‐coil hydrodynamic property behavior occurs. All DNAs are in identical, phosphate–EDTA, neutral‐pH buffers, 0.1M in NaCl. The extinction angle is a hydrodynamic property only and is thus particularly sensitive to effects of kinetic chain rigidity or internal viscosity. Our extinction angle results cannot be interpreted by any simple, single‐function theoretical expression. Rather, they must be divided into distinct high‐ and low‐molecular‐weight domains. The low‐molecular‐weight region is typical of rigid‐particle opticohydrodynamic property behaviour characterized primarily by particle orientation. The high‐molecular‐weight domain shows evidence for a finite internal viscosity effect, however, which can be interpreted as very nearly Kuhnian using Cerf's amplification of the Gaussian subchain model to include internal viscosity. It is found that the high‐molecular‐weight, monodisperse viral DNAs from T7, T5, and T2 bacteriophage show an internal viscosity contribution to the limiting extinction angle–shear rate ratio of ∼3 × 10−3 s. An effect of this magnitude may be marginally important in interpreting extinction angle and certain other hydrodynamic property data for high‐molecular‐weight DNA systems. Internal viscosity effects do not appear to be manifest in the ratio of flow birefringence to intrinsic viscosity, however, and the persistence length of the high‐molecular‐weight DNAs is found to be independent of molecular weight to within estimated experimental uncertainty.
Aggregation of apolar peptides in organic solvents. Concentration dependence of 1H‐nmr parameters for peptide NH groups in 310 helical decapeptide fragment of suzukacillin
Authors: Iqbal M. , Balaram P.
Published: December 2004

Peptide NH chemical shifts and their temperature dependences have been monitored as a function of concentration for the decapeptide, Boc‐Aib‐Pro‐Val‐Aib‐Val‐Ala‐Aib‐Ala‐Aib‐Aib‐OMe in CDCl3 (0.001–0.06M) and (CD3)2SO (0.001–0.03M). The chemical shifts and temperature coefficients for all nine NH groups show no significant concentration dependence in (CD3)2SO. Seven NH groups yield low values of temperature coefficients over the entire range, while one yields an intermediate value. In CDCl3, the Aib(1) NH group shows a large concentration dependence of both chemical shift and temperature coefficient, in contrast to the other eight NH groups. The data suggest that in (CD3)2SO, the peptide adopts a 310 helical conformation and is monomeric over the entire concentration range. In CDCl3, the 310 helical peptide associates at a concentration of 0.01M, with the Aib(1) NH involved in an intermolecular hydrogen bond. Association does not disrupt the intramolecular hydrogen‐bonding pattern in the decapeptide.
Far‐infrared absorption of nucleotides and poly(I)·poly(C) RNA
Authors: Beetz C. P. , Ascarelli G.
Published: December 2004

We have measured the ir absorption of 5′CMP, 5′IMP, and poly(I)·poly(C) from ∼25 to ∼500 cm−1. From a comparison of the data with the previously measured absorption of the corresponding nucleosides and bases we can identify several “lines” associated with the deformation of the ribose ring. Out‐of‐plane deformation of the bases contributes strongly to vibrations near 200 cm−1. The same ribose vibrations observed in the nucleotides are found in poly(I)·poly(C). They sharpen with increasing water absorption. A study of the spectra of poly(I)·poly(C) as a function of the adsorbed water indicates that water does not contribute in a purely additive fashion to the polynucleotide spectrum but depends on the conformation of the helix. However, the only spectral feature that shifts drastically with conformation is near 45 cm−1. Measurements at cryogenic temperatures indicate some sharpening of the spectrum of poly(I)·poly(C). Instead, no sharpening is observed in the spectrum of the nucleotides. Shear degradation of poly(I)·poly(C) produces significant spectral changes in the 200‐cm−1 region and sharpening of the features assigned to the low‐frequency ribose‐ring vibrations.
Examination of Haldane's first law for the partition of CO and O2 to hemoglobin A0
Authors: Wyman Jeffries , Bishop Gary , Richey Brough , Spokane Robert , Gill Stanley
Published: December 2004

A study of the oxygen replacement reaction of carbon monoxide‐saturated hemoglobin (HbA0) was carried out using spectroscopic, calorimetric, and pH titration methods. Under fully saturated conditions the replacement reaction can be defined by a single partition constant over all ratios of bound oxygen to carbon monoxide. This indicates that under saturating conditions Haldane's first law for the ligand binding of gas mixtures holds for any CO/O2 ratio. It further shows that there is no appreciable difference in relative CO‐O2 affinity between the α‐ and β‐chains. The same partition coefficient was found to hold for different pH, buffer, and allosteric effector conditions. The lack of any pH dependence of the partition coefficient was confirmed by the absence of proton changes for the replacement reaction. The temperature dependence of the partition coefficient and calorimetric results yield a value for the enthalpy of the reaction of −3.65 ± 0.29 kcal/mol/heme.
Model for the adsorption of cytochrome c at the water–mercury interface
Authors: Serre Paule‐Andrée , Haladjian Jean , Bianco Pierre
Published: December 2004

The effect of cytochrome c on the redox behavior of 1,4‐benzoquinone and cystine has been investigated by differential pulse polarography. The adsorption of cytochrome c on mercury surface produces a lowering of the reduction peak of 1,4‐benzoquinone and of the cystine prepeak. When the covering of the drop is maximal, no variation in peak height is observed. By using the Koryta equation, values between 1500 and 2300 Å2 for the surface area of one adsorbed cytochrome c molecule were obtained. The capacitance dependences on concentration and time have been determined by alternating‐current polarography, and lead to the surface area values of 2800 and 2700 Å2, respectively. Results are interpreted on the basis of an unfolding of cytochrome c molecules during the adsorption process. It is likely that a rather compact covering is obtained, but about 10% of the mercury surface seems to be unoccupied and corresponds to the accessible interstices between adjacent molecules.
Theory of protein secondary structure and algorithm of its prediction
Authors: Ptitsyn O. B. , Finkelstein A. V.
Published: December 2004

A molecular theory of protein secondary structure is presented that takes account of both local interactions inside each chain region and long‐range interactions between different regions, incorporating all these interactions in a single Ising‐like model. Local interactions are evaluated from the stereochemical theory describing the relative stabilities of α‐ and β‐structures for different residues in synthetic polypeptides, while long‐range effects are approximated by the interaction of each chain region with the averaged hydrophobic template. Based on this theory, an algorithm of protein secondary structure prediction is proposed and examples are given of “blind” predictions made before the x‐ray structural data became available.
Topological aspects of the conformational transformations in polypeptides and proteins
Authors: de Santis P. , Morosetti S. , Palleschi A.
Published: December 2004

The topological aspects of the conformational transformations in a polypeptide chain are investigated in relation to the problem of selecting the minimum‐energy pathways in protein folding.
Cis–trans peptide‐bond equilibria in cyclic hexapeptides
Authors: Kopple Kenneth D. , Zhu Peng‐Peng , Go Anita
Published: December 2004

Data are presented on the position of the equilibria of cyclo(Xxx‐Pro‐Yyy)2 backbones between forms with two cis Xxx‐Pro peptide bonds and forms with only trans peptide bonds. These data are interpreted in terms of two factors: a solvent‐independent steric interaction between the Xxx and Pro side chains, and the ability of solvent to influence the transannular electrostatic interaction between NH and CO groups of the Xxx units in the all‐trans form.