bluuebunny/crossref_metadata_2025 huggingface dataset:
Competitive cooperative bindings of a small ligand to a linear polymer. II. Investigations on the mechanisms of proflavine binding to poly(A) and DNA
Authors: Dourlent M. , Hogrel J. F.
Published: December 2004

Experimental binding isotherms relative to the interactions between proflavine and poly(A) or DNA are analyzed by comparison with theoretical models dealing with competitive cooperative bindings.

In the case of poly(A), there are apparently no specific binding sites for the positive co‐operative binding (complex I) leading to dye aggregation along the polyanionic chain. The second complex (complex II) seems to involve specific base‐dye interactions, but it cannot be said whether this binding displays negative cooperativity or noncooperativity. None of the two simpler theoretical models agree quantitatively with all experimental data. A plausible interpretation can be given if it is assumed that (i) the electrostatic binding of one isolated bound dye molecule (nucleus of complex I) involves a definite interaction between a phosphate group and the positive charge of the dye; (ii) the structure of complex II is such that a dye–phosphate ionic interaction is maintained.

In the case of DNA, our model of monoexclusive interactions fits the data more closely than does the model of biexclusive interactions. This gives experimental support for structural models in which the intercalated molecule interacts preferentially with one strand of the double helix and blocks only one phosphate for electrostatic binding. In order to propose a mechanism consistent with equilibrium and relaxation kinetic data, a modified reaction scheme is considered which takes account of the cooperativity effects in external binding and extends previous models.
Kinetic study of cooperative binding reaction of toluidine blue to poly(α,L‐glutamic acid) by means of the electric‐field pulse method
Authors: Ushio Hidetoshi , Yasunaga Tatsuy , Sano Takayuki , Tsuji Yoshikuni
Published: December 2004

Interaction of toluidine blue with helical and randomly coiled poly(α,L‐glutamic acid) was studied with absorption spectra, titration, and electric‐field pulse measurements. The obtained values of various parameters for the helical form of poly(α,L‐glutamic acid)differed from those for its coiled form. The difference of parameters in these two forms of poly(α,L‐glutamic acid) was attributed to differences of the binding mechanism in both forms. Furthermore, the binding of toluidine blue to poly(α,L‐glutamic acid) was considered to be due to hydrogen binding in the helical conformation and ionic interaction in the coiled conformation of the polymer.
An analysis of the association of collagen based on structural models
Authors: Cunningham Leon W. , Davies Hugh A. , Hammonds R. Glenn
Published: December 2004

The existence and distribution of vertical, interacting edges on cylindrical surfaces, which were derived from the basic structural features of the collagen molecule, have been examined as a function of the angle θ of the superhelix. Over the range θ = 26°–33° and near θ = 36°, the strongest intermolecular association was detected at 29.95°. This model exhibited three similar, self‐interacting edges, separated by approximately 120°. The potential for three similar but nonidentical edges lies in the geometry of the collagen molecule, but the existence of such edges and their ability to self‐associate is dependent upon the unique amino acid sequence. The relative strengths of association of each edge with itself and with the other edges are not identical, but the present analysis does not permit a judgment as to whether this variation could result in functional specificity in such interactions. All three chains participate in each edge though their contribution to the relative interaction strength is not identical.

These edges showed distinct maxima when displaced past one another by integral intervals of D, where D = 233 residue positions (quarter‐stagger). The strongest relative interaction occurs at a displacement of 1D.
An interpretation of the depolarization of the fluorescence of diphenylanthracene in solutions of polymers
Authors: Mazo Robert M.
Published: December 2004

It is argued that the decrease of fluorescence depolarization observed when diphenylanthracene is dissolved in poly(γ‐benzyl‐L‐glutamate) or polystyrene solution is due to short‐range interactions, and not to long‐range hydrodynamic interactions. Estimates of the hydrodynamic effect are given. Rough estimates of the effect to be expected on the short‐range hypothesis are in qualitative agreement with experiment.
Circular dichroism of collagen, gelatin, and poly(proline) II in the vacuum ultraviolet
Authors: Jenness Duane D. , Sprecher Cindy , Johnson W. Curtis
Published: December 2004

Circular dichroism spectra for acid‐soluble calfskin collagen, gelatin, and poly(proline) II in solution have been extended into the vacuum ultraviolet region. The extended spectrum of gelatin reveals that the circular dichroism of this unordered polymer is more closely related to the spectrum of charged polypeptides than might be evident from near ultraviolet work. A short‐wavelength band is found at about 172 nm, which corresponds in position, magnitude, and sign to a band recorded earlier for poly(L‐glutamic acid) at pH 8.0. This band is observed in a helical structure for the first time in the vacuum ultraviolet circular dichroism and absorption spectra of poly(proline) II. Both circular dichroism and absorption spectra point to the assignement of this band as the nσ*. Neither the nσ* nor the expected positive lobe of the ππ* helix band is observed in the extended circular dichroism spectrum of collagen. We postulate that these two bands cancel here in analogy to the case of α‐helical poly(L‐glutamic acid).
The importance of coulombic interactions for the induction of β structure in lysine oligomers by sodium dodecyl sulfate
Authors: Mattice Wayne L. , Harrison William H.
Published: December 2004

Circular dichroism spectra have been obtained for tri(L‐lysine), tetra(L‐lysine), and penta(L‐lysine) in aqueous sodium dodecyl sulfate at 25°C. None of the oligomers are affected significantly by sodium dodecyl sulfate at detergent concentrations exceeding 0.01 M. Literature results show that the high‐molecular‐weight polymer forms a β strucure under these conditions. At detergent concentrations near 3.5 × 10−4 M the penta(L‐lysine), but not the smaller oligomers, undergoes a conformational change. Its circular dichroism under these conditions is essentially identical to that observed with poly(L‐lysine) when it forms a β structure in sodium dodecyl sulfate. Solutions of the penta(L‐lysine), which exhibit this modified circular dichroism, are also turbid, leading to the conclusion that the oligomer has formed an intermolecular β structure. When these experiments are conducted in the presence of 0.1 M sodium hydroxide, the sodium dodecyl sulfate produces neither turbidity nor a modified circular dichroism spectrum. These observations provide compelling evidence that Coulombic interaction between the anionic detergent head and the cationic lysyl amino groups is essential for the conformational change induced in penta(L‐lysine) by sodium dodecyl sulfate.
Hyperfine structure in melting profile of bacteriophage lambda DNA
Authors: Gotoh Osamu , Husimi Yuzuru , Yabuki Sadato , Wada Akiyoshi
Published: December 2004

A high‐resolution plotter of differential melting profiles of DNA, RNA, or related biopolymers with an on‐line mini‐computer is described. With this device, more than 15 transition steps were identified in the thermal melting profile of DNA from bacteriophage lambda. These fine structures were found to be reproducible, and some of them disappear in the deletion mutant.

To Examine the melting profile, computer simulations for several hypothetical polynucleotide sequences were performed, and compared with experimental data. The sharp peaks that appeared in the differential melting profile of λ DNA may come from some homogeneous sequences of 500 bases or longer.
Structural investigations on DNA·protamine complexes
Authors: Herskovits T. T. , Brahms J.
Published: December 2004

Protamine·DNA complexes in film and in solution have been investigated by means of infrared linear dichroism, ultraviolet circular dichroism, and laser Raman spectroscopy. At high relative humidity and in solution both infrared linear dichroism and ultraviolet circular dichroism indicate the presence of a modified B form of DNA (designated as B* in our other papers27,28,46). This modified B form is characterized by a change of the orientation of the \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{OPO} $\end{document} bisector angle by about 4° with respect to the helical axis when compared to the B form of DNA. At decreasing relative humidities the same modified B form is maintained and no structural transitions B → A (or B → C) normally occurring in free DNA were observed. The absence of the A form in these complexes was also confirmed by laser Raman scattering studies of protamine·DNA complexes. On the basis of these results, a model of the protamine·DNA complex is proposed, which suggests that the presence of apolar amino‐acid residues, and probably the folding of the polypeptide chain, is responsible for preventing the B‐to‐A transition; this occurs either by protecting the high‐humidity modified B form against dehydration or by steric interference of this protein probably located in one of the DNA grooves.
Hydrogen‐deuterium exchange of the tryptophan residues in bovine α‐lactalbumin
Authors: Takesada Hiroko , Nakanishi Mamoru , Hirakawa Akiko Y. , Tsuboi Masamichi
Published: December 2004

Effects of deuteration on the Raman spectrum of a tryptophan residue have been examined. The 1386 cm−1 line of deuterated tryptophan residue has been found to be useful for tracing the hydrogen‐deuterium exchange reaction of this residue in a protein. An examination on bovine α‐lactalbumin at pH 6.4 and at 20°C indicates that two of the four tryptophan residues exchange with a rate constant much greater than 9 × 10−4 sec−1, while the other two exchange with a rate constant of 4 × 10−5 sec−1. The latter two have been assigned to Trp 28 and Trp 108 of this protein. The kinetics of hydrogen‐deuterium exchange reaction of completely “free” tryptophan residue have been examined by a proton magnetic resonance study on tryptophan itself. By taking the result of this examination into account, the chance of exposure to the solvent for Trp 28 or Trp 108 has been estimated to be 3 × 10−6 at pH 6.4 and at 20°C.
Influence of ribose 2′‐O‐methylation on GpC conformation by classical potential energy calculations
Authors: Stellman Steven D. , Broyde Suse B. , Wartell Roger M.
Published: December 2004

Potential energy calculations were employed to examine the effect of ribose 2′‐O‐methylation on the conformation of GpC. Minimum energy conformations and allowed conformational regions were calculated for 2′MeGpC and Gp2′MeC. The two lowest energy conformations of 2′MeGpC and Gp2′MeC are similar to those of GpC itself. The helical RNA conformation (sugar pucker‐C(3′)‐endo, ω′ and ω,g−g−, bases‐anti) is the global minimum, and a helix‐reversing conformation with ω′, ω in the vicinity of 20°, 80° is next in energy. However, subtle differences between the three molecules are noted. When the substitution is on the 5′ ribose (Gp2′MeC), the energy of the helical conformation is less than that of GpC, due to favorable interactions of the added methyl group. When the substitution is at the 3′ ribose (2′MeGpC) these stabilizing interactions are outweighed by steric restrictions, and the helical conformation is of higher energy than for GpC. Furthermore, the statistical weight of the 2′MeGpC g− g− helical region is substantially less than the corresponding weight for Gp2′MeC. In addition, 2′MeGpC′s methoxy group is conformationally restricted to a narrow range centered at 76°. This group has a broadly allowed region between 50 and 175° in Gp2′MeC. These differences occur because the appended methyl group in 2′MeGpC is located in the interior of the helix cylinder, as it would be in polynucleotide, while it hangs unimpeded in Gp2′MeC. These findings suggest that 2′‐O‐methylation has both stabilizing and destabilizing influences on the helical conformation of RNA. For 2′MeGpC the destabilizing steric hindrance imposed by the nature of the guanine base dominates.
The effect of changes in salt concentration and pH on the interaction between glycosaminoglycans and cationic polypeptides
Authors: Schodt Kathleen P. , Gelman Robert A. , Blackwell John
Published: December 2004

Circular dichroism (CD) spectroscopy has been used to investigate the effects of changes in salt concentration and pH on the interactions between basic polypeptides and connective tissue glycosaminoglycans in dilute aqueous solution. The polypeptides undergo conformation‐directing interactions in the presence of glycosaminoglycans, which are subject to transitions as the ionic strength and pH are varied. For poly(L‐lysine), the conformational change due to interaction breaks down as the ionic strength (monovalent ions) is increased. Based on the ionic strength at which disruption occurs, the glycosaminoglycans can be placed in order of increasing strength of interaction: chondroitin 6‐sulfate, hyaluronic acid, chondroitin 4‐sulfate, heparin, and dermatan sulfate. Prior to the conformational transition, scattering effects are observed, indicating the development of larger aggregates. Each glycosaminoglycan induces α‐helicity for poly(L‐arginine), which does not break down as the ionic strength is increased, indicating a stronger interaction for this polypeptide. The pH‐induced transitions are in the pH range 2.5–3.8 and are probably related to deionization of carboxyl groups. For poly(L‐lysine) the conformational effect is disrupted at low pH. For poly(L‐arginine), the transitions are not complete, but appear to correspond to an increase in scattering.
Kinetics of γ‐benzyl‐L‐glutamate NCA's polymerizations and molecular‐weight distributions on corresponding polymers
Authors: Rinaudo M. , Domard A.
Published: December 2004

The kinetics of γ‐benzyl‐L‐glutamate NCA's polymerizations in dioxane as solvent are discussed. The partial orders respective to [A], the NCA concentration and [I0], the initial initiator concentration are given; the rate constants are deduced and a mechanism is proposed to justify a rate of polymerization Vp = k[A][I0]2.

The dependence of the rate constants on the conformation of the growing chains is demonstrated; the acceleration is attributed to the ordered structures favorable to hydrogen bonding. The kinetics of aging have also been examined and discussed; it is shown that they cannot modify the kinetics of polymerization.

The DPn were obtained on the same samples before and after debenzylation; it is proved that at any concentration, DPn ≃ [A0]/[I0].

The molecular‐weight distributions were obtained by chromatography and a polydispersity lower than 1.3 was deduced for each sample. The trimodal distribution, appearing as soon as [A0]/[I0] is larger than 3, is attributed to the existence of the three structures σ, β, and α. The weight fraction of each of the structures was correlated to the kinetics of polymerization.
Fluorescence of proteins in aqueous neutral salt solutions. II. Influence of monovalent cation chlorides, particularly cesium chloride
Authors: Altekar Wijaya
Published: December 2004

The effects of varying concentrations of monovalent cation chlorides on the fluorescence of nine proteins were studied. These are discussed in terms of “direct” or “indirect” interactions with the aromatic amino acid residues. Cs+ is the only cation that quenches fluorescence of proteins due to “direct” interaction with aromatic amino acid residues. Quenching is due to collisional processes. An agreement with the Stern‐Volmer relationship is shown and the values of [(KQ)eff] and [(fa)eff] are calculated. These values confirm that the fraction of fluorescence accessible to Cs+ belongs to the “exposed” fluorophors. The mechanism of quenching by Cs+ is due to the heavy‐atom effect because phosphorescence enhancement is also seen at the same time.

The chlorides of Na+, K+, Rb+, NH4+, and Li+ do not have a similar effect on the fluorescence of all proteins. For a given protein a gradation of the same effect (i.e., quenching or dequenching) is seen. Interactions with factors that “inderectly” affect fluorescence of any protein are involved and the structural features of the protein are responsible for such “indirect” effects. The results indicate that neutral salts can act in more than one manner. The changes in fluorescence are indicative of electrostatic and lyotropic effects of ions. Only electrostatic interactions which occur in the vicinity of tryptophan in proteins are reflected. Li+ shows strong interactions with proteins. In 4 M LiCl, BSA, papain, and trypsin show fluorescence changes that are indicative of changes in protein structure.
Chiroptical properties of S‐proline conformational isomers
Authors: Richardson F. S. , Ferber S.
Published: December 2004

The chiroptical properties of S‐proline conformational isomers are examined on a theoretical model in which electronic wave functions are obtained from semiempirical molecular orbital calculations. The CNDO/S molecular orbital model is used to perform SCF‐MO calculations on ground state electronic structure and excited states are constructed in the virtual orbital‐configuration interaction approximation. Electronic rotatory strengths and dipole strengths are calculated directly from the complete (but approximate) molecular electronic wave functions. Zwitterionic, cationic, and anionic S‐proline structures are studied twotypes of conformational variables are represented in the calculations: (1) pyrrolidine ring conformation; and (2) rotation about the Cα‐COO− bond. Rotatory strengths are found to be somewhat sensitive to rotational isomerism about the Cα‐COO− bond, but are found to be rather insensitive to conformational changes within the pyrrolidine ring. The CD spectrum of zwitterionic S‐proline down to ∼160 nm appears to be well accounted for by the theoretically calculated results if conformational preferences with respect to rotation about the Cα‐COO− bond can be assumed to exist in solution media. Furthermore, spectra‐structure correlations are offered for the anionic and cationic forms of S‐proline in solution.
Theory of protein molecule self‐organization. I. Thermodynamic parameters of local secondary structures in the unfolded protein chain
Authors: Finkelstein A. V. , Ptitsyn O. B.
Published: December 2004

This paper presents the results of a stereochemical analysis of local interactions in unfolded protein chains (sterical repulsions, hydrogen, and hydrophobic bonds, etc.) by means of space‐filling modeles. On the basis of this analysis, an evaluation is made of thermodynamic parameters controlling the building‐in of all the 20 natural amino acid residues in all the physically possible position of local secondary structures (α‐helices, including α‐helices with short fragments of helices 310 at the C‐terminus; β‐bends of different types, helices 310, and their combinations) as well as thermodynamic parameters of separate hydrogen bonds of polar side groups with the neighbor peptide groups (“local contacts”). The accuracy of the obtained results is discussed.
31P Magnetic relaxation studies of yeast transfer RNAPhe
Authors: Hayashi Fumikazu , Akasaka Kazuyuki , Hatano Hiroyuki
Published: December 2004

The molecular mechanism of thermal unfolding of yeast tRNAPhe in 20 mM NaCl, 1 mM EDTA, and 10 mM MgSO4, pH 7.1 ± 0.1, has been examined by 31P magnetic relaxation and the nuclear Overhauser effect methods at 40.48 MHz in the temperature range of 22.5–80°C. Two partially resolved 31P resonance peaks of yeast tRNAPhe have been found to behave distinctively different in their longitudinal relaxation times. Individual intensities of the two partially resolved peaks have been quantitatively estimated by the use of relaxation data and the nuclear Overhauser effect as a function of temperature. The results of these observations largely support the earlier suggestion by Guéron and Shulman that the high‐ and low‐field parts of the main 31P resonance cluster originate from phosphorus nuclei belonging to the double‐helical and nonhelical regions of the tRNA, respectively. The spin‐lattice relaxation of the phosphorus nucleus has been found to be determined dominantly by the dipolar interaction with the surrounding ribose protons at this observing frequency. Rotational correlation times for the two portions of the ribose‐phosphate backbone of the tRNA have been separately deduced from the quantitative treatment of the 31P nuclear spin‐lattice relaxation times (T1) and the nuclear Overhauser effect. The result indicates that the two portions undergo internal motions at distinctively different rates of 108–1010 sec−1 order in the temperature range of 22.5–80°C, and that the thermal activation of these motions occurs at least in three distinctive steps, i.e., 22.5–31, 31–40, and 40–80°C. The rates of the internal motions and the associated activation energies in respective steps give some insight into the thermo‐induced change of the yeast tRNAPhe structure.
Poly(L–lysine)–DNA interactions in NaCl solutions: B → C and B → ψ Transitions
Authors: Weiskopf Manuel , Li Hsueh Jei
Published: December 2004

Thermal denaturation and circular dichroism (CD) properties of poly(L‐lysine)–DNA complexes vary greatly when these complexes are prepared differently, that is, whether by NaCl‐gradient dialysis starting from 2.0 M NaCl or by direct mixing at low salt. These differing properties were investigated in more detail by examining complexes, made by direct mixing in the presence of various concentrations of NaCl, both before and after the NaCl was dialyzed out of the complex solution. The precipitation curves of DNA due to polylysine binding indicate that such binding is noncooperative at zero salt; from 0.1 up to 1.0 M NaCl they exhibit varying degrees of cooperatively. Starting from zero salt, as the NaCl concentration used for complex formation is increased, both the CD and the melting properties of the complexes are shifted from those of directly mixed at zero salt to those of reconstitution: in the CD spectra there is a gradual shift from a B → C transition to a B → ψ transition; thermal denaturation results show a gradual increase in the melting temperatures of both free DNA (tm) and polylysine‐bound DNA (t′m). The progressive shift from B → C to B → ψ suggests a close relationship between these two transitions. Large aggregates of the complexes do not warrant the appearance of ψ‐type CD spectra: ψ‐spectra have been obtained in the supernatants of polylysine–DNA complexes made and measured at 1.0 M NaCl while slightly perturbed CD spectra in B → C transition have been observed in turbid solutions of fully covered complexes made at very low salt. If the complexes are made at intermediate salts and dialyzed to a very low salt, although up to 60% of the DNA is still bound by polylysine, the CD spectra of the complexes are shifted back to the B‐type CD characteristic of pure DNA.
Etude experimentale de L′auto‐association des molécules modèles dipeptidiques. III. Influence de la dimerisation stéréosélective sur les spectres de résonance magnétique protonique
Authors: Cung Manh Thông , Marraud Michel , Neel Jean
Published: December 2004

Proton magnetic resonance spectra of model dipeptide molecules R1–C′1O1–N2H2–CHR2–C′2O2–N3H3–R3 in CCl4 solutions exhibit splited signals when investigating on mixtures of L and D enantiomers differing from the racemic composition. The major effect is observed on amide proton signals which are the ones most sensitive to the ratio of aggregation. The stereoselective dimerization of enantiomeric molecules in the so‐called C5 conformational state is shown to be responsible for such a phenomenon, the intensity of which depends on the bulkiness of the side chain R2. A theoretical approach is proposed which gives predictions in close agreement with our own experimental findings.
Biphasic helix–coil transition of the ethidium bromide·poly(dA‐dT) and the propidium diiodide·poly(dA‐dT) Complexes. Stabilization of base‐pair regions centered about the intercalation site
Authors: Patel Dinshaw J. , Canuel Lita L.
Published: December 2004

The nonexchangeable base and sugar proton nmr resonances and the 260 and 278‐nm uv‐absorbance bands of the nucleic acid were utilized to monitor the temperature‐dependent duplex‐to‐strand transition of the alternating purine–pyrimidine deoxyribopolynucleotide poly(dA‐dT) in the absence and presence of ethidium bromide (EB) at phosphate/drug = 50, 28, and 15 and propidium diiodide (PI) at P/D = 50, 25, 15, 10, and 5 in 0.1 M salt between 50° and 100°C. The nmr and optical methods monitor a biphasic duplex‐to strand transition for the drug–poly(dA‐dT) complexes. We have monitored the dissociation of the drug from the complex at the ethidium bromide phenanthridine ring and side‐chain proton nmr resonances and the propidium diiodide 494 and 535‐nm uv‐absorbance bands and demonstrate that dissociation of the drug corresponds to the higher temperature transition in the biphasic nucleic acid melting curves. The lower temperature cooperative transition is assigned to the opening of drug‐free AT base‐pair regions in the drug–poly(dA‐dT) complex and exhibits an increase in transition midpoint and a decrease in cooperativity with increasing drug concentration. The higher temperature cooperative transition is assigned to the opening of AT base‐pair regions centered about the bound drug in the complex and exhibits an increase in the transition midpoint on raising the drug concentration. The large upfield shifts of the phenanthridine ring (but not side chain) protons of ethidium bromide on complex formation demonstrate intercalation of the drug between base pairs of the poly(dA‐dT) duplex. The nucleic acid base and sugar resonances of poly(dA‐dT) in 0.1 M phosphate undergo chemical shift changes between 0° and 50°C indicative of premelting conformational transition(s).
Interaction between poly(L‐lysine48, L‐histidine52) and DNA
Authors: Santella Regina M. , Li Hsueh Jei
Published: December 2004

Poly(Lys48, His52), a random copolypeptide of L‐lysine (48%) and L‐histidine (52%), was used as a model protein for investigating the effects of protonation on the imidazole group of histidines on protein binding to DNA. The complexes formed between poly(Lys48, His52) and DNA were examined using absorbance, circular dichroism (CD), and thermal denaturation. Although increasing pH reduces the charges on histidine side chains in the model protein, the protein still binds the DNA with approximately one positive charge per negative charge in protein‐bound regions. Nevertheless, CD and melting properties of poly(Lys48, His52)‐DNA complexes still depend upon the solution pH which determines the protonation state of imidazole group of histidine side chains. At pH 7.0, the complexes show two characteristic melting bands with a tm (46–51°C) for free base pairs and a t′m (94°C) for protein‐bound base pairs. The t′m of the complexes is reduced to 90°C at pH 9.2, although at this pH there is still one lysine per phosphate in protein‐bound regions. Presumably, the presence of deprotonated histidine residues destabilizes the native structure of protein‐bound DNA. The binding of this model protein to DNA causes a red shift of the crossover point and both a red shift and a reduction of the positive CD band of DNA near 275 nm. This phenomenon is similar to that caused by polylysine binding. These effects, however, are greatly diminished when histidine side chains in the model protein are deprotonated. The structure of already formed poly(Lys48, His52)·DNA complexes can be perturbed by changing the solution pH. However, the results suggest a readjustment of the complex to accommodate charge interactions rather than a full dissociation of the complex followed by reassociation between the model protein and DNA.
Amphipathic helixes and plasma lipoproteins: A computer study
Authors: Segrest Jere P. , Feldmann Richard J.
Published: December 2004

A molecular model for the lipid‐associating domains of the A and C plasma apolipoproteins was recently proposed. This model consists of helical regions with special properties termed amphipathic. In the present communication we present a computer analysis of the general occurrence of amphipathic helix patterns in proteins with known amino acid sequences.
Chromatin conformation: A systematic analysis of helical parameters from hydrodynamic data
Authors: Schmitz Kenneth S. , Ramsayshaw Barbara
Published: December 2004

Chromatin has a “bead‐and‐bridge” appearance when viewed by electron microscopy. We have used quasielastic light scattering and sedimentation velocity techniques to study the hydrodynamic properties of chicken erythrocyte chromatin multimers in an attempt to determine the superstructure in solution. The functional dependence of the friction factor on the number of core particles in the multimer was analyzed by the Garcia de la Torre‐Bloomfield formalism for a rigid array of odd‐sized beads. The hydrodynamic parameters of the monomeric and dimeric subunit components, i.e., bead size and separation, form the basis of a systematic determination of the superstructure. These calculations support a helical conformation for chromatin multimers containing up to twenty repeat units. It is also shown that an “equivalent” helix can be obtained if the bead separation distance is not constrained to that determined for the dimer.
Mutagen–nucleic acid complexes at the polynucleotide duplex level in solution: Intercalation of proflavine into poly(dA‐dT) and the melting transition of the complex
Authors: Patel Dinshaw J.
Published: December 2004

The nmr chemical shifts and line widths of the nucleic acid base and sugar proton resonances and the proflavine ring protons can be monitored through the melting transition of the proflavine + poly(dA‐dT) complex, phosphate/dye (P/D) ratio = 24 and 8 in 1M salt solution. The nucleic acid and mutagen protons in the complex are in fast exchange between duplex and strand states with the midpoint of the melting transition monitored at the nucleic acid resonances increasing from 72.6°C for poly(dA‐dT) to 78.1°C for the P/D = 24 complex and 83.4°C for the P/D = 8 complex in 1M salt solution. The melting transition monitored by the proflavine resonances were 80.0°C for the P/D = 24 complex and 84.3°C for the P/D = 8 complex in 1M salt solution. Since the nucleic acid is in excess at high P/D ratios, the nucleic acid transitions are an average for the opening of mutagen‐free and mutagen‐bound base‐pair regions, while the proflavine transitions monitor the melting of mutagen‐bound base‐pair regions. The observed 0.75 to 0.95 ppm unfield shift at all four proflavine protons on formation of the complex with poly(dA‐dT) provides direct evidence for intercalation of the mutagen between base pairs of the nucleic acid duplex. We have deduced the approximate overlap geometry between the proflavine ring and nearest‐neighbor base pairs at the intercalation site from a comparison between experimental proflavine complexation shifts and those calculated for various stacking orientations. The experimental chemical shift of the poly(dA‐dT) adenine H‐2 resonance in the duplex state in the absence and presence of proflavine suggests that intercalation occurs preferentially at dT‐dA sites. The selective chemical shift changes at the sugar H‐2′,2″ and H‐3′ resonances of the poly(dA‐dT) duplex on complex formation demonstrates changes in the sugar pucker and/or torsion angles of the sugar phosphate backbone at the intercalation site.
First‐neighbor frequencies of satellite DNAs from Drosophila nasutoides and Pagurus pollicaris from an analysis of their circular dichroism spectra
Authors: Gray Donald M. , Lee C. S. , Skinner Dorothy M.
Published: December 2004

From an analysis of their circular dichroism spectra, we find that the four (A + T)‐rich satellite DNAs of Drosophila nasutoides have distributions of first‐neighbor base paris that resemble those previously found for other (A + T)‐rich Drosophila satellites. We also apply our spectral analysis procedure for the first time to two (G + C)‐rich satellite DNAs, those from the hermit crab Pagurus pollicaris. We find that P. pollicaris satellite I cannot be accurately analyzed with our standard set of spectral components and that P. pollicaris satellite II appears to be much like the synthetic polymer poly[d(A‐G‐C‐)·d(G‐C‐T)] in its first‐neighbor content.
Laser Raman spectroscopy of acid phosphatase from rat liver
Authors: Twardowski Jacek
Published: December 2004

The Raman spectra of isoenzyme I and II in aqueous solution and in solid state are reported. The results reveal differences between these isoenzymes. These tertiary structures vary depending on whether the isoenzymes are solid or dissolved in H2O or D2O.
Measurement of the strongly held water of lysozyme by drying
Authors: Rao P. Bhaskara , Bryan William P.
Published: December 2004

A method for the measurement of water that is strongly held by lysozyme is described. This water is slowly removed by vaccum drying of lyophilized and can be titrated with the Karl Fischer reagent. Drying curves were obtained by mechanical pumping (moderate vacuum) and diffusion pumping (high vacuum) at 20°, 10°, 0°, −10° and −20°C. About 23 water molecules per lysozyme molecule are at least moderately held by the protein. These water molecules fall into several classes. Three to four of them are quite strongly held and may correspond to the three buried water molecules observed in the x‐ray analysis of lysozyme structure. The presence of tri‐N‐acetylglycosamine in the lysozyme active cleft has no effect on drying at 0°C. The method shows promise of being generally applicable to the measurement of small amounts of water which are strongly held by biological structures.
Relaxation and electrophoretic effects in polyelectrolyte solutions. I. Salt‐free solutions
Authors: Schmitt A. , Meullenet J. P. , Varoqui R.
Published: December 2004

Relations between relaxation and electrophoretic effects in salt‐free polyelectrolyte solutions are studied in terms of nonequilibrium thermodynamics and of binary friction coefficients. The significance and the method of determining these coefficients are explained. Consideration of experimental results and of long‐ and short‐range interactions suggests that the concept of “ion condensation” is needed to provide a consistent desciption of transport processes for linear flexible polyelectrolytes. Empirical relations previously used are shown to have only limited validity.
Helix‐coil transitions in nucleoprotein: Computer‐generated curves for independent melting of double‐stranded regions with fixed ends
Authors: Chipev C. C. , Staynov D. Z.
Published: December 2004

Helix‐coil transitions in nucleoprotein at low salt concentrations are known to be characterized by two phases of the process: independent melting of uncomplexed “naked” regions without rearrangement of proteins, followed, at higher temperatures, by melting of complexed DNA. Blocking at the ends of these regions increases their thermal stability and three is a shift of 10–20°C in tm of the melting profiles. In this study the basic assumption is that the loop entropy effect is mainly responsible for such stabilization. Calculations are made using conventional h‐c transition theory for a system of independently melted segments with fixed ends. Segments are either homosize or have randomly distributed lengths. Calculated melting curves are used to obtain tm, and transition width‐dependence on segment length (or average length when randomly distributed) and on the nucleation parameter σ. Base‐pair heterogeneity is taken into account by averaging over different base‐pair distributions in the individual segments, using Gaussian distribution around the overall (G+C)‐content. It is shown that this causes only an additional widening of the transition but no additional tm shift. Comparison is made with similar systems in the literature. The main conclusion drawn is that the treatment proposed may be useful for analysis of the lower temperature melting phase in nucleoprotein at low counterion concentrations. It may be used as an independent method to reveal the features of nucleoprotein structure.
Structural and conformational studies of polyriboadenylic acid in neutral and acid solution
Authors: Scovell William M.
Published: December 2004

Raman spectra of solutions of polyriboadenylic acid have been studied in the pH range of 7.2–5.2. Bands are identified which are sensitive to the characteristics of poly(rA) in the single‐and double‐stranded helical forms. Thermal melting profiles were obtained as a function of pH to monitor simultaneously the changes in (1) the phosphodiester backbone, (2) the base‐stacking interactions, (3) the perturbation of the PO unit, and (4) the degree of protonation at the N‐1 position in the adenine base. The temperature dependence of the intensity ratio of the bands at 725 and 705 cm−1 appears to be sensitive to the noncooperative and the cooperative thermal‐melting process for the single‐and double‐stranded forms of poly(rA), respectively. Concurrently, bands diagnostic of the degree of protonation reveal that the cooperative melting process for the “acid” poly(rA) clearly involves deprotonation.

The progressive perturbation of the 1100 cm−1 band with an increasing degree of protonation of poly(rA) is consistent with earlier suggestions regarding a PO‐(6)‐NH2 interaction in the double‐helical form of poly(rA). The stability of the double‐helix parallels the degree of protonation over the pH range studied as reflected in the tm values, which increase linearly with decreasing pH.
Experimental study on aggregation of model dipeptide molecules. V. Stereoselective association of leucine dipeptides
Authors: Cung Manh Thong , Marraud Michel , Neel Jean , Aubry André
Published: December 2004

Infrared spectroscopy and 1H nmr have been used to elucidate the association modes of leucine dipeptides in carbon tetrachloride solution. Two stereoselective types of aggregates have been evidenced. Homochiral molecules are associated in oligomeric aggregates and accommodate a β‐parallel‐like structure which was characterized by x‐ray diffraction. Heterochiral molecules are paired in centrosymmetrical dimers; the latter aggregation mode restricted to the dimer stage predominates in racemic solutions. A theoretical model proposed to account for this aggregation process is consistent with the experimental nmr data. Both homo‐ and heterochiral association constants are estimated from vapor pressure and nmr experiments.
A Raman and calorimetric investigation of 3′, 5′ GpG
Authors: Savoie Rodrigue , Klump Horst , Peticolas Warner L.
Published: December 2004

The Raman spectra of guanylyl (3′‐5′) guanosine (GpG) in solution in H2O and D2O at pH 3–7 have been recorded at various temperatures between 0 and 80°C. The results are consistent with the existence in the lower temperature range of stable aggregates formed by the stacking of GpG tetramers. The aggregates melt cooperatively near 60°C, which results in important changes in the spectra. Among these, a large increase in intensity of some of the bands assigned to the guanine residues shows that unstacking of the bases occurs at the melting. Also apparent in the spectra are changes in the intensity and frequency of band attributable to molecular groups involved in intermolecular hydrogen bonding between adjacent molecules in the complex. The melting temperature of GpG decreases by approximately 15°C upon lowering the concentration from 5 × 10−2 to 5 × 10−4M, as shown by Raman, calorimetric, CD, and uv measurements. The experimentally determined ΔH and ΔS for the melting transition are 9 Kcal/mol and 28 e.u./mol, respectively. The aggregation of GpG in 1.5 × 10−3M solutions was found to be very slow. The half‐time of the process, which roughly follows first‐order kinetics, is approximately 3 min at 10°C and 21 min at 35°C. The negative energy of activation associated with this reaction (−143 Kcal) indicated that the process involves intermediates whose concentrations decrease the temperatures raised, thus slowing down the overall process. The rate of disaggregation of GpG upon dilution to very low concentration is also extremely slow, indicating that the GpG aggregates, once formed, are very stable.
Ultraviolet photoelectron studies of 5‐halouracils
Authors: Padva A. , Peng S. , Lin J. , Shahbaz M. , Lebreton P. R.
Published: December 2004

Ultravoilet photoelectron spectroscopy has been employed to exmamin the valence electronic structure of 5‐fluorouracil, 5‐chlorouracil, 5‐bromouracil, and 5‐iodouracil. Photoelectron bands associted with the three highest π orbitals and the two oxygen atom lone‐pair orbitals were assigned by a comparison to similar bands observed in the photoelectron spectrum of uraciul. Bands arising from the halogen atom lone‐pair orbitals were assigned by comparing the present results with photoelectron spectra measured for halobenzenes, and by considering the linear dependence of halogen atom lone‐pair ionization potentials upon halogen atom electronegativities. The present spectroscopic results have been compared with results from studies of association constants of 5‐halouracil–adenine complexes. This examination in dicates that the complex association constants incresase as the ionization potentials of the highest occupied π orbital and the halogen atom lone‐pair orbitals of th halouracils decrease.
Experimental conformational study of two peptides containing α‐aminoisobutyric acid. Crystal structure of N‐acetyl‐α‐aminoisobutyric acid methylamide
Authors: Aubry A. , Protas J. , Boussard G. , Marraud M. , Neel J.
Published: December 2004

Some theoretical studies have predicted that the conformational freedom of the α‐aminoisobutyric acid (H‐Aib‐OH) residue is restricted to the α‐helical region of the Ramachandran map. In order to obtain conformational experimental data, two model peptide derivatives, MeCO‐Aib‐NHMe 1 and ButCO‐LPro‐Aib‐NHMe 2, have been investigated. The Aib dipeptide 1 crystallizes in the monoclinic system (a = 12.71 Å, b = 10.19 Å, c = 7.29 Å, β = 110.02°, Cc space group) and its crystal structure was elucidated by x‐ray diffraction analysis. The azimuthal angles depicting the molecular conformation (ϕ = −55.5°, ψ = −39.3°) fall in the α‐helical region of the Ramachandran map and molecules are hydrogen‐bonded in a three‐dimensional network. In CCl4 solution, ir spectroscopy provides evidence for the occurrence of the so‐called 5 and C7 conformers stabilized by the intramolecular i → i and i + 2 → i hydrogen bonds, respectively. The tripeptide 2 was studied in various solvents [CCl4, CD2Cl2, CDCl3, (CD3)2SO, and D2O] by ir and pmr spectroscopies. It was shown to accommodate predominantly the βII folded state stabilized by the i + 3 → i hydrogen bond. All these experimental findings indicate that the Aib residue displays the same conformational behavior as the other natural chiral amino acid residues.
Thermal perturbation techniques in characterizing ligand–macromolecule interactions: Theory and application to the proflavin‐α‐chymotryspin system
Authors: Sturgill Thomas W. , Johnson Robert E. , Biltonen Rodney L.
Published: December 2004

A thermal perturbation curve (TPC) is defined to be the derivative of the fractional degree of saturation, f, with respect to temperature, considered as a function of the natural logarithm of free ligand concentration, y. The theoretical framework for the use of such curves in the thermodynamic analysis of ligand binding to macromolecules is presented. The thermal perturbation curve either provides or complements the information obtained from the derivative binding isotherm ∂f/∂y. For a single set of identical and independent sites the TPC is identical to the derivative binding isotherm. Analysis of such a curve directly yield ΔH0 and ΔG0 for the binding reaction. In actual experimental work, however, the TPC can only be approximated because of “self‐buffering” effects relations between the parameter of the approximate curve and the thermodynamic quantities have been developed. This technique is applied to the proflavin‐α‐chymotryspin system to demonstrate its usefulness. The general features of thermal perturbation curves for cases of multiple sets of independent sites and cooperatively interacting sites have also been developed. The analysis of thermal perturbation curves in combination with other methods should provide a more powerful approach to the characterization of ligand‐macromolecule interactions.
Tail‐fiber attachement in bacteriophage T4D studied by quasielastic light scattering–band electrophoresis
Authors: Baran George J. , Bloomfield Victor A.
Published: December 2004

Mixtures of bacteriophage T4D particles with up to six tail fibres attached were seprated and analyzed in a quasielastic light scattering‐band electrophoresis apparatus. The electrophoretic mobilities and diffusion coefficients of the seprated bands were determined during the same experiment. Species differing in mobility by 0.05 × 10−4 cm2/V sec were resolved. Henry's electropheresis theory for spheres indicates that each tail fiber contributes about 140 effective positive charges to the phage structure. Estimate of the charge using the permanent dipole moment and the electrophorectic mobility (Bontje et. al. (1977) Biopolymers 16, 551–572) gives an effective charge of + 230 to −250 per tail fiber. The charge distribution on the fiberless particles was estimated to be −3380 on the head and −290 on the tail if the dipole moment was assumed positive and −1400 on the head and −1000 on the tail for a negative dipole. Tail‐fiber attachement does not proceed to completion in our invitro system, as substantial distributions as a function of tail‐fiber input indicates the reaction is a random, noncooperative process.
A quantitative analysis of excluded‐site effects for highly cooperative binding systems
Authors: Ramanathan Brinda , Schmitz Kenneth S.
Published: December 2004

Binding isotherms can provide quantitive information regarding the stability of a molecular complex. Theorectical studies in recent years have been directed to systems in which a single ligand can exclude more than one polymer site (excluded‐site effect). This system has minium of thre parameters to describe the binding data: the intrinsic binding constant, B; the remote‐neighbor cooperative paramaters, σq and the number of excluded sites, q. It is suggested in the present communication that precise values for these three parameters can be obtained by utilizing the characteristics of two forms of data representation: θ vs ln m and θ/m vs θ, where θ is the degree of saturation (0⩽θ⩽1) and m is the molality of free ligand. The matrix generation method is used to obtain empirical equations relating the midpoint location and slope at the midpoint of the θ vs ln m plot to the three molecular parameters. A modified Scatchard theory is also presented for highly cooperative systems, which results in an expression relaing the maximum in the θ/m vs θ plot to the molecular parameters σq and q, thus providing the third equation for the three unknown parameters. The novel method f analysis is illustrated with the AMP‐poly(L‐arginine) and oligocytidylate–T7 DNA sstems.
The effect of homologous amino acid replacement on the conformation of oligopeptides. I. Synthesis of co‐oligopeptides containing methionine and valine
Authors: Becker Jeffrey M. , Naider Fred
Published: December 2004

The preparation of a series of co‐oligopeptides Boc‐Val‐Metn‐OMe(n = 1–6), as sell as Boc‐Met3‐Val‐et2‐OMe and Boc‐Met3‐Val‐Met3‐Ome, is described. The synthesis was carried out by a classic method employing the mixed anhydride procedure (isobutylchloroformate) for all coupling reactions. All oligopeptides after purification were homogenous on silica thin layers and gave correct elemental analysis. They were judged to be optically pure using molar rotation studies at the sodium D line.