bluuebunny/crossref_metadata_2025 huggingface dataset:
Raman scattering of collagen, gelatin, and elastin
Authors: Frushour Bruce G. , Koenig Jack L.
Published: December 2004

The Raman spectra of collagen, gelatin, and elastin are presented. The Raman lines in the latter two spectra are assigned by deuterating the amide N‐H groups in gelatin and by studying the superposition spectra of the constituent amino acids. Two lines appear at 1271 and 1248 cm−1 in the spectra of collagen and gelatin that can be assigned to the amide III mode. Possibly, the appearance of two amide III lines is related to the biphasic nature of the tropocollagen molecule, i.e., proline‐rich (nonpolar) and proline‐poor (polar) regions distributed along the chain. The melting, or collagen‐to‐gelatin transition, in water‐soluble calf skin collagen is studied and the 1248‐cm−1 amide III line is assigned to the 31 helical regions of the tropocollagen molecule.

Elastin is thought to be mostly random and the Raman spectrum confirms this assertion. Strong amide I and III lines appear at 1668 and 1254 cm−1, respectively, and only weak scattering is observed at 938 cm−1. These features have been shown to be characteristic of the disordered conformation in proteins.
Nmr studies of mixtures of poly‐L‐lysine hydrobromide with water
Authors: Darke A. , Finer E. G.
Published: December 2004

1H, 2H, 13C, and 81Br nmr measurements of mixtures of poly‐L‐lysine hydrobromide with water have been carried out over a range of temperatures and water contents. When n (number of molecules of water per residue) ∼13 at room temperature, a transition occurs from a gel to a liquid phase. The liquid phase contains polymer molecules that are flexible, but contain more intramolecular structure than the same molecules in trifluoracetic acid solution. The gel phase contains junction zones of hexagonally packed α‐helices, linked by flexible regions of polypeptide chain. The α‐helical residues impart to their associated water molecules a slight anisotropy of motion, which is dectable by 2H nmr. These residues bind up to about seven molecules of water each; the other six required to complete the gel–liquid transition space out the polymer molecules, allowing increased segmental motion of the residues in the flexible regions. This increased motion reduces the energy of the flexible regions and thus increases the proportion of residues in them (increasing the temperature has the same effect); the transition occurs when insufficient residues remain in the α‐helical junction zones.
Quasi‐elastic light scattering by calf thymus DNA and λDNA
Authors: Schmitz K. S. , Pecora R.
Published: December 2004

The quasi‐elastic light‐scattering (homodyne) time‐correlation functions of calf thymus and λDNA are shown to contain contributions from at least two relaxation processes. A method of asymptotic analysis is described and used to obtain an estimate of the longest relaxation time as well as the “average” relaxation time and the mean‐squared dispersion in this average. Most theories of scattering from macromolecules in the limit of inifinite dilution predict that the longest relaxation time is due to translational self‐diffusion. The data obtained, however, indicate that the longest time is not simply related to the translational self‐diffusion coefficient of unaggregated macromolecules. It is also shown that the longest relaxation time of λDNA decreases in the later stages of the denaturation transition region. Some possible mechanisms for the origin of this long time are discussed, including a model of restricted motion of a molecule by its neighbors.
Circular dichroism of some mononucleosides
Authors: Brunner Wendel C. , Maestre Marcos F.
Published: December 2004

The circular dichroism (CD) and absorption spectra of uridine, thymidine, purine ribonucleoside, and the four adenine derivatives 2′‐deoxyadenosine, adenosine, adenosine‐3′,5′‐cyclic phosphate, and arabinosyl adenine were measured in water at pH 7 and pH 2. The absorption and CD spectra of the pyrimidines were simultaneously fitted to four Gaussian bands, and the dipole and rotational strengths of the electronic transitions determined. Adenine‐derivative CD spectra were determined by computer averaging six runs. The spectra showed CD bands at 268, 226, 209, and 195 nm. The band at 226 nm probably is an n–π* transition; the band at 209 nm cannot be detected without a computer. The CD and absorption spectra of purine ribonucleoside indicate three transitions in the 230–310‐nm region.
Spécificité de l'interaction DNA‐platine dosage du platine, pH métrie
Authors: Macquet J. P. , Theophanides T.
Published: December 2004

Interaction between the sodium salt of a DNA extracted from salmon sperm (41% GC) with [Pt(NH3)4]Cl2, [Pt(NH2(CH2)2NH(CH2)2NH2Cl]Cl,cis‐Pt(NH2(CH2)2NH2)Cl2,cis‐Pt(NH3)2Cl2,trans‐Pt(NH3)2Cl2, K[Pt(C2H4)Cl3], and K2[PtCl4) indicates at least three types of complexation. A correlation is found between the change of pH and the number of platinum atoms fixed per (AT + GC) unit. The first binding site is located on the G‐C pairs (guanine–cytosine), most likely the N‐7(G) site, as it was shown in a previous study of the guanosine‐platinum salts. The fixation of the second platinum atom by the pair (AT + GC) takes place with liberation of protons. In the case of the complexescis‐Pt(NH2(CH2)2NH2)Cl2,cis‐Pt(NH3)2Cl2, andtrans‐Pt(NH3)2Cl2the second interaction seems to involve simultaneously the N‐7(A) and the N‐1(G) and N‐3(C) sites. This latter intercrosslink between guanine and cytosine obviously liberates protons and the decrease of pH is related in this case to thetranseffect of the platinum compounds. The first two platinum atoms in the reaction of K2PtCl4] or the Zeise salt, K[Pt(C2H4)Cl3] with DNA are fixed on the G‐C pairs. A maximum of six platinum atoms per (AT + GC) unit were fixed in this case. Preliminary experiments with a DNA extracted from bacteriaMicrococcus lysodeikticus(72% GC) give similar results.
Conformational studies of alanine oligopeptides by nuclear magnetic resonance
Authors: Goodman M. , Ueyama N. , Naider F.
Published: December 2004

We have studied the nmr spectra of the series of alanine oligopeptides containing a methoxyethoxyethoxyacetyl blocking group on the N‐terminal residue and a morpholino blocking group on the C‐terminal residue. Spectra were measured in chloroform–trifluoroacetic acid solvent systems. For oligomers with chain lengths of five or more, “double peaks” are observed for the α‐CH protons. Addition of trifluoroacetic acid causes the peaks to coalesce. The amount of trifluoroacetic acid necessary for coalescence increases from the pentamer to the nonamer. These findings are general since alanine oligomers with different blocking groups exhibit similar “double peak” phenomena. We explain the “double peak” phenomenon in terms of specific folded forms of the oligopeptides which arise from intramolecular hydrogen bonding. Additional evidence for such hydrogen bonding is presented based upon infrared studies. Slight aggregation probably occurs for the pentamer and hexamer which may stabilize the folded forms.
Infrared spectroscopy of collagen and collagen‐like polypeptides
Authors: Doyle Barbara Brodsky , Bendit E. G. , Blout Elkan R.
Published: December 2004

The set of synthetic polytripeptides and polyhexapeptides which can adopt a triple‐helical form constitute a good model system for investigating collagen structure. Here we consider previous and new infrared spectroscopic studies on collagen and present the infrared spectra of a number of polymers with collagen‐like features.

The amide A band position for all triple‐helical polypeptides is higher than that observed for most proteins and polypeptides, and this high frequency appears to be related to the degree of supercoiling of the triple helix. It is possible that with increased supercoiling of the three chains the angles between the groups involved in the intramolecular hydrogen bonds become less favorable, or these bonds may become unusually long.

The frequency of the amide I band varies considerably for triple‐helical polypeptides with different amino acid sequences, and often minor bands are observed. This finding contrasts with the observations for polypeptides in a pleated sheet or α‐helical form, where the same amide I frequency is observed regardless of the amino acid composition. An explanation for this variation is proposed in terms of the hydrogen bonding properties of imino acids.

Significant spectral changes in the amide I region are observed on hydration in the spectra of some triple‐helical polypeptides, but corresponding changes have not been found in the collagens examined.
Differences in the red fluorescence of acridine orange bound to single‐stranded RNA and DNA
Authors: Ichimura Sachiko
Published: December 2004

Fluorescence of acridine orange bound to RNA or DNA in the single‐stranded form including single‐stranded synthetic polyribo‐ or polydeoxyribonucleotides was measured in the expectation that some distinct structural characteristic between single‐stranded RNA and DNA might be reflected by a specific fluorescent behaviour of bound dyes. It was found that the complex of the dye with single‐stranded RNA emits a weaker red fluorescence around 650 nm than the complex with single‐stranded DNA at low phosphate‐to‐dye ratios. The fact could be explained neither by a direct interaction of bound dyes with the 2′‐hydroxyl group of ribose in RNA nor by the difference in the G‐C content of the nucleic acids. On the basis of the character of dye molecules emitting the red fluorescence, it was suggested that the bases in single‐stranded RNA might be buried in some hydrophobic environment that would make the dyes less likely to interact with them, compared with the bases in single‐stranded DNA. It was further inferred that some conformational rigidity of single‐stranded RNA may partially be responsible for the weaker red fluorescence.
The nonplanar peptide unit III. Quantum chemical calculations for related compounds and experimental X‐ray diffraction data
Authors: Kolaskar A. S. , Lakshminarayanan A. V. , Sarathy K. P. , Sasisekharan V.
Published: December 2004

The possible nonplanar distortions of the amide group in formamide, acetamide, N‐methylacetamide, and N‐ethylacetamide have been examined using CNDO/2 and INDO methods. The predictions from these methods are compared with the results obtained from X‐ray and neutron diffraction studies on crystals of small open peptides, cyclic peptides, and amides. It is shown that the INDO results are in good agreement with observations, and that the dihedral angles θN and Δω defining the nonplanarity of the amide unit are correlated approximately by the relation θN = −2Δω, while θC is small and uncorrelated with Δω. The present study indicates that the nonplanar distortions at the nitrogen atom of the peptide unit may have to be taken into consideration, in addition to the variation in the dihedral angles (ϕ,ψ), in working out polypeptide and protein structures.
Synthesis and conformational study of sequential polypeptides, (L‐Ala‐L‐Val‐Gly)n and (L‐Val‐L‐Ala‐Gly)n
Authors: Katakai Ryoichi , Oya Masanao , Iwakura Yoshio
Published: December 2004

As an approach for elucidating the role of sequences of amino acids in protein structures, model polypeptides having the same composition but different sequences of amino acids, (L‐Ala‐L‐Val‐Gly)n and (L‐Val‐L‐Ala‐Gly)n, have been prepared by the method involving facile monomer synthesis using N‐carboxy α‐amino acid anhydrides and N‐hydroxysuccinimide esters. The yields and the molecular weights of the polypeptides formed by polycondensation do not depend on the monomer concentrations, but on the sequences of the amino acids in the monomers. Infrared spectra in the solid state showed that (L‐Ala‐L‐Val‐Gly)n can take the α‐helical conformation but (L‐Val‐L‐Ala‐Gly)n cannot. The results suggest that the conformations of polypeptides are influenced by the sequences of the amino acids in the polypeptides.
Sedimentation of generalized systems of interacting particles. I. Solution of systems of complete Lamm equations
Authors: Claverie Jean‐Michel , Dreux Henri , Cohen René
Published: December 2004

A very general approach to the chemical equilibria between many interacting molecules during sedimentation (boundary, band, or active enzyme) taking into account boundary conditions, cell geometry, equilibrium constants, diffusion, enzyme kinetics, etc., is presented. Through a Fortran program, the method has been applied to two very simple but typical cases. With only minor adjustments, the method presented here for sedimentation studies can be extended to all sorts of problems in which “pools” of various species are interacting with each other.
Competitive cooperative bindings of a small ligand to a linear homopolymer. I. Extension of the Ising model to the case of two competitive interactions
Authors: Dourlent M.
Published: December 2004

The theoretical study of the cooperative binding of a small ligand to a linear homopolymer is extended to systems in which two different complexes can form. The binding isotherms are derived under the assumption that the cooperative interactions exist only between molecules belonging to the same type of binding mode and are limited to nearest neighbors (Ising model). The binding to a single‐stranded chain is first considered and two extreme cases are studied: (1) the two complexes can form independently from each other (model of independent classes of binding sites); (2) only one class of binding site exists, each possessing two different states of complexation (three‐state model).

Binding to a double‐helical chain is also considered. Three simple types of competition between the different modes of binding are distinguished. The corresponding models are defined as: (1) the model of independent classes of binding sites; (2) the model of monoexclusive interactions between the different kinds of complexes (the symmetric and asymmetric cases are both considered); (3) the model of biexclusive interactions. The comparative study of the different cases shows that the binding isotherms are very similar at large polymer‐to‐ligand concentration ratios, while they can be very different at low polymer‐to‐ligand ratios. This can be used to obtain information on the mechanism of dye binding to nucleic acids by equilibrium studies as shown in a subsequent paper.
Helix–coil transition kinetics in aqueous poly(α,L‐glutamic acid)
Authors: Cummings Arthur L. , Eyring Edward M.
Published: December 2004

A polarimetric electric‐field‐jump relaxation apparatus is described and used to determine the relaxation spectrum for the helix–coil transition of poly(α,L‐glutamic acid) in water at 24°C. A maximum relaxation time of 1.7 μc occurs at the transition midpoint (pH = 5.9) yielding a rate constant for helical growth of 6 × 107 sec−1.
Effects of Na+ and Mg++ ions on the helix–coil transition of DNA
Authors: Record M. Thomas
Published: December 2004

The effects of monovalent (Na+) and divalent (Mg++) cations on the temperature and breadth of the helix–coil transition of phage DNA have been investigated. The experimental results confirm the findings of Dove and Davidson [J. Mol. Biol. 5, 467–478 (1962)] for the limiting cases of zero divalent ion concentration and saturating levels of divalent ion, and extend their findings to the intermediate region of Mg++ concentrations. A theory for the dependence of transition temperature on the ion concentrations is developed, utilizing the approach of Wyman [Adv. Protein Chem. 19, 223–286 (1964)], modified to account for electrostatic nonideality of the polyelectrolytes. The theory is in agreement with Manning's treatment of the experiments of Dove and Davidson [Biopolymers 11, 937–949, 951–955 (1972)] and is in fair agreement with experimental data over the entire range of ion concentrations. Further investigation of the structure and ion‐binding properties of the denatured form will be required before a quantitative comparison between theory and experiment can be performed.
Co‐oligopeptides of aromatic amino acids and glycine with a variable distance between the aromatic residues. I. Synthesis of co‐oligopeptides of tryptophan and glycine
Authors: Guarnaccia Rocco , Lorenzi Gian Paolo , Rizzo Vincenzo , Luisi Pier Luigi
Published: December 2004

The preparation of the co‐oligopeptides of the series H‐Gly‐Trp‐(Gly)n‐Trp‐Gly‐OH (n = 0, 1, and 2) and of a number of other unprotected co‐oligopeptides of glycine and tryptophan is reported. The syntheses have been carried out by conventional methods, using, in general, N‐hydroxysuccinimide esters for the coupling steps. All the oligopeptides were obtained after purfication as colorless and crystalline products, and gave only one spot on thin‐layer chromatography. Specfic problems connected with the synthesis and purficiation of optically pure tryptophan‐containing peptides are discussed.
Premelting effects in DNA under saltfree conditions
Authors: Grassi Henri , Rix‐Montel Marie‐Agnès , Kranck Hubert , Vasilescu Dane
Published: December 2004

We have studied the electrical conductivity of NaDNA solutions under “saltfree” conditions at temperatures well below the melting point of DNA, using radio‐frequency dielectric and noise measurements. A conductivity discontinuity is observed at a temperature well below that at which the usual denaturation processes and trans conformation may commence. The radio‐frequency permittivity also exhibits a discontinuity at the same temperature. For the premelting phase, the conductivity versus temperature curves consist of two linear regions with a change in slope occurring at 23°C. This effect is related to the behavior of the ionic sheath covering the DNA macromolecule. The activation energy of the alternative current conductivity as well as that the equivalent noise conductivity results as 3.11 kcal/mole below and 4.08 kcal/mole.
The A and B conformations of DNA and RNA subunits. Potential energy calculations for dGpdC
Authors: Broyde Suse B. , Stellman Steven D. , Wartell Roger M.
Published: December 2004

In order to obtain a molecular picture of the A and B forms of a DNA subunit, potential energy calculations have been made for dGpdC with C(3′)‐endo and C(2′)‐endo [or C(3′)‐exo] sugar puckerings. These are compared with results for GpC. The global minima for dGpdC and GpC are almost identical. They are like A‐form duplex DNA and RNA, respectively, with bases anti, the ω′, ω angle pair near 300°, 280°, and sugar pucker C(3′)‐endo. For dGpdC, a B‐form helical conformer, with sugar pucker C(2′)‐endo and ω′ = 257°, ω = 298°, is found only 0.4 kcal/mol above the global minimum. A second low‐energy conformation (2.3 kcal/mol) has ω′ = 263°, ω = 158° and ψ near 180°. This has dihedral angles like the original Watson–Crick model of the double helix. In contrast, for GpC, the C(2′)‐endo B form is 6.9 kcal/mol above the global minimum. These theoretical results are consistent with experimental studies on DNA and RNA fibers. DNA fibers exist in both A and B forms, while RNA fibers generally assume only the A form. A low‐energy conformation unlike the A or B forms was found for both dGpdC and GpC when the sugars were C(3′)‐endo. This conformation—ω′,ω near 20°,80°—was not observed for C(2′)‐endo dGpdC. Energy surface maps in the ω′,ω plane showed that C(2′)‐endo dGpdC has one low‐energy valley. It is in the B‐form helical region (ω′ ∼ 260°, ω ∼ 300). When the sugar pucker is C(3′)‐endo, dGpdC has two low‐energy regions: the A‐form helical region and the region with the minimum at ω′ = 16°, ω = 85°.
Polynucleotide circular dichroism calculations: Use of an all‐order classical coupled oscillator polarizability theory
Authors: Cech Carol L. , Hug Werner , Tinoco Ignacio
Published: December 2004

An all‐order classical coupled oscillator theory in which monomer band shapes are explicity taken into account is applied to the calculations of polynucleotide circular dichroism. Calculations are shown for ApA and oligoadenylic acid of varying chain lengths, in both RNA and B‐DNA geometry, and the advantages of this theory are assessed. By introducing an effective dielectric constant, good agreement with measured spectra is obtained. Variations in monomer parameters are tested in an attempt to eliminate remaining discrepancies between calculated and measured spectra.
An X‐ray study of poly(L‐prolyl‐L‐α‐phenylglycyl‐L‐proline)
Authors: Pra A. Del , Palumbo M. , Goodman M.
Published: December 2004

X‐ray diffraction studies have been made on the polytripeptide poly(L‐prolyl‐L‐α‐phenylglycyl‐L‐proline). Its structure has been found to be helical, with a poly(L‐proline) II conformation, packed in an orthorhombic lattice, space group P21212, with a = 14.3 Å, b = 13.5 Å, and c = 9.4 Å.
Models for depolymerizing enzymes. Application to α‐amylases
Authors: Thoma John A.
Published: December 2004

Several research groups have explored the action pattern of depolymerizing enzymes by examining the distribution of products during the early stages of digestion. Mathematical models for the various mechanisms that have been proposed for the behaviour of depolymerizing enzymes are developed in this paper. Published data for several amylases are reexamined in light of this theoretical analysis. It is concluded that following an initial random attack on a long polymer substrate, the enzyme frequently releases only one of the substrate fragments. The retained fragment may be repetitively hydrolyzed near one end to release a series of oligosaccharides before the enzyme substrate–fragment complex finally dissociates. Near optimum conditions Bacillus subtilis (var. amyloliquefaciens) amylase is unique among the enzymes tested because it does not repetitively attack substrate fragments.
Cooperative disordering of single‐stranded polynucleotides through copper crosslinking
Authors: Rifkind Joseph M. , Shin Yong A. , Heim Jane M. , Eichhorn Gunther L.
Published: December 2004

The thermal transitions of single‐stranded polynucleotides are noncooperative. In contrast, Cu(II) cooperatively disorders the single‐stranded helical structures of poly(A) and poly(C), as demonstrated by ORD and UV spectral changes as a function of the Cu2+ activity, and by a dramatic chain‐length dependence of the spectral changes. Equilibrium dialysis binding studies indicate that the cooperative disordering is paralleled by a somewhat less cooperative binding process.

The difference between the thermal‐ and Cu(II)‐induced transition is explained by the following mechanism. (1) Cu(II) initially binds in a noncooperative fashion to phosphate. (2) The Cu(II) so bound forms a second bond to a nonadjacent base site on the same polymer strand or another strand. These intramolecular and intermolecular crosslinks to the bases are responsible for the disordering. (3) The initial crosslinks formed provide nuclei for the cooperative formation of additional crosslinks, producing cooperative spectral changes paralleled by cooperative binding.

A comparison of the spectral and binding transitions indicates that there is appreciable noncooperative binding of copper to phosphate, which produces no spectral changes in the presence of added electrolyte. This comparison also indicates that each copper crosslink disorders several bases. The formation of intermolecular crosslinks is demonstrated by a polymer concentration dependence of the disordering. The formation of intramolecular crosslinks can be deduced from the fact that the “cooperative unit” required to explain the differences between the hexamer, which does not readily form intramolecular crosslinks, and the polymer is considerably larger than the cooperative unit determined from the polymer results.

The poly(A) disordering transition is less symmetrical than that of poly(C), particularly at low polymer concentrations. These results, together with other phenomena, are explained by a greater flexibility of poly(A), which favors the formation of small intramolecular loops.
The X‐Pro peptide bond as an nmr probe for conformational studies of flexible linear peptides
Authors: Grathwohl Christoph , Wüthrich Kurt
Published: December 2004

The equilibrium between the cis and trans forms of X‐Pro peptide bonds can readily be measured in the 13C nmr spectra. In the present paper we investigate how observation of this equilibrium could be used as an nmr probe for conformational studies of flexible polypeptide chains. The experiments include studies by 13C nmr of a series of linear oligopeptides containing different X‐L‐Pro peptide bonds, with X = Gly, L‐Ala, L‐Leu, L‐Phe, D‐Ala, D‐Leu, and D‐Phe. Overall the study confirms that X‐Pro peptide bonds can generally be useful as 13C nmr probes reporting the formation of nonrandom conformation in flexible polypeptide chains. It was found that the cis–trans equilibrium of X‐Pro is greatly affected by the side chain of X and the configuration of the α‐carbon atom of X. On the basis of these observations some general rules are suggested for a practical applications of the X‐Pro nmr probes in conformational studies of polypeptide chains.
Nmr studies of the molecular conformations in the linear oligopeptides H‐(L‐Ala)n‐L‐Pro‐OH
Authors: Grathwohl Christoph , Wüthrich Kurt
Published: December 2004

The molecular conformations of the linear oligopeptides H‐(L‐Ala)n‐L‐Pro‐OH, with n = 1,2 and 3, have been investigated. 13C nmr observation of the equilibrium between the cis and trans forms of the Ala‐Pro peptide bond indicated the occurrence of nonrandom conformations in solutions of these flexible peptides. The formation of the nonrandom species containing the cis form of the Ala‐Pro bond was found to depend on the deprotonation of the carboxylic acid group of proline, the solvent, and the ionic strength in aqueous solution. The influence of intramolecular hydrogen bonding on the relative conformational energies of the species containing the cis and trans Ala‐Pro peptide bond was studied by comparison of the peptides H‐(Ala)n‐Pro‐OH with analogous molecules where hydrogen bond formation was excluded by the covalent structure. In earlier work a hydrogen bond between the protonated terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue had been suggested to stabilize conformations including trans proline. For the systems described here this hypothesis can be ruled out, since the cis:trans ratio is identical for molecules with methyl ester protected and free protonated terminal carboxylic acid groups of proline. Direct evidence for hydrogen bond formation between the deprotonated terminal carboxylic acid group and the amide proton of the penultimate amino acid residue in the molecular species containing cis proline was obtained from 1H nmr studies. However, the cis:trans ratio of the Ala‐Pro bond was not affected by N‐methylation of the penultimate amino acid residue, which prevents formation of this hydrogen bond. Overall the experimental observations lead to the conclusion that the relative energies of the peptide conformations including cis or trans proline are mainly determined by intramolecular electrostatic interactions, whereas in the molecules considered, intramolecular hydrogen bonding is a consequence of specific peptide backbone conformations rather than a cause for the occurrence of energetically favored species. Independent support for this conclusion was obtained from model consideration which indicated that electrostatic interactions between the terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue could indeed account for the observed relative conformational energies of the species containing cis and trans proline, respectively.
Packing analysis of carbohydrates and polysaccharides. IV. A new method for detailed crystal structure refinement of polysaccharides and its application to V‐amylose
Authors: Zugenmaier Peter , Sarko Anatole
Published: December 2004

A method is described for predicting and solving crystal structures of linear homopolysaccharides. The method is based on the refinement of the structure with respect to either stereochemical constraints or x‐ray diffraction intensities. In the refinement process, all conformational and packing features of the molecule, such as bond lengths, bond angles, conformational angles, nonbonded contacts, hydrogen bonds, etc., can be allowed to vary until the structure reaches both a conformation and crystalline packing that are in minimum disagreement with the stereochemical restraints and the diffraction data. In this fashion, both packing and conformational features of the structure can be simultaneously refined, and not separately as has been the custom in the past. The refinement procedure is based on a method of constrained optimization which possesses improved characteristics of reaching a solution and avoiding false minima, in comparison with least squares methods. The procedure is, in addition, capable of easily finding molecules of solvent of crystallization. The method was applied to further refining the previously solved crystal structure of V‐amylose. The results indicated that contrary to the previously found six‐fold molecular symmetry in the P212121 space group, the V‐amylose molecule exhibits only two‐fold symmetry with the asymmetric unit consisting of three glucose residues in one‐half turn of the helix. The three residues are nonequivalent principally due to unequal rotational positions of the hydroxymethyl groups. The crystal structure of V‐amylose predicted from stereochemical refinement was identical in all details with that obtained from refining against X‐ray data. The excellent agreement with the diffraction data was indicated by the crystallographic disagreement index R = 0.25.
Fluctuations and mechanical strength of α‐helices of polyglycine and poly(L‐alanine)
Authors: Suezaki Yukio , Gō Nobuhiro
Published: December 2004

By using the static correlations of fluctuations in the dihedral angles of the α‐helices of polyglycine and poly(L‐alanine) calculated previously, geometrical fluctuations of a section (consisting of up to 18 peptide units) of the α‐helices of infinite length are calculated. These fluctuations are found to differ in some respects (e.g., the dependence of amplitudes on the length of section) from those of a circular rod made of homogeneous continuous material. However, the moduli of the mechanical strengths (tensile Young's modulus, bending Young's modulus, and the shear modulus) of a circular rod are calculated, whose geometrical fluctuations are approximately equal to the fluctuations of a section consisting of 18 peptide units. They are of the order of 1011 dyn/cm2. The tensile rigidity, flexural rigidity, and torsional rigidity are calculated to be 1.20 × 10−3 dyn, 2.46 × 10−19 dyn·cm2 and 1.79 × 10−19 dyn·cm2 for polyglycine, and 1.96 × 10−3 dyn, 4.05 × 10−19 dyn·cm2 and 3.28 × 10−19 dyn·cm2 for poly(L‐alanine), respectively.
Probing DNA quaternary ordering with circular dichroism spectroscopy: Studies of equine sperm chromosomal fibers
Authors: Sipski M. Leonide , Wagner Thomas E.
Published: December 2004

Studies are described which strongly support a cholesteric liquid crystal‐like quaternary structure for the DNA molecules of a biologically native chromosomal preparation from equine sperm cells. Discrete chromosomal fibers released from the head pieces of equine spermatozoon cells were prepared intact and probed for liquid crystalline ordering using reflectance and linear dichroism spectroscopy. Assuming cholesteric liquid crystalline order for the DNA molecules within the chromatin fibers, parameters measured experimentally were used to calculate the circular dichroism (CD) of the fibers. The calculated results compare remarkably well with the experimentally measured CD of the sperm chromosomal fibers and suggest a specific cholesteric liquid crystal‐like quanternary structural ordering of DNA molecules in equine sperm chromatin fibers. The potential of CD spectroscopy as a tool for the study of long‐range ordering of macromolecules is discussed.
The triple helix ⇌ coil conversion of collagen‐like polytripeptides in aqueous and nonaqueous solvents. Comparison of the thermodynamic parameters and the binding of water to (L‐Pro‐L‐Pro‐Gly)n and (L‐Pro‐L‐Hyp‐Gly)n
Authors: Engel Jürgen , Chen Han‐Tee , Prockop Darwin J. , Klump Horst
Published: December 2004

The collagen‐like peptides (L‐Pro‐L‐Pro‐Gly)n and (L‐Pro‐L‐Hyp‐Gly)n with n = 5 and 10, were examined in terms of their triple helix ⇌ coil transitions in aqueous and nonaqueous solvents. The peptides were soluble in 1,2‐propanediol containing 3% acetic acid and they were found to form triple‐helical structures in this solvent system. The water content of the solvent system and the amount of water bound to the peptides were assayed by equilibrating the solvent with molecular sieves and carrying out Karl Fischer titrations on the solvent phase. After the solvent was dehydrated, much less than one molecule of water per tripeptide unit was bound to the peptides. Since the peptides remained in a triple‐helical conformation, the results indicated that water was not an essential component of the triple‐helical structure. Comparison of peptides with the same chain length demonstrated that the presence of hydroxyproline increased the thermal stability of the triple helix even under anhydrous conditions. The results, therefore, did not support recent hypotheses that hydroxyproline stabilizes the triple helix of collagen and collagen‐like peptides by a specific interaction with water molecules. Analysis of the thermal transition curves in several solvent systems showed that although the peptides containing hydroxyproline had tm values which were 18.6° to 32.7°C higher, the effect of hydroxyproline on ΔG was only 0.1 to 0.3 kcal per tripeptide unit at 25°C. The results suggested, therefore, that the influence of hydroxyproline on helical stability may be explained by intrinsic effects such as dipole–dipole interactions or by changes in the solvation of the peptides by alcohol, acetic acid, and water. A direct calorimetric measurement of the transition enthalpy for (L‐Pro‐L‐Pro‐Gly)n in 3% or 10% acetic acid gave a value of −1.84 kcal per tripeptide unit for the coil‐to‐helix transition. From the value for enthalpy and from data on the effects of different chain lengths on the thermal transition, it was calculated that the apparent free energy for nucleation was +5 kcal/mol at 25°C (apparent nucleation parameter = 2 × 10−4 M−2). The value was dependent on solvent and on chemical modification of end groups.
Spectroscopic studies on the interaction of Au(III) with nucleosides, nucleotides, and dimethyl phosphate
Authors: Chatterji D. , Nandi U. S. , Podder S. K.
Published: December 2004

A series of complexes of Au(III) with nucleosides and nucleotides and their methyl derivatives in different stoichiometry have been prepared. Ultraviolet, visible, ir, and nmr studies have been performed to determine the site of binding of these ligands with the metal ion. In (1:4) Au(III): guanosine complex, N7 is the binding site, whereas at 1:1 complex, a bidentate type of chelation through C6O and N7 is observed. C6‐NH2 is favored over N1 as coordinating site at all stoichiometry in the adenosine complex. Inosine binds through N1 at r = 1. In cytidine, N1 is the binding site, whereas thymidine reacts only at high pH. In the case of nucleotides a bidentate type of chelation through the phosphate and the ring nitrogen occurs. The phosphate binding ability of Au(III) was further confirmed by studying the interaction of Au(III) with dimethyl phosphate—a conformational analog of the phosphate backbone in DNA chain.
Infinite‐dilution viscoelastic properties of fibrinogen and intermediate fibrin polymer
Authors: Nemoto Norio , Nestler F. Henry M. , Schrag John L. , Ferry John D.
Published: December 2004

The storage and loss shear moduli, G′ and G″, have been measured for dilute solutions of bovine fibrinogen in 68% aqueous glycerol and of intermediate fibrin polymer in 6M hexamethylene glycol, by the Birnboim‐Schrag multiple‐lumped resonator apparatus with titanium alloy resonators. The frequency range was 100–5800 Hz, the concentration range 1–6 g/l., and the temperatures 10.0 and 25.0°C. The shear moduli G′ and G″ at finite concentration, and the extrapolated instrinsic shear moduli [G′] and [G″], as functions of frequency, were compared with the predictions of various molecular theories. For fibrinogen, the frequency dependence agreed quite well with the calculations of Hassager for a trinodular rod as modified for the presence of small amounts of dimeric and trimeric aggregates which were deduced from parallel measurements of oscillatory flow birefringence. It was not possible, however, to distinguish between a linearly rigid configuration and one which is freely jointed at the central nodule. A model of a soft elastic sphere (simulating the cage model of Köppel) appeared to be very unlikely. The relaxation time for a rigid trinodular rod and the longest relaxation time for a jointed trinodular rod, calculated from molecular dimensions on the basis of electron microscope measurements, are somewhat smaller than the corresponding observed values; the discrepancy suggests that the molecule is swollen in solution. For the intermediate polymer (which was formed under conditions where ligation is expected), the frequency dependence agreed quite well with that predicted either for a prolate ellipsoid (Cerf‐Scheraga‐Saitō) or for a cylindrical rod (Yamakawa). The relaxation time obtained by fitting to theory agrees quite well with that calculated for a cylindrical rod with molecular dimensions based on a degree of polymerization of 20 and lateral binary association with staggered overlapping.
Packing analysis of carbohydrates and polysaccharides. V. Crystal structures of two polymorphs of pachyman triacetate
Authors: Bluhm Terry L. , Sarko Anatole
Published: December 2004

The crystal structures of two polymorphic forms of pachyman triacetate, the fully acetylated derivative of a naturally occuring β‐(1 → 3)‐D‐glucan, were determined by a combination of stereochemical and x‐ray diffraction analysis. The two polymorphs could be obtained depending on the temperature and the degree of stretching of film specimens of the substance: polymorph I resulted from stretching 25–50% at 125°C and polymorph II resulted from further stretching to 300% at 215°C. Both polymorphs had previously been shown to have sixfold helical chain conformations, but of unequal pitch. Subsequent detailed structure refinement performed with bond lengths, bond angles, conformational angles, and helix‐packing parameters as refinement variables, and the simultaneous minimization of packing and conformational energy and the crystallographic R‐factor as refinement criteria, resulted in a complete determination of the two crystal structures. Pachyman triacetate I was found to be a right‐handed helix packing with antiparallel polarity and space group P212121 symmetry (unit‐cell parameters a = 11.0, b = 19.0, c (fiber repeat) = 22.38 Å). The acetate groups were nearly planar and the O(2) and O(4) acetates were oriented in such a fashion that the carbonyl double‐bond nearly eclipsed the corresponding C—H bond of the ring. The O(6) was in the tg position and its acetate was oriented in such a fashion that the bond sequence C(6)—O(6)—C(6C)—C(6M) was nearly trans‐planar, with the carbonyl double‐bond bisecting the tetrahedral angle formed by C(6) and its two hydrogens. The final R = 0.221. Pachyman triacetate II was similarly found to be a right‐handed helix, but packing as a 50:50 mixture of parallel and antiparallel polarities (unit‐cell parameters a = 11.49, b = 20.13, c (fiber repeat) = 18.6 Å). The acetate positions in pachyman triacetate II were substantially the same as in pachyman triacetate I. The final R for the 50:50 mixture was 0.234. Probable reasons for the change in packing polarities are discussed, as are the difficulties encountered in the structure refinement of acetate derivatives.
Intrachain reactions of a pair of reactive groups attached to polymer ends. V. Formation of disulfide linkages in the air‐oxidation of sulfhydryl groups attached to ends of polysarcosine chain
Authors: Sisido Masahiko , Tamura Fumihide , Imanishi Yukio , Higashimura Toshinobu
Published: December 2004

Polysarcosine having sulfhydryl groups attached to both ends was synthesized by the NCA method and its air‐oxidation was investigated in aqueous solution with cupric‐ion or ferric‐ion catalysts. Air‐oxidation was also conducted for a polysarcosine having one terminal sulfhydryl group. The product of the air‐oxidation was fractionated by gel chromatography. The product analysis of the fully oxidized monofunctional polymer showed that the sulfhydryl groups were converted into disulfide bonds exclusively. There was no evidence for the interchange between two disulfide linkages or between a disulfide linkage and a sulfhydryl group during the air‐oxidation. The analysis of the products from the bifunctional polysarcosine showed that they were composed of a series of cyclic “monomer,” “dimer,” “trimer,” and higher “oligomers.” The cyclic structure was characterized by the larger elution volume in the gel chromatogram than that for a linear homologue having the same molecular weight. The weight fraction of each cyclic oligomer was determined by gel chromatography. The fraction of cyclic monomer F1 decreased monotonously with increasing the chain length. Smaller values of F1 were observed with cupric‐ion catalyst than with ferric‐ion catalyst. The dependence of F1 on the polymer concentration was much smaller than that expected from a simple competition mechanism between intra‐ and intermolecular reactions. These results indicate that the choice between intra‐ and intermolecular reactions is governed by the mode of the coordination of sulfhydryl groups to transition metal ions.
Conformational studies on polynucleotide chains. I. Hartree‐fock energies and description of nonbonded interactions with Lennard‐Jones potentials
Authors: Matsuoka Osamu , Tosi Camillo , Clementi Enrico
Published: December 2004

The sugar–phosphate–sugar complex C10H18O8P, a unit of the polynucleotide chains, was analyzed, making use of 100 conformational energies computed in the Hartree‐Fock approximation with a small basis set of Gaussian type orbitals. The geometry of the conformations [which corresponds to the C(2′)‐endo deoxy system], the basis set, and the computed total energies are reported in this work. In addition, a number of attempts are presented where we searched for a computationally very simple analytical expression apt to fit, with reasonable accuracy, the computed energies. Lennard‐Jones type potential seems to offer an appropriate form capable of reproducing the positions of the maxima and the minima resulting from ab initio computations, but neither the 6‐12 nor other similar forms seem to be able to correctly reproduce the intensity of the barriers. Form a details analysis of the barriers to rotation about the bonds O(5′)—C(5′) and C(5′)—C(4′) in terms of nonboned interactions, we found that a substantial improvement in the fit of analytical to ab initio energies may be obtained by distinguishing between atoms characterized by the same atomic number but having different chemical characteristics, like the oxygen atoms of the phosphate group, on one hand, and the oxygen atoms of the sugar rings and the hydroxyl groups, on the other.
Laser‐Raman spectroscopy of biomolecules. XI. Conformational study of poly(L‐valine) and copolymers of L‐valine and L‐alanine
Authors: Fasman Gerald D. , Itoh Koichi , Liu Christopher S. , Lord Richard C.
Published: December 2004

Raman spectroscopic studies have been carried out on polymers of L‐valine ranging in degree of polymerization (DP) from 2 to 930. The spectrum of the hexapeptide (DP = 6) is closely similar over the entire range 40–1750 cm−1 to those of polymers with much higher DP, and the structure is clearly shown to be that of the antiparallel pleated sheet (β‐structure) by the amide I and III frequencies. The formation of a little α‐helical structure occurs in polymers with DP above 500, although the amount does not appear to be a linear function of DP. The α‐helical structure is unstable and readily destroyed in samples cast from trifluoroacetic acid solution. It is stabilized by the incorporation of L‐alanine, a strong helix‐former; polymers of the latter may in turn be forced into a α‐structure in copolymers sufficiently rich in L‐valine.
Determination of the number of cross‐links in a protein gel from its mechanical and swelling properties
Authors: Van Kleef F. S. M. , Boskamp J. V. , Van Den Tempel M.
Published: December 2004

The relation between the chemical structure of a protein and the physical properties of a heat‐set gel of that protein has been investigated. The physical properties of the gel are determined by means of mechanical experiments in which the viscoelastic properties of the gel are determined in terms of the storage shear modulus, the loss modulus and the stress‐strain curve. The storage shear modulus defined the solid (elastic) character of the gel. The chemical structure of the protein and the nature of the solvent determine the nature and number of cross‐links in the gel. The cross‐links in gels formed by heating concentrated solutions of ovalbumin in 6M urea solutions were found to be disulfide bridges and the mechanical properties of these ovalbumin/urea gels approximated those of an ideal rubber. The latter finding enables one to calculate the number of cross‐links per ovalbumin molecule from the value of the storage modulus, using the classical theory of rubber elasticity. This theory, together with the Flory‐Huggins lattice model, can also be used to calculate the number of cros‐links per ovalbumin molecule from the swelling behavior of ovalbumin/urea gels. The number of cross‐links per ovalbumin molecule calculated from these two types of experiments are in mutual agreement and correspond with the number of thiol groups in ovalbumin. We conclude, thereforee, that theories of polymer physics can be used to relate the chemical structure of a protein to the physical properties of its gel.
Structures and populations of conformers of nucleoside monophosphates in aqueous solution. I. General methods of conformation search with lanthanide‐ion probes and spin‐coupling constants and application to uridine‐5′‐monophosphate
Authors: Inagaki Fuyuhiko , Tasumi Mitsuo , Miyazawa Tatsuo
Published: December 2004

The Ln(III)‐induced shifts and Gd(III)‐induced changes of the spin‐lattice relaxation times were observed for the 1H and 13C resonances of uridine‐5′‐monophosphate (5′‐UMP) in 2H2O solutions at pH 1.7–2.0. The vicinal spin‐coupling constants changed little by the addition of lanthanide cations, indicating that the conformations of this mononucleotide remained almost the same upon complex formation.

A general method was worked out for conformation studies of flexible molecules with lanthanide‐ion probes and spin‐coupling constants. This method was applied in an extensive computer search for 5′‐UMP, and it was concluded that the observed Ln(III)‐induced shifts, Gd(III)‐induced changes of relaxation times, and vicinal spin‐coupling constants could only be accounted for by a mixture of conformers. The populations of the major conformers, gg‐3′‐endo‐anti, and gg‐2′‐endo‐anti, amount to 46 ± 12% and 29 ± 11%, respectively. The correlation between local conformations are discussed on the basis of the present results.
Empirical calculations of dinucleotide optical activity
Authors: Johnson Neil P. , Switkes Eugene
Published: December 2004

In this paper we present calculations of dinucleotide optical activity based on the exciton‐coupled oscillator and generalized susceptibility theories of CD. Our application of these methods utilizes experimental transition moment data for the nucleic acids and does not require explicit wavefunctions for the monomers. In addition to near‐uv π‐π* states, the calculations include n‐π* and far‐uv π‐π* transitions recently characterized by Clark. We also show that correlated motions of electrons in the ground state of a system is reflected in the net CD summed over all transitions. Sample calculations for dinucleotides in several conformations illustrate the methods.