bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectroscopic studies on the structure of poly(8‐bromoadenylic acid): Effect of glycosidic torsion angle on the conformation and flexibility in polyribonucleotides
Authors: Govil Girjesh , Fisk Cherie L. , Howard Frank B. , Miles H. Todd 
Published: December 2004

AbstractThe helix–coil transition and conformational structure of poly(8‐bromoadenylic acid) [poly(8BrA)] have been investigated using 1H‐ and 13C‐nmr, CD, and ir spectroscopy. The results have been compared with the structure of the related 5′‐mono‐ and polynucleotides. The chemical shifts of H(2′), H(3′), C(2′), and C(3′) nmr signals show an interesting correlation with both the puckering of ribose ring and glycosidic bond torsion angle. Poly(8BrA) shows an upfield shift of the C(3′) signal and a downfield shift of the H(3′) signal compared to the chemical shifts in poly(A). These shifts are consistent with a C(3′) endo‐syn conformation for poly(8BrA). A similar effect has been reported previously and is also observed here on the C(2′) and H(2′) signals when the preferred conformation is C(2′)endo‐syn (e.g., in 5′‐8BrAMP). The chemical‐shift parameters thus act as a probe for studying syn ⇄ anti and N ⇄ S equilibria in solutions. The three‐bond 1H‐′13C coupling constants between H(1′) and C(8) and C(4) have been measured in poly(8BrA) and 5′‐8BrAMP and their structural implications have been discussed. The observed preference of a C(3′)endo‐syn conformation for poly(8BrA), coupled with other evidence, throws doubt on the validity of a correlation previously reported whereby a syn conformation is associated with a C(2′)endo ribose pucker. The backbone conformation of randomly coiled poly(8BrA) is very similar to the structures found in polyribonucleotides: poly(A) and poly(U). All three polymers show strong preferences for the backbone angles found in RNA helices. The CD spectrum of poly(8BrA) has a striking relationship to that of poly(A). The signs of all extrema are inverted, and the magnitudes are related by a constant factor. We suggest that these differences result from a change in the angle between coupled transition moment vectors in the two polymers. Infrared spectra of poly(8BrA) in H2O and D2O solution are reported for the frequency range below 1400 cm−1. The antisymmetric >PO stretching vibration is observed at an unusually low frequency in the helix (1214 cm−1). The symmetric >PO stretch occurs at ∼1095 cm−1 but is not resolved from a ring vibration near this frequency. A conformationally sensitive band, characteristic of helical RNA structures, is observed at 817 cm−1 and disappears when the helix is melted. This observation confirms the conclusion that ordered poly(8BrA) has a regular helical structure with an RNA backbone conformation. A stereochemical explanation is provided for the failure of poly(8BrA) (or other syn polymers) to form double helices with anti‐polyribonucleotides.
13C‐Nmr studies of ACTH: Assignment of resonances and conformational features
Authors: Toma Flavio , Fermandjian Serge , Löw Miklos , Kisfaludy Lajos 
Published: December 2004

AbstractThe biologically active ACTH(1–32) and ACTH(1–24) and other shorter peptide segments of the native hormone ACTH(1–39) were studied in aqueous solution by 13C‐nmr. In order to identify the 13C resonances—except those of the carbonyls—both high‐field nmr spectroscopy measurements and substitution of residues with amino acids enriched to 85% in 13C were carried out. The main results are (1) the direct characterization of the cis–trans isomerism of proline 24 and its effects on the directly connected and sequentially neighboring residues and (2) findings that the conformational features agree with an α‐helix type organization in the N‐terminal part of the ACTH molecule which is responsible for the biological activity.
Noninteracting local‐structure model of folding and unfolding transition in globular proteins. I. Formulation
Authors: GŌ Nobuhiro , Abe Haruo 
Published: December 2004

AbstractA statistical‐mechanical model (a noninteracting local structure model) of folding and unfolding transition in globular proteins is described and a formulation is given to calculate the partition function. The process of transition is discussed in this model within the framework of equilibrium statistical mechanics. In order to clarify the range of applicability of such an approach, the characteristics of the folding and unfolding transition in globular proteins are analyzed from the statistical‐physical point of view. A theoretical advantage is pointed out in studying folding and unfolding processes taking place as conformational fluctuations in individual protein molecules under macroscopic equilibrium at the melting temperature. In this case, paths of folding and unfolding are shown to be identical in the statistical sense. A key to the noninteracting local structure model lies in the concept of local structures and the assumption of the absence of interactions between local structures. A local structure is defined as a continuous section of the chain which takes the same or similar local conformation as in the native conformation. The assumption of the absence of inter‐actions between local structures endows the model with the remarkable character that its partition function can be calculated exactly; thereby the equilibrium population of various conformations along the folding and unfolding paths can be discussed only by a knowledge of the folded native conformation.
X‐Pro peptides: Solution and solid‐state conformation of benzyloxycarbonyl‐(Aib‐Pro)2methyl ester, a type I β‐turn
Authors: Venkatachalapathi Y. V. , Nair C. M. K. , Vijayan M. , Balaram P. 
Published: December 2004

AbstractThe synthesis of the tetrapeptide benzyloxycarbonyl(α‐aminoisobutyryl‐L‐prolyl)2‐methyl ester (Z‐(Aib‐Pro)2‐OMe) and an analysis of its conformation in solution and the solid state are reported. Stepwise synthesis using dicyclohexylcarbodiimide leads to racemization at Pro(2). Evidence for the presence of diastereomeric tetrapeptides is obtained from 270‐MHz1H‐nmr and 67.89‐MHz 13C‐nmr. The all‐L tetrapeptide is obtained by fractional crystallization from ethyl acetate. The NH of Aib(3) is shown to be involved in an intramo‐lecular hydrogen bond by variable‐temperature 1H‐nmr and the solvent dependence of NH chemical shifts. The results are consistent with a β‐turn conformation with Aib(1) and Pro(2) at the corners stabilized by a 4 → 1 hydrogen bond. The molecule crystallizes in the space group P212121, with a = 8.839, b = 14.938, and c = 22.015 Å. The structure has been refined to an R value of 0.051. The peptide backbone is all‐trans, and a 4 → 1 hydrogen bond, between the CO group of the urethane moiety and Aib(3) NH, is observed. Aib(1) and Pro(2) occupy the corner positions of a type I β‐turn with ϕ = −55.4°, Ψ = −31.3° for Aib(1) and ϕ = −71.6°, Ψ = −38° for Pro(2). The tertiary amide unit linking Pro(2) and Aib(3) is significantly distorted from planarity (Δω = 14.3°).
Structure in solution of biscyclo(dipeptide) restricted by CSSC gauche effect
Authors: Ueyama Norikazu , Araki Takeo 
Published: December 2004

AbstractBiscyclo(Cys‐Sar) [I] and biscyclo(Cys‐Pro) [II] were prepared by the extension of amino acid moieties from cystine. Compound I equilibrates between two rotamers around the CSSC bond of the cystine residue in methanol, showing dual negative CD transitions (CS‐SC) at 270 and 255 nm, and dual S‐S vibrations at 507 and 539 cm−1 in Raman spectra. In contrast, a conformation of P‐helix type is suggested in CH3CN, which shows a distinct negative CD at 270 nm and only one Raman band at 507 cm−1 for the S‐S bond. Compound II rotates freely in dimethylsulfoxide (Me2SO) but takes a relatively stable conformer of P‐helix type in methanol, chloroform/Me2SO (9:1), and chloroform/trifluoroacetic acid (9:1). The conformation in chloroform is retained even on addition of trifluoroacetic acid. A more complete conformation of compound II in water was determined from the negative CD of S‐S transition and 1H‐nmr spectra of the Cys‐β‐CH2 protons.
Conformation study of poly(γ‐methyl‐L‐glutamate) in helicogenic solvents by small‐angle X‐ray scattering
Authors: Ishimuro Yoshitaka , Yamaguchi Saburo , Hamada Fumiyuki , Nakajima Akio 
Published: December 2004

AbstractSmall‐angle x‐ray scattering of poly(γ‐methyl‐L‐glutamate), [Glu(OMe)]n, in m‐cresol and in pyridine was measured to determine the mass per unit length, Mq, and the radius of gyration of the cross section, 〈S〉1/2. It was confirmed from the values of Mq that [Glu(OMe)]n exists in an α‐helical conformation in these solvents. It was elucidated from the calculations on 〈S〉1/2 that the side chains come in moderately close contact with the main chain in these solvents. It was indicated from the analysis of the outer portion of the scattering curves that the side‐chain conformation varied depending on the solvent.
Conformational aspects of polypeptides. VIII. Helical assignments via far ultraviolet absorption spectra and optical activity
Authors: Goodman Murray , Listowsky Irving , Masuda Yukio , Boardman Franklin 
Published: December 2004

AbstractWe determined the onset of helical structures in solution for oligopeptides by means of the decrease in intensity of the 190 mμ band (hypochromism), and related these findings to optical rotatory dispersion data. Measurements of ultraviolet absorption spectra in trifluoroethanol show that helical conformations commence at about the tetradecamer for peptides derived from β‐methyl‐L‐aspartate. In the γ‐methyl‐L‐glutamate series the hypochromic effect starts at the nonamer, increasing in magnitude with peptide chain length. Essentially the same results were obtained by using optical rotatory dispersion. By dividing the b0 (Moffitt‐Yang constant) for the oligopeptides into helical and nonhelical components, we have better indications that in previous work for the onset of helicity. We have also studied the far ultraviolet spectra and optical rotatory dispersion for high polymers derived from β‐methyl‐L‐aspartate and γ‐methyl‐L‐glutamate. Assuming complete helicity for these high polymers, we assigned helical contents to the oligopeptides. In addition, ultraviolet spectra were measured for the polymer from γ‐methyl‐DL‐glutamate in order to determine its helical content.
Dialysis studies. V. The behavior of different preparations of bovine ribonuclease
Authors: Craig L. C. , King T. P. , Crestfield Arthur M. 
Published: December 2004

AbstractStudies of different preparations of ribonuclease A by thin film dialysis and countercurrent distribution have shown the existence of conformational isomers. These forms are slowly interconvertible in a particular solvent environment. They show the minimum molecular weight of ribonuclease and do not differ enzymatically or by rotatory dispersion.
The orientation and dissociation field effect of DNA in solution
Authors: Ise N. , Eigen M. , Schwarz G. 
Published: December 2004

AbstractBy means of a previously described experimental technique the orientation field effect (orientation of polyions and anisotropy of conductivity in an electric field) has been found for a special sample of desoxyribonucleic acid (DNA) in aqueous solution. The results can be described fairly well by the theory. The fact that the polyions of undenatured DNA are rather rigid rods due to their helical structure is, as expected, clearly noticeable in the concentration dependence of the effect. This phenomenon is discussed in comparison with the data for the flexible polyphosphate ions. Also measurements of the dissociation field effect of the substance have been performed. The results can be understood in the light of the structure of the DNA.
Helix–coil stability constants for the naturally occurring amino acids in water. XXI. Glutamine parameters from random poly(hydroxypropylglutamine‐co‐L‐glutamine) and poly(hydroxybutylglutamine‐co‐L‐glutamine)
Authors: Denton J. B. , Powers S. P. , Zweifel B. O. , Scheraga H. A. 
Published: December 2004

AbstractWater‐soluble, random copolymers containing L‐glutamine and either N5‐(3‐hydroxypropyl)‐L‐glutamine or N5‐(4‐hydroxybutyl)‐L‐glutamine were synthesized, fractionated, and characterized. The thermally induced helix–coil transitions of these copolymers were studied in water. A short‐range interaction theory was used to deduce the Zimm‐Bragg parameters σ and s for the helix–coil transition in poly(L‐glutamine) in water from an analysis of the melting curves of the copolymers in the manner described in earlier papers. The computed values of s indicate that L‐glutamine is helix‐indifferent at low temperature and a helix‐destabilizing residue at high temperature in water. At all temperatures in the range of 0–70°C, the glutamine residue promotes helix–coil boundaries since the computed value of σ is large.
Changes in Raman vibrational bands of calf thymus DNA during the B‐to‐A transition
Authors: Martin James C. , Wartell Roger M. 
Published: December 2004

AbstractThe B‐to‐A conformational transition of calf thymus DNA fibers was followed employing Raman spectroscopy. The transition was induced by soaking DNA fibers in water/ethanol mixtures increasing from 60 to 85% ethanol (v/v). Intensity changes of 17 Raman vibrational bands were quantified in the region from 400 to 860 cm−1. Two bands at 500 and 784 cm−1 were employed as internal standards. These bands do not appear to change in intensity with ethanol concentration. Large intensity changes relative to these two bands are observed between 70 and 74% ethanol for backbone vibrations at 708, 808, and 835 cm−1, and base vibrations at 682, 730, and 750 cm−1. These results indicate that a highly cooperative conformational change takes place between different portions of DNA in the B‐to‐A transition. Relative intensity changes preceding the onset of the major transition are observed in only two bands; at 835 cm−1, assigned to a ribose–phosphate vibration, and at 750 cm−1, assigned to thymine. The implications of these pretransition changes are discussed.
Adsorption of the polypeptides on a solid surface. III. Behavior of stiff chains in a pore
Authors: Zhulina E. B. , Gorbunov A. A. , Birshtein T. M. , Skvortsov A. M. 
Published: December 2004

AbstractA strict analytical theory has been developed describing the behavior of a model lattice polymer chain of arbitrary stiffness in a slitlike pore at polymer–adsorbent interaction energies –ε. The thermodynamic characteristics of the system were calculated. It was shown that the transition of the macromolecule from the solution volume inside a pore occurs by the first‐order phase transition with evolution of latent heat of adsorption. The transition point –ε = –εc is determined by the chain stiffness and is independent of the pore width D. It is shown that in the precritical range, –ε < –εc, the free energy ΔF of the macromolecules in the pores is adequately described by the universal dependence ΔF = ΔF(D*/A), where D* is some effective pore width depending on the value of –ε, and A is the length of the Kuhn segment. At high attraction energies, –ε ≫ –εc, the macromolecules are bonded to the pore walls by a great number of units and their free energy depends only on –ε and the chain stiffness, ΔF = ΔF(A, ε). Close to the critical energy –ε ≃ –εc (transition range), ΔF is determined by both the stiffness of the macromolecule and the pore width D: ΔF ∼ A2D−1 for fairly high values of A and D. The possibilities of using porous media as protein stabilizers are discussed, and the value of the stabilizing effect depending on the chain stiffness is estimated.
Cyclodextrin–adamantanecarboxylate inclusion complexes: A model system for the hydrophobic effect
Authors: Harrison John C. , Eftink Maurice R. 
Published: December 2004

AbstractThermodynamic studies of the binding of adamantanecarboxylate to cyclodextrins have been made as a function of temperature and added organic cosolvent (methanol) using flow microcalorimetry. The negative heat capacity change associated with the adamantanecar‐boxylate/β‐cyclodextrin interaction and the fact that the interaction is weakened by the addition of methanol implicate the binding process as being a hydrophobically driven one. The negative enthalpy change (ΔH0 = −5.5 kcal/mol) and near‐zero entropy change (ΔS0 = 1.5 cal/mol deg) are quite different from the values normally expected for a hydrophobic bond, indicating that other bonding forces are important in addition to the hydrophobic effect. The relative contribution of the hydrophobic effect and other bonding forces (most likely van der Waals forces) to the overall binding was judged from an analysis of the dependence of the thermodynamics of the association process on the surface tension of the water–methanol mixtures following a model for “solvophobic” bonding described by Sinanoglu [Molecular Associations in Biology (1968) Academic Press, New York, pp. 427–445]. From this analysis, adamantane–carboxylate/cyclodextrin complex formation is found to be driven to the extent of −1.9 kcal/mol by the hydrophobic effect. Furthermore, the hydrophobic driving force is found to be characterized by a positive ΔS0 of 10 cal/mol deg. The remaining free energy of binding (and the ΔH0 of binding of ∼−6 kcal/mol) is then due to the intrinsic (surface‐tension‐independent) van der Waals interaction between the ligand and cyclodextrin cavity.
Equilibrium dialysis studies of polyamine binding to DNA
Authors: Braunlin W. H. , Strick T. J. , Record M. T. 
Published: December 2004

AbstractBinding constants and binding site sizes for the interactions of the polyamines spermine (+4), spermidine (+3), and putrecine (+2) with helical DNA have been determined as a function of ionic conditions and temperature by equilibrium dialysis using 14C‐labeled polyamines. In addition, competition equilibrium dialysis has been used to determine binding parameters for the divalent cations putrescine and Mg2+ from the competitive effect of these ions on the binding of spermine or spermidine. In all cases, the logarithm of the binding constant (log Kobs) varies linearly with the logarithm of the monovalent salt concentration; the slopes d log Kobs/d log[NaCl] are proportional to the valence of the ligand, and values of the extrapolated binding constants at 1M NaCl obtained from the intercepts are small (of order 1–10M−1). In those cases examined, Kobs is insensitive to temperature; the free energy of binding is predominantly entropic. Consequently, polymines as DNA‐binding ligands behave analogously to the oligolysìnes investigated previously [cf. Record, Lohman & de Haseth (1976) J. Mol. Biol. 107, 145–158; Lohman, de Haseth & Record (1980) Biochemistry 19, 3522–3530]. The interactions of these oligocations with DNA are predominantly electrostatic and are driven by the release of thermodynamically bound electrolyte ions from the vicinity of the DNA. The extent to which these oligocations are localized at individual phosphate binding sites or delocalized on the DNA molecule is currently not known.
Helix–coil transition of poly(α,L‐glutamic acid) at an interface: Correlation with static and dynamic membrane properties
Authors: Pefferkorn Emile , Schmitt Adrien , Varoqui Raphaël 
Published: December 2004

AbstractWhen adsorbed from an aqueous dilute solution at high pH into the pores of an inert cellulose acetate filter, poly(α,L‐glutamic acid) remains strongly anchored to the pore walls. The existence of the helix–coil transition for the adsorbed polypeptide in a certain pH range is evidenced by static and dynamic membrane properties displayed by the “activated” filter, such as excess cation uptake, membrane potential, and hyraulic permeability. In particular, the variations of the hydrodynamic thickeness present a sigmoidal shape characteristic of the helix–coil transition at the interface, a transition apparently less sharp than in solution.
Evidence for the role of 4‐hydroxyproline localized in the third position of the triplet (Gly‐X‐Y) in adaptational changes of thermostability of a collagen molecule and collagen fibrils
Authors: Burjanadze Tengiz V. 
Published: December 2004

AbstractAn analysis of the available data on the thermostability and imino acid content of various collagens has shown that the change of the denaturation temperature (tm) of the collagen triple helix, as well as the temperature of hydrothermic shrinkage (ts) of collagen fibrils, depends on the number of hydroxyproline residues localized in the third position of the collagen triplet. This change does not depend on the content of proline and 3‐ and 4‐hydroxyproline localized in the second position of the triplet. Empiric equations have been obtained connecting tm and ts with the content of 4‐hydroxyproline. The results of the analysis are in good agreement with one of the collagen structure models recently proposed by the Ramachandran school.
Studies of fibrin film. I. Stress relaxation and birefringence
Authors: Roska Fred J. , Ferry John D. 
Published: December 2004

AbstractMeasurements of stress relaxation in uniaxial extension and associated time‐dependent birefringence have been made on bovine fibrin film, prepared by gentle compaction of coarse fibrin clots, containing 13–22% fibrin plasticized with either aqueous buffer or glycerol. Both unligated and ligated (i.e., with α‐α and γ‐γ ligation by fibrinoligase, factor XIIIa) films were studied. Both types showed two stages of stress relaxation, with time scales of approximately 10 and 103–104 s, respectively, with a plateau region between. In the plateau, the nominal (engineering) stress for ligated glycerol‐plasticized film is proportional to In λ, where λ is the stretch ratio, up to λ ≅ 2, and it decreases with increasing temperature. For unligated glycerol‐plasticized film, the stresses are smaller by a factor of one‐half to one‐third. For ligated film, the second stage of relaxation is relatively slight, and recovery after release of stress is often nearly complete. For unligated film, the second stage involves a substantial drop in stress, and after recovery there is a significant permanent set. A second relaxation for ligated film reproduces the first, but for unligated film it reproduces the first only if the initial relaxation is terminated before the second stage; otherwise, the second relaxation shows a weaker structure. The behavior of water‐plasticized film is similar to that of glycerol‐plasticized except that the second stage of relaxation occurs at shorter times. During the first stage of stress relaxation, up to about 100 s, the birefringence and the stress‐optical coefficient increase; during the plateau zone of stress relaxation, the birefringence of ligated films is approximately constant and is proportional to 2λ2/(λ2 + 1) − 1, where λ is the stretch ratio. This dependence is predicted by a two‐dimensional model in which rodlike elements in the plane of the film are oriented with independent alignment. During the final stage of stress relaxation, the birefringence of ligated films decreases slightly; that of unligated films decreases substantially, but less rapidly than the stress, corresponding to a further increase in the stress‐optical coefficient. With additional information from small‐angle x‐ray scattering reported in an accompanying paper, the first stage of relaxation is attributed to partial release of bending forces in the fibers by orientation, accompanied by increased birefringence. The second stage is attributed, for ligated films, to an internal transition in the fibrin units accompanied by elongation of some of the fibers; and in the unligated films, to a combination of the latter transition with slippage of protofibrils lengthwise within the fiber bundles that causes some loss of orientation, which diminishes the birefringence.