bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rigidity of myosin and myosin rod by electric birefringence
Authors: Hvidt Søren , Chang Taihyun , Yu Hyuk 
Published: December 2004

AbstractThe rotational relaxation times of rabbit myosin and myosin rod have been determined by electric birefringence measurement. The relaxation time of myosin measured in 10 mM pyrophosphate buffers in a pH range of 7.6–9.5 was found to have substantial concentration and pH dependences. The infinite‐dilution limit of the relaxation time, τ°, was determined as 38 ± 2 μs, and it was found to be independent of pH. For myosin rod, a possible thermally induced conformational change was investigated in a temperature range of 1–43°C. The rotational relaxation time of myosin rod shows no clear indication of conformational change in this temperature range, and the radius of gyration measurement by light scattering was shown to be consistent with this observation. The steady‐state birefringence, however, decreases substantially above around 40°C. This, the myosin rod appears to be only slightly flexible even at physiological temperature, but the possibility of a “melting” or “hinging” of the myosin rod cannot completely be ruled out on the basis of these experiments.
Effect of cationic surfactants on the conformation and aggregation of poly(L‐glutamic acid)
Authors: Maeda Hiroshi , Kato Hiroshi , Ikeda Shoichi 
Published: December 2004

AbstractThe effects of three cationic surfactants, dodecylammonium chloride (DAC), dodecyldimethylammonium chloride (DDAC), and dodecyldimethylammonium chloride (DTDAC), on the conformation of poly(L‐glutamic acid) and at neutral pH were examined by CD. The maximum extent of the α‐helix induction occurs for each surfactant when the mixing ration is about unity. Different effects specific to each surfactant, as described below, appear in the range of mixing ratios larger than that required for the maximum induction. In the case of DTAC, the α‐helices disintegrate into random coils. In the case of DDAC, the aggregation of α‐helices takes place eventually leading to precipitation. Solubilization of the precipitates occurs at high mixing ratios. The most complex behavior is seen in the case of DAC; aggregation of α‐helices occurs only to a small extent and the formation of a small complex predominates over aggregation takes place again as DAC concentration increases further. Induction of the α‐helix is favored by dilution at a constant mixing ratio but is suppressed by the addition of NaCl.
Conformation of oligopeptides with L‐leucyl‐L‐leucyl‐L‐alanyl and L‐methionyl‐L‐methionyl‐L‐leucyl repeating units
Authors: Katakai Ryoichi , Iizuka Yasuko 
Published: December 2004

AbstractThe conformation of oligopeptides with hydrophobic side chains, Nps‐(L‐Leu‐L‐Leu‐L‐Ala)n‐OEt and Nps‐(L‐Met‐L‐Met‐L‐Leu)n‐OEt(n = 1–6), in the solid state, obtained either by evaporation of the solvent or by precipitation with diethyl ether from a 1,1,1,3,3,3‐hexafluoropropan‐2‐ol (HFIP) solution, has been studied with ir spectroscopy and x‐ray powder‐diffraction measurements. The conformation of these peptides in the HFIP solution has been studied by CD spectroscopy. Due to a strong preference of the amino acids to form an α helix, the peptides begin forming α helices at the dodecapeptide in the HFIP solution, and in the solid state by evaporation. In the solid state, with precipitation, the α‐helical conformation is first observed at the octadecapeptide and the lower peptides assume a β structure. The conformational change, from the α helix to the β structure of the peptides with 12 to 15 amino acid residues, during the precipitation process, is due to a strong tendency of the amino acids to form the β‐structure in rather short peptide lengths.
Helix formation by hydroxyamyl‐L‐glutaminyl residues in water and aqueous sodium dodecyl sulfate
Authors: Overgaard Trina , Erie Dorothy , Darsey J. A. , Mattice Wayne L. 
Published: December 2004

AbstractConformational properties of the hydroxyamyl‐L‐glutaminyl residue have been deduced from a CD study of two copolypeptides containing hydroxypropyl‐L‐glutaminyl residues. Mole fractions of hydroxyamyl‐L‐glutaminyl residues were 0.17 and 0.45. Zimm–Bragg statistical weights for the hydroxyamyl‐L‐glutaminyl residue in water are found to be similar to those determined by P.H. von Dreele, N. Lotan, V.S. Ananthan‐arayanan, R.H. andreatta, D. Poland, and H.A. Scheraga [(1971) Macromolecules 4, 408–417] for the hydroxybutyl‐L‐glutaminyl residue. Sodium dodecyl sulfate has only a marginal effect on the helix‐forming tendency of hydroxyamyl‐L‐glutaminyl residues in water.
Temperature‐dependent reversible transition of poly(dCdG) · poly(DcdG) in ethanolic and methanolic solutions
Authors: Hall K. B. , Maestre M. F. 
Published: December 2004

AbstractUsing CD we investigated the transitions of poly(dCdG) · poly(dGdC) from B‐to‐Z form and from Z‐to‐Z′ form. We have found experimental conditions that allow the cooperative transition to occur as a function of temperature in ethanolic solutions. The transition is reversible and can be repeated as often as desired. There is no evidence of strand separation during the cooperative transition as monitored by absorbance. For purposes of calculation, we have assumed a two‐state model for the B‐to‐Z transition, although the data indicate that such a model is too simplistic. The calculations allow the estimation of the change in enthalpy per mole of cooperative unit for the transition as a function of ethanol concentration. The values range from ±140 to ±200 kcal/mol for ethanol concentrations between 10 and 20%. Investigations of the noncooperative Z‐to‐Z′ transition show that it is a reversible two‐state transition. The different forms of poly(dCdG) · poly(dGdC) give no scattering contributions to the CD as shown by fluorescent‐detected CD or fluorscat techniques. This indicates that the CD spectra are true spectra, and contain no contributions from differential scattering of the polynucleotide. This is particularly significant in the case of the Z′ form, since it exists at high ethanol concentrations (80%) where condensation of polynucleotides can provide large contributions to the CD spectra. Analogous investigations using methanol show that the two transitions also occur, but the final Z′ form in methanol is qualitatively different from the ethanol form.
Calorimetric study of 2U:1A three‐stranded complexes formed between poly(U) and adenine dinucleotides: ApA and diastereoisomers of nonionic adenine dideoxyribonucleoside methyl phosphonate
Authors: Wierzchowski Kazimierz L. , Zielenkiewicz Anna , Miller Paul S. 
Published: December 2004

AbstractMelting parameters of 2U:1A complexes formed by polyuridylic acid [poly(U)] and three adenine dinucleotides, diribonucleoside monophosphonate ApA and diastereoisomers of dideoxyribonucleoside methyl phosphonate [(dApA)1 and (dApA)2], in 1M NaCl and at a number of dinucleotide concentrations were obtained from differential scanning microcalorimetric data and interpreted in terms of the theory of helix–coil equilibrium in oligonucleotide–polynucleotide systems. The apparent binding constant, 1/cm, at 39°C and melting temperatures, Tm, at 1 × 10−3 M dinucleotide concentration indicate the following order of thermodynamic stability of the complexes: 2 poly(U) · (dApA)2 (2.27 × 103M−1, 44.2°C) > 2 poly(U) · (dApA)1 (9.9 × 102M1, 39.2°C) > 2 poly(U) · (ApA) (5.9 × 102M−1, 35.8°C). Corresponding calorimetric enthalpies of melting, ΔHm: 13.5, 12.7, and 12.8 kcal/mol (UUA base triplets) were found to be considerably lower than the van't Hoff enthalpies, ΔHapp: 29.4, 16.2, and 16.2 kcal/mol, respectively, evaluated from the dependence of the melting temperatures on dinucleotide concentration. Self‐association of dinucleotides and their simultaneous binding as monomers, dimers, and higher‐order associated species is suggested as the most probable cause of the differences between ΔHm and ΔHapp values. The differences in thermodynamic properties of the complexes formed by (dApA)1 and (dApA)2 diastereoisomers are discussed in connection with their known conformational properties. The higher and essentially enthalpic stability of the 2 poly(U) · (dApA)2 complex correlates with a lower degree of intramolecular stacking of the (dApA)2 isomer. The hydrophobically enhanced strong self‐association of the latter greatly influences the thermodynamics of its complex formation with poly(U) and results in ΔHapp/ΔHm = 2.3.
Molecular‐Mechanical studies of the mismatched base analogs of d(CGCGAATTCGCG)2:d(CGTGAATTCGCG)2, d(CGAGAATTCGCG)2, d(CGCGAATTCACG)2, d(CGCGAATTCTCG)2, and d(CGCAGAATTCGCG)·d(CGCGAATTCGCG)
Authors: Keepers Joe W. , Schmidt Paul , James Thomas L. , Kollman Peter A. 
Published: December 2004

AbstractMolecular‐mechanical simulations have been carried out on “mismatched base” analogs of the DNA double‐helical structure d(CGCGAATTCGCG)2, in which the base pairs CG at the 3 and 10 positions have been replaced by CA, AG, TC, and TG base pairs, as well as an insertion analog in which an extra adenine has been incorporated into one strand of the above structure between bases 3 and 4. The results of these simulations (calculated relative stabilities, structures, and nmr ring‐current shifts) have been compared with calorimetric and nmr data. The calculated relative stabilities of the double‐helical parent dodecamer and the various “wobble” base pairs qualitatively correlate with the experimental melting temperatures. The base‐pairing structure for the GT wobble pair is in agreement with that previously determined from nmr experiments. For the GA base pair, the structure with both bases anti has a slightly more favorable energy from base pairing and stacking than a structure with non‐Watson‐Crick H‐bonding with adenine syn, in agreement with nmr experiments. The CA wobble base is calculated to favor an adenine 6NH2 …︁ cytosine N3 H‐bond over cytosine 4NH2 …︁ adenine N1, again, in agreement with nmr experiments. There is no definitive experimental data on the TC base pair, but the existence of (somewhat long and weak) H‐bonds involving cytosine 4NH2 …︁ thymine 4CO and cytosine N3 …︁ thymine HN3 seems reasonable. We find a structure in which the extra adenine base of the insertion analogs sits “inside” the double helix.
Differential scattering of circularly polarized light by chromatin modeled as a helical array of dielectric ellipsoids within the born approximation
Authors: Belmont Andrew S. , Zietz Stanley , Nicolini Claudio 
Published: December 2004

AbstractTheoretical predictions within the Born approximation of the expected differential light scattering of circularly polarized light (CIDS) were made for the 300‐Å chromatin fiber, modeled as a helical array of dielectric ellipsoids. Computed CIDS values were strongly dependent on the exact geometry of the solenoid model, depending particularly on parameters relaed to the chiral nature of the fiber and the orientation of the nucleosomes within the helix, in contrast to the values of the total light scattering, which mainly probed size and shape. In particular, both a superbead model and a strict linear 110‐Å nucleosome filament would be predicted as giving rise to zero CIDS (in disagreement with the finite values observed). At the same time, helical models in which the normal vectors to the nucleosome faces were exactly parallel to the helical axis also yielded zero CIDS. Confirming earlier expectations, CIDS values were significantly less dependent on helical length than total light scattering. Finally, comparison of these calculated results from those extrapolated from available experimental data indicates that predicted CIDS values, based on currently accepted models of solenoid structure, are within an order of magnitude of those experimentally observed. Together, these results indicate the potential of differential light scattering measurements as a probe of chromatin higher‐order structure, complementary to existing scattering measurements.
Effect of the electric field on the apparent mobility of large DNA fragments in agarose gels
Authors: Stellwagen Nancy C. 
Published: December 2004

AbstractThe electrophoresis of a series of DNA fragments ranging in size from 0.5 to 12 kilobase pairs, has been studied as a function of agarose gel concentration and electric field strength. The apparent mobility of all fragments decreased with decreasing electric field strength and with increasing gel concentration. When extrapolated to zero electric field strength and zero agarose concentration, the apparent mobility of all DNA fragments extrapolated to a common value (2.0 ± 0.1) × 10−4 cm2/V s. The square roots of the retardation coefficients of the various fragments were found to be linearly related to the root‐mean‐square radii of gyration of the fragments, as predicted by pore‐size distribution theory. As predicted by reptation theory, the molecular weights of the various fragments were found to be linearly related to the reciprocal of the apparent mobilities. An equation is given for estimating the apparent pore size of agarose gels between 0.25 and 1.5% in concentration.
Phase‐structure transitions of the elastin polypentapeptide–water system within the framework of composition–temperature studies
Authors: Urry D. W. , Trapane T. L. , Prasad K. U. 
Published: December 2004

AbstractThe temperature dependence of the composition of coacervate and equilibrium phases is examined for the polypentapeptide of elastin (L‐Val1‐L‐Pro2‐Gly3‐L‐Val4‐Gly5)n in water. This provides for the development of a phase diagram. CD data is presented that provides information on associated polypeptide structure changes that, when added to previous CD, nmr, and dielectric relaxation data at lower water composition, allow construction of a phase‐structure diagram of the polypentapeptide–water system. The molecular‐weight dependence of phase change (coacervation) is included. The volume–composition studies as a function of temperature also provide temperature coefficients of expansion and of composition important in analyzing the mechanism of elasticity.
Spermine–nucleic acid interactions: A theoretical study
Authors: Zakrzewska Krystyna , Pullman Bernard 
Published: December 2004

AbstractThe interaction of spermine with nucleic acids is simulated theoretically using refined semi‐empirical energy formulae and an advanced minimization procedure. Various nucleic acids are considered: model homopolymeric DNA's, a dodecamer (CGCGAATTCGCG) of type B‐DNA, as well as a transfer RNA, tRNAPhe. The dominant role of electrostatic potential in determining the preferential binding sites of spermine is demonstrated in each of these cases and the role of counterions, nucleic acid structure, and base‐pair sequence is analyzed.
Structural variation of native cellulose related to its source
Authors: Okano Takeshi , Koyanagi Akio 
Published: December 2004

AbstractX‐ray diffraction diagrams of 80 specimens, mainly from woody plants, were recorded and resolved into characteristic reflections of cellulose I. Significant differences were observed in d‐spacings and integrated intensity ratios between softwoods and hardwoods. Of the lattice parameters, the monoclinic angle was found to be correlated with plant taxonomy and tended towards the right angle in the more advanced taxonomic groups. We have therefore demonstrated that the crystal structure of natural cellulose shows some variations related to the source of the cellulose.
Peptide‐bond distortions and the curvature of α‐helices
Authors: Chakrabarti P. , Bernard M. , Rees D. C. 
Published: December 2004

AbstractSolvent accessible peptide bonds in proteins exhibit a 1–3° compression of the OCN bond angle and a corresponding expansion of the NCCa bond angle, relative to buried peptide bonds. These changes are consistent with an increase in hydrogen bonding to the carbonyl oxygen accompanying solvent exposure (J. D. Dunitz and F. K. Winkler, (1975) Acta Cryst. B31, 251–263). For amphiphilic structures such as α‐helices, systematic differences in peptide‐bond geometry between solvent‐exposed and buried residues will generate significant curvature. A decrease of 4° in the OCN bond angle between hydrophilic and hydrophobic sides of an amphiphilic helix will lead to smooth bending, with a radius of curvature of about 70 Å. This curvature is in the range observed for α‐helices in proteins. Helix curvature is estimated to have only a small effect on the magnitude and direction of the helical dipole moment.
Conformation of mucous glycoproteins in aqueous solvents
Authors: Shogren R. L. , Jamieson A. M. , Blackwell J. , Jentoft N. 
Published: December 2004

AbstractLight‐scattering techniques have been used to measure the z‐average radius of gyration Rg z‐average translational diffusion coefficient Dt and weight–average molecular weight Mw of porcine submaxillary mucin (PSM) in solution. PSM isolated at low shear in the presence of protease inhibitors has a Mw about twice as large as a sample prepared without these precautions. The former sample has a Mw of 17 × 106 in 0.1M NaCl, which decreases to 8 × 106 in 6M guanidine hydrochloride (GdnHCl) and then to 2 × 106 on addition of 0.1M mercaptoethanol to the 6M GdnHCl solution. The Rg or D values obtained for PSM in this work superimpose with those of other authors for different mucin glycoproteins, leading to linear log–log relationships to the molecular weight of the protein core. Comparison of these results with those in the literature for denatured proteins suggest that mucins are linear random coils in which the protein core is stiffened by the presence of the oligosaccharide side chains. The length of the oligosaccharides and the nature of the solvent have little effect on the extension of the protein core. This suggests that the stiffness of the protein core is maintained by steric repulsion of the residues at the beginning of the oligosaccharide chains.
Prediction of protein structural class from the amino acid sequence
Authors: Klein Petr , Delisi Charles 
Published: December 2004

AbstractThe multidimensional statistical technique of discriminant analysis is used to allocate amino acid sequences to one of four secondary structural classes: high α content, high β content, mixed α and β, low content of ordered structure. Discrimination is based on four attributes: estimates of percentages of α and β structures, and regular variations in the hydrophobic values of residues along the sequence, occurring with periods of 2 and 3.6 residues. The reliability of the method, estimated by classifying 138 sequences from the Brookhaven Protein Data Bank, is 80%, with no misallocations between α‐rich and β‐rich classes. The reliability can be increased to 84% by making no allocation for proteins classified with odds close to 1. Classification using previously developed secondary structural prediction methods is considerably less reliable, the best result being 64% obtained using predictions based on the Delphi method.
The distribution of charged groups in proteins
Authors: Barlow D. J. , Thornton J. M. 
Published: December 2004

AbstractThe distributions of charged groups in 32 proteins of known three‐dimensional structure have been analyzed to determine how regularly the groups are spread over the molecule's surfaces, and to identify and to study those proteins where charge asymmetry would seem important for their function. The distributions have been analyzed in terms of charge “polarity,” surface “charge density,” and electric dipole moments. More detailed studies of the distributions for individual proteins are made using map projections specifically developed for this purpose. In the light of the results obtained we discuss the role of charged groups in relation to protein function.
Conformational properties of somatostatin. VI. In a methanol solution
Authors: van den Berg E. M. M. , Jans A. W. H. , van Binst G. 
Published: December 2004

AbstractThe peptide hormone, somatostatin, has been studied by nmr at 500 MHz in a methanol solution and at low temperature (263 K) in order to investigate a possible similarity with conformationally restricted biologically active analogs. The more pronounced predominancy of one conformer already present in a water solution is demonstrated. No evidence has been shown for interactions between Phe11 and other Phes in the molecule.
Thermodynamics of water–biopolymer interactions: Irreversible sorption by a single, uniform sorbent phase
Authors: Bryan William P. 
Published: December 2004

AbstractSorption isotherms of water vapor by solid biopolymers are necessary for the determination of thermodynamic quantities for water–biopolymer interactions. Such isotherms are generally irreversible, so equilibrium thermodynamics may not be applicable. General relationships are derived for thermodynamic quantities of sorption when the sorbent is a single uniform phase. In general, use of the Clausius–Clapeyron equation allows correct determination of differential entropies of sorption. However, calorimetric data are also necessary for the correct determination of other thermodynamic quantities. The single uniform phase model appears more useful than a domain model in explaining the hysteresis seen in water–biopolymer sorption isotherms.
Cytochrome c chimerae from natural and synthetic fragments: Significance of the biological properties
Authors: Wallace Carmichael J. A. , Corradin Giampietro , Marchiori Fernando , Borin Gianfranco 
Published: December 2004

AbstractAnalogs of natural proteins have application in basic research, in medicine, and increasingly, in industry. Of the many methods developed for the fabrication of modified proteins, semisynthesis has so far been the most productive [R. E. Offord (1983) Proc. Eur. Peptide Symp., 17 31–42]. The technique of fragment‐condensation semisynthesis takes as its basic raw material the native protein; fragments derived from it are manipulated by sequential degradation and resynthesis before recombination. While gene manipulation may overtake protein manipulation in general usefulness, certain types of analogs will remain accessible only by semisynthesis. Fragment condensation semisynthesis, as described above, has been used in preparing cytochrome c analogs [C. J. A. Wallace (1979) Proc. Am. Peptide Symp. 6, 609–612]. To overcome the difficulty of replacing amino acids far from convenient cleavage sites, a number of variants of the method have also been used. These include fragment‐specific chemical modification [C. J. A. Wallace & K. Rose (1983) Biochem. J. 215, 651–658] and solid‐phase synthesis of small [P. J. Boon, G. I. Tesser, H. H. K. Brinkhof & R. J. F. Nivard (1981) Proc. Eur. Peptide Symp. 16, 127–130] or large fragments [L. E. Barstow, R. S. Young, E. Yakali, J. J. Sharp, J. C. O'Brien, P. W. Berman & H. A. Harbury (1977) Proc. Natl. Acad. Sci. USA 74, 4148–4250]. The latter study gave low final recoveries, so we have prepared large peptides (38–42 residues) by classical solution methods. We have examined both their use in the reformation of the complete protein, and the physical and biochemical properties of the product analogs compared with those of the native proteins.