bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational energy calculations for dinucleotide molecules: A study of the nucleotide coenzyme nicotinamide adenine dinucleotide (NAD+)
Authors: Thornton Janet M. , Bayley Peter M. 
Published: December 2004

AbstractA study of the conformational states of the dinucleotide coenzyme NAD+ has been made using semiempirical energy calculations. Taking low‐energy mononucleotide structures as starting conformations, energy minimizations have been performed. The lowest energy states are stacked structures, with interactions between the adenine and nicotinamide rings. Some structures show stabilization gained from electrostatic attractions between the positively charged nicotinamide and negatively charged phosphate oxygens. These predictions correlate well with the available experimental data.
Effect of charge density of cationic polyelectrolytes on complex formation with DNA
Authors: Mita Kazuei , Zama Mitsuo , Ichimura Sachiko 
Published: December 2004

AbstractThe interaction between DNA and ionen polymers, ‐[N+(CH3)2(CH2)mN+(CH3)2(CH2)n], with m‐n of 3–3, 6–6, and 6–10 were examined in order to know how the binding behavior of cationic polymers with DNA depends on the charge density of polycation. The ionen polymer has no bulky side chain and the binding forces with DNA would be attributed mainly to electrostatic interaction. When 3–3 ionen polymers were added to DNA solution, precipitable complexes with the ratio of cationic residue to DNA phosphate (+/−) of 1/1 and the free DNA molecules were segregated, while 6–6 and 6–10 ionen polymers formed soluble complexes with DNA molecules up to (+/−) = 0.5. This suggests that 3–3 ionen polymers bind cooperatively with DNA while 6–6 and 6–10 ionen polymers bind noncooperatively. The cooperative binding of 3–3 ionen polymer and the noncooperative binding of 6–6 ionen polymer were also supported by the thermal melting and recooling profiles from the midpoint between first and second meltings. It was concluded that the charge density of DNA phosphate is a critical value determining whether the ionen polymers bind to DNA by a cooperative or by a noncooperative binding, since the distance between successive cationic charges of 3–3 ionen polymer is shorter than that between successive phosphate charges on DNA double helix and those of 6–6 and 6–10 ionen polymers are longer.
Flexibility of the pyrrolidine ring in proline peptides
Authors: Madison Vincent 
Published: December 2004

AbstractA survey of over 50 crystal structures indicates that both imino acid and peptide derivatives of proline populate ring conformers consistent with the torsional potentials about single bonds. In both cases, lower barriers for rotation about CN bonds relative to those about CC bonds favor smaller values for dihedral angles about the former bonds. In peptides a minimum in the torsional potential about CN bonds occurs at zero dihedral angle, further favoring small angles. The pyrrolidine‐ring dihedral angles of the proline compounds in the solid state obey a cyclopentane‐type pseudorotation function. Thus the puckering of the five‐membered ring can be quantitatively described by two parameters. Consistent with small dihedral angles about CN bonds, Cβ and/or Cγ are puckered out of the mean plane of the ring in nearly all of the nonstrained compounds.Utilizing the consistent force‐field method of Lifson and coworkers [see A. Warshel, M. Levitt, and S. Lifson (1970) J. Mol. Spectrosc. 33, 84] the intramolecular energy of five proline peptides was minimized with respect to all internal coordinates. In addition, the energy surface near minima was explored by constraining a particular dihedral angle and reminimizing the energy with respect to all remaining variables. In linear peptides two types of pyrrolidine‐ring conformers have identical predicted energies. In the cyclic dipeptide cyclo (Pro‐Gly) one of the ring conformers is favored by about 3 kcal/mol, while the cyclic tripeptide cyclo(Pro‐Gly‐Gly) favors the other conformer by a comparable margin. In agreement with observations in the solid state and in solution, Cβ and/or Cγ are puckered in the predicted conformers. A correlation between proline Φ and the details of the puckered conformation was predicted and found to match precisely conformers observed in crystals.For the diamides N‐acetyl‐L‐proline‐N′‐methyl‐amide and N‐acetyl‐L‐proline‐N′,N′‐dimethylamide (AcProMe2A) 30% and 60% cis acetyl peptide bonds were predicted in good agreement with observations in nonpolar solvents for the respective compounds. The conformational distributions with respect to proline Ψ are also in accord with experimental observations. For AcProMe2A, a model for a ‐Pro‐Pro‐sequence in a peptide chain, this study is the first to predict stable conformers for proline Ψ either ca. −50° or 140° for both cis and trans peptides.
The application of infinite‐order perturbation theory to biological polymers
Authors: Groskreutz Harvey , Wu Shi‐Yu , Schwartz Manuel 
Published: December 2004

AbstractQuantum mechanical perturbation theory of infinite order is applied to an infinitely long biological polymeric chain. The resulting ensemble‐averaged density of electronic states is approximately calculated by truncation according to a method introduced by S. Y. Wu [(1974) J. Math. Phys. 15, 947–949]. The results are found to require reasonable computational facilities and the method may be applied to a study of mutagenicity.
Conformational studies on polynucleotide chains. III. Intramolecular energy maps and comparison with experiments
Authors: Tosi Camillo , Clementi Enrico , Matsuoka Osamu 
Published: December 2004

AbstractConformational energy maps for the four combinations of two consecutive torsional angles of the backbone structure of polydeoxyribonucleotides are presented. Both the C(2′)‐endo and the C(3′)‐endo conformation of sugar rings were considered. The energies were evaluated with an analytical expression representing the best fit to ab initio energies computed in the Hartree‐Fock approximation, and consisting of a contribution from nonbonded interactions of the Lennard‐Jones 6‐12 type and an intrinsic torsional potential. It is shown that the minima of these maps are in excellent agreement with the most stable conformations as obtained from x‐ray crystallographic analysis of nucleic acids and polynucleotides.
Conformational studies of the copolymer poly(L‐lysine, L‐tyrosine) 1:1 in aqueous solution
Authors: Garnier Arlette , Tosi Lucia 
Published: December 2004

AbstractThe absorption and circular dichroism spectra of the 1:1 copolymer (L‐Lys, L‐Tyr)n have been investigated in aqueous solutions at pH ranging from 3 to 13. The spectral patterns indicate that the fully charged polympholyte assumes a nonperiodic conformation on the acid and basic sides of the isoelectric point. At pH ranging from 9.2 to 11.6, the polymer is largely ordered and takes mostly an antiparallel β‐structure as is shown by the infrared spectra in D2O solutions. Moreover, the rotational strength of the La transition of tyrosyl is independent of the polymer conformation, whereas that of the Lb transition is strongly sensitive to it.
Statistical mechanical deconvolution of thermal transitions in macromolecules. I. Theory and application to homogeneous systems
Authors: Freire Ernesto , Biltonen Rodney L. 
Published: December 2004

AbstractThe theoretical basis for the statistical mechanical deconvolution of a thermally induced macromolecular melting profile is presented. It is demonstrated that all the thermodynamic quantities characterizing a multistate macromolecular transition can be obtained from the average excess enthalpy function, 〈ΔH〉, of the system, without any assumption of the particular model or mechanism of the reaction.Experimentally, 〈ΔH〉 is obtained from scanning calorimetric data by direct integration of the excess apparent molar heat capacity function, ΦCp. Once 〈ΔH〉 is known as a continuous function of the temperature, the partition function, Q, of the system can be calculated by means of the equation

From the partition function all the thermodynamic quantities of the system can be obtained. It is shown that the number of discrete macroscopic energy states, the enthalpy and entropy changes between them, and the relative population of each state as a function of temperature can be calculated in a recursive form.
Compressibility studies of three proteins in CsCI solutions in the analytical ultracentrifuge
Authors: Sharp Dan S. , Fujita Norman , Kinzie Kathleen , Ifft James B. 
Published: December 2004

AbstractThe compositional buoyant densities, ρ;, of human γ‐immunoglobulin, bovine serum mercaptalbumin, and egg albumin have been measured in CsCl solutions in the analytical ultracentrifuge as a function or pressure. Standard pressure coefficients, ψ0, and standard partial specific volumes of the solvated proteins, υ,0, have been computed from these data. The ψ0 values obtained are strikingly different from each other and from the only other pressure coefficients which have been measured, those values obtained for nucleic acids and nucleoproteins. The ψ value for γ‐immunoglobulin is negative, the first nonpositive value obtained, and suggests an unusual internal structure for this protein. The pressure coefficient of mercaptalbumin is not constant. A second‐order relation is derived and utilized to interpret these data. The slope of the ρ(P) plot for egg albumin was constant and negative and yielded values of ψ0 which are about 20% as large as those reported for DNA. Evaluation of published isopiestic data for egg albumin in CsCl solutions provided the dependence of preferential hydration on water activity. This quantity, (dΓ′/da) as well as α, were found to be negative. The values of ψ0 and α were used to compute the effective density gradient from which the correct molecular weight of egg albumin was obtained. The apparent specific volume of egg albumin in a buoyant CsCl solution was measured using the Mettler‐Paar densimeter.
Brownian motion of highly charged poly(L‐lysine). Effects of salt and polyion concentration
Authors: Lin Sung‐Chang , Lee Wylie I. , Schurr J. Michael 
Published: December 2004

AbstractThe Brownian motion of a single sample of high‐molecular‐weight poly(L‐lysine) [(Lys)n, n = 955] has been studied by dynamic light scattering over a wide range of NaBr concentrations and at three different polyion concentrations. A substantial decrease in scattered intensity is associated with the transition from the ordinary phase to the low‐salt extraordinary phase. At the salt concentration where the transition takes place the relaxations are non‐exponential and appear to exhibit at all angles a rapid relaxation (τ ≅ 10 μsec) that is presumed to be a manifestation of the kinetics of the transition process. The K2 dependence of the slow relaxation rates in the extraordinary phase has been confirmed within the experimental error. The extrapolated infinite‐dilution values of the diffusion coefficients in the ordinary phase are observed to decline precipitously below 10−2M salt to astonishingly small values, indicating a dramatic rise in the friction factors of the isolated polyions. An extensive discussion of these findings in relation to the theory employed here and to existing data in the literature is also given.
Solubilities of amino acids
Authors: Bull Henry B. , Breese Keith , Swenson Charles A. 
Published: December 2004

AbstractThe Mettler/Paar precision density meter DMA‐02D has been used to determine the concentration of saturated solutions of amino acids at 20.0, 25.0, and 29.8 °C. The technique has proven itself an elegant and precise method. The solubilities of all of the amino acids with the exceptions of proline, lysine, and cystine have been measured. The Gibbs free energies of transfer from saturated water solution to 1M Na2SO4 and to 1M Gu·HCL along with the van't Hoff heats and entropies have been calculated. The van't Hoff heats have been compared with the calorimetrically determined heats for some of the amino acids. The Lumry‐Rajender relation between the entropy and heats has been observed. The process of transfer of the amino acids from water to the solvents is primarily enthalpic rather than entropic.
The antibody–antigen interaction at an aqueous–solid interface: A study by means of polarized infrared ATR spectroscopy
Authors: Ockman N. 
Published: December 2004

AbstractThe determination of structural changes in antibodies due to their specific interaction with antigenic proteins is an important problem in understanding immunological responses. The method of polarized ATR infrared spectroscopy applied to protein films adsorbed on an appropriate solid surface can give information about the conformation of the polypeptide chains, as well as their orientation with respect to the surface. The adsorption of anti‐rabbit serum albumin onto monomolecular films of rabbit serum albumin, bovine serum albumin, and ovalbumin, and of anti‐ovalbumin onto films of rabbit serum albumin and ovalbumin at a Ge‐aqueous interface have been studied by this technique. The intensity of the amide I absorption indicates that the strengths of binding of these three albumin proteins with anti‐rabbit serum albumin is, under appropriate conditions, in the order rabbit > bovine ≫ ovalbumin; with anti‐ovalbumin, it is ovalbumin ≫ rabbit. Since the frequencies of the amide I band appear near 1655 cm−1 for all the proteins and protein complexes studied, the major contributions to their conformation comes from α‐helix and random‐coil structures. The average orientation of the transition moments of the amide I and A bands has been shown to be about 75° with respect to the surface normal. This indicates that the polypeptides chains are on the average approximately parallel to the surface for all the systems studied. Consequently, the effect of the specific antibody‐antigen interaction on the conformation and orientation of the former seems negligible in these films.
Boundary analysis of sedimentation‐velocity experiments with monodisperse and paucidisperse solutes
Authors: Van Holde K. E. , Weischet Wolfgang O. 
Published: December 2004

AbstractA method is presented which allows one to calculate a distribution of sedimentation coefficients from the boundries of sedimentation‐velocity experiments with mono‐ or pauci‐disperse solutes. With two solutes differences in S value as small as 20% can be resolved. In absence of heterogeneity and concentration‐dependent effects, the analysis also provides values for the diffusion coefficient within an accuracy of −10 to +5%. Tests with both simulated data and ultracentrifugation experiments on short DNA fragments show the value and the limitations of the method.
Optical properties of sugars. VI. Circular dichroism of amylose and glucose oligomers
Authors: Lewis Donald G. , Johnson W. Curtis 
Published: December 2004

AbstractThe CD spectra of amylose, the maltose oligomers, cellobiose, and the cyclodextrins are measured in aqueous solution to 1640 Å. Two bands are found in this region. An examination of chromophorically equivalent but conformationally different glucans demonstrates that the CD of glucans is sensitive to conformation. However, the conformation of the subunits in the maltose oligomer series appears independent of chainlength. The conformations of the interior maltosyl groups of this series are all approximately equivalent. A comparison of the amylose and cycloamylose spectra indicates that amylose is substantially biased in its chirality. Since there is little chainlength dependence, the oligomers should have a similar chirality bias. The butanol complex of amylose, which is believed to have a V‐form helical conformation, has a CD similar to free aqueous amylose. This is consistent with conformational calculations on amylose which predict that the maltosyl subunits of amylose are restricted to a small region on its conformational map which includes the V‐form helix. It is also consistent with the idea that amylose a loosely wound and extended helix in aqueous solution.
Studies on protein folding, unfolding, and fluctuations by computer simulation. II. A. Three‐dimensional lattice model of lysozyme
Authors: Ueda Yuzo , Taketomi Hiroshi , Gō Nobuhiro 
Published: December 2004

AbstractA three‐dimensional lattice model of protein designed to assimilate lysozyme is introduced. An attractive interaction is assumed to work between preassigned specific pairs of units, when they occupy the nearest‐nighbor lattice points. The behavior of this lattice lysozyme is studied by a Monte Carlo simulation method. Because of the specific interunit interactions,“native state” of the lattice lysozyme is stable at low temperatures. Conformational fluctuations in the native state are observed to occur at both termini and loop regions of the main chain existing on the surface. The process of unfolding and denatured states of this model are discussed. Complete refolding from a denatured state was not observed. However, by starting from partially folded structures, the native conformation could be attained. From these observation it is concluded that, in the process of folding of proteins as simplified in a lattice model, nulceation is a rate‐limiting factor. The artificial character of this model and possible improvement are discussed.
Comparison of conformation and antimicrobial activity of synthetic analogs of gramicidin S: Stereochemical consideration of the role of D‐phenylalanine in the antibiotic
Authors: Kawai M. , Nagai U. 
Published: December 2004

AbstractIn order to study the role of D‐amino acid residues in keeping the stable β‐sheet conformation and in the antimicrobial activity of gramicidin S (GS), the four analogs of GS containing D‐Ala, L‐Ala, Gly, and Aib (α‐aminoisobutyric acid) in place of D‐Phe were synthesized. D‐Ala‐and Gly‐containing analogs showed antimicrobial activity, while those containing L‐Ala and Aib showed no activity. Conformation of these analogs and their derivatives were studied by comparison of ORD and CD spectra and by slective methylation method. It is concluded that the biologically active analogs have β‐sheet conformation while inactive analogs have a much different conformation from that of GS. This indicates that D‐Ala‐Pro and Gly‐Pro sequences favor taking a β‐bend form but L‐Ala‐Pro and Aib‐Pro sequences do not because the presence of L‐side methyl group on the α‐carbon atom of LAla and Aib residues destabilizes the β‐bend form. This would explain why the inactive analogs which take a different conformation from that of the active ones result in the loss of activity.
Photon correlation spectroscopy of hemoglobin: Diffusion of Oxy‐HbA and Oxy‐HbS
Authors: Jones C. Ronald , Jhonson Charles S. , Penniston John T. 
Published: December 2004

AbstractTranslation diffusion coefficients have been measured for oxyhemoglobin A and oxyhemoglobin S over the concentration range 0.1–37 g/dl by means of photon correlation spectroscopy. The solutions were 0.1 M in KCl and in each case the pH was adjusted to the isoelectric point of the hemoglobin species present. No significant differences were found between the HbA and HbS results; and after correction to water at 20°C, the diffusion coefficients could be described by the equation

where Do = (6.93 ± 0.06) × 10−7 cm2/sec and c ids the concentration in units of g/dl. No evidence was found for the aggregation of oxy‐HbS at high concentrations which was reported by Lindstrom et. al. [(1976) Biophys. J. 16, 679–689].
Model nucleoproteins: Binding of actinomycin D to complexes of DNA with lysine‐containing polypeptides
Authors: Votavoá H. , Bláha K. , Šponar J. 
Published: December 2004

AbstractComplexes of DNA with histone H1 and random and sequential polypeptides containing 30–100% of lysine were studied using actinomycin D as a probe. The binding of actinomycin D was measured by spectrophotometric titration in 0.15M NaCl and in 0.01M Tris buffer. The excluded‐site model was used for the evaluation of binding data. Polypeptides reduce the number of binding sites on DNA available for actinomycin D binding. The extent of this change depends mainly on the content and distribution of basic lysine residues. Of the hydrophobic residues constituting the peptides, only leucine strongly depresses the actinomycin D binding. The helix‐forming and helix‐breaking amino acid residues are without effect.
Ellipsometry as a tool to study the adsorption behavior of synthetic and biopolymers at the air–water interface
Authors: De Feijter J. A. , Benjamins J. , Veer F. A. 
Published: December 2004

AbstractThe application of ellipsometry of the study of the adsorption behavior of proteins and synthetic macromolecules at the air‐water interface has been investigated. It is shown that for macromolecules the amount adsorbed per unit area, Γ, as determined by ellipsometry, only has a well‐defined physical meaning if the refractive‐index increment remains constant up to high concentrations present in the adsorbed layer. It has been found experimentally that this conditioned is fulfilled for proteins. The ellipsometric Γ values of some protein agree satisfactorily with those obtained by two independent techniques has been used to investigate the adsorption from solution of κ‐casein, bovine serum albumin, and polyvinyl alcohol. For bovine serum albumin, Γ reaches a plateau value of 2.9 mg/m2 for concentrations ≥ 0.05 wt%. The thickness of the adsorbed molecules. For κ‐casein, Γ steadily increases with increasing centration and multilayers are formed. The technique provides interesting information on conformational changes in adsorbed macromolecules, on the rate of the process, and on the conditions under which these occur.
Synthesis of sequential polypeptides containing lysine and tyrosine
Authors: St. Pierre S. , Ingwall R. T. , Goodman M. 
Published: December 2004

AbstractSequential polypeptides with the repeating units L‐tyrosyl‐L‐lysyl, L‐tyrosyl‐(L‐lysyl)2, and L‐tyrosyl‐(L‐lysyl)3 have been synthesized by solution polymerization of the N‐hydroxy‐succinimide esters of the corresponding di‐, tri‐, and tetrapeptides. The monomers for the polytripeptide and polytetrapeptide were prepared by fragment condensation, using the mixed carbonic anhydride coupoling method. Moderately high molecular weight polypeptides were obtained.
Proton magnetic relaxation in solid poly(L‐alanine), poly(L‐leucine), poly(L‐valine), and polyglycine
Authors: Andrew E. R. , Gaspar R. , Venart W. 
Published: December 2004

AbstractMolecular motion in solid poly(L‐alanine), Poly(L‐leucine), poly(L‐valine), and polyglycine has been investigated through measurement of the portion spin‐lattice relaxation time at 30 and 60 MHz between 110 and 350°K. Rapid random reoriention of sied‐chain methyl groups provides the dominent source of relaxation in the first three; activation energies are 10.5 ± 1 1, 8.5 ± 1 kJ/mol, respectively, significantly lower than in the monomeric crystals. Relaxation times in poyglycine are two orders of magnitude longer than in the monomeric crystals. Relaxation times in polyglycine, significantly lower than in the monomeric crystals. Relaxation times in polyglycine are two orders of magnitude longer and are attributed mainly to segmental motions of the polymer chains. Evidence of nonexponential recovery of nuclear magnetization was encountered in the first three homopolyamino acids but not in polylycine, and was attributed to the correlated time to characterize these motions gave quite good agreement with the data; some improvement was obtained for two polymers using a Cole‐Davidson distribution of correlation times. For biopolymers using a Cole‐Davidson distribution of correlation times. For biopolymers generally it is concluded that rapid methyl group reorientation is a common dynamical feature and an important source of nuclear magnetic relaxation.