bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sedimentation equilibrium in macromolecular solutions of arbitrary concentration. II. Two protein components
Authors: Chatelier Ronald C. , Minton Allen P. 
Published: May 2005

AbstractRelations describing sedimentation equilibrium in solutions containing two macromolecular solute components are derived for the following cases: (1) two nonassociating proteins at arbitrary concentration, (2) one dilute self‐associating protein in the presence of a second inert protein at arbitrary concentration, and (3) two proteins at arbitrary concentration that can associate to form a single heterocomplex of arbitrary composition. As in earlier work (R. C. Chatelier and A. P. Minton (1987) Biopolymers, 26, 507–524), the relations are obtained by using scaled particle theory to calculate the thermodynamic activity of each species present at a given radial distance in the centrifuge. The results of numerical simulations of sedimentation equilibrium are presented as the dependence of apparent molecular weights, or apparent weight‐average molecular weights, upon solution composition. Semiempirical methods are presented, by means of which the weight‐average molecular weights of self‐ and heteroassociating proteins in highly nonideal solutions may be estimated from experimental data. It is found that the semiempirical methods yield reasonably accurate estimates of the true weight‐average molecular weight over a broad range of experimental conditions, providing that the partial specific volumes of two components in a heteroassociating system do not differ by more than about 0.05 mL/g.
Prediction of the native conformation of a polypeptide by a statistical‐mechanical procedure. III. Probable and average conformations of enkephalin
Authors: Paine Gregory H. , Scheraga Harold A. 
Published: May 2005

AbstractThe program SMAPPS (Statistical‐Mechanical Algorithm for Predicting Protein Structure) was originally designed to determine the probable and average backbone (ϕ, ψ) conformations of a polypeptide by the application of equilibrium statistical mechanics in conjunction with an adaptive importance sampling Monte Carlo procedure. In the present paper, the algorithm has been extended to include the variation of all side‐chain (χ) and peptide‐bond (ω) dihedral angles of a polypeptide during the Monte Carlo search of the conformational space. To test the effectiveness of the generalized algorithm, SMAPPS was used to calculate the probable and average conformations of Met‐enkephalin for which all dihedral angles of the pentapeptide were allowed to vary. The total conformational energy for each randomly generated structure of Met‐enkephalin was obtained by summing over the interaction energies of all pairs of nonbonded atoms of the whole molecule. The interaction energies were computed by the program ECEPP /2 (Empirical Conformational Energy Program for Peptides). Solvent effects were not included in the computation. The results of the Monte Carlo calculation of the structure of Met‐enkephalin indicate that the thermodynamically preferred conformation of the pentapeptide contains a γ‐turn involving the three residues Gly2‐Gly3‐Phe4. The γ‐turn conformation, however, does not correspond to the structure of lowest conformational energy. Rather, the global minimum‐energy conformation, recently determined by a new optimization technique developed in this laboratory, contains a type II′ β‐bend that is formed by the interaction of the four residues Gly2‐Gly3‐Phe4‐Met5. A similar minimum‐energy conformation is found by the SMAPPS procedure. The thermodynamically preferred γ‐turn structure has a conformational energy of 4.93 kcal/mole higher than the β‐bend structure of lowest energy but, because of the inclusion of entropy in the SMAPPS procedure, it is estimated to be ∼ 9 kcal/mole lower in free energy. The calculation of the average conformation of Met‐enkephalin was repeated until a total of ten independent average conformations were established. As far as the phenylalanine residue of the pentapeptide is concerned, the results of the ten independent average conformations were all found to lie in the region of conformational space corresponding to the γ‐turn. These results further support the conclusion that the γturn conformation is thermodynamically favored.
Conformational constraints of amino acid side chains in α‐helices
Authors: Piela Lucjan , Nemethy George , Scheraga Harold A. 
Published: May 2005

AbstractThe conformational freedom of amino acid side chains is strongly reduced when the side chains occur on an α‐helix. A quantitative evaluation of this freedom has been carried out by means of conformational energy computations for all naturally occurring amino acids and for α‐aminobutyric acid when they are placed in the middle of a right‐handed poly(L‐alanine) α‐helix. One of the three possible rotameric states for rotation around the Cα  Cβ bond (viz. g+) is excluded completely on the helix because of steric hindrance, and the relative populations of the other two rotamers (t and g−) are altered because of steric interactions and the reduction of hydrogen‐bonding possibilities. The computed tendencies of the changes in distributions of rotamers, on going from an ensemble of all backbone conformations to the α‐helix, agree with the observed tendencies in proteins. Minimum‐energy side‐chain conformations in an α‐helix have been tabulated for use in conformational energy computations on polypeptides.
Ir spectra and conformational behavior of N‐acetyl‐(glycine, L‐alanine, L‐leucine)‐N′‐methylamides in chloroform
Authors: Jose Chalakkal I. , Belhekar Anagha A. , Agashe Mangala S. 
Published: May 2005

AbstractNH stretching bands of N‐acetyl‐(glycine, L‐alanine, L‐leucine)‐N′‐methylamides in dilute chloroform solution have shown that these dipeptides are present as a mixture of intramolecularly hydrogen‐bonded five‐membered ring species and nonhydrogen bonded species. Integrated absorption intensity measurements revealed that the concentration of the intramolecularly hydrogen bonded species decreased from 62% in glycine to 35% in the L‐leucine derivatives.
Enthalpy and entropy changes for the intercalation of small molecules to DNA. II. Ethidium and propidium fluoride
Authors: Hopkins Harry P. , Wilson W. David 
Published: May 2005

AbstractEnthalpy changes (ΔHB) for the binding of ethidium (a monocation) and propidium (a dication) to calf thymus DNA have been determined calorimetrically in piperazine‐N, N′‐bis(2‐ethanesulfonic acid) buffer with the fluoride ion as the counterion. Heats of dilution for the fluoride salts of ethidium and propidium were substantially less than the corresponding values found for other halide salts of these cations. At a Na+ ion concentrations of 0.019, ΔHB = −8.3 and −7.9 ± 0.3 kcal mol−1 for ethidium and propidium, respectively. For these two cations, just as was observed for the naphthalene monoimide (monocation) and diimide (dication) [H. P. Hopkins, K. A. Stevenson, and W. D. Wilson, (1986) J. Sol. Chem. 15, 563–579], ΔHB is within the same experimental error for both cations. Apparently, charge–charge interactions in DNA–cation complexes produce only small changes in the enthalpy for the system. In the concentration range 0.019–0.207, the ΔHB values for propidium did not depend appreciably on the Na+ ion concentration, and a similar pattern was shown to exist for ethidium. When these results were combined with ΔGB values for the binding of these cations to DNA, we found the variation of ΔSB with Na+ ion concentration to be remarkably close to the predictions of modern polyelectrolyte theory, i.e., propidium binding to DNA causes approximately twice as many Na+ ions to be released into the bulk solution as does the binding of ethidium. The much stronger binding of propidium, relative to ethidium, at low ionic strengths is thus seen to be primarily due to entropic effects.
The effect of anisotropic properties of randomly oriented particles on polarized light: An operational calculus for spatially heterogeneous distributions
Authors: Maestre Marcos F. 
Published: May 2005

AbstractRecent publication of the application of Mueller–Stokes calculus to a model of optical microdomains by Hjelm et al. [(1986) Biopolymers 25, 1359–1378] states that the CD of randomly orientated microdomains show apparent CD due to the linear dichroism components. In this paper we show that these conclusions are erroneous due to a misapplication of the Mueller calculus to the model proposed by Hjelm et al. We show in detail where the errors were committed, and prove that the ordinary Mueller matrices cannot be used to compute the interaction of light with heterogeneous distributions of optical microdomains that lay in a plane perpendicular to the direction of the irradiation of light. We further prove that ordinary Stokes vectors do not represent the polarization properties of light in systems that are a heterogeneous distribution of optical microdomains in the plane perpendicular to the light beam. A modified optical calculus is proposed, in which extended space matrices and extended space polarization vectors will give the correct formulation for the heterogeneous distribution of microdomains. We prove that, for randomly orientated microdomains in space, the linear dichroism and linear birefringence components cancel, and the only remaining terms are those due to the intrinsic CD and circular birefringence. This result negates the explanation of Hjelm et al. about the induced CD in the Soret region of sickle hemoglobin gels.
Conformational behavior of the polysaccharide backbone of murein
Authors: Leps B. , Labischinski H. , Bradaczek H. 
Published: May 2005

AbstractThe energetically possible conformations for the alternating heteropolysaccharide backbone of murein, consisting of N‐acetylglucosamine and N‐acetylmuramic acid, were calculated using an empirical approach. The calculations were carried out for regular as well as for random‐chain polymers, resulting in a model for the saccharide strands featuring extended chains with a length increment of 0.98–1.02 nm per disaccharide unit and peptide attachment sites at every second saccharide residuum pointing into all directions with propagation angles of 80–100° between consecutive sites.
Vibrational CD of polypeptides. X. A study of α‐helical oligopeptides in solution
Authors: Yasui S. C. , Keiderling T. A. , Katakai Ryoichi 
Published: May 2005

AbstractWe have measured the vibrational CD (VCD) of a series of heterooligopeptides—o‐nitrophenylsulfenyl(L‐Met‐L‐Met‐L‐Leu) n‐OEt, n = 6,8,10,11–in the amide A, I, and II regions. These spectra are identical in shape and magnitude, within our signal to noise limits. The VCD in each band are of exactly the shape expected for a right‐handed α‐helix and imply that VCD of the polypeptide α‐helix is relatively unaffected by chain length down to the 18‐subunit level.
Theoretical conformational analysis of a μ‐selective cyclic opioid peptide analog
Authors: Wilkes Brian C. , Schiller Peter W. 
Published: May 2005

AbstractThe allowed conformations of the μ‐receptor‐selective cyclic opioid peptide analog
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were determined using a grid search through the entire conformational space. Energy minimization of the 13‐membered ring structure lacking the exocyclic Tyr1 residue and the Phe3 side chain using the molecular mechanics program Maximin resulted in only four low‐energy conformations. These four ring structures served as templates for a further energy minimization study with the Tyr1 residue and Phe3 side chain added to the molecule. The results indicated that the Tyr1 and Phe3 side chains enjoy considerable orientational freedom, but nevertheless, only a limited number of low‐energy side‐chain configurations were found. The obtained low‐energy conformers are discussed in relation to various proposed models of the bioactive conformation of enkephalins and morphiceptin.
Conformations of the glycine dipeptide
Authors: Lau Wan F. , Montgomery Pettitt B. 
Published: May 2005

AbstractIntegral equation theory is applied to the determination of the intramolecular potential of mean force for the glycine dipeptide, N‐acetyl glycyl‐N‐methylamide, in aqueous solution. The solvated free energy for the dipeptide as a function of the dihedral angles ϕ and ψ (Ramachandran plot) is determined and compared with the vacuum surface. Conformations forbidden in vacuum are found to be populated in aqueous solution. The results of the glycine dipeptide are compared to a parallel study on the alanine dipeptide. Solvent effects are found to be responsible for the extent of many of glycines properties related to flexibility.
Shape effects in elastic scattering by orientationally random ensembles of simple model viruses
Authors: McClain W. M. , Ghoul W. A. 
Published: May 2005

AbstractRecent theoretical work has shown that the complete set of polarized elastic light scattering studies should yield information about particle structure that has so far hardly been utilized. We present calculations of such light‐scattering properties for a number of model structures, exploring particularly the size limit at which the new effects should become visible. The particles are assumed to be randomly oriented in aqueous suspension, and all identical to each other. We compare several particle models of differing geometrical shape, but with identical forward scattering power and identical radii of gyration. We find that one of the ten observables shows particularly desirable properties as a general large‐particle characterization parameter: it is nonzero for all structures, it approaches zero as particle size decreases, and it shows an angular dependence that distinguishes among models of different shape. Assuming incident light at 350 nm, it differentiates between different shaped particles with radii of gyration as small as 50 nm. Such particles are well below the optical resolution limit and about the size of many types of viruses.
Conformational perturbation due to an extra adenosine in a self‐complementary oligodeoxynucleotide duplex
Authors: Roy Siddhartha , Sklenar Vladimir , Appella Ettore , Cohen Jack S. 
Published: May 2005

AbstractThe conformation of an oligodeoxynucleotide pentadecamer, d(CGCGAAATTTACGCG), self‐complementary except for an additional adenosine nucleotide at position 11, has been investigated with nmr spectroscopy. This oligomer was found to exist predominantly in the duplex form in solution rather than in the hairpin loop form, as observed previously for an analogous 13‐mer sequence. Nuclear Overhauser effects indicate that the B‐form conformation is disrupted by the extra A base, which forms a wedge within the duplex, producing a bent junction and an overall S‐like structure. A downfield‐shifted phosphate resonance was assigned using a two‐dimensional 1H–31P correlation method, and was found to be P12‐13. This and other results indicate that the extra A causes conformational distortions at some distance along the duplex structure.
Cyclic retro–inverso dipeptides with two aromatic side chains. I. Synthesis
Authors: Nunami Ken‐Ichi , Yamazaki Toshimasa , Goodman Murray 
Published: May 2005

AbstractA series of cyclic retro–inverso dipeptides—2‐[(4‐hydroxy)benzyl]‐5‐benzyl‐4,6(1H,2H,3H,5H)‐pyrimidinedione (c[mPhe‐gTyr]), 2‐benzyl‐5‐[(4‐hydroxy)benzyl]‐4,6(1H,2H,3H,5H)‐pyrimidinedione (c[mTyr‐gPhe]), and 2‐benzyl‐5‐amino‐5‐[(4‐hydroxy)benzyl]‐4,6(1H,2H,3H,5H)‐pyrimidinedione {c[(α‐amino)mTyr‐gPhe]}—were synthesized in order to define the minimum structural requirements for binding affinity with opiate receptors and biological activity. Although the first two compounds lack a free amine proposed to be necessary for receptor recognition, the c[mPhe‐gTyr] and c[mTyr‐gPhe] analogues serve as model molecules in conformational studies of the target analogue, c[(α‐amino)mTyr‐gPhe]. The cis‐ and trans‐c[(α‐amino)mTyr‐gPhe] contain all the functional groups such as the amine and phenolic groups in the tyrosine, and the aromatic group in the phenylalanine, necessary for opiate activity. In addition, the c[(α‐amino)mTyr‐gPhe] analogues possess similar geometries to the Tyr‐Pro part of morphiceptin (Tyr‐Pro‐Phe‐Pro‐NH2) whose high μ‐receptor activity is attributed to conformations with the Tyr‐Pro amide bond in a cis conformation because the peptide bonds assume a cis conformation. However, both analogues are inactive in the guinea pig ileum and the mouse vas deferens assays. This may result from wrong orientation of the benzyl group of the gPhe residue with respect to the (α‐amino)mTyr residue.Conformational studies of these molecules using 1H‐nmr spectroscopy and molecular mechanics calculations will be reported in the following paper. Results of conformational analysis should provide information about backbone–side‐chain interactions in the retro–inverso peptide chains since all the fundamental structural elements of the retro–inverso peptides are included in these model systems even though the peptide bonds must assume a cis conformation.
Distance‐dependent dielectric constants and their application to double‐helical DNA
Authors: Mazur J. , Jernigan R. L. 
Published: May 2005

AbstractDetailed studies of structures of biological macromolecules, even in simplified models, involve many costly and time‐consuming calculations. Any thorough methods require sampling of an extremely large conformation and momentum space. Calculations of electrostatic interactions, which depend on many physical factors, such as the details of solvent, solvent accessibility in macromolecules, and molecular polarizability, are always developed in a compromise between more rigorous, detailed models and the need for immediate application to complicated biological systems. In this paper, a middle ground is taken between the more exact theoretical models and the simplest constant values for the dielectric constant. The effects of solvent, counterions, and molecular polarizability are incorporated through a set of adjustable parameters that should be determined from experimental conditions. Several previous forms for the dielectric function are compared with the new ones. The present methods use Langevin functions to span the region of dielectric constant between bulk solvent and cavity values. Application of such dielectric models to double‐helical DNA is important because base‐stacking preferences were previously demonstrated [A. Sarai, J. Mazur, R. Nussinov, and R. L. Jernigan (1988) Biochemistry, vol. 27, pp. 8498–8502] to be sensitive to the electrostatic formulation. Here we find that poly (dG) · poly(dC) can be A form for high screening and B form for low screening. By contrast, poly (dA) · poly(dT) can only take the B form. Base stacking is more sensitive to the form of the dielectric function than are the sugar–phosphate backbone conformations. Also in B form, the backbone conformations are not so affected by the base types as in A form.
Salt dependence and ion specificity of the coil–helix transition of furcellaran
Authors: Zhang Wei , Piculell Lennart , Nilsson Svante 
Published: May 2005

AbstractThe conformational transition and the cation‐binding properties of aqueous furcellaran (a gel‐forming, low‐sulfated polysaccharide of the carrageenan family) in various salts and salt mixtures was studied by optical rotation and by 133Cs‐nmr. The results were compared with theoretical predictions based on the Poisson–Boltzmann cell model (PBCM). The conformational transition of furcellaran occurs in a single step, which implies a nonblocklike distribution of sulfate groups along the polymer chain. The chloride salts of sodium, lithium, and tetramethylammonium are equally potent in inducing helix formation of furcellaran, indicating that these ions act by nonspecific electrostatic interactions. In contrast, the potassium and cesium ions specifically promote helix formation and aggregation (gelation) of furcellaran. The divalent calcium and magnesium ions are nonspecific, but more potent than the nonspecific monovalent ions in inducing helices. Anions differ in their capacity to stabilize the furcellaran helix in the sequence Cl− < NO < Br− < SCN− < I−. The iodide and thiocyanate anions impede aggregation and gel formation. 133Cs‐nmr chemical shifts indicate specific binding of cesium ions to the furcellaran helix. Thus, with respect to its ion specificity and ion‐binding properties, furcellaran, with 0.6 sulfate group per repeating disaccharide, resembles κ‐carrageenan (1 sulfate/disaccharide) but differs from ι‐carrageenan (2 sulfates/disaccharide). The conformational transition temperatures of furcellaran are, however, generally higher than those of κ‐carrageenan under comparable conditions, and in mixtures of the two polysaccharides, separate transitions still occur, indicating that no mixed helices are formed. The observed ion sensitivity and cation‐binding properties of furcellaran agree with predictions, by the PBCM, for a K‐carrageenan with a reduced charge density.
Conformational preferences of oligopeptides rich in α‐aminoisobutyric acid. I. Observation of a 310/α‐helical transition upon sequence permutation
Authors: Basu Gautam , Bagchi Ken , Kuki Atsuo 
Published: May 2005

AbstractThe solution conformation of peptides rich in the α,α‐dialkylated amino acid Aib has proven to be a subtle problem, not because of helix/coil transitions, but rather because of α‐helical/310‐helical competition. A special series of peptides containing 75% Aib has been synthesized that feature identical amino acid composition but differing sequences; they are sequence permutation isomers. Nuclear magnetic resonance hydrogen‐bonding studies reveal that there is a sequence permutation induced transition between the two alternative helical forms within this set. The implications for the design and conformational prediction of helical Aib‐rich peptides are discussed.
Molecular dynamics simulation of oligosaccharides containing N‐acetyl neuraminic acid
Authors: Mukhopadhyay Chaitali , Bush C. Allen 
Published: May 2005

AbstractαD‐N‐acetyl neuraminic acid (Neu5Ac, sialic acid) is a commonly occurring carbohydrate residue in various cell surface glycolipids and glycoproteins. This residue is linked terminally or internally to Gal residues via an α(2 → 3) or α(2 → 6) linkage. In the cell surface receptor, sialyl‐LewisX, a terminal α(2 → 3) linkage is present. Previous studies from our laboratory have shown that in solution LewisX adopts a relatively rigid structure. In order to model the Neu5Ac residue, vacuum molecular dynamics of this monosaccharide were compared with simulations that explicitly include solvent water. The dynamical average of the monosaccharide conformation obtained from the two simulations was similar. Vacuum calculations for the disaccharide Neu5Ac α(2 → 3) Gal β‐O‐methyl show that a number of low energy minima are accessible to this disaccharide. Molecular dynamics simulations starting from the low energy minima show conformational transitions with a time scale of 10–50 ps among several of the minima while large barriers between other minima prevent transitions on the time scale studied. Simulations of this disaccharide in the presence of solvent show fewer conformational transitions, illustrating a dampening effect of the solvent that has been observed in some other studies. Our results are most consistent with an equilibrium among multiple conformations for the Neu5Ac α(2 → 3) Gal β linkage. © 1994 John Wiley & Sons, Inc.