bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heavy metal binding to heparin disaccharides. II. First evidence for zinc chelation
Authors: Whitfield Dennis M. , Sarkar Bibudhendra 
Published: December 2004

AbstractTo map out the heavy metal binding sites of iduronic acid containing oligosaccharides isolated from human kidneys, we studied Zn (II) binding by nuclear magnetic resonance (NMR) and molecular modeling to two disaccharides isolated after nitrous acid depolymerization of heparin and two synthetic disaccharides representative of the heparin structure, namely, IdopA2S(α1,4) AnManOH, 1a, IdopA2S(α1,4)AnManOH6S, 1b, IdopA2S‐(α1,4) GlcNSαMe, 2a, and IdopA2S(α1,4)GlcNS6SαMe, 2b (see previous article in this series). A conformational analysis of the metal free and metal bound solutions was made by comparing calculated 〈(NOE)〉s, 〈T1〉s, and 〈J〉s to experimental values. The 1C4, 4C1, and 2S0 conformations of the L‐idopyranosiduronate ring and the 4E and 4T3 of the anhydro‐D‐mannitol ring are evaluated as are rotations about the C5–C6 hydroxymethylene of the AnManOH (6S) or GlcNS(6S) residues. The NOE between IdopA2S H1 and H3 and the known NOE between H2 and H5, as well as the T1 of IdopA2S H3, are introduced as NMR observables sensitive to the IdopA2S ring conformation. Similarly, a NOE between IdopA2S H5 and AnManOH (6S) or GlcNS (6S) H3 was observed that directly restricts the allowed interglycosidic conformational space. For all disaccharides, the Zn(II) bound spectral data are consistent with models in which these motions are partially “frozen” such that the 1C4 conformation of the IdopA2S is stabilized along with the 4T3 conformation of the AnManOH (6S) ring. The interglycosidic conformation is also stabilized in one of two minima. Electrostatic potential energy calculations gave the best overall agreement with experiment and suggest metal binding conformations with the carboxylate and ring oxygen of the IdopA2S residues (1C4 conformation) and either O3 of the GlcNS (6S) residues or the sulfate oxygens of the 6‐sulphate for 2b providing additional chelating sites. These chelation models concur with the observation of marked 13C and 1H NMR chemical shifts for the IdopA2S resonances and of GlcNS H3 for 2a and GlcNS6S C6 for 2b. This study of model compounds implicates the IdopA2S(α1,4) GlcNS6S group as part of the heavy metal binding site in biologically important acidic oligosaccharides such as heparin.
The nature of folded states of globular proteins
Authors: Honeycutt J. D. , Thirumalai D. 
Published: December 2004

AbstractWe suggest, using dynamical simulations of a simple heteropolymer modelling the α‐carbon sequence in a protein, that genetically the folded states of globular proteins correspond to statistically well‐defined metastable states. This hypothesis, called the metastability hypothesis, states that there are several free energy minima separated by barriers of various heights such that the folded conformations of a polypeptide chain in each of the minima have similar structural characteristics but have different energies from one another. The calculated structural characteristics, such as bond angle and dihedral angle distribution functions, are assumed to arise from only those configurations belonging to a given minimum. The validity of this hypothesis is illustrated by simulations of a continuum model of a heteropolymer whose low temperature state is a well‐defined β‐barrel structure. The simulations were done using a molecular dynamics algorithm (referred to as the “noisy” molecular dynamics method) containing both friction and noise terms. It is shown that for this model there are several distinct metastable minima in which the structural features are similar.Several new methods of analyzing fluctuations in structures belonging to two distinct minima are introduced. The most notable one is a dynamic measure of compactness that can in principle provide the time required for maximal compactness to be achieved. The analysis shows that for a given metastable state in which the protein has a well‐defined folded structure the transition to a state of higher compactness occurs very slowly, lending credence to the notion that the system encounters a late barrier in the process of folding to the most compact structure. The examination of the fluctuations in the structures near the unfolding → folding transition temperature indicates that the transition state for the unfolding to folding process occurs closer to the folded state.
The use of flory–huggins theory in interpreting partitioning of solutes between organic liquids and water
Authors: Holtzer Alfred 
Published: December 2004

AbstractSolute partitioning data for dilute solutions have almost invariably been interpreted by equating experimental values of –RT In Kx (wherein Kx is the mole fraction partition coefficient) to Δμ∞, the standard Gibbs energy change for solute transfer from one solvent to another. Recently, it has been alleged that this relation is insufficiently general. Instead, the statistical mechanical Flory‐Huggins (FH) theory has been recommended for use, because it is designed to account for disparities in molecular size between solute and solvent. Our examination of the thermodynamics of partitioning shows that: (1) The customary interpretation is not only entirely correct (providing only that the solute is dilute), but is model‐independent. (2) The dilute limit of the FH theory is seen to agree entirely with the usual interpretation of –RT In Kx, once certain misnomers are cleared away. (3) The use of FH theory being urged upon us in fact serves only to extract from Δμ∞; (the latter quite correctly determined as –RT In Kx) the contact part of Δμ∞ in order to obtain information on hydrophobic interactions. Some caveats are cited concerning such use of the FH statistical mechanical model.
Hydration of DNA bases: Analysis of crystallographic data
Authors: Schneider Bohdan , Cohen Dawn , Berman Helen M. 
Published: December 2004

AbstractWe present a systematic analysis of water structure around nucleic acid bases. We have examined 28 crystal structures of oligonucleotides, and have studied the patterns of water around the four bases, guanine, cytosine, adenine, and thymine. The geometries of water positions were calculated up to 4.00 Å from base atoms. We have found conformation‐dependent differences in both the geometry and extent of hydration of the bases.
Conformational states of a TT mismatch from molecular dynamics simulation of duplex d(CGCGATTCGCG)
Authors: Venable Richard M. , Widmalm Göran , Brooks Bernard R. , Egan William , Pastor Richard W. 
Published: December 2004

AbstractThe TT mismatch region in duplex d(CGCGATTCGCG) was studied using a 500‐ps molecular dynamics (MD) simulation in water, and a series of 1‐ps MD simulations and energy minimizations in vacuum. The DNA maintained its duplex structure, although the mismatch region showed significantly higher flexibility than the GC regions. The predominant conformation in the 500‐ps MD simulation involved an average −42° propeller twist between T6 and T′6, and a −22° buckle between A5 and T′7, One hydrogen bond was formed between T6 and T′6, and another between T6 and the O2 of T′7 with both Watson‐Crick hydrogen bonds between A5 and T′7 remaining intact. The minimizations resulted in conformations with the equivalent hydrogen‐bonding pattern, as well as ones with “wobble pair” hydrogen bonds between T6 and T′6. However, the wobble pair conformation was found to be unstable in the water simulation.
Flow linear dichroism spectra of four filamentous bacteriophages: DNA and coat protein contributions
Authors: Clack Beatrice A. , Gray Donald M. 
Published: December 2004

AbstractIn this study, we have separated the contributions of DNA and protein to the absorption and linear dichroism (LD) of each of four phages: fd, IKe, Pf1, and Pf3. We have found that the DNA packaged in each of the phages is hypochromic relative to the purified single stranded DNA, suggesting that bases are stacked in all of the phages. We have oriented the phages by flow and for the first time report the intrinsic LD from 320 to 190 nm for each of these phages. From the intrinsic LD of the phages and the isotropic absorption of the individual components, we have determined the reduced dichroism of the DNA within the phages and, subsequently, the maximum angle of inclination of the DNA bases (from the helix axis) for the packaged DNA. The maximum angles were 63° and 64° for the DNAs of class I phages fd and IKe, respectively. The angles were significantly less, 51° and 49°, for the DNAs of the class II phages Pf1 and Pf3, respectively. Thus, the two classes of phage differ in the structures of their packaged DNA, the DNA bases of the class II phages being more parallel to the long axis of the phage than are the DNA bases of the class I phages.
Effects of hydration on scale factors for ab initio force constants. IV. trans and cis N‐methylacetamide
Authors: Williams Robert W. 
Published: December 2004

AbstractScaled quantum mechanical force fields have been calculated using the 4‐31G basis for trans and cis conformers of both isolated and water‐solvated N‐methylacetamide (NMA). (1) A single set of scale factors for isolated NMA yields relatively correct predictions of the shifts in vibrational frequencies between the trans and cis conformers. This is also true of a single set of scale factors for trans and cis NMA in water. The total standard deviation between measured and calculated frequencies for trans NMA in both isolated and solvated states is 6 cm−1. This implies that it should be possible to use a single set of scale factors to accurately predict the vibrational spectra of a peptide in a variety of conformational states. (2) The computationally predicted effect of hydration on force constants for the supermolecule NMA · nH2O are generally consistent with the experimentally measured effects of hydration on scale factors. These results indicate that supermolecule calculations can be useful in predicting the effects of hydration on spectra. (3) Three types of scale factors are calculated as follows: (a) first from ab initio calculations on an isolated molecule using frequencies measured from isolated molecules; (b) second from calculations on an isolated molecule using frequencies measured from water‐solvated or otherwise hydrogen‐bonded molecules; (c) and third from supermolecule calculations on a molecule hydrogen‐bonded to water, using frequencies measured from water‐solvated molecules. (4) The third type of scale factors are similar to the first type, for confidently measured modes, even though some of the force constants are very different. This suggests that one set of scale factors may be transferable to both isolated and hydrogen‐bonded molecules, and that the simple representation of hydration used here may be a useful approximation. The second type of scale factors yield accurate frequencies, but they may not be generally transferable.
Studies of DNA dumbbells. II. Construction and characterization of DNA dumbbells with a 16 base‐pair duplex stem and Tn end loops (n = 2, 3, 4, 6, 8, 10, 14)
Authors: Amaratunga Mohan , Snowden‐Ifft Elizabeth , Wemmer David E. , Benight Albert S. 
Published: December 2004

AbstractThe preparation and characterization of DNA dumbbells that contain the 16 base‐pair duplex sequences 5′G‐C‐A‐T‐A‐G‐A‐T‐G‐A‐G‐A‐A‐T‐G‐C3′ (set 1) and 5′G‐C‐A‐T‐C‐A‐T‐C‐G‐A‐T‐G‐A‐T‐G‐C3 ′(set 2) are reported. The dumbbells of set 1 have the duplex stem nucleated on both ends by Tn (n = 2, 3, 4, 6, 8, 10, and 14) loops. The dumbbells of set 2 have Tn (n = 2, 4, 8, 10) end loops. For the molecules of set 1, effects of end loop size on the electrophoretic mobility, CD and UV absorbance spectra, and cleavage by restriction enzymes, were investigated. Effects of loop size on the CD spectra and restriction enzyme cleavage of the molecules of set 2 were also examined. Optical melting curves of the molecules of set 1 were collected as a function of sodium ion concentration from 30 to 120 mM. These investigations revealed that as loop size decreases, the electrophoretic mobilities, rates of enzyme cleavage, and optical melting temperatures increase. For end loops with at least three T's the observed increases are inversely proportional to loop size. The behavior of the dumbbell with T2 end loops departs from this linear dependence and is anomalous in every experimental context. For molecules with end loops comprised of at least four T's CD spectra were virtually indistinguishable. However, these spectra differed considerably from the CD spectrum of the T2‐looped molecule. The CD spectrum of the dumbbell with T3 end loops displayed features common to the dumbbells with larger loops and T2 end loops. Thermodynamic evidence that the terminal G · C base pairs (bps) nucleating the T2 end loops were intact was obtained from a comparison of the melting temperature of this molecule with that of a DNA dumbbell containing the 14 central bps of the set 1 duplex sequence linked instead by end loops comprised of the four base sequence, C‐T‐T‐C. The tm of this latter molecule was determined to be 9°C less than that of the former dumbbell assumed to contain a 16‐bp stem and T2 end loops. One‐ and two‐dimensional proton nmr measurements performed on the dumbbell of set 2 with T2 end loops and the same sequence with unpaired T's on the ends also verified formation of the T2 end loops, indicated the duplex residues of the dumbbell were in the B form, and showed that the first 3 bps adjoining the loops are distorted. Results are compared with several recently published relevant studies.
Origins and consequences of ligand‐induced multiphasic thermal protein denaturation
Authors: Shrake Andrew , Ross Philip D. 
Published: December 2004

AbstractThe presence of subsaturating levels of a high‐affinity ligand has been demonstrated both by experiment and calculation to have far‐reaching consequences on thermally induced protein denaturation due to the coupling between the protein denaturation and ligand‐binding equilibria. Under such circumstances, a protein may undergo biphasic denaturation even though in the absence of ligand it exhibits a thermogram comprised of a single essentially symmetric endotherm. Up to now, the presence of just 2 maxima in the thermogram has been presented merely as an experimental observation or as the result of equilibrium computations. Here we develop a thermodynamic description of the linkage between these equilibria in which the number of cusps present in the thermogram correlates with the number of resolved steps in the plot of saturation level of remaining native protein vs temperature (i.e., the thermal binding curve). During thermally induced denaturation, the concentration of native protein decreases; thus, the native protein in effect is titrated with ligand at constant total ligand concentration. The free ligand concentration increases substantially through the release of bound ligand by unfolding protein thereby increasing the saturation level of the remaining native protein. The form of this thermal binding curve is a function of the number of ligand‐binding sites on the protein, the magnitudes of the association constants, and the total ligand and total protein concentrations. As a result, the model predicts multiphasic denaturation of a single cooperative unit when the thermal binding curve consists of discrete multiple steps. The presence of only 2 maxima (i.e., a single cusp) in a thermogram for a protein with multiple sites on the native species derives from the form of the thermal binding curve, which in this case is a single‐step sigmoidal plot, and not from the predominant denaturation of unliganded and fully liganded native species. In addition, it is shown that, in general, the contributions from the denaturation of individual native protein species are decidedly non‐two‐state in character; thus, simple deconvolutton should not be carried out. The effects of nonzero values of ΔCP and dΔCP/dT for denaturation and of changes in enthalpy and in heat capacity for ligand binding, as well as the interaction of ligand with the denatured protein, are explored also.
Synthesis of new hydrophilic microspheres: Optimized carriers for microparticle‐enhanced nephelometric immunoassays
Authors: Marchand J. , Varcin P. , Riochet D. , Montagne P. , Cuilliere M. L , Duheille J. , Pau B. 
Published: December 2004

AbstractTo optimize antigen–antibody reactions, we have synthesized chemically well‐defined hy‐drophilic microspheres. Proteins or haptens were covalently linked to these carriers. When the microsphere conjugates were agglutinated by the corresponding antiserum, the size of the complex artificially increased during the immunological reaction. After optimizing var‐ious parameters such as the hydrophilic character, repulsion charges, and amount of antigen coupled to the microspheres, we developed a rapid and sensitive immunoassay based on laser light scattering by the complexes.
Conformational studies of anionic melittin analogues: Effect of peptide concentration, pH, ionic strength, and temperature—models for protein folding and halophilic proteins
Authors: Ramalingam Kalaiyarasi , Aimoto Saburo , Bello Jake 
Published: December 2004

AbstractMelittin (MLT), a 26‐residue cationic (net charge +5 at pH 7.2) peptide from bee venom, is well known to be a monomeric, approximately random coil; but when its charges are reduced by titration, by acetylation (net charge +2) or succinylation (net charge −2), or by screening by salt, it goes over to tetrameric α‐helix. The conversion is promoted by raising the peptide concentration. The tetramer is held together by hydrophobia forces. We have changed the net charge to −6 by acylation with acetylcitric anhydride (a new acylating agent); this anionic derivative forms tetrameric helix at neutral pH, without salt, and at relatively low concentration, conditions under which the cationic MLT does not become helical. Thus, a high net charge is not sufficient to prevent association and helix formation. We have synthesized an anionic melittin analogue of MLT (E‐MLT; net charge −4) in which all five lysine and arginine residues are replaced with glutamate, and acetyl and succinyl derivatives of E‐MLT (net charges −5 and −6). All three of these are resistant to helix formation. They require much higher NaCl or NaClO4 concentration for helix formation than does MLT. Even CaCl2, MgCl2, and spermine. 4HC1 are less effective in helicizing E‐MLT than MLT. MLT, at pH 7.2, shows increasing helix as the peptide concentration increases (8‐120 μM), but E‐MLT and its acyl derivatives do not. MLT and acylated MLTs in the helical tetramer show both cold‐ and heat‐induced unfolding, with maximum stability near room temperature. At high temperature, a significant amount of residual structure remains. Heating (to 100°C) monomeric MLT (i.e., MLT at low concentration) or E‐MLT results in a monotonic increase in negative ellipticity. In 1.0M NaCl, E‐MLT (at sufficiently high concentration) also shows cold and hot unfolding. The results are discussed in respect to charge–charge and charge‐dipole interactions, and hydrophobic effects. E‐MLT is also discussed in relation to proteins of halophilic bacteria, which have higher proportions of anionic residues than do corresponding proteins of non‐halophiles.
Discontinuous volume transitions in ionic gels and their possible involvement in the nerve excitation process
Authors: Tasaki I. , Byrne P. M. 
Published: December 2004

AbstractDiscontinuous volume changes in polymer gels carrying negatively ionized groups were studied by varying the molarities of univalent and bivalent cations in the bathing solution. These studies offer a sound basis for elucidating the origin of rapid swelling and heat production in nerve fibers associated with the process of excitation.
The use of UV‐visible spectroscopy for the determination of hydrophobic interactions between neuropeptides and membrane model systems
Authors: Young John K. , Graham William H. , Beard Debbie J. , Hicks Rickey P. 
Published: December 2004

AbstractUltraviolet‐visible spectroscopy has been used as a rapid method to evaluate the hydrophobia interactions between a series of cationic and zwitterionic neuropeptides and dipeptides with the hydrophobia core of two membrane model systems; sodium dodecyl sulfate and lysophosphatidylcholine micelles. If a hydrophobia interaction occurs, a 1−nm bathochromic shift is observed in the uv‐visible spectrum of the aromatic side chains when going from aqueous solution to a micellar solution. The aromatic residues of substance P, bradykinin, and Des‐Arg9 bradykinin all exhibited the 1−nm bathochromic shift in the presence of sodium dodecyl sulfate while those of Met‐enkephalin did not. The opposite effects were observed in the presence of lysophosphatidylcholine micelles. © 1992 John Wiley & Sons, Inc.
Hydrophobicity of amino acid residues: Differential scanning calorimetry and synthesis of the aromatic analogues of the polypentapeptide of elastin
Authors: Luan Chi‐Hao , Parker Timothy M. , Gowda D. Channe , Urry Dan W. 
Published: December 2004

AbstractRelative hydrophobicities of aromatic amino acid residues are investigated by using differential scanning calorimetry (DSC) on 10 synthetic copolypentapeptides of poly(VPGVG) of elastin. Utilizing the hydrophobic‐driven process of the inverse temperature transition exhibited by these polypentapeptides in aqueous solution, the relative hydrophobicities of Phe, Trp, and Tyr residues are determined by the critical temperature and heat of the transition. The DSC data for the aromatic residue containing copolypentapeptide aqueous solution indicate that tryptophan is the most hydrophobic amino acid residue, phenylalanine the third most hydrophobic on basis of transition temperature and the second on basis of transition heat. For tyrosine, significant differences are observed between the phenolic and the phenoxide anionic states. At pH 7, where tyrosine is protonated, it is found to be the second most hydrophobic amino acid residue on the basis of the transition temperature, whereas on the basis of the heat of transition, it is loss hydrophobic than both tryptophan and phenylalanine. Changing the pH from pH 7 to pH 12, for example, for poly[0.8(VPGVG), 0.2(VPGYG)] in aqueous solution shifts the transition temperature from 7 to 49°C with a dramatically reduced heat. On the basis of both the transition temperature scale and the heat of transition, the hydroxylated tyrosine appears less hydrophobic than glycine. © 1992 John Wiley & Sons, Inc.
Structural investigation of helices II, III, and IV of B. megaterium 5S ribosomal RNA by molecular dynamics calculations
Authors: Kim Jong Hwa , Marshall Alan G. 
Published: December 2004

AbstractThe structures of the helices II‐III region and the helix IV region of B. megaterium 5S rRNA have been examined by means of energy minimization and molecular dynamics calculations. Calculated distances between neighboring hydrogen‐bonded imino protons in helices II, III, and IV were between 3.5 and 4.5 Å. The overall axis for the helices II‐III region is warped rather than straight. Formation of additional Watson‐Crick base pairs in loop B and loop C was not evident from the atomic positions calculated by molecular dynamics. Bases in loop C are well stacked, showing no significant change during dynamics. Bulge migration in helix III does not seem to be possible; the helices II‐III region prefers one conformation. Helix II is more stable than helix III. Five base pairs in helix IV were sufficiently stable to establish that helix IV is terminated by a hairpin loop of three nucleotides. U87 protrudes from loop D. Structures of the helices II‐III segment and the helix IV segment of B. megaterium 5S rRNA obtained by molecular dynamics were generally consistent with the solution structure inferred from high‐field proton nmr spectroscopy. © 1992 John Wiley & Sons, Inc.