bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for similar function of transmembrane segments in receptor and membrane‐anchored proteins
Authors: Brandl Christopher J. , Deber Raisa B. , Hsu Lynn C. , Woolley G. Andrew , Young Xenia K. , Deber Charles M. 
Published: December 2004

AbstractTransmembrane (TM) regions of receptor proteins should have unique structural and/or chemical characteristics if these regions contain residues functional in TM signal transduction. However, in a survey of the membrane‐occurring residues in 37 integral membrane proteins, we found that amino acid compositions of TM regions of receptor proteins (n = 11) could not be distinguished statistically from corresponding regions of membrane‐anchored proteins (e.g., recognition molecules) with a functional external domain attached to a single hydrophobic membrane‐spanning anchor segment (n = 16). TM regions in both categories of proteins differed from the compositions of TM regions in membrane‐transport proteins (n = 10). The analysis implies that TM regions in receptor proteins may function mainly to anchor (and position) receptors in their cellular membranes, and therefore residues in receptors that participate in signal transduction need not be restricted to these regions. In addition to mechanisms involving receptor aggregation, ligand‐activated conformational perturbation of a receptor external aqueous domain, resulting in membrane penetration of hydrophobic segment(s) of this domain to produce intramembranous contact with its cytoplasmic domain, is hypothesized as a further possible mode of signal transduction.
Counterion exchange reactions on DNA: Monte Carlo and Poisson–Boltzmann analysis
Authors: Paulsen Mark D. , Anderson Charles F. , Record M. Thomas 
Published: December 2004

AbstractIn solutions containing DNA and cations of more than one type, the competitive interactions of these cations with DNA can be modeled as an ion exchange process that can be described quantitatively by means of the theoretical approach reported in this paper. Under conditions of experimental interest the radial distribution function of each type of counterion is calculated from the results of canonical Monte Carlo (MC) simulations using the primitive model for DNA (having a helical charge distribution) and for the electrolyte ions. These ions consist of monovalent coions, monovalent counterions intended to represent Na+, and counterions of a second type designated Mz+, having variable size and charge (z ≥ 1). The competitive association of these counterions with DNA is described in terms of D, a parameter analogous to an ion exchange equilibrium quotient. Values of D are calculated from the results of our MC simulations and compared with corresponding predictions of the Poisson–Boltzmann (PB) cell model and with results inferred from analyses of previously published nmr measurements. Over typical experimental concentration ranges (0.02M < [Na+] < 0.20M, 0.001 < [Mz+] < 0.160M), DMC and DPB both are predicted to be relatively independent of the bulk ion concentrations. For various specifications of the size and charge of the competing cation (Mz+), DMC and DPB exhibit similar trends, although the MC simulations consistently predict that the cations bearing a higher charge density than that of Na+ are somewhat stronger competitors than indicated by the PB calculations. For monovalent and divalent competitors of varying radii, theoretical predictions of D are compared with values obtained by fitting nmr measurements. If the hard‐sphere radii specified in the simulations are the (hydrated) ionic radii determined from conductance measurements, then the MC predictions and the corresponding nmr results are in reasonable agreement for various monovalent competitors and for a divalent polyamine, but not for Ca2+ and Mg2+.
Metal‐Induced sequential transitions among DNA conformations
Authors: Shin Yong A. , Butzow James J. , Sinsel Lisa D. , Clark Patricia , Pillai Rajasekharan P. , Johnson W. Curtis , Eichhorn Gunther L. 
Published: December 2004

AbstractThe action of [Co(NH3)6]Cl3 on poly(dGdC) · poly(dGdC) can lead to a series of consecutive reactions, in which B‐DNA is first converted to Z‐DNA [M. Behe and G. Felsenfeld (1981) Proc. Natl. Acad. Sci USA 78, 1619–1623], which in turn is transformed into an unidentified conformer that we tentatively call “U”, and finally the highly associated anisotropic ψ‐DNA is produced. Conditions are given under which the sequence B ⇄ Z ⇄ “U” ψ(+) can be stopped at any point in the direction from left to right. The reverse processes, from right to left, occur when ψ(+) or “U”‐DNA are treated with various amounts of salt concentrations and lowering temperature. Thus it is demonstrated that four conformers of poly(dGdC) · poly(dGdC) are readily interconvertible, and that Z‐DNA and “U” conformers are intermediates in the reversible transformations of B‐ and ψ‐DNA.
The interaction of multiply charged intercalating heterocycles with DNA
Authors: Fairley Terri , Molock Frank , Boykin David W. , Wilson W. David 
Published: December 2004

AbstractThe interaction with DNA of two aromatic nitrogen heterocycles, 1 and 2, which at pH 6 have two positive charges on their ring systems and two cationic side chains, have been determined. A third similar compound, 3, with a single side chain and reduced ring charge, was analyzed as a control. Viscometric titrations with sonicated DNA indicated that all three compounds bind to DNA by intercalation. Spectrophotometric binding studies as a function of ionic strength indicated that both 1 and 2 bind to DNA as tetracations at pH 6. These are the first examples of intercalators with two charges directly on the intercalating ring system. Dissociation kinetics experiments as a function of ionic strength confirmed that 1 and 2 bind to DNA as tetracations. Compound 1 has a G · C base‐pair binding preference, 2 seems to prefer binding to alternating pyrimidine–purine sequences regardless of the composition, and 3 has no significant binding specificity.
Statistical mechanical theory of melting transition in supercoiled DNA
Authors: Sen Srikanta , Majumdar Rabi 
Published: December 2004

AbstractThe melting curve for a covalently closed circular DNA has been analyzed on the basis of an expression for the supercoiling energy derived in terms of the elastic parameters of the macromolecule, treated as a homopolymer. The result obtained by applying the usual methods of statistical mechanics indicate close agreement with the available experimental data. It is found that the elevation of the melting temperature, as compared to that of the nicked circular or linear DNA, is a natural consequence of the fact that the supercoiled molecule is constrained by an invariant linking number. The flattening of the melting curve, on the other hand, arises as the closed circular duplex melts into a loose helix rather than random coils.
Binding of nogalamycin to model tetranucleotides
Authors: Trinquier Georges , Chen Kai‐Xian , Gresh Nohad 
Published: December 2004

AbstractIntercalated complexes of the antitumor antibiotic nogalamycin (NGM) with the double‐stranded oligonucleotides d(GCGC)2, d(ATAT)2, and d(ACAC) · d(GTGT) are investigated with the theoretical method SIBFA. The amino sugar part of the drug locates preferentially in the minor groove. An intrinsic preference for the d(ATAT)2 sequence over the d(ACAC) · d(GTGT) and d(GCGC)2 sequences is obtained, corresponding to relative energies 0, 11, and 15 kcal/mole, respectively. A mixed sugar‐puckering pattern is preferred in the d(ATAT)2 complex while a uniform sugar‐puckering pattern is preferred for the other sequences. No direct specific interaction involves the N+—H part of protonated NGM. The location of the amino sugar as well as the sequence selectivity is due to the global electrostatic interaction of the dimethylammonium group with the given groove. The two hydroxyl groups of the amino sugar and the carbonyl of the carbomethoxy group encounter partners for hydrogen bonding at the intercalation site, but these interactions do not appear to govern the base sequence selectivity. The nogalose part is not found to be directly involved in the binding or in the selectivity. The conformations of isolated and intercalated NGM are discussed.
Ions around DNA: Monte Carlo estimates of distribution with improved electrostatic potentials
Authors: Conrad Joan , Troll Mark , Zimm Bruno H. 
Published: December 2004

AbstractCoulomb's law for the electrostatic interactions between ions is modified when discontinuities in dielectric constant (relative permittivity) occur. In a DNA solution such a discontinuity occurs at the interface between the DNA molecular helix and the surrounding water. We take the modified interaction potentials from a previous report [Macromolecules (1986) 19, 1186–1194] and use them with the Monte Carlo method to find the distribution of univalent and bivalent counterions around the DNA helix in the absence of coions (i.e., no added salt). In comparing the ion distribution with the modified potential to the distribution without, we find that the effects of the modifications to the potentials are considerable. The modifications tend to drive the ions out of the grooves of the helix, especially out of the major groove. This result comes partly from the repulsion exerted on the ions by the low‐permittivity helix and partly from the concentration of the field of the phosphates at the surface of the helix, a concentration that is also caused by the discontinuity in permittivity.
Conformational behavior of cyclic CCK‐related peptides determined by 400‐MHz 1H‐nmr: Relationships with affinity and selectivity for brain receptors
Authors: Roy P. , Charpentier B. , Durieux C. , Dor A. , Roques B. P. 
Published: December 2004

AbstractThe conformational study of a homogenous series of cyclic analogues of CCK8, selective for central receptors, such as Boc‐ X‐Tyr(SO3H)‐Nle‐D‐Lys‐Trp‐Nle‐Asp‐Phe‐NH2, where X = L‐Glu, D‐Glu, or γ‐D‐Glu, was performed by 400‐MHz 1H‐nmr. The regular increase in affinity for central receptors when going from [L‐Glu] to [γ‐D‐Glu] is correlated to (a) an enhancement in internal flexibility of the cyclic moiety, (b) an external orientation of the tyrosine side chain, and (c) a restructuring of the C‐terminal part of the peptide. All these results could permit a modeling of biologically active conformation of CCK8 for both receptors types to be performed.
Conformational properties of 2,3‐methanopyroglutamic acid in peptides: Nmr and X‐ray diffraction studies
Authors: Mapelli C. , Elrod L. F. , Switzer F. L. , Stammer C. H. , Holt E. M. 
Published: December 2004

AbstractThe effects of replacing L‐pyroglutamic acid with the cyclopropane analogue 2,3‐methanopyroglutamic acid (2,3‐MeGlp) on conformation and enzymatic stability have been investigated in 2,3‐MeGlp‐NHMe and the novel thyrotropin releasing hormone (TRH) analogue [2,3‐MeGlp1]‐TRH by x‐ray diffraction and nmr. While 2,3‐MeGlp‐NHMe adopts a folded conformation (small ψ angle) in the solid state, several conformations are available to the molecule in solution. 1H‐nmr of the diastereomeric mixture [(±)‐2,3‐MeGlp1]‐TRH indicates a close orientation of the pyrrolidone and imidazole rings. The 2,3‐MeGlp‐His amide bond is considerably more stable to pyroglutamate aminopeptidase than the Glp‐His bond in TRH.
Conformationally constrained D,L‐alternating oligopeptides
Authors: Fenude Emma , Tomasic Lera , Lorenzi Gian Paolo 
Published: December 2004

AbstractThe possibility of selectively reducing the number of β‐helical structures theoretically possible for a D,L‐alternating peptide by using a N‐methyl group as conformational constraint is considered. Some 1H‐nmr data regarding Boc(L‐Nle‐D‐Nle)3‐L‐Nle‐D‐MeNle‐L‐Nle‐D‐Nle‐L‐Nle‐OMe (I), its formyl analogue (II), and the pentadecapeptide Boc(D‐Leu‐L‐Leu)5‐D‐MeLeu‐(L‐Leu‐D‐Leu)2‐OMe (III) are presented. It is shown that these alternating stereocooligopeptides with a N‐methyl group in the (n − 3) (I and II) or (n − 4) position (III) differ drastically in their behavior from the corresponding nonmethylated compounds. In chloroform, I and II form predominantly ↑↓ β7.2‐helices and III forms almost exclusively ↑↓ β5.6 or ↑↓ β7.2‐helices. The helices are in every case those having the maximum possible number of interchain H bonds.
Stereoselective electron transfer between chiral substrates and metal chelates anchored to polypeptides
Authors: Pispisa B. , Palleschi A. , Paradossi G. 
Published: December 2004

AbstractElectron transfer from ortho‐dihydroxy substrates, such as L(+)‐ascorbic acid, L‐adrenaline, and L‐dopa, to iron(III) in [Fe(tetpy)(OH)2]+ ions anchored to sodium poly(L‐glutamate) (FeTL) or poly(D‐glutamate) (FeTD) was found to proceed stereoselectively when structurally ordered and partially shielded actives sites prevent easy approach for redox partner. Oxidant‐reductant interactions are then mediated by the polypeptide, whose conformational asymmetry ensures an efficient sterically discriminating environment. Evidence is produced that stereoselectivity chiefly arises from transition state effects, while thermodynamic discrimination is of minor importance. Theoretical models of the diastereomeric electron‐transfer complexes were constructed by conformational energy calculations based on Coulombic, nonbonded, and hydrogen‐bonded energy terms. The molecular parameters of the models enabled “differential” thermodynamic functions of the diastereomeric pairs and stereoselectivity to be evaluated and satisfactorily compared with those experimentally determined. The models give good insight into the observed topochemical phenomena and support the idea that stereoselevtivity is coupled with a remote attack mechanism on the central metal ion where the peripheral tetpy ligand of the active sites acts as an electron‐transfer agent.
Synthesis of the dodecapeptide corresponding to domain III of bovine brain calmodulin: α‐β Shift side reactions during the synthesis by the classical method in solution
Authors: Borin Gianfranco , Calderan Andrea , Ruzza Paolo , Pezzoli Anna , Marchiori Fernando , Peggion Evaristo 
Published: December 2004

AbstractWe report details of the chemical synthesis of the dodecapeptide corresponding to the calcium binding loop III of bovine brain calmodulin (sequence 93–104) and its fragments 96–04, 93–98, and 99–104.The preparation of the peptides employed classical solution methods and a fragment‐condensation strategy. The major difficulties were encountered during the synthesis of the peptides containing the N‐terminal sequences‐Gly‐Asn‐Gly‐ and ‐Asp‐Lys‐Asp‐Gly‐Ans‐Gly‐, in which α‐β shift side reactions were observed.
Conformational analysis of cyclic peptides in solution
Authors: Kessler Horst , Bats Jan‐Willem , Wagner Klaus , Will Martin 
Published: December 2004

AbstractThe strategy and tactics of conformational analysis of cyclic peptides in solution is demonstrated by the example of cyclo(‐D‐Pro‐Phe‐Thr‐Phe‐Trp‐Phe‐). Spin‐locked experiments like rotating frame nuclear Overhauser enhancement spectroscopy (ROESY), ROTO, and TOCSY are successfully applied to assign all proton signals and to obtain distance information. A crude conformational model was built using the nmr data. This starting model was refined by restrained molecular dynamics (MD) calculations using ROE derived distances and fixed bond angles as determined from homo‐ and heteronuclear coupling constants. To mimic the solvent and to reduce artifacts in an in vacuo calculation the charges of the solvent‐exposed NH protons were gradually reduced according to the temperature gradients. The thus obtained “conformation” (mean of a 40 ps MD trajectory) shows very close similarity to x‐ray structures in an orthorhombic and in two monoclinic crystal modifications of the same compound. The main difference is the breaking of an intermolecular hydrogen bond of the theronine hydroxyl group on dissolution of the crystal and forming an intramolecular hydrogen bond in solution.
Two‐dimensional 1H‐nmr study of synthetic peptides containing the main immunogenic region of the Torpedo acetylcholine receptor
Authors: Cung M. T. , Marraud M. , Hadjidakis I. , Bairaktari E. , Sakarellos C. , Kokla A. , Tzartos S. 
Published: December 2004

AbstractA comparative 1H‐NMR spectral study of a synthetic decapeptide containing the main immunogenic region of the Torpedo acetylcholine receptor (AChR; WNPADYGGIK, representing the α67–76 fragment of Torpedo AChR) with four analogous peptides (WNP3‐D5YGGIK, WNPAA5YGGIK, WNPADYGGA9K, and WNPD4DYGGV9K) has been carried out in dimethyl sulfoxide.One‐ and two‐dimensional nmr experiments [correlated spectroscopy (COSY), relayed COSY, and phase‐sensitive nuclear Overhauser enhancement spectroscopy (NOESY)] were performed to obtain complete assignments of the proton resonances. The presence of strong and multiple short‐ and long‐range NOEs, and especially a strong long‐range NOE between the two Asn2‐CαH and Gly7‐CαH protons, argues in favor of a rigid folded structure in all five cases. Temperature dependence measurements indicate the existence of three intramolecular interactions involving the Asp3, Gly8, and Lys10 amide protons.
CD spectra of isoionic DNA solutions
Authors: Davydova O. V. , Kuznetsov I. A. , Florentiev V. L. 
Published: December 2004

AbstractThe ion‐exchange transition of Na‐DNA → H‐DNA in concentrated salt‐free solutions is accompanied by strong variations in CD spectra. The rotational force of the negative band |Δε249| decreases when going to H‐DNA by about 4 times, and the value of Δε279, by 1.2 times. These changes are irreversible to a considerable extent, which is evident because the spectra of Na‐DNA obtained by neutralizing isoionic H‐DNA solutions with NaOH or by the ion‐exchange method significantly differ from those of Na‐DNA taken by dissolving solid Na‐DNA in deionized water. It has been shown that additions of NaCl to an isoionic solution of DNA leads to variations of spectra, typical for deprotonation processes as well as for an increase in DNA hydration.
Harmonic dynamics of a DNA hexamer in the absence and presence of the intercalator ethidium
Authors: Rudolph Barbara R. , Case David A. 
Published: December 2004

AbstractVibrational normal mode calculations are presented for a DNA hexanucleoside pentaphosphate, d(CpGpCpGpCpG)2, and for its complex with the cationic interclator ethidium. Two intercalation sites are modeled that differ in DNA backbone torsion angles. Normal mode frequencies for the DNA fragment itself are significantly lower than those reported earlier using different force fields, but an analysis of “effective” frequencies suggests that somewhat higher frequencies are more appropriate. Intercalation leads to significant lowering of mobility for the base pairs adjacent to the drug; in this sequence, the ethidium binding affects the guanosine atoms more strongly than the cytosine atoms. Motions of the bases and the intercalator are analyzed in terms of “twist” about the local helix axis and a “tilt” angle relative to this axis, and the results are compared to fluorescence studies of ethidium‐DNA complexes.
Phonon interpretation of inelastic neutron scattering in DNA crystals
Authors: Schroll W. K. , Prabhu V. V. , Prohofsky E. W. , Van Zandt L. L. 
Published: December 2004

AbstractThe calculated spectrum of longitudinal compressional waves on DNA polymer chains is shown to be in excellent agreement with recently performed inelastic neutron scattering measurements in hydrated, oriented DNA crystals. This opens up a previously unexplored frequency regime of DNA science and establishes the validity of the phonon extended wave description of DNA elementary excitations in this region.
New x‐ray diffraction results from agarose: Extended single helix structures and implications for gelation mechanism
Authors: Foord S. A. , Atkins E. D. Y. 
Published: December 2004

AbstractA new series of x‐ray fiber diffraction patterns is reported from agarose films dried at temperatures close to 100°C from water or dimethylacetamide solutions, cooled to room temperature, stretched above 40°C, and finally x‐rayed at room temperature. This procedure gives x‐ray patterns showing highly crystalline forms of agarose with projected axial advances (h) per repeating disaccharide in the range of 0.888–0.973 nm, and favoring extended and single agarose chains. Stretching the films below 40°C yields an oriented but fairly diffuse x‐ray pattern, similar to that reported previously for agarose, and that has been interpreted in terms of a model with two semicontracted agarose chains, with a value of h = 0.634 nm, draping around each other to form a double helix.The new data requires that double‐helix to single‐chain transitions be considered in condensed films as well as in solution. Alternatively, two populations of double‐helix and single‐helix conformations may coexist in the same film, or the original case for the double‐helix model may be flawed, perhaps through misinterpretation of the diffuse x‐ray pattern. The new results have prompted a critical discussion of evidence for the double‐helix model and to indicate that there is potential to improve the data experimentally with a view to gaining a clearer insight into the molecular mechanisms involved in gelation of agarose.
The stabilization of β‐lactoglobulin by glycine and NaCl
Authors: Arakawa Tsutomu 
Published: December 2004

AbstractEffect of glycine and NaCl on the thermal denaturation of β‐lactoglobulin was examined. The results showed that the transition temperature of β‐lactoglobulin is increased by the addition of glycine and NaCl at 0.5 and 1M. This observed stabilization by glycine and NaCl was interpreted in terms of their favorable interactions with the native state of β‐lactoglobulin and unfavorable interactions with the denatured state.
Free energy of hydration of collagen models and the enthalpy of the transition between the triple‐helical coiled‐coil and single‐stranded conformations
Authors: Némethy George , Scheraga Harold A. 
Published: December 2004

AbstractInteractions with water make an important contribution to the free energy of stabilization of the collagen triple helix, but they do not alter the structure of the triple helix, i.e., the packing geometry of the three strands. Conformational energy computations have been carried out on poly(tripeptide) analogues of collagen, with the introduction of a newly developed form of a hydration shell model to compute the free energy of hydration. The most stable triple helix formed by poly(Gly‐Pro‐Pro), obtained earlier from conformational energy computations [M. H. Miller & H. A. Scheraga (1976) J. Polym. Sci. Polym. Symp. 54, 171], with a structure that is very closely similar to the observed structure, is strongly favoured over other three‐strand complexes, both in the absence and the presence of hydration. The hydration shell model does not provide an explanation for the increased stability of the poly(Gly‐Pro‐Hyp) triple helix as compared to poly(Gly‐Pro‐Pro). It appears that the difference should be attributed to specific binding of water, an effect that is not yet included in the present version of the hydration shell model. On the other hand, this model accounts for the observed enthalpy of unfolding of a poly(Gly‐Pro‐Pro) triple helix to isolated single chains in solution in terms of intramolecular noncovalent interactions and the free energy of hydration.
CD and small‐angle x‐ray scattering of silk fibroin in solution
Authors: Canetti Maurizio , Seves Alberto , Secundo Francesco , Vecchio Giuseppe 
Published: December 2004

AbstractWe investigated the structure of silk fibroin dissolved in water and in water–organic solvent mixtures by CD and small‐angle x‐ray scattering (SAXS). CD spectra indicated a disordered secondary structure in water and a β‐sheet conformation in aqueous organic solvents, such as methanol, dioxane, and trifluoroethanol (in trifluoroethanol a transient form evolving toward β‐sheet conformation was seen just after dissolution). The SAXS technique indicated the presence of fibroin particles of lamellar shape. The molecular weight was 188,000 daltons in water and 302,000 daltons in aqueous methanol.