bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interaction of calcium ions with gastrin fragments of increasing chain length
Authors: Peggion E. , Foffani M. T. , Wünsch E. , Moroder L. , Goodman M. , Mammi S. 
Published: May 2005

AbstractThe interaction of a series of biologically active gastrin fragments with calcium ions has been investigated by CD in trifluoroethanol. It was found that the gastrin octapeptide pGlu10,Nle15‐HG[10–17] binds one calcium ion per molecule. The hypothesis is made that the binding involves the C‐terminal, biologically important tetrapeptide. When the chain is elongated to the gastrin nonamer pGlu9,Nle15‐HG[9–17], a second binding site is available, which is most likely situated at the N‐terminal part of the molecule. Further elongation of the peptide chain up to the dodecapeptide pGlu6,Nle15‐HG[6–17] does not provide any additional binding site. Saturation of the two sites in the shorter peptides produces different changes in the chiroptical properties in the near‐ and far‐uv. As the chain is elongated, this difference tends to disappear. This result is consistent with an increased conformational order of the longer peptides. In the shorter fragments, the strength of this second binding is appreciably lower than that of the first, while in the longer peptides, the strength of the two bindings is comparable. On the assumption that the variation of the CD properties is proportional to the extent of binding, the constant for the binding of the second ion was determined to be of the order of 5 × 105 L/mol for the nonapeptide.
The dynamics of the DNA hydration shell at gigahertz frequencies
Authors: Tao N. J. , Lindsay S. M. , Rupprecht A. 
Published: May 2005

AbstractWe have used Brillouin scattering to measure the linewidths and frequencies of GHz acoustic phonons in Na‐ and Li‐DNA films as a function of temperature between 300 and 140 K for samples that were dry, lightly, and heavily hydrated. The linewidths decrease with falling temperature and water contents, indicating that coupling to a water relaxation is the main source of phonon damping. The strength of the relaxation was determined using measurements of the phonon linewidth as a function of frequency, and confirmed by comparison of measured and calculated spectral profiles. The relaxation strength is anisotropic, being greater for phonons propagating perpendicular to the helix axis. The hydrated DNA exhibits both a rapid relaxation (≤ 10−11 s per radian) giving rise to a classical f2 damping, and a slower motion with a relaxation time that varies from ∼ 4 × 10−11 s per radian (primary hydration shell) to ∼ 2 × 10−12 s per radian (secondary hydration shell) at room temperature. In the frequency interval that bounds these relaxation times (∼ 4 to 80 GHz) we expect degrees of freedom associated with the primary hydration shell to be important. The sample with primary hydration follows a simple Arrhenius behavior with ΔH ∼ 5 kcal mole−1. The effective activation energy for the sample with secondary hydration is somewhat higher (indicating a more cooperative water relaxation) and varies strongly with temperature. The elastic moduli change much more than can be accounted for by relaxation, indicating the importance of water motion in softening interatomic potentials. The extent of the softening caused by the “unfreezing” of water motion is similar to the degree of softening caused by hydrating the sample.
The biological functions of low‐frequency vibrations (phonons). VI. A possible dynamic mechanism of allosteric transition in antibody molecules
Authors: Chou Kuo‐Chen 
Published: May 2005

AbstractBy means of the quasi‐continuity theory developed recently [Chou, K.‐C. (1983) Biochem. J. 209, 573–580; Chou, K.‐C. (1984) Biochem. J. 221, 27–31; Chou, K.‐C. (1985) Biophys. J. 48, 289–297], the low‐frequency breathing motions of the β‐barrels in the 12 domains of an IgG antibody molecule have been calculated. The results are in very good agreement with the observed low‐frequency peaks in the Raman spectra. Based on this, the resonant couplings among the domains located at its different regions are discussed. It turns out that some very interesting functions of antibody molecules, such as the “chelate effect” and “trigger effect” whose dynamic principle has been so far unknown, can be clearly elucidated in terms of a fundamental natural law; i.e., it is through the channel of low‐frequency resonance that the “signal” (or energy) in an antibody is transmitted from one location to the other, so as to be able to induce the relevant conformational change required for operating those important biological functions. The physical picture illustrated here once again provides us with a classic example that structure and function in nature are highly harmonized.
Thermodynamics of water–biopolymer interactions: Irreversible sorption by two uniform sorbent phases
Authors: Bryan William P. 
Published: May 2005

AbstractIn order to understand the mutual interactions between water and a biopolymer, thermodynamic analysis of sorption isotherms of water vapor by the biopolymer is necessary. These isotherms are irreversible and show sorption hysteresis. The reasons for such behavior are not established. As a continuation of previous work, general relationships for thermodynamic quantities of sorption are derived for the general case when the sorbent consists of two uniform phases. As in the case of a single sorbent phase, the Clausius–Clapeyron equation can be used to obtain differential entropies of sorption. Two special cases for the two‐phase situation—equilibrium hysteresis and partial equilibrium hysteresis—are plausible models for the irreversibility seen in water–biopolymer interactions. When differential entropy of sorption is plotted as a function of amount of water sorbed per mole of biopolymer, irregularities are generally seen. It is suggested that these irregularities reflect changes in conformation and/or dynamics of the biopolymer molecule.
Brownian dynamics simulation of protein folding: A study of the diffusion‐collision model
Authors: Lee Sangyoub , Karplus Martin , Bashford Donald , Weaver David 
Published: May 2005

AbstractThe dynamic aspects of protein folding are described by a series of diffusion‐collision steps involving structural units (microdomains) of various sizes that combine to form the protein in its native state. A method is introduced for obtaining the rate constants for the basic diffusion‐collision step by use of Brownian dynamics. The method is applied to an investigation of the folding dynamics of two α‐helices connected by a flexible (random‐coil) polypeptide chain. The results of this full three‐dimensional treatment are compared with simplified model calculations for the diffusion‐collision step. Of particular interest are the nature of the collision dynamics and the role of the intervening peptide chain.
Conformational transitions of calmodulin as studied by vacuum‐UV CD
Authors: Hennessey John P. , Manavalan Parthasarathy , Johnson W. Curtis , Malencik Dean A. , Anderson Sonia R. , Schimerlik Michael I. , Shalitin Yechiel 
Published: May 2005

AbstractCD measurements were made for calmodulin and its calcium (Ca2+) complexes at different ionic strengths and Ca2+ concentrations. Calmodulin at an ionic strength of 0.00M and in the absence of Ca2+ exists as an α‐helical protein with a negligible amount of β‐sheet. An increase in ionic strength, whether or not Ca2+ is present, increases α‐helix at the expense of “other” (coil) structure. The changes in β‐sheet and β‐turns are insignificant. Binding of Ca2+ at low ionic strength occurs in stages with at least one folding intermediate before attaining the final stable state. Binding of Ca2+ at an ionic strength of 0.165M causes only a slight increase in α‐helix, so that the secondary structure of the protein depends on ionic strength and is insensitive to the nature of the cation (i.e., Ca2+). Thus, the activation of calmodulin by Ca2+ must be due to a structural reorientation rather than to a major secondary structural alteration. The CD estimation of secondary structure with 4 mol Ca2+/calmodulin (61% α‐helix, 2% antiparallel β‐sheet, 2% parallel β‐sheet, 21% β‐turns, and 14% other) is in excellent agreement with the x‐ray results.
A CD study of the role of metal ions in the conformation of poly(L‐lysine)
Authors: Watanabe S. , Saito T. 
Published: May 2005

AbstractThe effect of LiCl, NaCl, and CsCl as univalent salts, and of CaCl2, ZnCl2, and MgCl2 as divalent salts, on the α and antiparallel β‐sheet, and random conformations of poly(L‐lysine) (PLL), in water at room temperature were examined by means of CD and compared quantitatively on the basis of elliptical strength at the maximal peak. Changes in the α‐helical and antiparallel β‐sheet helical conformations of PLL were markedly dependent on the salt concentrations of LiCl, NaCl, and CsCl, which induced decreases in negative intensity in that order. The CD spectrum of the random conformation, the most disordered form, displayed positive cotton effect in concentrations of these salts up to 3.0M and a negative peak in concentrations of 6.0M. The effect of these salts on the random conformation of PLL was stronger than that on the α‐ and β‐conformations in higher concentrations. The CD spectrum of the random conformation in the presence of CaCl2, ZnCl2, and MgCl2, on the other hand, showed negative cotton effect in salt concentrations as low as 3.0M. It was impossible, however, to measure the effect on α‐ and β‐conformations of ZnCl2 and MgCl2 above concentrations of 10 mM because of a solubility problem with salts in alkaline solution.
Order parameters of gels and gelation kinetics of aqueous agarose systems: Relation to the spinodal decomposition of the sol
Authors: Leone M. , Sciortino F. , Migliore M. , Fornili S. L. , Vittorelli M. B. Palma 
Published: May 2005

AbstractHydrogels of a significant biostructural polymer (agarose) were studied turbidometrically in the course of their isothermal self‐assembly. Supramolecular order was characterized by an order parameter and associated correlation length. This type of characterization, in general, may help more in the quantitative measurement of order in biostructures. The picture of processes leading to isothermal gelation appears much richer than expected, and it is probably of more general validity, as it agrees with predictions based on the statistical model of site‐bond correlated percolation. At the higher temperatures a spinodal decomposition occurs well before, and possibly triggers [P. L. San Biagio, et al. (1986) Biopolymers 25, 2255–2269], the start of gelation. In this case, the spatial modulation of concentration, as well as topological features of the gel, appear to reflect those of the spinodally decomposed sol. When an upper limit is approached for the temperature of isothermal gelation, both the order parameter and the correlation length exhibit a critical‐like behavior. At lower temperatures, the sequence of processes and the resulting features of the gel appear dictated by the (temperature‐ and concentration‐dependent) interplay of spinodal decomposition and gelation processes and kinetics. The present results are believed to provide a basis for a deeper understanding of the relation between the processes of gelation and of spinodal decomposition, and between their time scales.
Conformational analysis of the 2′‐deoxyribofuranose ring from proton–proton coupling constants: Analysis of a nucleoside‐carcinogen adduct formed from 2‐acetylaminofluorene utilizing a three‐state model
Authors: Evans Frederick E. , Levine Robert A. 
Published: May 2005

AbstractThe conformation of the sugar moiety of 8‐(N‐fluoren‐2‐ylamino)‐2′‐deoxyguanosine in solution has been examined as a function of temperature by 1H‐nmr spectroscopy. Analysis of coupling constants shows that lowering the temperature to −50°C in methanol shifts the conformational equilibrium of the sugar ring resulting in a C2′‐endo conformation at a mole fraction of 0.97. The computed phase angle of pseudorotation and amplitude of pucker are 154° and 36°, respectively, with very little discrepancy between the five calculated coupling constants and coupling constants extrapolated from the temperature profiles. A computer program has been written enabling a three‐state best‐fit analysis. The three‐state analysis indicates an equilibrium between C2′‐endo, C3′‐endo, and 04′‐endo conformations. In aqueous solution, the computed mole fraction of the 04′‐endo form is 0.18 at 30°C. The conformation associated with the sugar ring and the C4′C5′ bond is compared to that of 2′‐deoxyguanosine.
Cooperative lengths of DNA during melting
Authors: Blake R. D. 
Published: May 2005

AbstractThe mean cooperative length of domains of DNA, determined from the variance in (G + C) content in derivative melting curves of large bacterial DNAs, varies from 230 base pairs (bp) for (A − T)‐rich domains to 580 bp for (G − C) domains. These values correspond to values for the cooperativity parameter of 2(±2) × 10−5 and 3(±2) × 10−6, respectively, and to +7.2 and +9.6 kcal for the free energy of helix interruption in those regions.
Asymmetric oscillations in cyclodextrin—a molecular dynamics study
Authors: Prabhakaran M. , Harvey Stephen C. 
Published: May 2005

AbstractA 30‐ps molecular dynamics simulation of motions of cyclodextrin is completed on the free molecule and with two model substrates. Even with its cyclic constraint, the molecule traversed through large conformational space, showing high flexibility. The asymmetric oscillations of the free molecule are evident from the time course behavior of the ratio of the second moments (anisotropic ratio) of the atomic motions along the first two principal axes. The study also shows the stability of the molecule derived from specific substrate. The preference of chair conformation by glucose is also evident from these studies.
Fluorescence dynamics studies of troponin C
Authors: Steiner Robert F. , Norris Lynn 
Published: May 2005

AbstractThe time decay of fluorescence anisotropy for a dansylaziridine (DANZ) conjugate with Met‐25, which lies within the N‐terminal lobe of troponin C (TnC), shows at 10 and 25°C a longer correlation time characteristic of the entire molecule and a shorter correlation time arising from a more localized motion of the probe. In the absence of Ca2+, the amplitude of the shorter correlation time increases, suggesting an increased mobility of the probe. At 40°C, in both the absence and presence of Ca2+, a significant increase in probe mobility occurs. A 2,6‐toluidinyl naphthalene sulfonate (2,6‐TNS) complex with Ca2+‐liganded TnC shows only the longer correlation time at 12 and 25°C. An N‐(iodoacetylaminoethyl‐5‐naphthylamine‐1‐sulfonate) conjugate with Cys‐98 shows both a long and a short correlation time; the amplitude of the shorter correlation time is greater than for the DANZ conjugate. At 9, 25, and 40°C in the presence of Ca2+, and at 9°C in its absence, the magnitude of the long correlation time is consistent with motion of the entire molecule; at higher temperatures in the absence of Ca2+ it is substantially smaller, suggesting the presence of internal rotation. For Ca2+‐liganded TnC at temperatures of 25°C or lower, the results with all three labels are interpretable in terms of the crystallographic structure of TnC.
Comparison by 1H‐nmr spectroscopy of the conformation of the 2600 dalton antifreeze glycopeptide of polar cod with that of the high molecular weight antifreeze glycoprotein
Authors: Rao B. N. Narasinga , Bush C. Allen 
Published: May 2005

AbstractThe antifreeze glycopeptide (AFGP‐8) from polar cod, B. saida, is a 14‐amino acid polypeptide having alternating glycotripeptide sequences of Ala‐[Gal(β1 → 3)GalNAc(β1 → O)]‐Thr‐Pro and Ala‐[Gal(β1 → 3)GalNAc(β1 → O)]‐Thr‐Ala, with alanyl residues at amino and carboxy terminals. Conformational studies of AFGP‐8 have been carried out by 1H‐nmr and empirical energy calculations to investigate the difference in its antifreeze behavior from that of the more active high‐molecular weight AFGP 1‐4 of P. borchgrevinki. The 1H‐nmr spectra, including the resonances of the exchangeable amide protons, were assigned by two‐dimensional correlated spectroscopy (COSY), one‐dimensional difference decoupling, and nuclear Overhauser effect (NOE) measurements. For the four threonyl residues, the amide proton coupling constants and the small coupling constants between Hα and Hβ indicate similar conformations, despite significant chemical shift differences. The strong NOE between the α protons and the amide protons of the residue following together with large temperature coefficients of chemical shifts, indicate an extended conformation not consisting of α‐helix, turns or bends. Energy computations indicate several low‐energy conformations consistent with the observed coupling constants for ϕ. Among these, a left‐handed helical conformation with three repeating residues per turn has been proposed, which is in accordance with the observed NOE between the methyl group of the α‐GalNAc and Ala Hβs. While the observed Overhauser effects in the threonyl side chain suggest a certain amount of conformational averaging, the effect involving the acetmido methyl of α‐GalNAc and Hβs of Ala indicate that it as is a major conformer. In view of the close similarity between the conformations of AFGP‐8 and the more active antifreeze polymer, AFGP 1‐4, we propose that the difference in their activities is due to the length of the regular repeating structure with glycosylation at every third amino acid residue, and not due to any fundamental difference in their conformations.
Molecular mechanics modeling of oligonucleotide adducts of the antitumor drug cis‐diamminedichloroplatinum(II)
Authors: Kozelka Jiří , Archer Sharon , Petsko Gregory A. , Lippard Stephen J. , Quigley Gary J. 
Published: May 2005

AbstractIn order to assess the geometric changes caused when the antitumor drug cis‐diammine‐dichloroplatinum(II) (cis‐DDP) binds to DNA, molecular mechanics calculations were performed on two double‐stranded and two single‐stranded oligonucleotides and their adducts with cis‐{Pt(NH3)2}2+. For the platinated duplexes, three model structures have been derived, one involving only local disruption of base pairing with retention of the helix directionality, and two models showing pronounced kinking of the double helix. One of the kinked models is stabilized by bridging sodium ions. The other kinked duplex model shows retention of all Watson–Crick base pairing, including that of the coordinated guanines. All models exhibit hydrogen bonds connecting one ammine ligand of platinum with one or two phosphate groups located at the 5′ side of the platinated strand.
Influence of hydrogen bonding, main chain–side chain interactions, and protecting groups on the excimer formation of bis(pyrenylalanine) peptides
Authors: Goedeweeck R. , Ruttens F. , López‐Arbeloa F. , De Schryver F. C. 
Published: May 2005

AbstractDipeptides of the aromatic fluorescent amino acid, pyrenylalanine, are studied using both stationary and transient fluorescence techniques. Since the conformational transitions of the peptide chain are slow compared to the decay of the pyrene excited state, both ground state conformations, adopted by the peptide, i.e., C5 and C7, can be monitored separately. Kinetic models are proposed to describe the molecular dynamics of the peptide chain as probed by the intramolecular excimer formation between both pyrene chromophores. These kinetic schemes explain the influence of solvent, chain chirality, main chain–side chain interactions, and nature of the protecting groups on the emission spectrum and the fluorescence decay profile of these model peptides. These schemes also provide a tool to calculate rate constants of conformational transitions and excimer formation. By comparing the kinetic and thermodynamic parameters of the various compounds, the influence of a structural modification on the molecular dynamics of the peptide chain is determined.
Vibrational CD studies of the solution conformation of N‐urethanyl‐L‐amino acid derivatives
Authors: Chernovitz Anita C. , Freedman Teresa B. , Nafie Laurence A. 
Published: May 2005

AbstractThe solution conformations of several N‐urethanyl‐L‐amino acids in 0.2–0.002M chloroform and 0.2M dimethylsulfoxide have been investigated by using vibrational circular dichroism (VCD), ir absorption, and 13C‐nmr spectroscopies. Both the N‐carbobenzoxy (N‐CBZ) and N‐t‐butoxycarbonyl derivatives of L‐alanine, L‐proline, L‐valine, and L‐phenylalanine, and N‐CBZ‐serine were studied. The 13C‐nmr results indicate that the molecules occur predominantly as the cis isomer about the CN peptide bond at room temperature. The interpretation of the strong VCD couplet in the carbonyl‐stretching region using the degenerate coupled oscillator model is consistent with the conformational range of ϕ = −60° to −90° and ψ = 30° to 90° for molecules forming acid dimers. Conformations with an intramolecularly hydrogen‐bonded C7 ring are also present, which give rise to biased VCD features in the NH‐, CH‐, and CO‐stretching regions that can arise due to vibrationally generated ring currents.
Loop energy in DNA
Authors: Blake R. D. , Delcourt Scott G. 
Published: May 2005

AbstractThe loop function ƒ(N), representing the statistical weight of N complementary residues in a closed ring, has been determined by analysis of high‐resolution melting curves of a series of recombinant homopoly(A · T)N inserts in pBR322 DNA, where 150 > N > 50 base pairs (bp). Loops are found more stable and therefore presumably less elastic than expected for an ideal, freely jointed chain. A value of 97 ± 2 bp is obtained for the empirical orientation‐stiffness parameter D in the expression for nonideal chains, ƒ(N) = (N + D)−1.7. The 10% increase in apparent stiffness over that of an ideal chain closely coincides with the extent of residual stacking in the loop. It is thus concluded that the more favorable loop energy, such as expected of smaller loops, is due to the incipient helical orientation of some residues, predisposing the loop to reclosure. A quantitative loop function is essential for the prediction and assignment of domains in DNA.
The Hodgkin–Huxley Na+ channel model versus the five‐state Markovian model
Authors: Chay Teresa Ree 
Published: May 2005

AbstractIn describing the Na+ channel‐gating kinetics, it is generally believed the Hodgkin–Huxley model is inadequate and other types of Markovian models are more appropriate. In this paper, we perform detailed kinetic analyses to find out whether the Hodgkin–Huxley model is really unacceptable. Specifically, we consider two models for the analyses: A five‐state Markovian model that allows inactivation to take place before opening and a Hodgkin–Huxley eight‐state model. The criteria used to check the goodness of the two models are (a) Akaike's information criterion; (b) χ2 tests on the waiting‐time, open‐time, and closed‐time distributions, and the number of openings per record; and (c) comparison between all latency distributions and the probability of the open state predicted from the two models. In order to do this, we first develop a method of constructing probability density histograms of a specified event (e.g., waiting time, closed time, open time, number of openings per patch) from the multichannel patch‐clamp recordings. The goodness of our method is checked by simulating multichannel patch recordings using a multinomial random number generator. Our kinetic analysis on the single Na+ channel recordings from the cardiac cells revealed that (a) on the basis of Akaike's information criterion, the Hodgkin–Huxley model is definitely a better model than the five‐state model, but (b) on the basis of χ2 tests on the probability density functions, the latter model is slightly better than the former. We find no evidence that the Hodgkin–Huxley model is inferior to the five‐state model for this cell type.