bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic light scattering measurements of the diffusion of probes in filamentous actin solutions
Authors: Newman Jay , Mroczka Nicholas , Schick Kenneth L. 
Published: December 2004

AbstractThe diffusion coefficients of monodisperse polystyrene latex spheres in solutions of polymerized actin were measured using dynamic light scattering. Four different probes with radii R, ranging from 50 to 500 nm, were separately used in actin solutions with concentrations c, ranging from 1.5 to 21 μM, which had been polymerized with either 1 mM MgCl2, 1mM CaCl2, or 100 mM KCl. Under all conditions, and at four different scattering angles in the range of 30°–90°, the measured average diffusion coefficients D of the probes were systematically smaller for samples of increased actin concentration or of increased probe radius. Control experiments indicated that the probes did not bind to the actin. These data for Mg2+‐ and Ca2+ ‐polymerized actin agree and were found to be quite well summarized by the scaling relation D/D0 = exp[–αRδCν], where D0 is the measured diffusion coefficient of the probes in water (and, as also measured, in the starting actin solutions prior to polymerization with added salt), with values of δ = 0.73 ± 0.05, ν = 1.08 ± 0.09, and α = (1.1 ± 0.6) × 10−3 (with c in μM and R in nm). Data for KCl‐polymerized actin show much more restricted diffusivities of the probes at comparable actin concentrations. Inhomogeneities in the solution are reflected in the “effective polydispersity” of the probe diffusion coefficients, which depend on local microviscosity differences.
Solvated helical backbones: X‐ray diffraction study of Boc‐Ala‐Leu‐Aib‐Ala‐Leu‐Aib‐OMe · H2O
Authors: Karle I. L. , Flippen‐Anderson J. L. , Uma K. , Balaram P. 
Published: December 2004

AbstractA second example of insertion of a water molecule into the helical backbone of an apolar peptide is presented here and compared to a similar occurrence in a longer peptide with the same type of sequence of residues, i.e., Boc‐Aib‐(Ala‐Leu‐Aib)3‐OMe. The backbone of the title compound assumes an approximate 310‐helical form with three 4 → 1 hydrogen bonds. In the place of a fourth 4 → 1 hydrogen bond, a water molecule is inserted between O(1) and N(4), and acts as a bridge by forming hydrogen bonds N(4) … W(1) (2.95 Å) and W(1) … O(1) (2.81 Å). The water molecule participates in a third hydrogen bond with a neighboring peptide molecule, W(1) … O(4) (2.91 Å). The insertion of the water molecule causes the apolar peptide to mimic an amphiphilic helix. Crystals grown from ethyl acetate/petroleum ether (reported here) or from methanol/water solution are in space group P212121 with a = 12.024(4) Å, b = 15.714(6) Å, c = 21.411(7) Å, Z = 4 and dcalc = 1.124 g/cm3 for C32H58N6O9 · H2O. The overall agreement factor R is 6.3% for 2707 reflections observed with intensities > 3σ(F) and the resolution is 0.90 Å.
Comparison of α‐helix stability in peptides having a negatively or positively charged residue block attached either to the N‐ or C‐terminus of an α‐helix: The electrostatic contribution and anisotropic stability of the α‐helix
Authors: Takahashi Sho , Kim Eui‐Ho , Hibino Takeshi , Ooi Tatsuo 
Published: December 2004

AbstractAn estimation of the thermodynamic effects of a charged random coil, which is attached either to the N‐ or C‐terminus of polyalanine, upon α‐helix stability is attempted. A temperature‐induced helix‐coil transition of Ala20Lys20Phe and Lys20Ala20Phe was studied under various conditions of salt concentration and pH. By combining the results with previous ones for Ala20Glu20Phe and Glu20Ala20Phe, which have opposite electric charges to the present system [S. Ihara et al. (1982) Biopolymers 21, 131–145], the free energy of the coil to helix transition of the polyalanine block could be separated into two terms—one term for the electrostatic interaction of electric charges in the random‐coil block with the α‐helix dipole, and a second term for the intrinsic stability of the helix. The first term indicates the significance of the helix dipole‐charge interactions, which affects the helix stability depending on the attaching side of the charged block and on the sign of the charges. This clearly shows the anisotropic stability of the α‐helix. Furthermore, analysis of the dependence of these thermodynamic quantities on salt concentrations showed, assuming that the effect of the attached electric charges was symmetric (in other words, the absolute values of the electrostatic interaction terms were independent of the sign of electric charges), that the intrinsic stability of the α‐helix was dependent on which side of the helix was attached to the random coil: a random coil attached to the N‐terminus of the α‐helix had little effect while that attached to a C‐terminal significantly destabilized the helix.
Small‐angle x‐ray scattering studies of fibrin film: Comparisons of fine and coarse films prepared with thrombin and ancrod
Authors: Müller Michael F. , Ferry John D. , Lin J. S. 
Published: December 2004

AbstractMeasurements of small‐angle x‐ray scattering have been made on films prepared from fine and coarse (i.e., formed at high and low, respectively, pH and ionic strength) clots of bovine fibrin by osmotic shrinkage or compression in one dimension. Intensity profiles were obtained with pinhole geometry on films stretched up to a stretch ratio of 1.43. In unstretched coarse films, repeat spacings were seen at about 245, 120, and 77–80 Å. These peaks can probably be identified with the first, second, and third orders of the well‐known fibrin repeat of 225 Å. In unstretched fine films, only the 77–80 Å spacing was seen. In this case, the first two orders may be weak because the half‐staggered arrangement of monomer units giving rise to the 225 Å reflection is not reinforced by lateral aggregation of protofibrils; the third order may be strong since the molecular subdomains appear to divide the repeat roughly into thirds. After stretching, the 77–80 Å spacing persisted in the meridional direction but almost disappeared in the equatorial. Experiments on unstretched films prepared with ancrod substituted for thrombin gave similar results.
Temperature and concentration behavior of anomalous microwave resonances in DNA
Authors: Davis M. E. , Van Zandt L. L. 
Published: December 2004

AbstractWe have calculated the expected absorption of microwave radiation in the gigaHertz frequency range by fixed‐length DNA polymer molecules dissolved in saline solution. While the effects of counterions and solvent dynamics have been accounted for in detail, the features of the absorption are completely dominated by the interaction between the charged polymer and the so‐called first hydration layer, that is, the nearest layer of solvent water molecules not actually bonded to the polymer. The relevant parameters of the interaction are the strength of the water‐to‐polymer coupling and the average persistence time of the individual water‐to‐polymer bonds. These are presumably hydrogen bonds to the oxygen atoms of the backbone phosphate structure. Using a given parameterization we can obtain the structured absorption corresponding to compressional wave phonon excitations on the polymer, “organ pipe” modes, such as have been claimed to be seen by Edwards, Davis, Swicord, and Saffer. While further studies have not confirmed these resonances, at some frequency and hydration these modes must become visible because of the high relaxation time measured by Lindsay, the existence of the resonances in relatively dry fibers and films of DNA, and the existence of underdamped modes in the ir spectrum of DNA in solution.We have examined the effects of varying slat concentration and the system temperature. In both cases the effects are virtually nil, in the former because of the Manning condensation phenomenon that preserves a remarkably constant polymer environment over a wide range of bulk ionic strength, and in the latter case because of a fortuitous competition between effects of bulk viscosity and persistence time changes with temperature. Hence any effects seen in the experimental variation of temperature or salinity could be wholly attributed to their modification of the hydration layer properties.
Properties of amidated pectins. II. Polyelectrolyte behavior and calcium binding of amidated pectins and amidated pectic acids
Authors: Racape E. , Thibault J. F. , Reitsma J. C. E. , Pilnik W. 
Published: December 2004

AbstractThe intrinsic pK values, as well as the free fractions of sodium and calcium counterions, were determined on salt‐free solutions of amidated pectinates and amidated pectates. The apparent pK values were non dependent of the degree of amidation but only to the effective charge density of the pectic polymers and an unique value of 2.9 ± 0.1 was found for the intrinsic pK value. The results obtained by conductimetry and with (sodium and calcium) specific electrodes showed a blockwise distribution of amide and acid groups in amidated pectates and a blockwise distribution of amide groups and a rather statistical distribution of acid groups in amidated pectinates.
Dielectric relaxation in synthetic melanin
Authors: Osak Władysław , Tkacz Katarzyna , Sławiński Janusz , Czternastek Halina 
Published: December 2004

AbstractThe charging and discharging currents were investigated in a synthetic melanin sample. The presence of long‐lasting dielectric relaxation was established. The steady state was reached after a long time, from 103 to 105 s, which depends both on temperature and voltage.The temperature dependence of polarization was of an activation character (Eα = 0.67 eV). The kind of electrode material did not influence the current curves.
Bisintercalation of ditercalinium into a d(CpGpApTpCpG)2 minihelix: A 1H‐ and 31P‐NMR study
Authors: Delepierre M. , Dinh T. Huynd , Roques B. P. 
Published: December 2004

AbstractThe structure of the complex formed in aqueous solution between ditercalinium, a bisintercalating drug, and the self‐complementary hexanucleotide d(CpGpApTpCpG)2 is investigated by 400‐MHz 1H‐nmr and 162‐MHz 31P‐nmr. Whatever the drug to thlix ratio, ditercaliniun occurred in the bound form, whereas free and complexed hexanucleotide and are in slow exchange. This allows unambiguous resonance assignm, ent through two‐dimensional chemical exvhange experiments. The strong upfield shifts measured on most aromatic protons on both drug and bases as well as on DNA imino protons are consistent with bisintercalation of the dimer. Nuclear Overhauser effects observed between drug and nucleeotide protons give a defined geometry for complexation, and suggest a DNA conformational change upon drug binding.
Conformation‐Activity relationships of cyclic dermorphin analogues
Authors: Wilkes Brian C. , Schiller Peter W. 
Published: December 2004

AbstractA theoretical conformational analysis (molecular mechanics study) of nine cyclic tetrapeptides, structurally related to the highly μ‐receptor‐selective dermorphin analogue , was performed. These compounds display considerable diversity in their μ‐receptor affinity and selectivity. A systematic search and subsequent energy minimization in absence of the exocyclic Tyr1 residue and Phe3 side chain revealed the constrained nature of the 11–13 membered ring structures contained in these analogues. No more than four low‐energy conformers (within 2 kcal/mol of the lowest energy conformation) were found in each case. After attachment of the Tyr1 moiety and Phe3 side chain to the “bare” low‐energy ring structures, a systematic search and energy minimization of these exocyclic moieties resulted in a limited number of low‐energy conformational families for all compounds. Five analogues with high μ‐receptor affinity—
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(A2 bu: alpha;, γ‐diaminobutyric acid) and
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—all showed a tilted stacking interaction between the Tyr1 and Phe3 aromatic rings in the lowest or second lowest energy conformation found. The same kind of stacking was not possible in low‐energy conformers of the four analogues with poor affinity for the μ‐receptor
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: [Nα‐methylphenylalanine], and
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It is concluded that a tilted stacking arrangement of the two aromatic rings may represent a structural requirement for high μ‐receptor affinity of the examined cyclic dermorphin analogues.
Use of t‐butyldimethylsilyl cyanoacetate for preparation of α‐cyano ketones
Authors: Ghosh Soumitra S. 
Published: December 2004

AbstractThe synthesis of t‐butyldimethylsilyl cyanoacetate and the reactions of its anion with acyl donors are described. The reagent was found to be the method of choice for the syntheses of α‐cyano ketone substrate analogues for carboxypeptidase A. These compounds have been shown to be potent mechanism‐based inactivators for the enzyme.
Enkephalin analogues containing β‐naphthylalanine at the fourth position
Authors: Mierke Dale F. , Said‐Nejad Odile E. , Schiller Peter W. , Goodman Murray 
Published: December 2004

AbstractTo examine the importance of the aromatic side chains of enkephalin on opiate activity, we report the synthesis and conformational analysis of a series of analogues related to enkephalin with β‐naphthylalanine in place of phenylalanine at the fourth position. Three linear analogues (Tyr‐D‐Ala‐Gly‐(L and D)‐β Nal(1)‐Leu‐NH2 and Tyr‐D‐Ala‐Gly‐β Nal(2)‐Leu‐NH2) were initially synthesized to examine the effect of the substitution on biological activity. The increased activity of these peptides at the μ‐opiate receptor, compared to native Leu‐enkephalin, prompted us to examine the more conformational constrained analogues, Tr‐c[D‐A2bu‐Gly‐(L and D)‐β Nal(1)‐Leu], incorporating a α,γ‐diaminobutyric acid at the second position and cyclization to the carboxylic end of the leucine. These two cyclic analogues provide insight into the necessity for the L chirality of the aromatic residue at position 4. The Tyr‐c[D‐A2bu‐Gly‐L‐β Nal(1)‐Leu] analogue is highly potent and displays a slight preference for the μ receptor. The conformational analysis indicates that despite the high flexibility of the tyrosine side chain, the aromatic rings of the tyrosine and naphthylalanine are relatively distant from each other. The presence of two intramolecular hydrogen bonds help maintain the conformation of the 14‐membered backbone ring that keeps the side chains directed away from each other. These findings are in agreement with our model of an extended structure required for μ selectivity and a folded form with close aromatic ring placement for δ selectivity.
SV40 Large T‐antigen nuclear signal analogues: Successful nuclear targeting with bovine serum albumin but not low molecular weight fluorescent conjugates
Authors: Lobl Thomas J. , Mitchell Mark A. , Maggiora Linda L. 
Published: December 2004

AbstractThe signal sequence of a nuclear‐directed protein encodes the necessary information for targeting the attached proteins to the cell nucleus. The sequence/structural requirements for a functional transport signal were explored with a series of peptides derived from the simian virus 40 large T‐antigen nuclear signal 126–134 (CPKKKRKVED‐NH2, wild type) conjugated to bovine serum albumin (BSA) through an N‐terminal Cys (1) with m‐maleimidobenzoyl‐N‐hydroxysuccinimide ester. Nuclear accumulation was virtually complete 15 min after microinjection into green monkey kidney cells (TC‐7). Peptides with Asn, Orn, and Gln substituted for Lys128, the reverse wild‐type peptide (DEVKRKKKPC‐NH2) and the long 34‐residue wild‐type analogue (CYDDEATADSQHSTPPKKKRKVEDPKDFESELLS‐NH2), were synthesized and conjugated similarly to BSA. The Orn peptide and the 34‐residue wild‐type analogue conjugated to BSA also transported to the nucleus but at a slower rate than 1. The reverse wild‐type, Asn‐ and Gln‐BSA conjugates of these signal analogues did not show transport to the nucleus after 6 h of incubation. In an effort to learn if such signal sequences would also target a small molecule such as a fluorescent tag to the nucleus, 1 fluorescently tagged with monobromobimane was prepared and microinjected into TC‐7 cells. The peptide was distributed throughout the cell. These results support the notion that a positively charged residue at position 128 is needed for rapid nuclear transport and that the intracellular transport machinery has spatial recognition. The results with fluorophore‐peptide conjugates suggest nuclear localization of these low molecular weight peptides will be difficult to attain even if attached to a functional nuclear localization sequence.
Applications of simulated annealing to peptides
Authors: Wilson Stephen R. , Cui Weili 
Published: December 2004

AbstractWe report the application of a new conformation searching algorithm called simulated annealing to the location of the global miniumum energy conformation of peptides. Simulated annealing is a Metropolis Monte Carlo approach to conformation of generation in which both the energy and temperature dependence of the Boltzmann distribution guides the search for the global minimum. Both uphill and downhill moves are possible, which allows the molecule to escape from local minima. Applications to the 20 natural amino acid “dipeptide models” as well as to polyalanines up to Ala80 are very successful in finding the lowest energy conformation. A history file of the simulated annealing process allows reconstruction and examination of the random walk around conformation space. A separate program, Conf‐Gen, reads the history file and extracts all low‐energy conformations visited during the run.
Synergism through direct covalent bonding between agents: A strategy for rational design of chemotherapeutic combinations
Authors: Rideout Darryl , Calogeropoulou Theodora , Jaworski James , McCarthy Michael 
Published: December 2004

AbstractSelf‐assembling chemotherapeutic agents are mixtures of relatively nontoxic precursors that can combine chemically under physiological conditions to form products with greater cytotoxic and/or antimicrobial activity than either of the precursors. Combinations that form products more rapidly in or near the target (tumor, pathogen, virally infected cell) than in normal tissues will exhibit target‐selective synergism, thus exhibiting an antitarget selectivity that is greater than the selectivities of the product (e.g., a hydrazone) and of either precursor (e.g., a hydrazine derivative or ketone) used singly.This paper describes the target‐selective cytotoxic synergism of a cationic aldehyde (A) and a cationic acylhydrazine (B) containing a triarylalkylphophonium moiety against Ehrlich ascites carcinoma cells (ELA) in culture, in addition to reviewing previous work on self‐assembling cytotoxins. The synergism between A and B is carcinoma selective when the ELA cells (the target) are compared to CV‐1, A, B and the hydrazone C resulting from their reaction are lipophilic delocalized cations that selectively inhibit ELA growth relative to CV‐1 growth. The hydrazone C is more growth inhibitory than either A or B for both cell lines. A combination of A with an unreactive analogue of B and a combination of B with an unreactive analogue of A did not synergistically inhibit ELA proliferation. The degree of synergism is greater against the ELA cells than against the CV‐1 cells. These data, together with hydrazone formation kinetics, suggest that A and B are both concentrated together selectively inside the ELA due to the transmembrane potentials, reacting inside the ELA cells at a higher velocity than inside the CV‐1 cells to form the more growth‐inhibitory hydrazone C.
17O‐ and 14N‐nmr studies of Leu‐enkephalin and enkephalin‐related fragments in aqueous solution
Authors: Karayannis Theodoros , Gerothanassis Ioannis P. , Sakarellos‐Daitsiotis Maria , Sakarellos Constantinos , Marraud Michel 
Published: December 2004

Abstract17O‐ and 14N‐nmr chemical shifts and line widths of the carboxyl and amino terminal groups of Leu‐enkephalin—Tyr‐Gly‐Gly‐Phe‐[17O]Leu‐Oh—and enkephalin‐related fragments—[17O]Leu‐OH, Phe‐[17O]Leu‐OH, Gly‐Phe‐[17O]Leu‐OH, and Gly‐Gly‐Phe‐[17O]Leu‐OH—were measured in aqueous solution over the entire pH range. Enrichment in 17O was achieved by saponification of the corresponding O‐methyl esters. Ionization constants and titration shifts were obtained by nonlinear least‐squares fits to one‐protion titration curves. [17O]Leu‐OH exhibits a profound pH‐dependent solvation change on deprotonation of the carboxyl group, as shown by 17O‐ and 14N‐nmr line widths. In contrast, the peptides studied do not exhibit pH‐dependent conformational (solvation) changes on deprotonation of the carboxyl group, and a head‐to‐tail intramolecular association between the ionic terminal groups should be excluded. It is shown that the peptides do not exhibit isotropic overall molecular motion and that segmental motion rather than fast internal motion influences the effective correlation times at the sites of the carboxyl oxygens and the amino nitrogen.
Assessment of protien reorientational diffusion in solution by 13C off‐resonance rotating frame spin–lattice relaxation: Effect of anisotropic tumbling
Authors: Morgan Courtesy F. , Schlieich Thomas , Caines G. Herbert , Michael David 
Published: December 2004

AbstractThe 13C off‐resonance rotating frame spin‐lattice relaxation technique is applicable to the study of protien rotational diffusion behaviour in a variety of experimental situations. The original formalism of James and co‐workers (1978) (J. Amer. Chem. Soc. 100, 3590–3594) was constrained by the assumption of random isotropic reorientational motion. Here we include in the formalism anisotropic tumbling, and present the results of computer simulations illustrating the differences between anisotropic and isotropic reorientational motion for the off‐resonance rotating frame spin–lattice relaxation experiment. In addition, We have included chemical shift anisotropy of the peptide carbonyl carbon as an additional relaxation mechanism contribution, to permit high field nmr protein rotational diffusion measurements.
Restrained energy refinement with two different algorithms and force fields of the structure of the α‐amylase inhibitor tendamistat determined by nmr in solution
Authors: Billeter M. , Schaumann Th. , Braun W. , Wüthrich K. 
Published: December 2004

AbstractThe solution structure of an α‐amylase inhibitor, tendamistat, calculated from nmr data with the distance geometry program DISMAN is subjected to restrained energy minimization. To study the influence of force field parametrizations and the convergence behavior of refinement algorithms, two different programs were used. AMBER is an established software package including a steepest descent and/or conjugent gradient optimizer in the Euclidian space; the name AMBER also represents a force field. The program FANTOM (fast Newton–Raphson torsion angle energy minimizer) is a new restrained energy refinement implementation of the Newton–Raphson algorithm, which uses second derivatives of the conformational energy in dihedral angle space with the ECEPP/2 force field. For both programs the normal energy force field was supplemented with an additional potential of the form ΣA(di − ui)6 (if di > ui), which enforces upper limits ui to selected distances di as measured by nmr. Improvements of the intramolecular interactions with a decrease of the internal energies of about 1000 kcal/mol could be achieved without increasing the distance constraint violations. The restrained energy refinements caused only small changes of the molecular geometries: The root mean square distance values for the backbone atoms between the initial DISMAN structure and the refined structures are about 0.5 Å for AMBER and about 0.7 Å for FANTOM. Local conformational changes during the restrained energy minimizations are analyzed with respect to hydrogen‐bond formation, and with respect to comparisons of the solution structure and the crystal structure.