bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐Resolution solid‐state 13C‐nmr of peptides: A study of chain‐length dependence for 310‐helix formation
Authors: Saitô Hazime , Tabeta Ryoko , Formaggio Fernando , Crisma Marco , Toniolo Claudio 
Published: December 2004

AbstractHigh‐resolution solid‐state 13C‐nmr spectra of two series of fully protected oligopeptides, Z‐(Aib)n‐OMe (n = 3−8) and Z‐(Aib)n‐L‐Leu‐(Aib)2‐OMe (n = 0−5), were recorded to gain insight into main‐chain length dependence for 310‐helix formation. We found that all the oligopeptides examined adopt an incipient or a fully developed 310‐helical structure, as judged from the characteristic splitting of the Cβ signals as well as the conformation‐dependent displacements of the Cα and CO peaks.
17O‐nmr studies of the conformational and dynamic properties of enkephalins in aqueous and organic solutions using selectively labeled analogues
Authors: Sakarellos Constantinos , Gerothanassis Ioannis P. , Birlirakis Nicolaos , Karayannis Theodoros , Sakarellos‐Daitsiotis Maria , Marraud Michel 
Published: December 2004

AbstractThe synthesis of Leu‐enkephalin selectively 17O‐enriched in Gly2 and Gly3 is reported. The 17O‐nmr chemical shifts of [17O‐Gly2, Leu5]‐ and [17O‐Gly3, Leu5]‐enkephalins in H2O are almost identical and independent of the pH. Since hydrogen bonding is the dominant factor governing the chemical shifts of the peptide oxygen, it can be concluded that the hydration state of both oxygens is identical and independent of the pH. The 17O chemical shifts of the [17O‐Leu5]‐enkephalin terminal carboxyl group at pH ∼ 1.9 and 5.6 are very different in H2O but very similar in CH3CN/DMSO (4:1) solution. This suggests that the protonation state of the carboxyl group at both pH values in CH3CN/DMSO solution is the same and consequently that Leu‐enkephalin exists in the neutral form at pH ∼ 5.6. In this organic mixed solvent system both Gly2 and Gly3 oxygen resonances exhibit a significant shift to high frequency by the same extent (Δδ ∼ 30 ppm). It is concluded that both peptide oxygens are not hydrogen bonded to an appreciable extent and that no specific 2 ← 5 hydrogen bonding exists to an appreciable extent. This conclusion is in agreement with the energy of activation for molecular rotation, as determined from T1 measurements, which was found to be almost identical for both [17O‐Gly2, Leu5]‐ and [17O‐Gly3, Leu5]‐enkephalins in CH3CN/DMSO (4:1) mixed solvent.
Conformationally constrained tachykinins: N‐methylated analogues of neurokinin A
Authors: Rovero P. , Pestellini V. , Patacchini R. , Santicioli P. , Maggi C. A. , Meli A. 
Published: December 2004

AbstractLimited conformational constraints have been introduced in the sequence of the C‐terminal fragment of the peptide neurotransmitter neurokinin A by N‐methylation of individual peptide bonds, and the biological activities of the peptides thus obtained were evaluated in order to assess the effect of such conformational constraint on receptor selectivity. The analogue methylated in position 7 shows enhanced selectivity toward NK‐1 receptor.
Structure of the ion channel peptide antibiotic gramicidin A
Authors: Langs David A. 
Published: December 2004

AbstractThe crystal structure of the uncomplexed orthorhombic form of gramicidin A has been determined at 0.86 Å resolution. The polypeptide crystallizes from ethanol as a left‐handed, double‐stranded, antiparallel β5.6‐helical dimer that is 31 Å long and an average of 4.8 Å in diameter. The uncomplexed channel does not contain ions or solvent molecules, and its diameter is not uniform but varies from a minimum of 3.85 Å to a maximum of 5.47 Å. There are three empty cavities in the channel that have a diameter exceeding 5.25 Å and appear to be large enough to accommodate water molecules or potassium ions in a chemically reasonable coordination environment. The observed crystal structure does not offer any obvious clues as to why an antiparallel β5.6‐helix cannot function as an ion channel in lipid bilayers.
A theoretical investigation of the intercalative binding of 7‐H pyrido[4.3C]carbazole chromophore into a d(CpG)2 minihelix
Authors: Maroun Rachid , Gresh Nohad 
Published: December 2004

AbstractTheoretical computations are performed of the intercalative binding to a model d(CpG)2 minihelix of 7‐H pyrido[4.3C]carbazole, the precursor of the antitumor bisintercalating drug ditercalinium. The conformations of the intercalation site are generated by the AGNAS procedure (algorithm to generate nucleic acid structures) of Miller and co‐workers. The ligand‐nucleotide interactions and the nucleotide conformational energies are computed with the SIBFA procedures (sum of interactions between fragments ab intio computed), which use formulas of empirical origin that reproduce ab initio SCF (self‐consistent field) computations. Among the candidate intercalation sites most favored energetically, one has a pattern of conformational angles related to the one determined crystallographically by Sobell et al. in a series of x‐ray structural studies of small intercalator–dinucleotide monophosphate complexes. Optimal values of the unwinding angle, found in the range of −12° to −14°, are consistent with available experimental data on DNA.
Calorimetric study of the effect of intrachain cross‐linking on lysozyme unfolding
Authors: Segawa Shin‐Ichi , Sugihara Mitsuru , Maeda Tomoko , Mitsuhisa Yukio , Kodama Michiko , Seki Syûzô , Sakiyama Minoru 
Published: December 2004

AbstractThermodynamics of unfolding of lysozyme cross‐linked between Glu 35 and Trp 108 were studied in solutions of various concentrations of 1‐propanol (1‐PrOH) at pH 3.7 by means of scanning microcalorimetry. The transition temperature for the cross‐linked lysozyme increases by 17–19°C due to cross‐linking at every concentration of 1‐PrOH. This corresponds to the increase in the unfolding Gibbs free energy of about 28 kJ · mol−1, which is independent of the concentration of 1‐PrOH. It was found that the unfolding enthalpy of cross‐linked lysozyme is only slightly larger than that of intact one, and the unfolding entropy of the cross‐linked one is nearly equal to that of the intact one, if both are compared at the same temperature. The stabilization mechanism for the cross‐linked lysozyme is discussed on the basis of these calorimetric data.
Site‐specific laser modification (cleavage) of oligodeoxynucleotides
Authors: Benimetskaya L. Z. , Bulychev N. V. , Kozionov A. L. , Koshkin A. A. , Lebedev A. V. , Novozhilov S. Yu. , Stockman M. I. 
Published: December 2004

AbstractSequence‐specific photomodification of oligodeoxynucleotide pAGAGTATTGACTTA (“a target”) has been carried out with the aid of complementary fluorescent probes. Such a probe consisted of oligodeoxynucleotide pAATACTCT and a chromophore group attached to its 5′ end. Three different derivatives of ethidium bromide were used as a chromophore. The photomodification was induced by nitrogen laser radiation (337 nm, 15 MW /cm2). The irradiation induces the following photodamages: target cleavage at the specific binding site with a cutting off of the 8‐mer from its 5′ end (yield up to 12%), formation of specific covalent adduct target‐probe with a yield of 20–70%, and piperidine‐sensitive target modifications with a 7–27% yield (for different chromophores). The total yield of specific photodamages of all kinds is 50–80%. The target cleavage and generation of piperidine‐sensitive modifications are optically nonlinear processes. Piperidine treatment of the irradiated samples led to specific cleavage of the target with the yield up to 40%. All kinds of observed modifications are not influenced by high concentrations of free radical scavengers: 1.3M tBuOH and 10 mM cystamine. The pattern of cleavage indicates that the most probable position of the chromophore is between T8 and G9 of the target, i.e., the chromophore stacks on top of the last A · T base pair of the duplex. The aggregate of evidence is in agreement with the mechanism of nonlinear photomodification (the cleavage and generation of piperidine‐sensitive modifications) based on the transfer of two‐photon excitation energy from the chromophore to the target.
Raman spectroscopy of supercoiled and nicked ColE1 plasmid
Authors: Christens‐Barry William A. , Martin James C. , Lebowitz Jacob 
Published: December 2004

AbstractNative supercoiled and nicked Co1E1 DNA were examined using laser Raman spectroscopy. Co1E1 contains 6646 base pairs (bp) and, when supercoiled, approximately 47 negative supercoils. An analytical buoyant density gradient centrifugation technique developed by Burke and Bauer was scaled to preparative quantities, and used to isolate the supercoiled plasmid fraction from its nicked counterpart. This procedure allowed enriched fractions of the supercoiled plasmid to be extracted without the use of the optical contaminant ethidium bromide. The intensities of several Raman bands were altered between the spectra of the two topological forms. Notably absent were any changes in bands arising from cytosine and guanine vibrations. The observed changes are interpreted in terms of the polymorphic structures which have been observed in many DNA structural studies. The results of this study suggest that accommodation of supercoiling takes place chiefly in A‐T base pairs and backbone moieties, without substantial modification of G‐C base‐pair structure. Premelting effects may account for the observed changes, including a slight shift to lower frequency of a band known to be responsive to base‐pair disruption. Heteronomous ribose sugar pucker is evident in both supercoiled and nicked plasmid species. No gross conformational transitions were detected for native supercoiled DNA, and consequently, subtle rearrangements appear sufficient to absorb the supercoiling deformations.
Local dynamics in biological macromolecules
Authors: Perico Angelo 
Published: December 2004

AbstractThe diffusive approach in the optimized Rouse–Zimm approximation to segment relaxation in the nanosecond time domain (ORZLD) is extended to consider chains of nonequivalent units as occurring in biological macromolecules. The correlation times for second‐order time correlation functions of each virtual bond on the chain are calculated for some homopolypeptides, and random and regular copolypeptides. The expected correlation times for biological macromolecules organized in multiple domains are discussed via a simple model of the ORZLD hierarchy. Dynamic bond correlation times are compared with static local presistence lengths.
1H‐nmr studies of a monointercalating drug into a d(CpGpApTpCpG)2 minihelix
Authors: Delepierre M. , Dinh T. Huyhn , Roques B. P. 
Published: December 2004

AbstractThe structure of the complex formed between the 7H‐pyridocarbazole monomer [{(2‐piperidyl)‐2,1‐ethane‐y1} {10‐methoxy‐7H‐pyrido[4,3‐c]carbazolium} dimethane sulfonate] and the autocomplementary hexanucleotide d(CpGpApTpCpG)2 in aqueous solution is analyzed by 270‐ and 400‐MHz 1H‐nmr. The large upfield shifts observed for both the drug and the self‐complementary hexanucleotide protons provide evidence for intercalated complexes. The observation of intermolecular nuclear Overhauser effects between drug and the hexanucleotide protons gives a privileged orientation of the durg in the intercalation site with the quaternarizing ethyl piperidine chain protruding in the major groove. Moreover, the data suggest an intercalation based on the neighbor exclusion site principle in the three alternating sequences.
Linear dichroism studies of the complexes between CT–DNA and distamycins
Authors: Forni A. , Moretti I. , Marconi G. , Mongelli N. , Samorí B. 
Published: December 2004

AbstractThe study of the monomeric chromophore of the distamycins reported in Ref. 1 was used here to build up a description of the electronic states of the whole oligopeptide by the exciton theory. Liquid crystal–linear dichroism (LC–LD) spectra of the distamycins were recorded by using as orienting solvents both thermotropic and lyotropic mesomorphic media. The agreement between the LD spectra and the polarization assignments by the exciton treatment is satisfactory. On this basis the flow‐LD spectra of the complex between distamycin V and DNA was interpreted in terms of the preferred relative orientations of the guest and host molecules. A single site location of the distamycin within the minor groove does not perfectly match the experimental order parameters. This orientational distribution function could be too simple to explain the experimental data. It may therefore be assumed that a small fraction of the guest molecules are preferentially aligned more parallel to the host chain axis than the minor groove. Alternatively, and probably more likely, the partial mismatch of the experimental data with the minor groove location may be seen as a manifestation of the well‐known stiffening and bending effects at the binding sites, which have already been observed by other techniques.
Characterization of the reaction products of adult human hemoglobin and disuccinimidyloxalate
Authors: Marini M. A. , Christensen S. , Snell S. , Jessee R. , Medina F. , Zegna A. 
Published: December 2004

AbstractA number of chemically modified hemoglobin preparations have been proposed for use as an emergency resuscitation fluid. The purpose for forming these hemoglobin derivatives is to decrease the oxygen binding (i.e., to increase the P50) and to increase the intravascular retention time. These goals have been met with various degrees of success by using the reaction with pyridoxyl 5‐phosphate to raise the P50, followed by the addition of glutaraldehyde to increase circulating half‐life by polymerization.1,2 Other derivatives have been formed with polyethylene glycol,3,4 bis‐(3,5‐dibromosalicyl) fumarate,5,6 glycolaldehyde,7 and 2‐nor‐2‐formylpyridoxal 5‐phosphate,8,9 as well as with other compounds. All these derivatives introduce a foreign molecule into the hemoglobin, which may not always be desirable. Recently Tharp and Day10 used cyanogen to form intersubunit amide cross‐links in hemoglobin without the incorporation of cyanogen. This approach is attractive if the appropriate functional properties can be attained. Takeda et al.11 showed that equimolar concentrations of amino acids and disuccinimidyloxalate could form peptide bonds in high yield. We report the characteristics of the hemoglobin molecule modified by internal covalent amide bonds, which may be a suitable candidate for a resuscitation fluid.
Structural and electrostatic effects on binding of trivalent cations to double‐stranded and single‐stranded poly[d (AT)]
Authors: Plum G. Eric , Bloomfield Victor A. 
Published: December 2004

AbstractWe have measured the thermal melting profile for poly[d(AT)] · poly[d(TA)] as a function of concentration of three trivalent cations: spermidine, me8spermidine, and hexammine cobalt(III). Using McGhee's (1976) theory of DNA melting in the presence of ligands, we have estimated association constants Kh, Kc and binding site sizes nh, nc for binding to double‐helical (h) and single‐stranded (c) polynucleotide. The results are as follows:

Cation
Kh (M−1)
nh (bp)
Kc (M−1)
nc (bases)

Spermidine
9 × 105
2.2
1.3 × 104
4.5

Me8spermidine
2 × 105
1.4
7 × 103
3

Hexammine cobalt(III)
1.1 × 105
1.5
6 × 102
6

The binding parameters for spermidine and hexammine cobalt(III) to double helical molecules agree fairly well with direct equilibrium dialysis measurements, and are in reasonable accord with predictions of counterion condensation theory. However, despite their identical charges, the three ligands bind to single‐stranded DNA with quite different affinities. Estimates of the charge spacing of single‐stranded DNA suggest that poly[d(AT)] is less elongated in the presence of spermidine and hexammine cobalt (III) than it is when complexed with me8spermidine.
Structural dependence of oligonucleotide photooxidation
Authors: Rokita Steven E. , Lau Bernard , Romero‐Fredes Lorraine 
Published: December 2004

AbstractOxidative photosensitization was used to characterize the conformational‐dependent reactivity of various structures formed by oligonucleotides 14–15 nucleotides in length. The rate and product composition from a single hit process was analyzed using quantitative ion exchange chromatography under native and denaturing conditions. The primary damage incurred under aerobic acetone sensitization was base oxidation that, in turn, would induce strand scission upon a secondary treatment with piperidine. The reactive intermediates of this process were not consistent with diffusible radical species or singlet oxygen, as indicated by isotope and quenching studies. Derivatization was most likely initiated through a type I photoprocess with a direct interaction between DNA bases and excited state acetone preceding an irreversible oxidation step. This dominant reaction demonstrated no obvious sequence or site specificity for initial modification; the relative reactivity among the oligonucleotides did not correspond to any simple trend of base composition or near neighbor analysis. Likewise, the steric requirements of base modification allowed for similar rates of oxidation for single‐strand, helical, and aberrant forms of DNA. Hybridization of the most reactive oligonucleotides, however, did suppress their relative single‐strand vs double‐strand reactivity by as much as fourfold.
Inhibition of protein kinase C and calmodulin by the geometric isomers cis‐ and trans‐tamoxifen
Authors: O'Brian Catherine A. , Ioannides Constantin G. , Ward Nancy E. , Liskamp Rob M. 
Published: December 2004

AbstractThe triphenylethylene antiestrogen trans‐tamoxifen is an effective antitumor agent used in the treatment of human breast cancer. While the antiestrogenic activity of trans‐tamoxifen clearly plays an important role in its tumoricidal action, some of the biological effects of trans‐tamoxifen are independent of estrogen. Therapeutic concentrations of trans‐tamoxifen inhibit protein kinase C (PKC) and calmodulin‐dependent enzymes. PKC and calmodulin play critical roles in growth regulation, and there is evidence that inhibition of PKC and calmodulin by trans‐tamoxifen may contribute to the antiumor activity of the drug in vivo.The geometric isomers cis‐ and trans‐tamoxifen have a number of opposing biological activities that have been attributed to their interactions with the estrogen receptor, Cis‐tamoxifen is generally estrogenic, whereas trans‐tamoxifen is generally antiestrogenic. In this report, we compared the effects of cis‐ and trans‐tamoxifen on PKC activity and on calmodulin‐dependent cAMP phosphodiesterase activity. Cis‐ and trans‐tamoxifen inhibited the Ca2+‐ and phosphatidylserine‐ (PS‐) dependent activity of purified rat brain PKC with indistinguishable potencies, but cis‐tamoxifen was somewhat more potent than the trans isomer in the inhibition of the Ca2+‐ and PS‐independent activity of PKC. In addition, cis‐tamoxifen was the more potent isomer in the inhibition of T lymphocyte activation, an event that entails a PKC‐requiring signal transduction pathway. A modest preference of the cis isomer was also observed in the inhibition of a calmodulin‐dependent cAMP phosphodiesterase. These results suggest a congruence between triphenylethylene binding sites on PKC and on the activated calmodulin–cAMP phosphodiesterase complex. We conclude that the interactions of cis‐ and trans‐tamoxifen with PKC and the activated calmodulin–cAMP phosphodiesterase complex offer a criterion for distinguishing biological effects of triphenylethylenes that are due to interactions with the estrogen receptor from the biological effects resulting from their inhibitory activities against PKC and calmodulin‐dependent processes.
A comparative analysis of single‐ and multiple‐residue substitutions in the alkaline phosphatase signal peptide
Authors: Kendall Debra A. , Doud Suzanne K. , Kaiser Emil Thomas 
Published: December 2004

AbstractThe alkaline phosphatase signal peptide participates in transport of the enzyme to the periplasmic space of Escherichia coli. The signal sequence, like that of other signal peptides, is composed of a polar amino‐terminal segment, a central region rich in hydrophobic residues and a carboxy‐terminal region recognized by signal peptidase. We have previously shown that an alkaline phosphatase signal peptide mutant containing a polyeucine core region functions efficiently in transport of the enzyme [D. A. Kendall, S. C. Bock, and E. T. Kaiser (1986) Nature 321, 706–708]. In this study, some of the amino acid changes involved in the polyleucine sequence are examined individually. A Phe to Leu substitution as the sole change results in impaired transport properties in contrast to when it is combined with three other amino acid changes in the polyleucine‐containing sequence. A mutant with a Pro to Leu substitution in the hydrophobic core region is comparable to wild type while the same type of substitution (Pro to Leu) in the carboxy‐terminal segment results in substantial accumulation of the mutant precursor. Finally, introduction of a basic residue into the hydrophobic segment (Leu to Arg substitution) results in a complete export block. These results exemplify the spectrum of properties produced by individual residue changes and suggest there is some interplay between hydrophobicity and conformation for signal peptide function.
Fluctuation and linkage relations in macromolecular solution
Authors: Schellman John A. 
Published: December 2004

AbstractIt is shown in the appendix that the derivatives of the excess free energy of a macromolecule in solution, with respect to the activities of other solution components, lead to fluctuation and linkage relations among these other components. Solution fluctuation theory is used, but it is specialized to the fluctuations and correlations associated with the presence of a macromolecule, and is developed with a modified ensemble.The relations of the appendix are used to analyze the interaction of two solution components, A and B, with the macromolecule and with one another. Three cases are considered: (1) A and B are ligands that bind stoichiometrically to the macromolecule. This case reduces to Wyman's binding polynomial analysis. (2) A and B are tow substances at high concentration that interact selectively with the macromolecule. (3) A is a species that binds stoichiometrically to the macromolecule, while B is a component at high concentration that interacts weakly with the macromolecule.
Resolution power of regularization algorithm for binary systems in dynamic light scattering
Authors: Timchenko A. A. , Griko N. B. , Serdyuk I. N. 
Published: December 2004

AbstractThe resolving ability of the SIPP program operating on the regularzation principle was studied in computer experiments and in real experiments on a mixture of particles was two different dimensions as well as on tobacco mosaic virus. It has been shown that the limit of resolution in real dynamic light scattering experiments is achieved when the ratio of the characteristic times of the components is 1:2, provided that the contribution of the “slow” component to scattering is about twice that of the “fast” component.Some practical rules that serve to obtain the best resolution of the two compnoents have been formulated.