Home About us Contact
|
Home About us Contact | ||
|
|
||
Dissociation Process (dissociation + process)
Selected AbstractsEnergetic aspects of locked nucleic acids quadruplex association and dissociationBIOPOLYMERS, Issue 6 2006Luigi Petraccone Abstract The design of modified nucleic acid aptamers is improved by considering thermodynamics and kinetics of their association/dissociation processes. Locked Nucleic Acids (LNA) is a promising class of nucleic acid analogs. In this work the thermodynamic and kinetic properties of a LNA quadruplex formed by the TGGGT sequence, containing only conformationally restricted LNA residues, are reported and compared to those of 2,-OMe-RNA (O-RNA) and DNA quadruplexes. The thermodynamic analysis indicates that the sugar-modified quadruplexes (LNA and O-RNA) are stabilized by entropic effects. The kinetic analysis shows that LNA and O-RNA quadruplexes are characterized by a slower dissociation and a faster association with respect to DNA quadruplex. Interestingly, the LNA quadruplex formation process shows a second-order kinetics with respect to single strand concentration and has a negative activation energy. To explain these data, a mechanism for tetramer formation with two intermediate states was proposed. © 2006 Wiley Periodicals, Inc. Biopolymers 83: 584,594, 2006 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Strikingly fast microtubule sliding in bundles formed by Chlamydomonas axonemal dynein,CYTOSKELETON, Issue 6 2010Susumu Aoyama Abstract Chlamydomonas axonemal extracts containing outer-arm dynein bundle microtubules when added in the absence of ATP. The bundles dissociate after addition of ATP (Haimo et al., Proc Natl Acad Sci USA 76:5759,5768, 1979). In the present study, we investigated the ATP-induced bundle dissociation process using caged ATP. Application of ,0.5 mM ATP induced microtubule sliding at ,30 ,m·s,1, which was 1.5 times faster than the microtubule sliding observed in protease-treated axonemes and five times faster than microtubule gliding on glass surfaces coated with outer-arm dynein. Bundles formed by mutant dynein molecules that lack one of the three heavy chains (HCs) displayed similar high-speed intermicrotubule sliding. These results suggest that Chlamydomonas outer-arm dynein molecules, when aligned, can translocate microtubules at high speed and that the high-speed sliding under load-free conditions does not require the complete set of the three HCs. It is likely that each of the three HCs has the ability to produce high-speed sliding, which should be an important property for their cooperation. © 2010 Wiley-Liss, Inc. [source] Determination of dissociation energy for ligand exchange reaction from EXAFSJOURNAL OF SYNCHROTRON RADIATION, Issue 2 2001T. Miyanaga EXAFS (extended X-ray absorption fine structure) experiments were performed at several different temperatures for a series of 3d transition metal ions (Cr3+, Fe3+, Fe2+, Ni2+, Co2+, Zn2+) in aqueous solutions. Anharmonic EXAFS analyses, which include up to third order cumulant, were carried out to study on the metal-oxygen bonding potential. According to the model in which the dissociation process is dominant for the ligand-water exchange reaction, the dissociation energy has been first evaluated from EXAFS in solution phase. [source] Influence of Grafting on the Solution Properties and the Dissociation Behavior of Ionic/Nonionic Grafted CopolymersMACROMOLECULAR CHEMISTRY AND PHYSICS, Issue 6 2007Jens Weber Abstract A new synthetic approach towards grafted terpolymers based on a poly[(methyl vinyl ether)- alt -(maleic anhydride)] backbone and poly(ethylene glycol) monomethyl ether (MPEG) side chains is presented. Resulting comb polymers with controllable grafting degree still have highly reactive anhydride moieties along the polymer backbone, as proved by IR spectroscopy. Grafting degree depends on the anhydride hydroxide stoichiometric ratio. It is not influenced by the molecular weight of MPEG. An increase in the grafting degree leads to a contraction of the polymer in the solution. Evaluation of potentiometric titration data gave a deeper insight into the dissociation process. The copolymers showed a two-step dissociation behavior. No significant influence of the grafting degree on the acidic strength was observed, whilst there is a strong effect of the grafting degree on the free energy change upon neutralization ,Gel. Grafting leads to a higher change in free energy ,Gel,1 for the first step but to lower ,Gel,2 required for the second step. [source] Binding specificity and the ligand dissociation process in the E. coli biotin holoenzyme synthetasePROTEIN SCIENCE, Issue 3 2002Keehwan Kwon Abstract The binding of the Escherichia coli biotin holoenzyme synthetase to the two ligands, biotin and bio-5,-AMP, is coupled to disorder-to-order transitions in the protein. In the structure of the biotin complex, a "glycine-rich" loop that is disordered in the apo-enzyme is folded over the ligand. Mutations in three residues in this loop result in significant changes in the affinity of the enzyme for both biotin and bio-5,-AMP. The kinetic basis of these losses in the affinity resides primarily in changes in the unimolecular rates of dissociation of the complexes. In this work, isothermal titration calorimetry has been employed to examine the detailed thermodynamics of binding of three loop mutants to biotin and bio-5,-AMP. The energetic features of dissociation of the protein,ligand complexes also have been probed by measuring the temperature dependencies of the unimolecular dissociation rates. Analysis of the data using the Eyring formalism yielded entropic and enthalpic contributions to the energetic barrier to dissociation. The thermodynamic results coupled with the known structures of the apo-enzyme and biotin complex have been used to formulate a model for progression from the ground-state complex to the transition state in biotin dissociation. In this model, the transition-state is characterized by both partial disruption of noncovalent bonds and acquisition of some of the disorder that characterizes the glycine-rich loop in the absence of ligand. [source] Discrete and continuum quantum states for the Kratzer oscillatorINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2002Adelio R. MatamalaArticle first published online: 2 JUL 200 Abstract Kratzer oscillator is a realistic zero-order model for describing the anharmonic ro-vibrational motion in diatomic molecules. Kratzer oscillator has an energy spectrum containing both discrete and continuum parts. Wavefunctions belonging to the continuum would be useful in the study of transitions to the continuum in molecular dissociation processes. In this article, bound and scattering wavefunctions of the Kratzer oscillator are reviewed and the bound,bound and the bound,free matrix elements are obtained. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002 [source] Influence of differently ionized species on fragmentation pathways and energetics of a potential adenosine receptor antagonist using a triple quadrupole and a multistage LTQ-OrbitrapÔ FTMS instrumentJOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 4 2009Wendy Zhong A systematic study was conducted to investigate the influence of differently ionized species on the fragmentation pathways and energetics of a piperazine-containing adenosine by using different cations or anions. Very different fragmentation mechanisms were observed in protonated- versus sodiated-molecules, which indicated that the proton is mobilized to promote the charge-direct fragmentation, whereas Na+ cation was fixed at the heterotricyclic ring structure provoking charge-remote fragment ions. This finding was also supported by the results observed in the fragmentation behaviors in the deprotonated-molecule. The energetics of these fragment ions were also explored by using the breakdown curves obtained from the triple quadrupole and LTQ-OrbitrapÔ instrument. The data indicated that the lowest energy pathways in the protonated-molecule [M+H]+ involve breaking a CN bond connecting an ethylene bridge and heterotricyclic ring structure. The lowest energy pathway is the cleavage of a CO bond connecting the methoxy ethyl group and phenolic oxygen to form a distonic radical ion for a sodiated-molecule [M+Na+]and a deprotonated-molecule [M-H],. The data suggest that by choosing the differently ionized species, one can probe different fragmentation channels that can provide additional structure information for an unknown impurity and possibly degradation product identification. In addition, by comparing the data obtained from triple quadrupole and LTQ-Orbitrap instruments, one can develop further understanding of the differences in the fragmentation behaviors due to the variations in the collision activation-dissociation process. From the side-by-side comparison with the breakdown curves obtained for both instruments, the difference in fragmentation behaviors caused by the difference in dissociation processes that occur in these two types of instruments can be probed. J. Heterocyclic Chem., (2009). [source] Photoionization studies on various quinones by an infrared laser desorption/tunable VUV photoionization TOF mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 12 2008Yang Pan Abstract Photoionization and dissociative photoionization characters of six quinones, including 1,2-naphthoquinone (1,2-NQ), 1,4-naphthoquinone (1,4-NQ), 9,10-phenanthroquinone (PQ), 9,10-anthraquinone (AQ), benz[a]- anthracene-7,12-dione (BAD) and 1,2-acenaphthylenedione (AND) have been studied with an infrared laser desorption/tunable synchrotron vacuum ultraviolet (VUV) photoionization mass spectrometry (IR LD/VUV PIMS) technique. Mass spectra of these compounds are obtained at different VUV photon energies. Consecutive losses of two carbon monoxide (CO) groups are found to be the main fragmentation pathways for all the quinones. Detailed dissociation processes are discussed with the help of ab initio B3LYP calculations. Ionization energies (IEs) of these quinones and appearance energies (AEs) of major fragments are obtained by measuring the photoionization efficiency (PIE) spectra. The experimental results are in good agreement with the theoretical data. Copyright © 2008 John Wiley & Sons, Ltd. [source] The nature of collision-induced dissociation processes of doubly protonated peptides: comparative study for the future use of matrix-assisted laser desorption/ionization on a hybrid quadrupole time-of-flight mass spectrometer in proteomicsRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 22 2001R. Cramer Comparative MS/MS studies of singly and doubly charged electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) precursor peptide ions are described. The spectra from these experiments have been evaluated with particular emphasis on the data quality for subsequent data processing and protein/amino acid sequence identification. It is shown that, once peptide ions are formed by ESI or MALDI, their charge state, as well as the collision energy, is the main parameter determining the quality of collision-induced dissociation (CID) MS/MS fragmentation spectra of a given peptide. CID-MS/MS spectra of singly charged peptides obtained on a hybrid quadrupole orthogonal time-of-flight mass spectrometer resemble very closely spectra obtained by matrix-assisted laser desorption/ionization post-source decay time-of-flight mass spectrometry (MALDI-PSD-TOFMS). On the other hand, comparison of CID-MS/MS spectra of either singly or doubly charged ion species shows no dependence on whether ions have been formed by ESI or MALDI. This observation confirms that, at the time of precursor ion selection, further mass analysis is effectively decoupled from the desorption/ionization event. Since MALDI ions are predominantly formed as singly charged species and ESI ions as doubly charged, the associated difference in the spectral quality of MS/MS spectra as described here imposes direct consequences on data processing, database searching using ion fragmentation data, and de novo sequencing when ionization techniques are changed. Copyright © 2001 John Wiley & Sons, Ltd. [source] | ||||||||||