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Millisecond Timescale (millisecond + timescale)

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Chemistry100%

Selected Abstracts

Cover Picture (Isr. J. Chem.

ISRAEL JOURNAL OF CHEMISTRY, Issue 3-4 2009
3-4/2009)
Structures of E. coli Adenylate Kinase in the open (4AKE) and closed (1ANK) states with cyanine dye derivatives modeled onto residues 128 and 194 for single-molecule Forster resonance energy transfer (FRET) studies of lid dynamics. The bottom of the figure displays a sample distance-vs.-time trajectory displaying spontaneous lid open,closed transitions on the millisecond timescale. The time-dependent potential of mean force along the lid coordinate measured by single-molecule FRET is also displayed. Further information can be found in Hanson et al., Proc. Natl. Acad. Sci. USA, 104, 18055,18060 (2007). With thanks to Haw Yang. [source]

All three Ca2+ -binding loops of photoproteins bind calcium ions: The crystal structures of calcium-loaded apo-aequorin and apo-obelin

PROTEIN SCIENCE, Issue 3 2005
Lu Deng
HLH, helix,loop,helix; HSQC, heteronuclear single quantum coherence; RMSD, root mean square deviation; SAD, single wavelength anomalous dispersion Abstract The crystal structures of calcium-loaded apoaequorin and apo-obelin have been determined at resolutions 1.7 Å and 2.2 Å, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium-loaded apo-proteins retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2-hydroperoxycoelenterazine, and also the same as the Ca2+ -discharged obelin bound with the product, coelenteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these subtle shifts are the basis of the ability of these photoproteins to sense Ca2+ concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed. [source]

Early Structural Evolution of Native Cytochrome c after Solvent Removal

CHEMBIOCHEM, Issue 15 2008
Michal Z. Steinberg
Abstract Electrospray ionization transfers thermally labile biomolecules, such as proteins, from solution into the gas phase, where they can be studied by mass spectrometry. Covalent bonds are generally preserved during and after the phase transition, but it is less clear to what extent noncovalent interactions are affected by the new gaseous environment. Here, we present atomic-level computational data on the structural rearrangement of native cytochrome c immediately after solvent removal. The first structural changes after desolvation occur surprisingly early, on a timescale of picoseconds. For the time segment of up to 4.2 ns investigated here, we observed no significant breaking of native noncovalent bonds; instead, we found formation of new noncovalent bonds. This generally involves charged residues on the protein surface, resulting in transiently stabilized intermediate structures with a global fold that is essentially the same as that in solution. Comparison with data from native electron capture dissociation experiments corroborates both its mechanistic postulations and our computational predictions, and suggests that global structural changes take place on a millisecond timescale not covered by our simulations. [source]

Osmium(II) and Ruthenium(II) Arene Maltolato Complexes: Rapid Hydrolysis and Nucleobase Binding

CHEMISTRY - A EUROPEAN JOURNAL, Issue 9 2007

Abstract Density functional calculations show that aquation of [Os(,6 -arene)(XY)Cl]n+ complexes is more facile for complexes in which XY=an anionic O,O-chelated ligand compared to a neutral N,N-chelated ligand, and the mechanism more dissociative in character. The O,O-chelated XY=maltolato (mal) [M(,6 - p -cym)(mal)Cl] complexes, in which p -cym=p -cymene, M=OsII (1) and RuII (2), were synthesised and the X-ray crystal structures of 1 and 2,2,H2O determined. Their hydrolysis rates were rapid (too fast to follow by NMR spectroscopy). The aqua adduct of the OsII complex 1 was 1.6,pKa units more acidic than that of the RuII complex 2. Dynamic NMR studies suggested that O,O-chelate ring opening occurs on a millisecond timescale in coordinating proton-donor solvents, and loss of chelated mal in aqueous solution led to the formation of the hydroxo-bridged dimers [(,6 - p -cym)M(,-OH)3M(,6 - p -cym)]+. The proportion of this dimer in solutions of the OsII complex 1 increased with dilution and it predominated at micromolar concentrations, even in the presence of 0.1,M NaCl (conditions close to those used for cytotoxicity testing). Although 9-ethylguanine (9-EtG) binds rapidly to OsII in 1 and more strongly (log,K=4.4) than to RuII in 2 (log,K=3.9), the OsII adduct [Os(,6 - p -cym)(mal)(9EtG)]+ was unstable with respect to formation of the hydroxo-bridged dimer at micromolar concentrations. Such insights into the aqueous solution chemistry of metal,arene complexes under biologically relevant conditions will aid the rational design of organometallic anticancer agents. [source]

Site-Specific Investigation of the Steady-State Kinetics and Dynamics of the Multistep Binding of Bile Acid Molecules to a Lipid Carrier Protein

CHEMISTRY - A EUROPEAN JOURNAL, Issue 37 2010
Dr. Clelia Cogliati
Abstract The investigation of multi-site ligand,protein binding and multi-step mechanisms is highly demanding. In this work, advanced NMR methodologies such as 2D 1H,15N line-shape analysis, which allows a reliable investigation of ligand binding occurring on micro- to millisecond timescales, have been extended to model a two-step binding mechanism. The molecular recognition and complex uptake mechanism of two bile salt molecules by lipid carriers is an interesting example that shows that protein dynamics has the potential to modulate the macromolecule,ligand encounter. Kinetic analysis supports a conformational selection model as the initial recognition process in which the dynamics observed in the apo form is essential for ligand uptake, leading to conformations with improved access to the binding cavity. Subsequent multi-step events could be modelled, for several residues, with a two-step binding mechanism. The protein in the ligand-bound state still exhibits a conformational rearrangement that occurs on a very slow timescale, as observed for other proteins of the family. A global mechanism suggesting how bile acids access the macromolecular cavity is thus proposed. [source]