Hydration dynamics and time scales of coupled water-protein fluctuations

We report experimental and theoretical studies on water and protein dynamics following photoexcitation of apomyoglobin. Using site-directed mutation and with femtosecond resolution, we experimentally observed relaxation dynamics with a biphasic distribution of time scales, 5 and 87 ps, around the site Trp7. Theoretical studies using both linear response and direct nonequilibrium molecular dynamics (MD) calculations reproduced the biphasic behavior. Further constrained MD simulations with either frozen protein or frozen water revealed the molecular mechanism of slow hydration processes and elucidated the role of protein fluctuations. Observation of slow water dynamics in MD simulations requires protein flexibility, regardless of whether the slow Stokes shift component results from the water or protein contribution. The initial dynamics in a few picoseconds represents fast local motions such as reorientations and translations of hydrating water molecules, followed by slow relaxation involving strongly coupled water-protein motions. We observed a transition from one isomeric protein configuration to another after 10 ns during our 30 ns ground-state simulation. For one isomer, the surface hydration energy dominates the slow component of the total relaxation energy. For the other isomer, the slow component is dominated by protein interactions with the chromophore. In both cases, coupled water-protein motion is shown to be necessary for observation of the slow dynamics. Such biologically important water-protein motions occur on tens of picoseconds. One significant discrepancy exists between theory and experiment, the large inertial relaxation predicted by simulations but clearly absent in experiment. Further improvements required in the theoretical model are discussed.     

Structural properties of an artificial protein that regulates the nucleation of inorganic and organic crystals

Technological advances have facilitated the generation of artificial proteins that possess the capabilities of recognizing and binding to inorganic solids and/or controlling nucleation processes that form inorganic solids. However, very little is known regarding the structure of these interesting polypeptides and how their structure contributes to functionality. To address this deficiency, we report structural investigations of an artificial protein, p288, that self-assembles and controls the nucleation of simple salts and organic compounds into dendrite-like crystals. Under aqueous conditions at low pH and in the presence of high salt, p288 is conformationally labile and exists primarily as a random coil conformer in equilibrium with other undefined secondary structures, including polyproline type II and beta turn. We note that p288 can fold into either a partial beta strand (at neutral pH) or a predominantly alpha helical (in the presence of TFE) conformation. Solid-state 13C-15N NMR experiments also reveal that p288 in the lyophilized, hydrated state possesses some degree of nonrandom coil structure. These results indicate that p288 is conformationally labile but can undergo conformational transitions to a more stable structure when water solvent loss/displacement occurs and protein concentrations increase. We believe that conformational instability and the ability to adopt different structures as a function of different environmental conditions represent important molecular features that impact p288 supramolecular assembly and crystal nucleation processes.     

High-throughput mutagenesis to evaluate models of stereochemical control in ketoreductase domains from the erythromycin polyketide synthase

Ketoreductase (KR) activities help determine the stereochemistry of the products of modular polyketide synthases (PKSs). For example, domains eryKR(1) and eryKR(2), contained, respectively, in the first and second extension modules of the erythromycin-producing PKS, reduce 3-ketoacyl-thioester intermediates with opposite stereospecificity. Amino acid motifs that correlate with stereochemical outcome have been identified in KRs. We have used saturation mutagenesis of these motifs in eryKR(1) and eryKR(2), and a microplate-based screen of such mutants for activity against (9R, S)-trans-1-decalone, to identify candidate enzymes potentially altered in stereocontrol. Active mutants were reassayed with (2R, S)-2-methyl-3-oxopentanoic acid N-acetylcysteamine thioester, and the alcohol products were analyzed by chiral HPLC. Variant enzymes were found with either altered substrate selectivity for the (2R) or (2S) substrate or altered stereospecificity of reduction, or both, further highlighting the importance of these motifs in stereochemical control.     

Submicrometer structure of surface-chemical gradients prepared by a two-step immersion method

Lateral force microscopy and microdroplet density measurements have been used to examine the microstructure of surface-chemical gradients of thiols on gold, prepared by a two-step immersion method. A single-component coverage gradient, generated by gradual immersion of a gold surface into a solution of a single thiol, yielded islands of approximately 25 nm in diameter at the end that had only been briefly immersed, whereas an increasingly continuous film was formed along the gradient. After saturation with a second thiol with a different end group, the structure generated during the initial immersion step was found to persist.     

Towards novel difluorinated sugar mimetics; syntheses and conformational analyses of highly-functionalised difluorinated cyclooctenones

Highly-functionalised difluorinated cyclooctenones were synthesised from trifluoroethanol using either metallated difluoroenol acetal or carbamate chemistry, followed by a [2,3]-Wittig rearrangement or aldol reaction. Efficient RCM reactions afforded the title compounds which showed rather restricted fluxional behaviour by VT (19)F NMR. Topological characterisation by molecular modelling and NOESY/ROESY experiments offered a number of challenges, but allowed the identification of two favoured boat-chair conformers which interconverted by pseudorotation with relatively large activation barriers.     

Thermal Decomposition and Crystallization of Aqueous Sol-Gel Derived Zirconium Acetate Gels: Effects of the Additive Anions

Zirconia powders were prepared by forming gels by desiccation of aqueous precursor solutions of zirconium acetate containing nitric or sulfuric acid at pH 2.4 and 1.4 and pyrolyzing the gels to temperatures up to 825°C. The structure development in the gels and solid pyrolysis products was investigated. The crystalline zirconia structures produced monoclinic (m), metastable cubic (c) and tetragonal (t) polymorphs. The structure transition temperatures were strongly dependent on the pH, the anions and the stoichiometry of the zirconium complex in the precursor solution. The monoclinic polymorph fraction in the zirconia formed by pyrolyzing the gel formed from the precursor solution containing sulfuric acid at pH 2.4 to 750°C approaches zero while this ratio in the zirconia formed by pyrolyzing the gel formed from the precursor solution containing nitric acid at pH 1.4 to 825°C is 0.7.     

Muonium in bulk fused quartz: Test case for RAHD relaxation theory

Muonium (μ ⁺ e ⁻) in bulk fused quartz is a unique system in that theμ ⁺ spin polarization (in the muonium state) relaxes almost entirely via random anisotropic hyperfine distortions (RAHD). As such, this system provides an excellent test case for a new RAHD spin relaxation theory. This theory is quantitatively compared to static zero field data and the functional characteristics in both the high field and dynamic limits are considered as well.