Cutinase-AOT interactions in reverse micelles: the effect of 1-hexanol

The protein-water nuclear Overhauser effect (NOE) as an indirect microscope for molecular surface mapping of interaction patterns

In this computational study, the intermolecular solute-solvent Nuclear Overhauser Effect (NOE) of the model protein ubiquitin in different chemical environments (free, bound to a partner protein and encapsulated) is investigated. Short-ranged NOE observables such as the NOE/ROE ratio reveal hydration phenomena on absolute timescales such as fast hydration sites and slow water clefts. We demonstrate the ability of solute-solvent NOE differences measured of the same protein in different chemical environments to reveal hydration changes on the relative timescale. The resulting NOE/ROE-surface maps are shown to be a central key for analyzing biologically relevant chemical influences such as complexation and confinement: the presence of a complexing macromolecule or a confining surface wall modulates the water mobility in the vicinity of the probe protein, hence revealing which residues of said protein are proximate to the foreign interface and which are chemically unaffected. This way, hydration phenomena can serve to indirectly map the precise influence (position) of other molecules or interfaces onto the protein surface. This proposed one-protein many-solvents approach may offer experimental benefits over classical one-protein other-protein pseudo-intermolecular transient NOEs. Furthermore, combined influences such as complexation and confinement may exert non-additive influences on the protein compared to a reference state. We offer a mathematical method to disentangle the influence of these two different chemical environments.

pH effects on the structural dynamics of cutinase from Trichoderma reesei: insights from molecular dynamics simulations

The influence of different pH conditions on conformational changes of Tr cutinase was investigated using molecular dynamics simulations.

The influence of hydrodynamic interactions on protein dynamics in confined and crowded spaces-assessment in simple models

We consider several systems that are confined within a softly repulsive sphere. The first one is a model protein, crambin, which is described by a structure-based coarse grained model. We demonstrate that the folding process is accelerated by the hydrodynamic interactions (HI) in a way that depends on the radius of the sphere. The tighter the encompassing sphere, the smaller the effect, independent of the nature of the starting conformations. The second system is a protein surrounded by protein-like softly repulsive spheres that make the confined space crowded. In this case, the HI shorten the folding times in a way which depends on the degree of crowdedness only weakly. The third system is a collection of spheres that are meant to represent molecules. We show that confinement increases association times. We also observe that the HI either facilitate or obstruct association of two spheres depending on the crowding conditions. The dependence of the association time on crowdedness in the confining sphere is qualitatively distinct from that derived by Wieczorek and Zielenkiewicz for a cube with the periodic boundary conditions.

The role of short-range Cys171-Cys178 disulfide bond in maintaining cutinase active site integrity: a molecular dynamics simulation

Understanding structural determinants in enzyme active site integrity can provide a good knowledge to design efficient novel catalytic machineries. Fusarium solani pisi cutinase with classic triad Ser-His-Asp is a promising enzyme to scrutinize these structural determinants. We performed two MD simulations: one, with the native structure, and the other with the broken Cys171-Cys178 disulfide bond. This disulfide bond stabilizes a turn in active site on which catalytic Asp175 is located. Functionally important H-bonds and atomic fluctuations in catalytic pocket have been changed. We proposed that this disulfide bond within active site can be considered as an important determinant of cutinase active site structural integrity.

Fluorescence lifetime imaging microscopy and fluorescence resonance energy transfer from cyan to yellow fluorescent protein validates a novel method to cluster proteins on solid surfaces

A novel method to distribute proteins on solid surfaces is proposed. Proteins microencapsulated in the water pool of reverse micelles were used to coat a solid surface with well-individualized round spots of 1 to 3 microm in diameter. The number of spots per unit area can be increased through the concentration of reverse micelles, and networks of spots were obtained at high concentrations of large reverse micelles. Moreover, depending on the pool size of the water reverse micelles, proteins can be deposited far from each other or in close proximity within the range of 50 to 70 A. This proximity obtained with small reverse micelles was proved through fluorescence lifetime imaging microscopy and fluorescence resonance energy transfer (FLIM-FRET) measurements for the most relevant FRET pair in cell biology studies, the cyan and yellow fluorescent proteins. This novel procedure has several advantages and reveals the potential for study of protein-protein interactions on solid surfaces and for developing novel biomaterials and molecular devices based on biorecognition elements.

Effects of confinement and crowding on folding of model proteins

We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding scenarios, but both effects are not dramatic. The influence of crowding on folding are studied by placing several identical proteins within the sphere, denaturing them, and then by monitoring refolding. If the interactions between the proteins are dominated by the excluded volume effects, the net folding times are essentially like for a single protein. An introduction of inter-proteinic attractive contacts hinders folding when the strength of the attraction exceeds about a half of the value of the strength of the single protein contacts. The bigger the strength of the attraction, the more likely is the occurrence of aggregation and misfolding.

Reverse micelles: inert nano-reactors or physico-chemically active guides of the capped reactions

Reverse micelles present self-assembled multi-molecular entities formed within specific compositional ranges of water-in-oil microemulsions. The structure of a reverse micelle is typically represented as nano-sized droplet of a polar liquid phase, capped by a monolayer of surfactant molecules, and uniformly distributed within a non-polar, oil phase. Although their role in serving as primitive membranes for encapsulation of primordial self-replicating chemical cycles that anticipated the very origins of life has been proposed, their first application for 'parent(hesis)ing' chemical reactions with an aim to produce 'templated' 2D arrays of nanoparticles dates back to only 25 years ago. Reverse micelles have since then been depicted as passive nano-reactors that via their shapes template the growing crystalline nuclei into narrowly dispersed or even perfectly uniform nano-sized particles. Despite this, numerous examples can be supported, where from deviations from the simple unilateral correlations between size and shape distribution of reverse micelles and the particles formed within may be reasonably implied. A rather richer, dynamical role of reverse micelles, with potential significance in the research and design of complex, self-assembly synthesis pathways, as well as possible adoption of their application as an aspect of biomimetic approach, is suggested herein.

Structure modifications of AOT reverse micelles due to protein incorporation

Structural modifications of AOT/water/isooctane reverse micelles due to incorporation of proteins were studied at various water contents and protein concentrations, using small-angle X-ray scattering (SAXS) experiments under static conditions, rheometry analysis, and SR-SAXS experiments under induced shear flow. Two proteins, lysozyme (pI 11.1, Mw 14,300 Da) and BSA (pI 4.3, Mw 66,700 Da), were chosen as models. SAXS analysis of protein-containing reverse micelles at low water content detected minima in the average micelle size versus protein concentration curve, for both proteins, below and above their isoelectric point. This minimum was attributed to changes in the size distribution of the reverse micelles. SAXS measurements of reverse micelles at high water content have shown them to have a cylindrical form. Incorporation of lysozyme at pH 7 into the cylindrical micelles induced a shape transition to spherical micelles, which was associated with a decreased viscosity. SR-SAXS measurements under induced shear flow and dynamic conditions revealed alignment of the cylindrical micelles in the flow direction. The anisotropy parameter, a measure of the degree of the spatial order, was found to increase with increasing shear rate and to decrease with increasing lysozyme concentration.