Mapping the Intramolecular Vibrational Energy Flow in Proteins Reveals Functionally Important Residues

Unveiling the mechanisms of energy relaxation in biomolecules is key to our understanding of protein stability, allostery, intramolecular signaling, and long-lasting quantum coherence phenomena at ambient temperatures. Yet, the relationship between the pathways of energy transfer and the functional role of the residues involved remains largely unknown. Here, we develop a simulation method of mapping out residues that are highly efficient in relaxing an initially localized excess vibrational energy and perform site-directed mutagenesis functional assays to assess the relevance of these residues to protein function. We use the ligand binding domains of thyroid hormone receptor (TR) subtypes as a test case and find that conserved arginines, which are critical to TR transactivation function, are the most effective heat diffusers across the protein structure. These results suggest a hitherto unsuspected connection between a residue`s ability to mediate intramolecular vibrational energy redistribution and its functional relevance.

On the Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors

The ligand binding domain (LBD) of nuclear hormone receptors adopts a very compact, mostly alpha-helical structure that binds specific ligands with very high affinity. We use circular dichroism spectroscopy and high-temperature molecular dynamics Simulations to investigate unfolding of the LBDs of thyroid hormone receptors (TRs). A molecular description of the denaturation mechanisms is obtained by molecular dynamics Simulations of the TR alpha and TR beta LBDs in the absence and in the presence of the natural ligand Triac. The Simulations Show that the thermal unfolding of the LBD starts with the loss of native contacts and secondary Structure elements, while the Structure remains essentially compact, resembling a molten globule state. This differs From most protein denaturation simulations reported to date and suggests that the folding mechanism may start with the hydrophobic collapse of the TR LBDs. Our results reveal that the stabilities of the LBDs of the TR alpha and TR beta Subtypes are affected to different degrees by the binding of the isoform selective ligand Triac and that ligand binding confers protection against thermal denaturation and unfolding in a subtype specific manner. Our Simulations indicate two mechanisms by which the ligand stabilizes the LBD: (1) by enhancing the interactions between H8 and H 11, and the interaction of the region between H I and the Omega-loop with the core of the LBD, and (2) by shielding the hydrophobic H6 from hydration.

Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations

Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus (RmLamR) determined at 1.95 angstrom resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis, for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting beta-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of charge-charge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases.

Interactions between Bacteriophage DNA and Cationic Biomimetic Particles

The interaction between giant bacteriophage DNA and cationic biomimetic particles was characterized from sizing by dynamic light-scattering, zeta-potential analysis, turbidimetry, determination of colloid stability, visualization from atomic force microscopy (AFM), and determination of cytotoxicity against E. coli from colony forming unities counting. First, polystyrene sulfate (PSS) particles with different sizes were covered by a dioctadecyldimethylammonium bromide (DODAB) bilayer yielding the so-called cationic biomimetic particles (PSS/DODAB). These cationic particles are highly organized, present a narrow size distribution and were obtained over a range of particle sizes. Thereafter, upon adding lambda, T5 or T2-DNA to PSS/DODAB particles, supramolecular assemblies PSS/DODAB/DNA were obtained and characterized over a range of DNA concentrations and particle sizes (80-700 nm). Over the low DNA concentration range, PSS/DODAB/DNA assemblies were cationic, colloidally stable with moderate polydispersity and highly cytotoxic against E. coli. From DNA concentration corresponding to charge neutralization, neutral or anionic supramolecular assemblies PSS/DODAB/DNA exhibited low colloid stability, high polydispersity and moderate cytotoxicity. Some nucleosome mimetic assemblies were observed by AFM at charge neutralization (zeta-potential equal to zero).

The Catalytic Acid in the Dephosphorylation of the Cdk2-pTpY/CycA Protein Complex by Cdc25B Phosphatase

The development of anticancer therapeutics that target Cdc25 phosphatases is now an active area of research. A complete understanding of the Cdc25 catalytic mechanism would certainly allow a more rational inhibitor design. However, the identity of the catalytic acid used by Cdc25 has been debated and not established unambiguously. Results of molecular dynamics simulations with a calibrated hybrid potential for the first reaction step catalyzed by Cdc25B in complex with its natural substrate, the Cdk2-pTpY/CycA protein complex, are presented here. The calculated reaction free-energy profiles are in very good agreement with experimental measurements and are used to discern between different proposals for the general acid. In addition, the simulations give useful insight on interactions that can be explored for the design of inhibitors specific to Cdc25.

Gas-Phase Nucleophilic and Elimination Reactions in Simple Alkyl Nitrates

There has been increasing interest in the gas-phase reactivity of alkyl nitrates because of their well-known applications as explosives and because of then role in atmospheric and in marine processes This manuscript describes an experimental study by FT-ICR techniques of the gas-phase reactions of OH(-) and F(-) with methyl and ethyl Innate For methyl nitrate, the main reaction channel is found to be an elimination process promoted by abstraction of an a proton from the methyl group. Nucleophilic displacement of nitrate anion through an S(N)2 process at the carbon center Is also found to he an important reaction channel with methyl nitrate In ethyl nitrate, Ruination of NO(3)(-) is greatly enhanced and this is attributed to the ease of an E2-type elimination process promoted by proton abstraction at the beta position of the ethyl group. Theoretical calculations at the MP2/6-311+G(3df,2p)//MP2/6-31+G(d) level of theory ale consistent with the relative importance of the reaction channels and suggest that these reactions proceed through a double well potential The calculations also predict that nucleophilic attack by OH(-) at the nitrogen center (Sn2@N) is energetically the rueful ad pathway but experiments with (18)OH(-) showed no evidence for this channel. Single-point calculations reveal a strong preference for approach to the emboli center and may explain the lack of reactivity at the nitrogen center. Calculations were also carried out or NH(2)(-) and SH(-) to establish the reactivity pattern to provide a better understanding of environmentally relevant nitrate esters.

Role of Polyelectrolyte for Layer-by-Layer Compact TiO(2) Films in Efficiency Enhanced Dye-Sensitized Solar Cells

Efficient compact TiO(2) films using different polyeleetrolytes are prepared by the layer-by-layer technique (LbL) and applied as an effective contact and blocking film in dye-sensitized solar cells (DSCs). The polyanion thermal stability plays a major role on the compact layers, which decreases back electron transfer processes and current losses at the FTO/TiO(2) interface. FESEM images show that polyelectrolytes such is sodium sullonated polystyrene (PSS) and sulfonated lignin (SE), in comparison to poly(acrylic acid) (FAA), ensure an adequate morphology for the LbL TiO(2) layer deposited before the mesoporous film, even triter the sintering step at 450 degrees C. The so treated photoanode in DSCs leads to a 30% improvement On the overall conversion efficiency. Electrochemical impedance spectroscopy (EIS) is employed to ascertain the role of die compact films with such polyelectrolytes. The significant increase in V(oc) of the solar cells with adequate polyelectrolytes in the LbL TiO(2) films shows their pivotal role in decreasing the electron recombination at the FTO surface and enhancing the electrical contact of FTO with the mesoporous TiO(2) layer.

Ether-Bond-Containing Ionic Liquids and the Relevance of the Ether Bond Position to Transport Properties

The ionic liquids (ILs) 1-ethoxyethyl-2,3-dimethylimidazolium bis(trifluoromethanesulfonyl)imide, [EtO-(CH(2))(2)MMI][Tf(2)N], and N-(ethoxyethyl)-N-methylmorpholinium bis(trifluoromethanesulfonyl)imide, [EtO(CH(2))(2)MMor][Tf(2)N] were synthesized, and relevant properties, such as thermal stability, density, viscosity, electrochemical behavior, ionic conductivity, and self-diffusion coefficients for both ionic species, were measured and compared with those of their alkyl counterparts, 1-n-butyl-2,3-dimethylimidazolium bis(trifluoromethanesulfonyl)imide, [BMMI][Tf(2)N], and N-n-butyl-N-methylpiperidinium bis(trifluoromethanesulfonyl)imide,[BMP][Tf(2)N] and N-n-butyl-N-methylmorpholinium bis(trilfuoromethanesulfonyl)imide [BMMor][Tf(2)N][. This comparison was done to evaluate the effects caused by the presence of the ether bond in either the side chain or in the organic cation ring. The salt, LiTf(2)N, was added to the systems to estimate IL behavior with regard to lithium cation transport. Pure [EtO(CH(2))(2)MMI][Tf(2)N] and their LiTf(2)N solutions showed low viscosity and the highest conductivity among the ILs studied. The H(R) (AC conductivity/NMR calculated conductivity ratio) values showed that, after addition of LiTf(2)N, ILs containing the ether bond seemed to have a greater number of charged species. Structural reasons could explain these high observed HR values for [EtO(CH(2))(2)MMor][Tf(2)N].

Effect of SO(2) on the Transport Properties of an Imidazolium Ionic Liquid and Its Lithium Solution

Transport coefficients have been measured as a function of the concentration of sulfur dioxide, SO(2), dissolved in 1-butyl-2,3-dimethylimidazolium bis(trifluoromethylsulfonyl)-imide, [BMMI][Tf(2)N], as well as in its lithium salt solution, Li[Tf(2)N]. The SO(2) reduces viscosity and density and increases conductivity and diffusion coefficients in both the neat [BMMI] [Tf(2)N] and the [BMMI][Tf(2)N]-Li[Tf(2)N] solution. The conductivity enhancement is not assigned to a simple viscosity effect; the weakening of ionic interactions upon SO(2) addition also plays a role. Microscopic details of the SO(2) effect were unraveled using Raman spectroscopy and molecular dynamics (MD) simulations. The Raman spectra suggest that the Li(+)-[Tf(2)N] interaction is barely affected by SO(2), and the SO(2)-[Tf(2)N] interaction is weaker than previously observed in an investigation of an ionic liquid containing the bromide anion. Transport coefficients calculated by MD simulations show the same trend as the experimental data with respect to SO(2) content. The MD simulations provide structural information on SO(2) molecules around [Tf(2)N], in particular the interaction of the sulfur atom of SO(2) with oxygen and fluorine atoms of the anion. The SO(2)-[BMMI] interaction is also important because the [BMMI] cations with above-average mobility have a larger number of nearest-neighbor SO(2) molecules.

DMSO-Induced Denaturation of Hen Egg White Lysozyme

We report on the size, shape, structure, and interactions of lysozyme in the ternary system lysozyme/DMSO/water at low protein concentrations. Three structural regimes have been identified, which we term the ""folded"" (0 < phi(DMSO) < 0.7), ""unfolded"" (0.7 <= phi(DMSO) < 0.9), and ""partially collapsed"" (0.9 <= phi(DMSO) < 1.0) regime. Lysozyme resides in a folded conformation with an average radius of gyration of 1.3 +/- 0.1 nm for phi(DMSO) < 0.7 and unfolds (average R(g) of 2.4 +/- 0.1 nm) above phi(DMSO) > 0.7. This drastic change in the protein`s size coincides with a loss of the characteristic tertiary structure. It is preceded by a compaction of the local environment of the tryptophan residues and accompanied by a large increase in the protein`s overall flexibility. In terms of secondary structure, there is a gradual loss of alpha-helix and concomitant increase of beta-sheet structural elements toward phi(DMSO) = 0.7, while an increase in phi(DMSO) at even higher DMSO volume fractions reduces the presence of both a-helix and beta-sheet secondary structural elements. Protein-protein interactions remain overall repulsive for all values of phi(DMSO) An attempt is made to relate these structural changes to the three most important physical mechanisms that underlie them: the DMSO/water microstructure is strongly dependent on the DMSO volume fraction, DMSO acts as a strong H-bond acceptor, and DMSO is a bad solvent for the protein backbone and a number of relatively polar side groups, but a good solvent for relatively apolar side groups, such as tryptophan.

Excited Electronic States, Transition Probabilities, and Radiative Lifetimes of CAs: A Theoretical Contribution and Challenge to Experimentalists

High-level CASSCF/MRCI calculations with a quintuple-zeta quality basis set are reported by characterizing for the first time a manifold of electronic states of the CAs radical yet to be investigated experimentally. Along with the potential energy curves and the associated spectroscopic constants, the dipole moment functions for selected electronic states as well as the transition dipole moment functions for the most relevant electronic transitions are also presented. Estimates of radiative transition probabilities and lifetimes complement this investigation, which also assesses the effect of spin-orbit interaction on the A (2)Pi state. Whenever pertinent, comparisons of similarities and differences with the isovalent CN and CP radicals are made.

Room Temperature Ionic Liquid-Lithium Salt Mixtures: Optical Kerr Effect Dynamical Measurements

The addition of lithium salts to ionic liquids causes an increase in viscosity and a decrease in ionic mobility that hinders their possible application as an alternative solvent in lithium ion batteries. Optically heterodyne-detected optical Kerr effect spectroscopy was used to study the change in dynamics, principally orientational relaxation, caused by the addition of lithium bis(trifluoromethylsulfonyl)imide to the ionic liquid 1-buty1-3-methylimidazolium bis(trifluoromethylsulfonyl)imide. Over the time scales studied (1 ps-16 ns) for the pure ionic liquid, two temperature-independent power laws were observed: the intermediate power law (1 ps to similar to 1 ns), followed by the von Schweidler power law. The von Schweidler power law is followed by the final complete exponential relaxation, which is highly sensitive to temperature. The lithium salt concentration, however, was found to affect both power laws, and a discontinuity could be found in the trend observed for the intermediate power law when the concentration (mole fraction) of lithium salt is close to chi(LiTf(2)N) = 0.2. A mode coupling theory (MCT) schematic model was also used to fit the data for both the pure ionic liquid and the different salt concentration mixtures. It was found that dynamics in both types of liquids are described very well by MCT.

Unraveling Dynamical Heterogeneity in the Ionic Liquid 1-Butyl-3-methylimidazolium Chloride

Heterogeneous dynamics within a time range of nanoseconds was investigated by molecular dynamics (MD) simulations of 1 -butyl-3-methylimidazolium chloride ([bmim]Cl). After identifying groups of fast and slow ions, it was shown that the separation between the location of the center of mass and the center of charge of cations, d(CMCC), is a signature of such difference in ionic mobility. The distance d(CMCC) can be used as a signature because it relaxes in the time window of the dynamical heterogeneity. The relationship between the parameter dcmcc and conformations of the side alkyl chain in [bmim] is discussed. Since the relatively slow relaxation of dcmcc is a consequence of coexisting polar and nonpolar domains in the bulk, the MD simulations reveal a subtle interplay between structural and dynamical heterogeneity in ionic liquids.

Picosecond Dynamics of the Prototropic Reactions of 7-Hydroxyflavylium Photoacids Anchored at an Anionic Micellar Surface

Three water-insoluble, micelle-anchored flavylium salts, 7-hydroxy-3-octyl-flavylium chloride, 4`-hexyl-7-hydroxyflavylium chloride, and 6-hexyl-7-hydroxy-4-methyl-flavylium chloride, have been employed to probe excited-state prototropic reactions in micellar sodium dodecyl sulfate (SDS). In SDS micelles, the fluorescence decays of these three flavylium salts are tetraexponential functions in the pH range from 1.0 to 4.6 at temperatures from 293 to 318 K. The four components of the decays are assigned to Four kinetically coupled excited species in the micelle: specifically, promptly deprotonable (AH(+)*) and nonpromptly deprotonable (AH(h)(+)*) orientations of the acid in the micelle. the base-proton geminate pair (A*center dot center dot center dot H(+)), and the free conjugate base (A*). The initial prompt deprotonation to form the germinate pair occurs at essentially the same rate (k(d) similar to 6-7 x 10(10) s(-1)) for all three photoacids. Recombination of the germinate pair is similar to 3-fold faster than the rate of proton escape from the pair (k(rec) similar to 3 x 10(10) s(-1) and k(diss) similar to 1 x 10(10) s(-1)), corresponding to an intrinsic recombination efficiency of the pair of similar to 75%. Finally, the reprotonation of the short-lived free A* (200-350 ps, depending oil the photoacid) has two components, only one of which depends oil the proton concentration in the intermicellar aqueous phase. Ultrafast transfer of the proton to water and substantial compartmentalization of the photogenerated proton at the micelle surface Oil the picosecond time scale strongly suggest preferential transfer of the proton to preformed hydrogen-bonded water bridges between the photoacid and the anionic headgroups. This localizes the proton in the vicinity of the excited base much more efficiently than ill bulk water, resulting ill the predominance of geminate re reprotonation at the micelle surface.

Electrostatic and Hydrophobic Interactions Involved in CNT Biofunctionalization with Short ss-DNA

This work is aimed at studying the adsorption mechanism of short chain 20-mer pyrimidinic homoss-DNA (oligodeoxyribonucleotide, ODN: polyC(20) and polyT(20)) onto CNT by reflectometry. To analyze the experimental data, the effective-medium theory using the Bruggemann approximation represents a Suitable optical model to account for the surface properties (roughness, thickness, and optical constants) and the size of the adsorbate. Systematic information about the involved interactions is obtained by changing the physicochemical properties of the system. Hydrophobic and electrostatic interactions are evaluated by comparing the adsorption oil hydrophobic CNT and oil hydrophilic silica and by Modulating the ionic Strength With and without Mg(2+). The ODN adsorption process oil CNT is driven by hydrophobic interactions only when the electrostatic repulsion is Suppressed. The adsorption mode results in ODN molecules in a side-on orientation with the bases (nonpolar region) toward the surface. This unfavorable orientation is partially reverse by adding Mg(2+). On the other hand, the adsorption oil silica is dominated by the strong repulsive electrostatic interaction that is screened at high ionic strength or mediated by Mg(2+). The cation-mediated process induces the interaction of the phosphate backbone (polar region) with the surface, leaving the bases free for hybridization. Although the general adsorption behavior of the pyrimidine bases is the same, polyC(20) presents higher affinity for the CNT Surface due to its acid-base properties.