Evidence of coexistence of change of caged dynamics at Tg and the dynamic transition at Td in solvated proteins

Mossbauer spectroscopy and neutron scattering measurements on proteins embedded in solvents including water and aqueous mixtures have emphasized the observation of the distinctive temperature dependence of the atomic mean square displacements, , commonly referred to as the dynamic transition at some temperature Td. At low temperatures, increases slowly, but it assume stronger temperature dependence after crossing Td, which depends on the time/frequency resolution of the spectrometer. Various authors have made connection of the dynamics of solvated proteins including the dynamic transition to that of glass-forming substances. Notwithstanding, no connection is made to the similar change of temperature dependence of obtained by quasielastic neutron scattering when crossing the glass transition temperature Tg, generally observed in inorganic, organic and polymeric glass-formers. Evidences are presented to show that such change of the temperature dependence of from neutron scattering at Tg is present in hydrated or solvated proteins, as well as in the solvents used unsurprisingly since the latter is just another organic glass-formers. The obtained by neutron scattering at not so low temperatures has contributions from the dissipation of molecules while caged by the anharmonic intermolecular potential at times before dissolution of cages by the onset of the Johari-Goldstein beta-relaxation. The universal change of at Tg of glass-formers had been rationalized by sensitivity to change in volume and entropy of the beta-relaxation, which is passed onto the dissipation of the caged molecules and its contribution to . The same rationalization applies to hydrated and solvated proteins for the observed change of at Tg.Comment: 28 pages, 10 figures, 1 Tabl

Time-Dependent Gene Network Modelling by Sequential Monte Carlo

Most existing methods used for gene regulatory network modeling are dedicated to inference of steady state networks, which are prevalent over all time instants. However, gene interactions evolve over time. Information about the gene interactions in different stages of the life cycle of a cell or an organism is of high importance for biology. In the statistical graphical models literature, one can find a number of methods for studying steady-state network structures while the study of time varying networks is rather recent. A sequential Monte Carlo method, namely particle filtering (PF), provides a powerful tool for dynamic time series analysis. In this work, the PF technique is proposed for dynamic network inference and its potentials in time varying gene expression data tracking are demonstrated. The data used for validation are synthetic time series data available from the DREAM4 challenge, generated from known network topologies and obtained from transcriptional regulatory networks of S. cerevisiae. We model the gene interactions over the course of time with multivariate linear regressions where the parameters of the regressive process are changing over time

Evidence of Coexistence of Change of Caged Dynamics at Tg and the Dynamic Transition at Td in Solvated Proteins

Mossbauer spectroscopy and neutron scattering measurements on proteins embedded in solvents' including water and aqueous mixtures have emphasized the observation of the distinctive temperature dependence of the atomic mean square displacements, , commonly referred to as the dynamic transition at some temperature T(d). At low temperatures, increases slowly, but it assumes,stronger temperature dependence after crossing T(d), which depends, on the time/frequency resolution of the spectrometer. Various authors, have made connection of the dynamics of solvated proteins, including the dynamic transition to that of glass-forming substances. Notwithstanding, no connection is made to the similar change of temperature dependence of obtained by quasielastic neutron scattering when crossing the glass transition temperature T(g), senerally observed in inorganic, organic, and polymeric glass-formers. Evidences are presented here to show that such a change of the temperature dependence of from neutron scattering at T(g) is present in hydrated or solvated proteins, as well as in the solvent used, unsurprisingly since the latter is just another organic glass-former. If unaware of the existence of such a crossover of at T(g), and if present, it can be mistaken as the dynamic transition at T(d) with the ill consequences of underestimating T(d) by the lower value T(g) and confusing the identification of the origin of the dynamic transition. The obtained by neutron scattering at not so low temperatures has contributions from the dissipation of molecules while caged by the anharmonic intermolecular potential at times before dissolution of cages by the onset of the Johari-Goldstein beta-relaxation or of the merged alpha-beta relaxation. The universal change of at T(g) of glass-formers, independent of the spectrometer resolution, had been rationalized by sensitivity to change in volume and entropy of the dissipation of the caged molecules and its contribution to . The same rationalization applies to hydrated and solvated proteins for the observed change of at T(g)

The role of primitive relaxation in the dynamics of aqueous mixtures, nano-confined water and hydrated proteins RID A-8503-2012

The relaxation scenario in aqueous systems, such as mixtures of water with hydrophilic solutes, nano-confined water and hydrated biomolecules, has been shown to exhibit general features, in spite of the huge differences in structure, chemical composition and complexity. Dynamics, in all these systems, invariably shows at least two relaxations: (i) a slower process, related to cooperative and structural motions of water and solute molecules (in the case of mixtures) or related to interfacial processes in the case of confined water and (ii) a faster process, with non-cooperative character originating from water. The latter has properties including timescale and temperature dependence similar or related in all the aqueous systems. This water-specific relaxation can be identified as the primitive relaxation, or the Johari-Goldstein beta-relaxation. The primitive process is the precursor of the many-body relaxation process which increases in length-scale with time until the terminal a-relaxation is reached. Using new experimental data (at atmospheric and high pressure) along with a revision of most of the recent literature on the dynamics of confined water and aqueous mixtures, we show that the two abovementioned relaxation processes are inter-related as evidenced by correlations in their properties. For instance, both relaxation time and dielectric strength of the water-specific relaxation exhibit a crossover from a stronger to a weaker dependence with decreasing T, at the temperature where the slow process attains a very long timescale (>1 ks) and becomes structurally arrested, exactly analogous to that found for beta-relaxation in van der Waals liquids. Moreover, the primitive relaxation of water is shown to play a pivotal role in determining the dynamics of hydrated biomolecules in general, including the "dynamic transition" observed by neutron scattering and Mossbauer spectroscopy. We show that the primitive relaxation of the solvent is responsible for the dynamic transition, even in the case that the solvent is not pure water or an aqueous mixture. (C) 2010 Elsevier B.V. All rights reserved

Resolving the ambiguity of the dynamics of water and clarifying its role in hydrated proteins

The dynamics of water in aqueous mixtures with various hydrophilic solutes can be probed over practically unrestricted temperature and frequency ranges, in contrast to bulk water where crystallization preempts such study. The characteristics of the dynamics of water and their trends observed in aqueous mixtures on varying the solutes and concentration of water, in conjunction with that of water confined in spaces of nanometer size, lead us to infer the fundamental traits of the dynamics of water. These include the universal secondary relaxation, here called the nu-relaxation, the low degree of intermolecular coupling/cooperativity, and the 'strong' character of the structural primary relaxation. The dynamics of hydration water in hydrated proteins at sufficiently high hydration levels are similar in every respect to that in aqueous mixtures. In particular, the nu-relaxation of hydration water has a relaxation time nearly the same as that of the nu-relaxation of aqueous mixtures above and below the glass transition temperature. This can explain the dynamics transition observed by Mossbauer spectroscopy and neutron scattering. The fact that it is coupled to atomic motions of the hydrated protein, like similar situation in aqueous mixtures, explains why the dynamic transition is observed by neutron scattering at the same temperature whether the hydration water is H(2)O or D(2)O. The possibility that the nu-relaxation of the solvent is instrumental for biological function of hydrated biomolecules is suggested by the comparable temperature dependences of the ligand escape rate and the reciprocal of the nu-relaxation time

The role of primitive relaxation in the dynamics of aqueous mixtures, nano-confined water and hydrated proteins

The relaxation scenario in aqueous systems, such as mixtures of water with hydrophilic solutes, nano-confined water and hydrated biomolecules, has been shown to exhibit general features, in spite of the huge differences in structure, chemical composition and complexity. Dynamics, in all these systems, invariably shows at least two relaxations: (i) a slower process, related to cooperative and structural motions of water and solute molecules (in the case of mixtures) or related to interfacial processes in the case of confined water and (ii) a faster process, with non-cooperative character originating from water. The latter has properties including timescale and temperature dependence similar or related in all the aqueous systems. This water-specific relaxation can be identified as the primitive relaxation, or the Johari-Goldstein beta-relaxation. The primitive process is the precursor of the many-body relaxation process which increases in length-scale with time until the terminal a-relaxation is reached. Using new experimental data (at atmospheric and high pressure) along with a revision of most of the recent literature on the dynamics of confined water and aqueous mixtures, we show that the two abovementioned relaxation processes are inter-related as evidenced by correlations in their properties. For instance, both relaxation time and dielectric strength of the water-specific relaxation exhibit a crossover from a stronger to a weaker dependence with decreasing T, at the temperature where the slow process attains a very long timescale (>1 ks) and becomes structurally arrested, exactly analogous to that found for beta-relaxation in van der Waals liquids. Moreover, the primitive relaxation of water is shown to play a pivotal role in determining the dynamics of hydrated biomolecules in general, including the "dynamic transition" observed by neutron scattering and Mossbauer spectroscopy. We show that the primitive relaxation of the solvent is responsible for the dynamic transition, even in the case that the solvent is not pure water or an aqueous mixture. (C) 2010 Elsevier B.V. All rights reserved

The JG β-relaxation in water and impact on the dynamics of aqueous mixtures and hydrated biomolecules

Although by now the glass transition temperature of uncrystallized bulk water is generally accepted to manifest at temperature Tg near 136 K, not much known are the spectral dispersion of the structural α-relaxation and the temperature dependence of its relaxation time τα,bulk(T). Whether bulk water has the supposedly ubiquitous Johari-Goldstein (JG) β-relaxation is a question that has not been answered. By studying the structural α-relaxation over a wide range of temperatures in several aqueous mixtures without crystallization and with glass transition temperatures Tg close to 136 K, we deduce the properties of the α-relaxation and the temperature dependence of τα,bulk(T) of bulk water. The frequency dispersion of the α-relaxation is narrow, indicating that it is weakly cooperative. A single Vogel-Fulcher-Tammann (VFT) temperature dependence can describe the data of τα,bulk(T) at low temperatures as well as at high temperatures from neutron scattering and GHz-THz dielectric relaxation, and hence, there is no fragile to strong transition. The Tg-scaled VFT temperature dependence of τα,bulk(T) has a small fragility index m less than 44, indicating that water is a "strong" glass-former. The existence of the JG β-relaxation in bulk water is supported by its equivalent relaxation observed in water confined in spaces with lengths of nanometer scale and having Arrhenius T-dependence of its relaxation times τconf(T). The equivalence is justified by the drastic reduction of cooperativity of the α-relaxation in nanoconfinement and rendering it to become the JG β-relaxation. Thus, the τconf(T) from experiments can be taken as τβ,bulk(T), the JG β-relaxation time of bulk water. The ratio τα,bulk(Tg)/τβ,bulk(Tg) is smaller than most glass-formers, and it corresponds to the Kohlrausch α-correlation function, exp[-(t/τα,bulk)1-n], having (1-n) = 0.90. The dielectric data of many aqueous mixtures and hydrated biomolecules with Tg higher than that of water show the presence of a secondary ν-relaxation from the water component. The ν-relaxation is strongly connected to the α-relaxation in properties, and hence, it belongs to the special class of secondary relaxations in glass-forming systems. Typically, its relaxation time τν(T) is longer than τβ,bulk(T), but τν(T) becomes about the same as τβ,bulk(T) at sufficiently high water content. However, τν(T) does not become shorter than τβ,bulk(T). Thus, τβ,bulk(T) is the lower bound of τν(T) for all aqueous mixtures and hydrated biomolecules. Moreover, it is τβ,bulk(T) but not τα(T) that is responsible for the dynamic transition of hydrated globular proteins