Dataset Information

Non-specific Interactions Between Macromolecular Solutes in Concentrated Solution: Physico-Chemical Manifestations and Biochemical Consequences.

ABSTRACT: A general thermodynamic formulation of the effect of hard and soft non-specific intermolecular interactions upon reaction equilibria is summarized. A highly simplified quantitative model for non-specific intermolecular interaction is introduced. This model is used to illustrate how the magnitudes of attractive and repulsive components of the overall intermolecular interaction, and the balance between them, influence the concentration-dependent properties of a highly concentrated solution of a single macromolecular solute. The properties calculated using the results of computer simulation and an approximate analytical model are found to agree qualitatively with the results of experimental measurements on protein solutions over a broad range of concentration.

SUBMITTER: Hoppe T

PROVIDER: S-EPMC6424865 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Non-specific Interactions Between Macromolecular Solutes in Concentrated Solution: Physico-Chemical Manifestations and Biochemical Consequences.

Hoppe Travis T Minton Allen P AP

Frontiers in molecular biosciences 20190313

A general thermodynamic formulation of the effect of hard and soft non-specific intermolecular interactions upon reaction equilibria is summarized. A highly simplified quantitative model for non-specific intermolecular interaction is introduced. This model is used to illustrate how the magnitudes of attractive and repulsive components of the overall intermolecular interaction, and the balance between them, influence the concentration-dependent properties of a highly concentrated solution of a si ...[more]

PMID: 30918892

Similar Datasets

Project description:Hydrodynamic interactions exert a critical effect on the dynamics of macromolecules. As the concentration of macromolecules increases, by analogy to the behavior of semidilute polymer solutions or the flow in porous media, one might expect hydrodynamic screening to occur. Hydrodynamic screening would have implications both for the understanding of macromolecular dynamics as well as practical implications for the simulation of concentrated macromolecular solutions, e.g., in cells. Stokesian dynamics (SD) is one of the most accurate methods for simulating the motions of N particles suspended in a viscous fluid at low Reynolds number, in that it considers both far-field and near-field hydrodynamic interactions. This algorithm traditionally involves an O(N(3)) operation to compute Brownian forces at each time step, although asymptotically faster but more complex SD methods are now available. Motivated by the idea of hydrodynamic screening, the far-field part of the hydrodynamic matrix in SD may be approximated by a diagonal matrix, which is equivalent to assuming that long range hydrodynamic interactions are completely screened. This approximation allows sparse matrix methods to be used, which can reduce the apparent computational scaling to O(N). Previously there were several simulation studies using this approximation for monodisperse suspensions. Here, we employ newly designed preconditioned iterative methods for both the computation of Brownian forces and the solution of linear systems, and consider the validity of this approximation in polydisperse suspensions. We evaluate the accuracy of the diagonal approximation method using an intracellular-like suspension. The diffusivities of particles obtained with this approximation are close to those with the original method. However, this approximation underestimates intermolecular correlated motions, which is a trade-off between accuracy and computing efficiency. The new method makes it possible to perform large-scale and long-time simulation with an approximate accounting of hydrodynamic interactions.

Project description:The interplay between environmental and genetic factors conditions the fruit ripening program in plants. Transcriptome analysis of grapevine fruits can help understanding these interactions to consciously cope with conditions leading to detrimental effects for viticultural purposes. However, considering the grapevine characteristic ripening asynchrony, which can be intensified by contrasting conditions, accurate grape sampling may be essential for molecular comparisons. In this study, berry density sorting according to floatability in NaCl solutions was assessed as a grape ripening staging strategy. Total sugar content was more correlated with berry density than with other non-invasive ripening parameters. The transcriptome was compared between three density classes collected near commercial maturity using grapevine whole-genome NimbleGen microarrays. Expression profiles clearly related with ripening progression were detected in a density series simultaneously collected from a vineyard of Albariño. By contrast, considerable differences were detected when the same density series was sampled on two different dates from the same vineyard of Tempranillo. Functional analysis indicated that environmental differences between both sampling moments determined most of these expression differences. Ripening degree-dependent responses to the environment were also detected. Finally, the effect of the sorting procedures on the grape transcriptome showed negligible when it was directly tested. Altogether, these findings evidence the convenience of homogenizing the developmental stage and the sampling time conditions for transcriptome comparisons. Berry density sorting proved useful to this end, although this method could be limited when the berry sugar concentration is not determined by the ripening developmental program. The potential berry transcriptional response to the high concentrated salt solutions used for berry density-sorting may involve a concern on the suitability of this method for transcriptomic studies. This possibility was directly tested by comparing the expression of berries immersed in a highly concentrated NaCl solution (170 g•L-1) during a relatively long time lapse (1 h) with that in berries kept at room air. This experiment was carried out using Tempranillo grapes at mid-véraison to standardize the ripening state by selecting berries with the same proportion of coloured skin surface (50%, corresponding to TSS of 9.9 ±0.3 ºBrix). Berries grown under watering (W) and no-watering (NW) conditions were analysed to test for possible irrigation-NaCl solution interactions affecting berry gene expression. No significant DEG was identified when the effect of the NaCl solution was analysed separately for berries collected from W or NW blocks (≥2-fold change and B-H adjusted P≤0.05 in 2-class limma). When W and NW samples were used together to analyse the effect of the NaCl immersion irrespectively of the irrigation treatment, 15 genes were detected with a B-H adjusted P≤0.05 and only 13 of these showed ≥2-fold change, confirming the slight effect. In summary, the effect of the NaCl immersion on the berry transcriptome is negligible and does not seem to interact with the transcriptomic response to other environmental cues.

Dataset Information

Non-specific Interactions Between Macromolecular Solutes in Concentrated Solution: Physico-Chemical Manifestations and Biochemical Consequences.

Publications

Non-specific Interactions Between Macromolecular Solutes in Concentrated Solution: Physico-Chemical Manifestations and Biochemical Consequences.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure