L-glutamate Receptor In Paramecium

Bernal-Martínez, Juan; Ortega‐Soto, Arturo

doi:10.1063/1.1811853

Cited by 2 publications

(2 citation statements)

References 13 publications

(23 reference statements)

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“…The computation of the minimum-distance distribution function was implemented as the module of our MDAnalysis software suite and is available at . A solvent molecule was considered to belong to the bulk domain if all of its atoms were farther from the protein than 8 Å.…”

Section: Methodsmentioning

confidence: 99%

Molecular Interpretation of Preferential Interactions in Protein Solvation: A Solvent-Shell Perspective by Means of Minimum-Distance Distribution Functions

Martı́nez

Shimizu

2017

J. Chem. Theory Comput.

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Preferential solvation is a fundamental parameter for the interpretation of solubility and solute structural stability. The molecular basis for solute-solvent interactions can be obtained through distribution functions, and the thermodynamic connection to experimental data depends on the computation of distribution integrals, specifically Kirkwood-Buff integrals for the determination of preferential interactions. Standard radial distribution functions, however, are not convenient for the study of the solvation of complex, nonspherical solutes, as proteins. Here we show that minimum-distance distribution functions can be used to compute KB integrals while at the same time providing an insightful view of solute-solvent interactions at the molecular level. We compute preferential solvation parameters for Ribonuclease T1 in aqueous solutions of urea and trimethylamine N-oxide (TMAO) and show that, while macroscopic solvation shows that urea is preferentially bound to the protein surface and TMAO is preferentially excluded, both display specific density augmentations at the protein surface in dilute solutions. Therefore, direct protein-osmolyte interactions can play a role in the stability and activity of the protein even for preferentially hydrated systems. The generality of the distribution function and its natural connection to thermodynamic data suggest that it will be useful in general for the study of solvation in mixtures of structurally complex solutes and solvents.

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Section: Methodsmentioning

confidence: 99%

Molecular Interpretation of Preferential Interactions in Protein Solvation: A Solvent-Shell Perspective by Means of Minimum-Distance Distribution Functions

Martı́nez

Shimizu

2017

J. Chem. Theory Comput.

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“…Lectins at the cytostomal cavity function in prey recognition by interacting with carbohydrates on the surface of algal cells as in Oxyrrhis marina (Roberts et al., ). AMPA/KA receptors allow an influx of cations when AMPA is bound (Bernal‐Martinez & Ortega‐Soto, ). The depolarization that results induces transient depolarizations via Na v as described above.…”

Section: Developing a Working Model Of Sensory Mechanisms Of Favellamentioning

confidence: 99%

Connecting alveolate cell biology with trophic ecology in the marine plankton using the ciliateFavellaas a model

Echevarria

Wolfe

Strom

et al. 2014

FEMS Microbiol Ecol

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Planktonic alveolates (ciliates and dinoflagellates), key trophic links in marine planktonic communities, exhibit complex behaviors that are underappreciated by microbiologists and ecologists. Furthermore, the physiological mechanisms underlying these behaviors are still poorly understood except in a few freshwater model ciliates, which are significantly different in cell structure and behavior than marine planktonic species. Here, we argue for an interdisciplinary research approach to connect physiological mechanisms with population-level outcomes of behaviors. Presenting the tintinnid ciliate Favella as a model alveolate, we review its population ecology, behavior, and cellular/molecular biology in the context of sensory biology and synthesize past research and current findings to construct a conceptual model describing the sensory biology of Favella. We discuss how emerging genomic information and new technical methods for integrating research across different levels of biological organization are paving the way for rapid advance. These research approaches will yield a deeper understanding of the role that planktonic alveolates may play in biogeochemical cycles, and how they may respond to future ocean conditions.

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L-glutamate Receptor In Paramecium

Cited by 2 publications

References 13 publications

Molecular Interpretation of Preferential Interactions in Protein Solvation: A Solvent-Shell Perspective by Means of Minimum-Distance Distribution Functions

Molecular Interpretation of Preferential Interactions in Protein Solvation: A Solvent-Shell Perspective by Means of Minimum-Distance Distribution Functions

Connecting alveolate cell biology with trophic ecology in the marine plankton using the ciliateFavellaas a model

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