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Distinct Protein Hydration Water Species Defined by Spatially Resolved Spectra of Intermolecular Vibrations.

ABSTRACT: In this molecular dynamics simulation study, we analyze intermolecular vibrations in the hydration shell of a solvated enyzme, the membrane type 1-matrix metalloproteinase, with high spatial resolution. Our approach allows us to characterize vibrational signatures of the local hydrogen bond network, the translational mobility of water molecules, as well as the molecular entropy, in specific local environments. Our study demonstrates the heterogeneity of water properties within the hydration shell of a complex biomolecule. We define a classification scheme based on the vibrational density of states that allows us to distinguish separate classes of hydration water species and facilitates the description of hydration water properties at distinct hydration sites. The results demonstrate that no single characteristic of the protein surface is sufficient to determine the properties of nearby water. The protein surface geometry, quantified here by the number of protein atoms in the vicinity of a hydration water molecule, as well as the chemical nature of a solvated protein functional group, influences dynamic and thermodynamic properties of solvating water molecules.

SUBMITTER: Pattni V

PROVIDER: S-EPMC5607456 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Distinct Protein Hydration Water Species Defined by Spatially Resolved Spectra of Intermolecular Vibrations.

Pattni Viren V Vasilevskaya Tatiana T Thiel Walter W Heyden Matthias M

The journal of physical chemistry. B 20170711 31

In this molecular dynamics simulation study, we analyze intermolecular vibrations in the hydration shell of a solvated enyzme, the membrane type 1-matrix metalloproteinase, with high spatial resolution. Our approach allows us to characterize vibrational signatures of the local hydrogen bond network, the translational mobility of water molecules, as well as the molecular entropy, in specific local environments. Our study demonstrates the heterogeneity of water properties within the hydration shel ...[more]

PMID: 28636363

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Project description:In mammalian brains, millions to billions of cells form complex interaction networks to enable a wide range of functions. The enormous diversity and intricate organization of cells have impeded our understanding of the molecular and cellular basis of brain function. Recent advances in spatially resolved single-cell transcriptomics have enabled systematic mapping of the spatial organization of molecularly defined cell types in complex tissues1-3, including several brain regions (for example, refs. 1-11). However, a comprehensive cell atlas of the whole brain is still missing. Here we imaged a panel of more than 1,100 genes in approximately 10 million cells across the entire adult mouse brains using multiplexed error-robust fluorescence in situ hybridization12 and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating multiplexed error-robust fluorescence in situ hybridization and single-cell RNA sequencing data. Using this approach, we generated a comprehensive cell atlas of more than 5,000 transcriptionally distinct cell clusters, belonging to more than 300 major cell types, in the whole mouse brain with high molecular and spatial resolution. Registration of this atlas to the mouse brain common coordinate framework allowed systematic quantifications of the cell-type composition and organization in individual brain regions. We further identified spatial modules characterized by distinct cell-type compositions and spatial gradients featuring gradual changes of cells. Finally, this high-resolution spatial map of cells, each with a transcriptome-wide expression profile, allowed us to infer cell-type-specific interactions between hundreds of cell-type pairs and predict molecular (ligand-receptor) basis and functional implications of these cell-cell interactions. These results provide rich insights into the molecular and cellular architecture of the brain and a foundation for functional investigations of neural circuits and their dysfunction in health and disease.

Dataset Information

Distinct Protein Hydration Water Species Defined by Spatially Resolved Spectra of Intermolecular Vibrations.

Publications

Distinct Protein Hydration Water Species Defined by Spatially Resolved Spectra of Intermolecular Vibrations.

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