Dataset Information

Structural Dynamics in the Presence of Water of Graphene Bilayers with Defects.

ABSTRACT: The dynamics of a bilayer of graphene containing one mono-vacancy in the top layer has been investigated in the framework of DFTB in the absence and in the presence of water. Due to the speed of the code, we can describe details of the behavior, which are not directly accessible experimentally and cannot be treated by DFT or classical molecular dynamics. The presence of water enhances the displacement of carbon atoms in the perpendicular direction to the surface. Our results explain very well a variety of experimental findings. In particular, the stabilization of the Jahn-Teller distortion by hydrogenation of one of the carbon atoms at the edge of a mono-vacancy has been elucidated. This work is the first analysis of the behavior of a graphene vacancy at room temperature in contact with water based on a quantum mechanical molecular dynamics method, where both graphene and solvent are treated at the same level.

SUBMITTER: Santos E

PROVIDER: S-EPMC10385876 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature

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Structural Dynamics in the Presence of Water of Graphene Bilayers with Defects.

Santos Elizabeth E

Nanomaterials (Basel, Switzerland) 20230710 14

The dynamics of a bilayer of graphene containing one mono-vacancy in the top layer has been investigated in the framework of DFTB in the absence and in the presence of water. Due to the speed of the code, we can describe details of the behavior, which are not directly accessible experimentally and cannot be treated by DFT or classical molecular dynamics. The presence of water enhances the displacement of carbon atoms in the perpendicular direction to the surface. Our results explain very well a ...[more]

PMID: 37513049

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Project description:B0AT1 (SLC6A19) is a major sodium-coupled neutral amino acid transporter that relies on angiotensin converting enzyme 2 (ACE2) or collectrin for membrane trafficking. Despite its significant role in disorders associated with amino acid metabolism, there is a deficit of comprehensive structure-function understanding of B0AT1 in lipid environment. Herein, we have employed molecular dynamics (MD) simulations to explore the architectural characteristics of B0AT1 in two distinct environments: a simplified POPC bilayer and a complex lipid system replicating the native membrane composition. Notably, our B0AT1 analysis in terms of structural stability and regions of maximum flexibility shows consistency in both the systems with enhanced structural features in the case of complex lipid system. Our findings suggest that diacylglycerol phospholipids significantly alter the pore radius, hydrophobic index, and surface charge distribution of B0AT1, thereby affecting the flexibility of transmembrane helices TM7, TM12, and loop connecting TM7-TM8, crucial for ACE2-B0AT1 interaction. Pro41, Ser190, Arg214, Arg240, Ser413, Pro414, Cys463, and Val582 are among the most prominent lipid binding residues that might influence B0AT1 functionality. We also perceive notable lipid mediated deviation in the degree of tilt and loss of helicity in TM1 and TM6 which might affect the substrate binding sites S1 and S2 in B0AT1. Considerably, destabilization in the structure of B0AT1 in lipid environment was evident upon mutation in TM domain, associated with Hartnup disorder through various structure-based protein stability tools. Our two-tiered approach allowed us to validate the use of POPC as a baseline for initial analyses of SLC transporters. Altogether, our all-atoms MD study provides a platform for future investigations into the structure-function mechanism of B0AT1 in realistic lipid mimetic bilayers and offers a framework for developing new therapeutic agents targeting this transporter.

Dataset Information

Structural Dynamics in the Presence of Water of Graphene Bilayers with Defects.

Publications

Structural Dynamics in the Presence of Water of Graphene Bilayers with Defects.

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