Summary
Information regarding pathways through voids in biomolecules and their roles in ligand transport is critical to our understanding of the function of many biomolecules. Recently, the advent of high-throughput molecular dynamics simulations has enabled the study of these pathways, and of rare transport events. However, the scale and intricacy of the data produced requires dedicated tools in order to conduct analyses efficiently and without excessive demand on users. To fill this gap, we developed the TransportTools, which allows the investigation of pathways and their utilization across large, simulated datasets. TransportTools also facilitates the development of custom-made analyses.
Availability and Implementation
TransportTools is implemented in Python3 and distributed as pip and conda packages. The source code is available at https://github.com/labbit-eu/transport_tools.
Supplementary information
Supplementary data are available at Bioinformatics online.
Green and nano-structured catalytic media are vital for bio-catalysis to attenuate the denaturation tendency of biocatalysts under severe reaction conditions. Hydrotropes with multi-faceted physiochemical properties represent promising systems for sustainable...
Green and nanostructured catalytic media are vital in biocatalysis to attenuate the denaturation tendency of biocatalysts under severe reaction conditions. Hydrotropes with multifaceted physiochemical properties can be envisaged as promising systems for sustainable protein packaging. Herein, the suitability of adenosine-5'-triphosphate (ATP) and cholinium salicylate ([Cho][Sal]) ionic liquid (IL) to form nanostructures and to nanoconfine Cytochrome c (Cyt c) were disclosed envisioning enhancement of stability and activity under multiple stresses. Experimental and computational validations were undertaken to explain nanostructuring phenomenon of ATP and IL, structural organizations of nanoconfined Cyt c, and site-specific interactions that stabilize protein structure. Both, ATP and IL form nanostructures in aqueous media and caged Cyt c via multiple non-specific soft interactions. Remarkably, the engineered molecular nano-cages of ATP (5-10 mM), IL (300 mg/mL), and ATP+IL around Cyt c resulted in 9-72 folds higher peroxidase activity than native Cyt c with exceptionally high thermal tolerance (110 degrees C). The polar interactions mediated by hydrotropes with the cardiolipin binding site of Cyt c well corroborated with the increased peroxidase activity. Further, higher activity trends were observed in the presence of urea, GuHCl, and trypsin without any protein degradation. Specific binding of hydrotropes at highly mobile regions of Cyt c (Omega 40-54 residues) and enhanced H-bonding with Lys and Arg offered excellent stability under extreme conditions. Additionally, ATP effectively counteracted reactive oxygen species (ROS) induced denaturation of Cyt c, which was enhanced by [Sal] counterpart of IL. Overall, this study explored the robustness of nanostructured hydrotropes having a higher potential for protein packaging with improved stability and activity in extreme conditions. Thus, the present work brings out a novel strategy for real-time industrial biocatalysis to protect mitochondrial cells from ROS-instigated apoptosis.
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