Role of Lipids in the Reaction Coordinate of GlpG Rhomboid Protease
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DOI: 10.1016/j.bpj.2016.11.1127
Abstract: Rhomboid proteases function in hydrated lipid membrane environments that can impact significantly the catalytic activity of the enzyme. How lipids participate in the reaction coordinate of rhomboid proteases is, however, unclear. We address this question… read more here.
Keywords: rhomboid protease; reaction coordinate; glpg; reaction ... See more keywords
Reaction Coordinate and Thermodynamics of Base Flipping in RNA.
Sign Up to like & getrecommendations! Published in 2021 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.0c01199
Abstract: Base flipping is a key biophysical event involved in recognition of various ligands by ribonucleic acid (RNA) molecules. However, the mechanism of base flipping in RNA remains poorly understood, in part due to the lack… read more here.
Keywords: thermodynamics; base flipping; flipping rna; base ... See more keywords
Accelerating All-Atom Simulations and Gaining Mechanistic Understanding of Biophysical Systems through State Predictive Information Bottleneck.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00058
Abstract: An effective implementation of enhanced sampling algorithms for molecular dynamics simulations requires a priori knowledge of the approximate reaction coordinate describing the relevant mechanisms in the system. In this work, we focus on the recently… read more here.
Keywords: predictive information; state predictive; reaction coordinate; biophysical systems ... See more keywords
A Rigorous Method for Identifying a One-Dimensional Reaction Coordinate in Complex Molecules.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00132
Abstract: Understanding the mechanism of functional protein dynamics is critical to understanding protein functions. Reaction coordinate (RC) is a central topic in protein dynamics, and the grail is to find the one-dimensional RC (1D-RC) that can… read more here.
Keywords: method; complex molecules; reaction coordinate; reaction ... See more keywords
Organic chemistry students’ interpretations of the surface features of reaction coordinate diagrams
Sign Up to like & getrecommendations! Published in 2018 at "Chemistry Education Research and Practice"
DOI: 10.1039/c8rp00063h
Abstract: Organic chemistry students struggle with understanding the energetics of chemical reactions. Reaction coordinate diagrams are one tool that is widely used in organic chemistry classrooms to assist students with visualizing and explaining the energy changes… read more here.
Keywords: chemistry; organic chemistry; surface features; reaction coordinate ... See more keywords
Cellular reprogramming dynamics follow a simple 1D reaction coordinate.
Sign Up to like & getrecommendations! Published in 2017 at "Physical biology"
DOI: 10.1088/1478-3975/aa90e0
Abstract: Cellular reprogramming, the conversion of one cell type to another, induces global changes in gene expression involving thousands of genes, and understanding how cells globally alter their gene expression profile during reprogramming is an ongoing… read more here.
Keywords: reaction coordinate; cellular reprogramming; gene expression;