Conformational Dynamics of thiM Riboswitch To Understand the Gene Regulation Mechanism Using Markov State Modeling and the Residual Fluctuation Network Approach

2018 ◽  
Vol 58 (8) ◽  
pp. 1638-1651 ◽  
Author(s):  
Manish Kesherwani ◽  
Kutumbarao N. H. V ◽  
Devadasan Velmurugan
Keyword(s):  
Gene Regulation ◽  
Conformational Dynamics ◽  
Regulation Mechanism ◽  
Network Approach ◽  
Markov State ◽  
Markov State Modeling

scholarly journals Understanding the Conformational Dynamics of a Pentameric Ligand-Gated Ion Channel through Markov State Modeling

2019 ◽  
Vol 116 (3) ◽  
pp. 395a-396a
Author(s):  
Cathrine C. Bergh ◽  
Laura Orellana ◽  
Rebecca J. Howard ◽  
Erik Lindahl
Keyword(s):  
Ion Channel ◽  
Conformational Dynamics ◽  
Markov State ◽  
Markov State Modeling

scholarly journals Markov state modeling of sliding friction

2016 ◽  
Vol 94 (5) ◽  
Author(s):  
F. Pellegrini ◽  
François P. Landes ◽  
A. Laio ◽  
S. Prestipino ◽  
E. Tosatti
Keyword(s):  
Sliding Friction ◽  
Markov State ◽  
Markov State Modeling

scholarly journals Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xinyi Wan ◽  
Filipe Pinto ◽  
Luyang Yu ◽  
Baojun Wang
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Protein Binding ◽  
Gene Networks ◽  
Dynamic Range ◽  
Gene Expression Regulation ◽  
Single Layer ◽  
Regulation Mechanism ◽  
Gene Circuits ◽  
Synthetic Dna

AbstractVersatile tools for gene expression regulation are vital for engineering gene networks of increasing scales and complexity with bespoke responses. Here, we investigate and repurpose a ubiquitous, indirect gene regulation mechanism from nature, which uses decoy protein-binding DNA sites, named DNA sponge, to modulate target gene expression in Escherichia coli. We show that synthetic DNA sponges can be designed to reshape the response profiles of gene circuits, lending multifaceted tuning capacities including reducing basal leakage by >20-fold, increasing system output amplitude by >130-fold and dynamic range by >70-fold, and mitigating host growth inhibition by >20%. Further, multi-layer DNA sponges for decoying multiple regulatory proteins provide an additive tuning effect on the responses of layered circuits compared to single-layer sponges. Our work shows synthetic DNA sponges offer a simple yet generalizable route to systematically engineer the performance of synthetic gene circuits, expanding the current toolkit for gene regulation with broad potential applications.

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