Perspective: a stirring role for metabolism in cells
J Losa, S Leupold, D Alonso‐Martinez… - Molecular Systems …, 2022 - embopress.org
Based on recent findings indicating that metabolism might be governed by a limit on the rate
at which cells can dissipate Gibbs energy, in this Perspective, we propose a new …
at which cells can dissipate Gibbs energy, in this Perspective, we propose a new …
How do nucleosome dynamics regulate protein search on DNA?
SK Mishra, A Bhattacherjee - The Journal of Physical Chemistry B, 2023 - ACS Publications
Nearly three-fourths of all eukaryotic DNA is occupied by nucleosomes, protein–DNA
complexes comprising octameric histone core proteins and∼ 150 base pairs of DNA. In …
complexes comprising octameric histone core proteins and∼ 150 base pairs of DNA. In …
Modelling chromosome-wide target search
L Hedström, L Lizana - New Journal of Physics, 2023 - iopscience.iop.org
The most common gene regulation mechanism is when a transcription factor (TF) protein
binds to a regulatory sequence to increase or decrease RNA transcription. However, TFs …
binds to a regulatory sequence to increase or decrease RNA transcription. However, TFs …
Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study
In a process known as facilitated diffusion, DNA-binding proteins find their target sites by
combining three-dimensional diffusion and one-dimensional scanning of the DNA …
combining three-dimensional diffusion and one-dimensional scanning of the DNA …
Enhancer-Insulator Pairing Reveals Heterogeneous Dynamics in Long-Distance 3D Gene Regulation
Cells regulate fates and complex body plans using spatiotemporal signaling cascades that
alter gene expression. Short DNA sequences, known as enhancers (50–1500 base pairs) …
alter gene expression. Short DNA sequences, known as enhancers (50–1500 base pairs) …
Probing the Modulation in Facilitated Diffusion Guided by DNA-Protein Interactions in Target Search Processes
D Thonnekottu, D CHATTERJEE - Physical Chemistry Chemical …, 2024 - pubs.rsc.org
Many fundamental biophysical processes involving gene regulation and gene editing rely, at
the molecular level, on an intricate methodology of searching and locating the precise target …
the molecular level, on an intricate methodology of searching and locating the precise target …
A minimal kinetic model for the interpretation of complex catalysis in single enzyme molecules
P Kundu, S Saha, G Gangopadhyay - Physical Chemistry Chemical …, 2024 - pubs.rsc.org
Multi-exponential waiting-time distribution and randomness parameter greater than unity
ascribe dynamic disorder in single-enzyme catalysis corroborated to the interplay of …
ascribe dynamic disorder in single-enzyme catalysis corroborated to the interplay of …
A general mechanism for enhancer-insulator pairing reveals heterogeneous dynamics in long-distant 3D gene regulation
Cells regulate fates and complex body plans using spatiotemporal signaling cascades that
alter gene expression. Enhancers, short DNA sequences (50-150 base pairs), help …
alter gene expression. Enhancers, short DNA sequences (50-150 base pairs), help …
Influence of Nonspecific Interactions between Proteins and In Vivo Cytoplasmic Crowders in Facilitated Diffusion of Proteins: Theoretical Insights
B Punia, S Chaudhury - The Journal of Physical Chemistry B, 2022 - ACS Publications
The binding of proteins to their respective specific sites on the DNA through facilitated
diffusion serves as the initial step of various important biological processes. While this …
diffusion serves as the initial step of various important biological processes. While this …
Exploring the role of heterogeneity in quorum sensing cells: a discrete state stochastic approach
P Jangid, S Chaudhury - Journal of Statistical Mechanics: Theory …, 2023 - iopscience.iop.org
Quorum sensing (QS) is a bacterial communication process in which cells detect the local
environment and collectively activate gene expression. The transcriptional activator (LuxR) …
environment and collectively activate gene expression. The transcriptional activator (LuxR) …