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 …

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 …

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 …

Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study

M Lüking, J Elf, Y Levy - The Journal of Physical Chemistry B, 2022 - ACS Publications
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 …

Enhancer-Insulator Pairing Reveals Heterogeneous Dynamics in Long-Distance 3D Gene Regulation

L Hedström, R Metzler, L Lizana - PRX Life, 2024 - APS
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) …

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 …

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 …

A general mechanism for enhancer-insulator pairing reveals heterogeneous dynamics in long-distant 3D gene regulation

L Hedström, R Metzler, L Lizana - arXiv preprint arXiv:2402.09209, 2024 - arxiv.org
Cells regulate fates and complex body plans using spatiotemporal signaling cascades that
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 …

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) …