Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity

DJ Huggins, PC Biggin, MA Dämgen… - Wiley …, 2019 - Wiley Online Library
Biomolecular simulation is increasingly central to understanding and designing biological
molecules and their interactions. Detailed, physics‐based simulation methods are …

Shelterin proteins and cancer

TNV Patel, R Vasan, D Gupta, J Patel… - Asian Pacific Journal of …, 2015 - koreascience.kr
The telomeric end structures of the DNA are known to contain tandem repeats of TTAGGG
sequence bound with specialised protein complex called the" shelterin complex". It …

Yangonin modulates lipid homeostasis, ameliorates cholestasis and cellular senescence in alcoholic liver disease via activating nuclear receptor FXR

L Kong, R Dong, K Huang, X Wang, D Wang, N Yue… - Phytomedicine, 2021 - Elsevier
Background: Alcoholic liver disease (ALD) is a progressive disease beginning with simple
steatosis but can progress to alcoholic steatohepatitis, fibrosis, cirrhosis, and even …

Dynamics and recognition within a protein–DNA complex: a molecular dynamics study of the SKN-1/DNA interaction

L Etheve, J Martin, R Lavery - Nucleic Acids Research, 2016 - academic.oup.com
Molecular dynamics simulations of the Caenorhabditis elegans transcription factor SKN-1
bound to its cognate DNA site show that the protein–DNA interface undergoes significant …

Low frequency variants associated with leukocyte telomere length in the Singapore Chinese population

X Chang, RL Gurung, L Wang, A Jin, Z Li… - Communications …, 2021 - nature.com
The role of low frequency variants associated with telomere length homeostasis in chronic
diseases and mortalities is relatively understudied in the East-Asian population. Here we …

Bisphenol A (BPA) binding on full‐length architectures of estrogen receptor

Y Liu, K Qu, Y Hai, C Zhao - Journal of Cellular Biochemistry, 2018 - Wiley Online Library
Previous research has shown that the major toxicity mechanism for many environment
chemicals is binding with estrogen receptor (ER) and blocking endogenous estrogen …

Identification of the initial steps in signal transduction in the α4β2 nicotinic receptor: insights from equilibrium and nonequilibrium simulations

ASF Oliveira, DK Shoemark, HR Campello… - Structure, 2019 - cell.com
Nicotinic acetylcholine receptors (nAChRs) modulate synaptic transmission in the nervous
system. These receptors have emerged as therapeutic targets in drug discovery for treating …

Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors

J Hörberg, K Moreau, MJ Tamás… - Nucleic Acids …, 2021 - academic.oup.com
Abstract Activator proteins 1 (AP-1) comprise one of the largest families of eukaryotic basic
leucine zipper transcription factors. Despite advances in the characterization of AP-1 DNA …

[HTML][HTML] Duplication of the mitochondrial control region is associated with increased longevity in birds

I Skujina, R McMahon, VPE Lenis, GV Gkoutos… - Aging (Albany …, 2016 - ncbi.nlm.nih.gov
Despite a number of biochemical and lifestyle differences which should increase risk of
oxidative damage to their mitochondrial DNA (mtDNA) and thus reduce expected lifespan …

Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA

J Rodriguez, F Battistini, S Learte-Aymamí… - RSC Chemical …, 2023 - pubs.rsc.org
We report the modelling of the DNA complex of an artificial miniprotein composed of two zinc
finger modules and an AT-hook linking peptide. The computational study provides for the …