A unifying mechanism for protein transport through the core bacterial Sec machinery

WJ Allen, I Collinson - Open Biology, 2023 - royalsocietypublishing.org
Encapsulation and compartmentalization are fundamental to the evolution of cellular life, but
they also pose a challenge: how to partition the molecules that perform biological functions …

Bridge: A graph-based algorithm to analyze dynamic H-bond networks in membrane proteins

M Siemers, M Lazaratos, K Karathanou… - Journal of chemical …, 2019 - ACS Publications
Membrane proteins that function as transporters or receptors must communicate with both
sides of the lipid bilayer in which they sit. This long distance communication enables …

Dynamic correlations: exact and approximate methods for mutual information

K Demirtaş, B Erman, T Haliloğlu - Bioinformatics, 2024 - academic.oup.com
Motivation Proteins are dynamic entities that undergo conformational changes critical for
their functions. Understanding the communication pathways and information transfer within …

Dynamic water hydrogen-bond networks at the interface of a lipid membrane containing palmitoyl-oleoyl phosphatidylglycerol

K Karathanou, AN Bondar - The Journal of Membrane Biology, 2018 - Springer
Lipid membrane interfaces are complex environments that host essential cellular processes
such as binding of proteins or drug molecules. A key open question is how water molecules …

The mechanism and energetics of a ligand-controlled hydrophobic gate in a mammalian two pore channel

S Milenkovic, IV Bodrenko, L Lagostena… - Physical Chemistry …, 2020 - pubs.rsc.org
In the last decade two-pore intracellular channels (TPCs) attracted the interest of
researchers, still some key questions remain open. Their importance for vacuolar (plants) …

The rational modification of the secretion pathway: the bidirectional grinding strategy on signal peptide and SecA in Bacillus subtilis

Z Jiang, L Zhang, W Zhou, H Li, Y Li, W Qin… - Biochemical …, 2023 - Elsevier
The secretory (Sec) pathway is essential for protein translocation in Bacillus subtilis. In
contrast to signal peptides (SPs), the key components of the Sec pathway lack excessive …

Using graphs of dynamic hydrogen-bond networks to dissect conformational coupling in a protein motor

K Karathanou, AN Bondar - Journal of Chemical Information and …, 2019 - ACS Publications
DExD/H-box proteins are soluble enzymes that couple binding and hydrolysis of adenosine
triphosphate (ATP) with reactions involving RNA metabolism or bind and push newly …

Dynamic hydrogen-bond networks in bacterial protein secretion

K Karathanou, AN Bondar - FEMS microbiology letters, 2018 - academic.oup.com
The Sec protein secretion machinery includes proteins whose reaction coordinates involve
large-scale conformational changes. Dynamic hydrogen-bond networks can provide …

Factors underlying asymmetric pore dynamics of disaggregase and microtubule-severing AAA+ machines

M Damre, A Dayananda, RA Varikoti, G Stan… - Biophysical Journal, 2021 - cell.com
Disaggregation and microtubule-severing nanomachines from the AAA+ (ATPases
associated with various cellular activities) superfamily assemble into ring-shaped hexamers …

Molecular dynamics of DNA translocation by FtsK

J Pajak, G Arya - Nucleic Acids Research, 2022 - academic.oup.com
The bacterial FtsK motor harvests energy from ATP to translocate double-stranded DNA
during cell division. Here, we probe the molecular mechanisms underlying coordinated DNA …