Pragmatic coarse-graining of proteins: models and applications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …
proteins with other molecules are often difficult to assess by experimental techniques …
Machines on genes through the computational microscope
Macromolecular machines acting on genes are at the core of life's fundamental processes,
including DNA replication and repair, gene transcription and regulation, chromatin …
including DNA replication and repair, gene transcription and regulation, chromatin …
Multibody terms in protein coarse-grained models: A top-down perspective
I Zaporozhets, C Clementi - The Journal of Physical Chemistry B, 2023 - ACS Publications
Coarse-grained models allow computational investigation of biomolecular processes
occurring on long time and length scales, intractable with atomistic simulation. Traditionally …
occurring on long time and length scales, intractable with atomistic simulation. Traditionally …
The marionette mechanism of domain–domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor
The human estrogen receptor α (hER α) is involved in the regulation of growth,
development, and tissue homeostasis. Agonists that bind to the receptor's ligand-binding …
development, and tissue homeostasis. Agonists that bind to the receptor's ligand-binding …
Unravelling how single-stranded DNA binding protein coordinates DNA metabolism using single-molecule approaches
Single-stranded DNA-binding proteins (SSBs) play vital roles in DNA metabolism. Proteins
of the SSB family exclusively and transiently bind to ssDNA, preventing the DNA double …
of the SSB family exclusively and transiently bind to ssDNA, preventing the DNA double …
Structural and dynamic basis of DNA capture and translocation by mitochondrial Twinkle helicase
Twinkle is a mitochondrial replicative helicase which can self-load onto and unwind
mitochondrial DNA. Nearly 60 mutations on Twinkle have been linked to human …
mitochondrial DNA. Nearly 60 mutations on Twinkle have been linked to human …
Joint Efforts of Replicative Helicase and SSB Ensure Inherent Replicative Tolerance of G‐Quadruplex
L Guo, Y Bao, Y Zhao, Z Ren, L Bi, X Zhang… - Advanced …, 2024 - Wiley Online Library
Abstract G‐quadruplex (G4) is a four‐stranded noncanonical DNA structure that has long
been recognized as a potential hindrance to DNA replication. However, how replisomes …
been recognized as a potential hindrance to DNA replication. However, how replisomes …
Exploring Abeta42 Monomer Diffusive Dynamics on Fibril Surfaces through Molecular Simulations
YW Ma, GF Wang, MY Tsai - bioRxiv, 2024 - biorxiv.org
Alzheimer's disease is closely linked to the aggregation of Abeta42 peptides, which follow a
complex pathway involving primary nucleation and secondary processes. While previous …
complex pathway involving primary nucleation and secondary processes. While previous …