Bottom-up coarse-graining: Principles and perspectives

J Jin, AJ Pak, AEP Durumeric, TD Loose… - Journal of chemical …, 2022 - ACS Publications
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …

Actin and actin-binding proteins

TD Pollard - Cold Spring Harbor perspectives in biology, 2016 - cshperspectives.cshlp.org
Organisms from all domains of life depend on filaments of the protein actin to provide
structure and to support internal movements. Many eukaryotic cells use forces produced by …

[HTML][HTML] Structural basis of actin filament assembly and aging

W Oosterheert, BU Klink, A Belyy, S Pospich… - Nature, 2022 - nature.com
The dynamic turnover of actin filaments (F-actin) controls cellular motility in eukaryotes and
is coupled to changes in the F-actin nucleotide state,–. It remains unclear how F-actin …

Mechanism of actin polymerization revealed by cryo-EM structures of actin filaments with three different bound nucleotides

SZ Chou, TD Pollard - … of the National academy of Sciences, 2019 - National Acad Sciences
We used cryo-electron microscopy (cryo-EM) to reconstruct actin filaments with bound
AMPPNP (β, γ-imidoadenosine 5′-triphosphate, an ATP analog, resolution 3.1 Å), ADP-Pi …

Enhancing important fluctuations: Rare events and metadynamics from a conceptual viewpoint

O Valsson, P Tiwary, M Parrinello - Annual review of physical …, 2016 - annualreviews.org
Atomistic simulations play a central role in many fields of science. However, their usefulness
is often limited by the fact that many systems are characterized by several metastable states …

Structural transitions of F-actin upon ATP hydrolysis at near-atomic resolution revealed by cryo-EM

F Merino, S Pospich, J Funk, T Wagner… - Nature structural & …, 2018 - nature.com
The function of actin is coupled to the nucleotide bound to its active site. ATP hydrolysis is
activated during polymerization; a delay between hydrolysis and inorganic phosphate (Pi) …

Biomimetic temporal self-assembly via fuel-driven controlled supramolecular polymerization

A Mishra, DB Korlepara, M Kumar, A Jain… - Nature …, 2018 - nature.com
Temporal control of supramolecular assemblies to modulate the structural and transient
characteristics of synthetic nanostructures is an active field of research within …

Machine learning-driven multiscale modeling: bridging the scales with a next-generation simulation infrastructure

HI Ingólfsson, H Bhatia, F Aydin… - Journal of Chemical …, 2023 - ACS Publications
Interdependence across time and length scales is common in biology, where atomic
interactions can impact larger-scale phenomenon. Such dependence is especially true for a …

Structures and mechanisms of actin ATP hydrolysis

Y Kanematsu, A Narita, T Oda… - Proceedings of the …, 2022 - National Acad Sciences
The major cytoskeleton protein actin undergoes cyclic transitions between the monomeric G-
form and the filamentous F-form, which drive organelle transport and cell motility. This …

Hybrid quantum mechanical/molecular mechanical methods for studying energy transduction in biomolecular machines

T Kubař, M Elstner, Q Cui - Annual review of biophysics, 2023 - annualreviews.org
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become
indispensable tools for the study of biomolecules. In this article, we briefly review the basic …