Two decades of Martini: Better beads, broader scope

SJ Marrink, L Monticelli, MN Melo… - Wiley …, 2023 - Wiley Online Library
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …

Single-chain inherent elasticity of macromolecules: from concept to applications

Y Bao, S Cui - Langmuir, 2023 - ACS Publications
“The Tao begets the One. One begets all things of the world.” These words of wisdom from
Tao Te Ching are of great inspiration to scientists in polymer materials science and …

Anisotropic friction in a ligand-protein complex

W Cai, M Jäger, JT Bullerjahn, T Hugel, S Wolf… - Nano Letters, 2023 - ACS Publications
The effect of an externally applied directional force on molecular friction is so far poorly
understood. Here, we study the force-driven dissociation of the ligand-protein complex biotin …

Understanding the driving forces that trigger mutations in SARS-CoV-2: mutational energetics and the role of arginine blockers in COVID-19 therapy

H Ridgway, CT Chasapis, K Kelaidonis, I Ligielli… - Viruses, 2022 - mdpi.com
SARS-CoV-2 is a global challenge due to its ability to mutate into variants that spread more
rapidly than the wild-type virus. Because the molecular biology of this virus has been studied …

GōMartini 3: from large conformational changes in proteins to environmental bias corrections

PCT Souza, L Borges-Araújo, C Brasnett, RA Moreira… - BioRxiv, 2024 - biorxiv.org
Coarse-grained modeling has become an important tool to supplement experimental
measurements, allowing access to spatio-temporal scales beyond all-atom based …

Engineering an artificial catch bond using mechanical anisotropy

Z Liu, H Liu, AM Vera, B Yang, P Tinnefeld… - Nature …, 2024 - nature.com
Catch bonds are a rare class of protein-protein interactions where the bond lifetime
increases under an external pulling force. Here, we report how modification of anchor …

Martini 3 OliGo̅mers: a scalable approach for multimers and fibrils in GROMACS

K Korshunova, J Kiuru, J Liekkinen… - Journal of Chemical …, 2024 - ACS Publications
Martini 3 is a widely used coarse-grained simulation method for large-scale biomolecular
simulations. It can be combined with a Go̅ model to realistically describe higher-order …

Single-chain mechanics at low temperatures: a study of three kinds of polymers from 153 to 300 K

S Lu, W Cai, S Zhang, S Cui - Macromolecules, 2023 - ACS Publications
The single-chain mechanics of three kinds of polymers (ie, polydimethylsiloxane,
polyoxymethylene, and poly (methyl methacrylate)) has been investigated from room …

Direct Comparison of Lysine versus Site‐Specific Protein Surface Immobilization in Single‐Molecule Mechanical Assays

H Liu, Z Liu, M Sá Santos… - Angewandte Chemie …, 2023 - Wiley Online Library
Single‐molecule force spectroscopy (SMFS) is powerful for studying folding states and
mechanical properties of proteins, however, it requires protein immobilization onto force …

Nanomechanical footprint of SARS-CoV-2 variants in complex with a potent nanobody by molecular simulations

LF Cofas-Vargas, GE Olivos-Ramirez, M Chwastyk… - Nanoscale, 2024 - pubs.rsc.org
Rational design of novel antibody therapeutics against viral infections such as coronavirus
relies on surface complementarity and high affinity for their effectiveness. Here, we explore …