Recent advances and emerging challenges in the molecular modeling of mechanobiological processes

G Stirnemann - The Journal of Physical Chemistry B, 2022 - ACS Publications
Many biological processes result from the effect of mechanical forces on macromolecular
structures and on their interactions. In particular, the cell shape, motion, and differentiation …

SOP-MULTI: A Self-Organized Polymer-Based Coarse-Grained Model for Multidomain and Intrinsically Disordered Proteins with Conformation Ensemble Consistent …

K Baratam, A Srivastava - Journal of Chemical Theory and …, 2024 - ACS Publications
Multidomain proteins with long flexible linkers and full-length intrinsically disordered
proteins (IDPs) are best defined as an ensemble of conformations rather than a single …

Conformational fluctuations and induced orientation of a protein, its solvation shell, and bulk water in weak non-unfolding external electric fields

Y Shuto, E Walinda, D Morimoto… - The Journal of Physical …, 2023 - ACS Publications
Extreme external electric fields have been reported to disrupt the tertiary structure of stably
folded proteins; however, the effects of weaker electric fields on many biomolecules …

Native Salt Bridges Are a Key Regulator of Ubiquitin's Mechanical Stability

T Nandi, SRK Ainavarapu - The Journal of Physical Chemistry B, 2022 - ACS Publications
Although it is known that various intramolecular interactions determine protein mechanical
stability, a detailed molecular-level understanding of the key regulators of protein …

Simulation-based inference of single-molecule force spectroscopy

L Dingeldein, P Cossio, R Covino - Machine Learning: Science …, 2023 - iopscience.iop.org
Single-molecule force spectroscopy (smFS) is a powerful approach to studying molecular
self-organization. However, the coupling of the molecule with the ever-present experimental …

[PDF][PDF] 同义密码子使用模式控制核糖体扫描节律的分子机制

高明阳, 吴玉湖, 杨宣叶, 王进千… - 农业生物技术 …, 2024 - journal05.magtech.org.cn
摘要翻译过程中新生多肽链的正确折叠是蛋白质具备生物学活性的基石, 但往往新生多肽链正确
形成空间构象需通过共翻译折叠机制才能实现. 在核糖体翻译mRNA 序列时同义密码子使用 …

The effect of pulling and twisting forces on chameleon sequence peptides

J Meadows, K Röder - ChemPhysChem, 2023 - Wiley Online Library
Chameleon sequences are amino acid sequences found in several distinct configurations in
experiment. They challenge our understanding of the link between sequence and structure …

Reconstruction of the Free Energy Profile for SUMO1 from Nonequilibrium Single-Molecule Pulling Experiments

T Nandi, SR Koti Ainavarapu - The Journal of Physical Chemistry …, 2022 - ACS Publications
Free energy profiles form the cornerstone in the study of protein folding and function. In this
study, the free energy profile of SUMO1 protein is directly reconstructed using an extension …

Molecular interpretation of single-molecule force spectroscopy experiments with computational approaches

G Stirnemann - Chemical Communications, 2022 - pubs.rsc.org
Single molecule force-spectroscopy techniques have granted access to unprecedented
molecular-scale details about biochemical and biological mechanisms. However, the …

Molecular interpretation of single-molecule force spectroscopy experiments with computational approaches

S Guillaume - 2022 - chemrxiv.org
Single molecule force-spectroscopy techniques have granted access to unprecedented
molecular-scale details about biochemical and biological mechanisms. However, the …