Protein design: From the aspect of water solubility and stability

R Qing, S Hao, E Smorodina, D Jin, A Zalevsky… - Chemical …, 2022 - ACS Publications
Water solubility and structural stability are key merits for proteins defined by the primary
sequence and 3D-conformation. Their manipulation represents important aspects of the …

Structure of fish Toll-like receptors (TLR) and NOD-like receptors (NLR)

BR Sahoo - International journal of biological macromolecules, 2020 - Elsevier
Innate immunity driven by pattern recognition receptor (PRR) protects the host from invading
pathogens. Aquatic animals like fish where the adaptive immunity is poorly developed …

Anton 3: twenty microseconds of molecular dynamics simulation before lunch

DE Shaw, PJ Adams, A Azaria, JA Bank… - Proceedings of the …, 2021 - dl.acm.org
Anton 3 is the newest member in a family of supercomputers specially designed for atomic-
level simulation of molecules relevant to biology (eg, DNA, proteins, and drug molecules) …

Advances in molecular dynamics simulations and enhanced sampling methods for the study of protein systems

R Lazim, D Suh, S Choi - International journal of molecular sciences, 2020 - mdpi.com
Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently
could provide reliable answers to questions pertaining to the structure-function relationship …

Principles governing the phase separation of multidomain proteins

P Mohanty, U Kapoor… - Biochemistry, 2022 - ACS Publications
A variety of membraneless organelles, often termed “biological condensates”, play an
important role in the regulation of cellular processes such as gene transcription, translation …

Structure of the Shaker Kv channel and mechanism of slow C-type inactivation

X Tan, C Bae, R Stix, AI Fernández-Mariño, K Huffer… - Biophysical …, 2022 - cell.com
294a Tuesday, February 22, 2022 channel exhibits a domain-swapped relationship
between voltage-sensing and pore domains, with the voltage-sensors in an activated state …

Computational prediction of protein–protein binding affinities

T Siebenmorgen, M Zacharias - Wiley Interdisciplinary Reviews …, 2020 - Wiley Online Library
Protein–protein interactions form central elements of almost all cellular processes.
Knowledge of the structure of protein–protein complexes but also of the binding affinity is of …

Protein-based bioactive coatings: from nanoarchitectonics to applications

C Fu, Z Wang, X Zhou, B Hu, C Li, P Yang - Chemical Society Reviews, 2024 - pubs.rsc.org
Protein-based bioactive coatings have emerged as a versatile and promising strategy for
enhancing the performance and biocompatibility of diverse biomedical materials and …

Development of a force field for the simulation of single-chain proteins and protein–protein complexes

S Piana, P Robustelli, D Tan, S Chen… - Journal of chemical …, 2020 - ACS Publications
The accuracy of atomistic physics-based force fields for the simulation of biological
macromolecules has typically been benchmarked experimentally using biophysical data …

AlphaDesign: A de novo protein design framework based on AlphaFold

M Jendrusch, JO Korbel, SK Sadiq - Biorxiv, 2021 - biorxiv.org
De novo protein design is a longstanding fundamental goal of synthetic biology, but has
been hindered by the difficulty in reliable prediction of accurate high-resolution protein …