Protein design: From the aspect of water solubility and stability

R Qing, S Hao, E Smorodina, D **, 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 …

Macromolecular modeling and design in Rosetta: recent methods and frameworks

JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle… - Nature …, 2020 - nature.com
The Rosetta software for macromolecular modeling, docking and design is extensively used
in laboratories worldwide. During two decades of development by a community of …

The Rosetta all-atom energy function for macromolecular modeling and design

RF Alford, A Leaver-Fay, JR Jeliazkov… - Journal of chemical …, 2017 - ACS Publications
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse
biological questions and engineering challenges ranging from interpretation of low …

Structures of the σ2 receptor enable docking for bioactive ligand discovery

A Alon, J Lyu, JM Braz, TA Tummino, V Craik… - Nature, 2021 - nature.com
The σ2 receptor has attracted intense interest in cancer imaging, psychiatric disease,
neuropathic pain,–and other areas of biology,. Here we determined the crystal structure of …

Coarse-grained protein models and their applications

S Kmiecik, D Gront, M Kolinski, L Wieteska… - Chemical …, 2016 - ACS Publications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

[HTML][HTML] Antidepressant drugs act by directly binding to TRKB neurotrophin receptors

PC Casarotto, M Girych, SM Fred, V Kovaleva… - Cell, 2021 - cell.com
It is unclear how binding of antidepressant drugs to their targets gives rise to the clinical
antidepressant effect. We discovered that the transmembrane domain of tyrosine kinase …

Recent advances in de novo protein design: Principles, methods, and applications

X Pan, T Kortemme - Journal of Biological Chemistry, 2021 - ASBMB
The computational de novo protein design is increasingly applied to address a number of
key challenges in biomedicine and biological engineering. Successes in expanding …

Caveolin-1 dolines form a distinct and rapid caveolae-independent mechanoadaptation system

FN Lolo, N Walani, E Seemann, D Zalvidea… - Nature cell …, 2023 - nature.com
In response to different types and intensities of mechanical force, cells modulate their
physical properties and adapt their plasma membrane (PM). Caveolae are PM nano …

Interdependence of a mechanosensitive anion channel and glutamate receptors in distal wound signaling

J Moe-Lange, NM Gappel, M Machado, MM Wudick… - Science …, 2021 - science.org
Glutamate has dual roles in metabolism and signaling; thus, signaling functions must be
isolatable and distinct from metabolic fluctuations, as seen in low-glutamate domains at …

Accurate computational design of multipass transmembrane proteins

P Lu, D Min, F DiMaio, KY Wei, MD Vahey, SE Boyken… - Science, 2018 - science.org
The computational design of transmembrane proteins with more than one membrane-
spanning region remains a major challenge. We report the design of transmembrane …