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 …

De novo protein design, a retrospective

IV Korendovych, WF DeGrado - Quarterly reviews of biophysics, 2020 - cambridge.org
Proteins are molecular machines whose function depends on their ability to achieve
complex folds with precisely defined structural and dynamic properties. The rational design …

[HTML][HTML] Protein structure prediction and design in a biologically realistic implicit membrane

RF Alford, PJ Fleming, KG Fleming, JJ Gray - Biophysical Journal, 2020 - cell.com
Protein design is a powerful tool for elucidating mechanisms of function and engineering
new therapeutics and nanotechnologies. Although soluble protein design has advanced …

Modeling membrane geometries implicitly in Rosetta

H Woods, JK Leman, J Meiler - Protein Science, 2024 - Wiley Online Library
Interactions between membrane proteins (MPs) and lipid bilayers are critical for many
cellular functions. In the Rosetta molecular modeling suite, the implicit membrane energy …

[HTML][HTML] A lipophilicity-based energy function for membrane-protein modelling and design

JY Weinstein, A Elazar… - PLoS computational …, 2019 - journals.plos.org
Membrane-protein design is an exciting and increasingly successful research area which
has led to landmarks including the design of stable and accurate membrane-integral …

Principles and methods in computational membrane protein design

AA Vorobieva - Journal of Molecular Biology, 2021 - Elsevier
After decades of progress in computational protein design, the design of proteins folding and
functioning in lipid membranes appears today as the next frontier. Some notable successes …

[HTML][HTML] Evaluation of transmembrane protein structural models using hpmscore

S Téletchéa, J Esque, A Urbain, C Etchebest… - …, 2023 - mdpi.com
Transmembrane proteins (TMPs) are a class of essential proteins for biological and
therapeutic purposes. Despite an increasing number of structures, the gap with the number …

Validation of de novo designed water-soluble and transmembrane proteins by in silico folding and melting

A Martin, C Berner, S Ovchinnikov, AA Vorobieva - bioRxiv, 2023 - biorxiv.org
In silico validation of de novo designed proteins with deep learning (DL)-based structure
prediction algorithms has become a mainstream practice. However, formal evidence of the …

[HTML][HTML] Upgraded molecular models of the human KCNQ1 potassium channel

G Kuenze, AM Duran, H Woods, KR Brewer… - PloS one, 2019 - journals.plos.org
The voltage-gated potassium channel KCNQ1 (KV7. 1) assembles with the KCNE1
accessory protein to generate the slow delayed rectifier current, IKS, which is critical for …

One‐shot design elevates functional expression levels of a voltage‐gated potassium channel

JJ Weinstein, C Saikia, I Karbat, A Goldenzweig… - Protein …, 2024 - Wiley Online Library
Membrane proteins play critical physiological roles as receptors, channels, pumps, and
transporters. Despite their importance, however, low expression levels often hamper the …