Recognition in the domain of molecular chirality: from noncovalent interactions to separation of enantiomers

P Peluso, B Chankvetadze - Chemical Reviews, 2022 - ACS Publications
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in
nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules …

Mapping the energetic and allosteric landscapes of protein binding domains

AJ Faure, J Domingo, JM Schmiedel… - Nature, 2022 - nature.com
Allosteric communication between distant sites in proteins is central to biological regulation
but still poorly characterized, limiting understanding, engineering and drug development …

Learning from Protein Engineering by Deconvolution of Multi‐Mutational Variants

F Hollmann, J Sanchis, MT Reetz - … Chemie International Edition, 2024 - Wiley Online Library
This review analyzes a development in biochemistry, enzymology and biotechnology that
originally came as a surprise. Following the establishment of directed evolution of …

Learning epistasis and residue coevolution patterns: Current trends and future perspectives for advancing enzyme engineering

M Wittmund, F Cadet, MD Davari - ACS catalysis, 2022 - ACS Publications
Engineering proteins and enzymes with the desired functionality has broad applications in
molecular biology, biotechnology, biomedical sciences, health, and medicine. The vastness …

Simultaneous native mass spectrometry analysis of single and double mutants to probe lipid binding to membrane proteins

HS Jayasekera, FA Mohona, M Ewbank… - Analytical …, 2024 - ACS Publications
Lipids are critical modulators of membrane protein structure and function. However, it is
challenging to investigate the thermodynamics of protein–lipid interactions because lipids …

Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions

J Lyu, T Zhang, MT Marty, D Clemmer, DH Russell… - Elife, 2024 - elifesciences.org
Structural and functional studies of the ATP-binding cassette transporter MsbA have
revealed two distinct lipopolysaccharide (LPS) binding sites: one located in the central cavity …

An intramolecular energetic network regulates ligand recognition in a SH2 domain

C Nardella, L Pagano, V Pennacchietti… - Protein …, 2023 - Wiley Online Library
In an effort to investigate the molecular determinants of ligand recognition of the C‐terminal
SH2 domain of the SHP2 protein, we conducted extensive site‐directed mutagenesis and …

[HTML][HTML] High-throughput affinity measurements of transcription factor and DNA mutations reveal affinity and specificity determinants

AK Aditham, CJ Markin, DA Mokhtari, N DelRosso… - Cell Systems, 2021 - cell.com
Transcription factors (TFs) bind regulatory DNA to control gene expression, and mutations to
either TFs or DNA can alter binding affinities to rewire regulatory networks and drive …

Supertertiary protein structure affects an allosteric network

L Laursen, J Kliche, S Gianni… - Proceedings of the …, 2020 - National Acad Sciences
The notion that protein function is allosterically regulated by structural or dynamic changes
in proteins has been extensively investigated in several protein domains in isolation. In …

[HTML][HTML] Cell phenotypes can be predicted from propensities of protein conformations

R Nussinov, Y Liu, W Zhang, H Jang - Current Opinion in Structural Biology, 2023 - Elsevier
Proteins exist as dynamic conformational ensembles. Here we suggest that the propensities
of the conformations can be predictors of cell function. The conformational states that the …