Biomolecular assemblies: moving from observation to predictive design

CJ Wilson, AS Bommarius, JA Champion… - Chemical …, 2018 - ACS Publications
Biomolecular assembly is a key driving force in nearly all life processes, providing structure,
information storage, and communication within cells and at the whole organism level. These …

Sensing new chemicals with bacterial transcription factors

V Libis, B Delépine, JL Faulon - Current opinion in microbiology, 2016 - Elsevier
Highlights•Transcription Factors represent a starting material of choice to build new
biosensors.•Evolution and rational design are making advances toward tailor-made …

Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria

OV Tsoy, DA Ravcheev, J Čuklina… - Frontiers in …, 2016 - frontiersin.org
Biological nitrogen fixation plays a crucial role in the nitrogen cycle. An ability to fix
atmospheric nitrogen, reducing it to ammonium, was described for multiple species of …

Substitutions at nonconserved rheostat positions modulate function by rewiring long-range, dynamic interactions

P Campitelli, L Swint-Kruse… - Molecular biology and …, 2021 - academic.oup.com
Amino acid substitutions at nonconserved protein positions can have noncanonical and
“long-distance” outcomes on protein function. Such outcomes might arise from changes in …

[HTML][HTML] Rheostats, toggles, and neutrals, Oh my! A new framework for understanding how amino acid changes modulate protein function.

L Swint-Kruse, AW Fenton - Journal of Biological Chemistry, 2024 - Elsevier
Advances in personalized medicine and protein engineering require accurately predicting
outcomes of amino acid substitutions. Many algorithms correctly predict that evolutionarily …

PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational …

L Swint-Kruse, LL Dougherty, B Page, T Wu… - Database, 2023 - academic.oup.com
Interpreting changes in patient genomes, understanding how viruses evolve and
engineering novel protein function all depend on accurately predicting the functional …

Deep representation learning improves prediction of LacI-mediated transcriptional repression

AS Garruss, KM Collins… - Proceedings of the …, 2021 - National Acad Sciences
Recent progress in DNA synthesis and sequencing technology has enabled systematic
studies of protein function at a massive scale. We explore a deep mutational scanning study …

Rheostat functional outcomes occur when substitutions are introduced at nonconserved positions that diverge with speciation

L Swint‐Kruse, TA Martin, BM Page, T Wu… - Protein …, 2021 - Wiley Online Library
When amino acids vary during evolution, the outcome can be functionally neutral or
biologically‐important. We previously found that substituting a subset of nonconserved …

Long‐term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive …

M Ghalayini, M Magnan, S Dion, O Zatout… - Molecular …, 2019 - Wiley Online Library
In vitro experimental evolution has taught us many lessons on the molecular bases of
adaptation. To move towards more natural settings, evolution in the mice gut has been …

Rheostatic contributions to protein stability can obscure a position's functional role

PT O'Neil, L Swint‐Kruse, AW Fenton - Protein Science, 2024 - Wiley Online Library
Rheostat positions, which can be substituted with various amino acids to tune protein
function across a range of outcomes, are a developing area for advancing personalized …