[HTML][HTML] Evolution, folding, and design of TIM barrels and related proteins

S Romero-Romero, S Kordes, F Michel… - Current Opinion in …, 2021 - Elsevier
Highlights•In-depth sequence analysis reveals that the protein fold universe is more
evolutionarily connected than previously assumed.•Short ancestral fragments are observed …

Protein sequence design by conformational landscape optimization

C Norn, BIM Wicky, D Juergens, S Liu… - Proceedings of the …, 2021 - National Acad Sciences
The protein design problem is to identify an amino acid sequence that folds to a desired
structure. Given Anfinsen's thermodynamic hypothesis of folding, this can be recast as …

Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase

JPT Zaragoza, AR Offenbacher, S Hu… - Proceedings of the …, 2023 - National Acad Sciences
The enzyme soybean lipoxygenase (SLO) provides a prototype for deep tunneling
mechanisms in hydrogen transfer catalysis. This work combines room temperature X-ray …

Natural oleogelators for the formulation of oleogels by considering their rheological and textural perspective; a review

B Hashemi, M Varidi, E Assadpour, F Zhang… - International Journal of …, 2024 - Elsevier
A well-known method for reducing or swapping out undesirable and controversial fats in
food is oleogelation. To quantify the effects of droplets-particle inclusion on the textural …

Instant thermal switching from soft hydrogel to rigid plastics inspired by thermophile proteins

T Nonoyama, YW Lee, K Ota, K Fujioka… - Advanced …, 2020 - Wiley Online Library
Proteins of thermophiles are thermally stable in a high‐temperature environment, adopting a
strategy of enhancing the electrostatic interaction in hydrophobic media at high temperature …

ProteinTools: a toolkit to analyze protein structures

N Ferruz, S Schmidt, B Höcker - Nucleic acids research, 2021 - academic.oup.com
The experimental characterization and computational prediction of protein structures has
become increasingly rapid and precise. However, the analysis of protein structures often …

Probing microscopic conformational dynamics in folding reactions by measuring transition paths

NQ Hoffer, MT Woodside - Current Opinion in Chemical Biology, 2019 - Elsevier
Transition paths comprise those parts of a folding trajectory where the molecule passes
through the high-energy transition states separating folded and unfolded conformations. The …

Rational design of formate dehydrogenase for enhanced thermal stability and catalytic activity in bioelectrocatalysis

H Shi, M Fu, T Zhang, X Zhang, L Yao… - Journal of Agricultural …, 2024 - ACS Publications
Formate dehydrogenase can be utilized as a biocatalyst in the bioelectrocatalysis of
converting CO2 into formic acid. However, its industrial application has been hindered by …

Constructing Phase Separation in Polymer Gels: Strategies, Functions and Applications

Z Wang, W Qiu, Q Zhang - Progress in Polymer Science, 2024 - Elsevier
Over the past decades, there has been a flourishing of phase-separated polymer gels.
Unlike traditional design methods that rely on chemical structure and polymer network …

[HTML][HTML] The stability landscape of de novo TIM barrels explored by a modular design approach

S Romero-Romero, M Costas, DAS Manzano… - Journal of Molecular …, 2021 - Elsevier
The ability to design stable proteins with custom-made functions is a major goal in
biochemistry with practical relevance for our environment and society. Understanding and …