[HTML][HTML] Evolution, folding, and design of TIM barrels and related proteins
S Romero-Romero, S Kordes, F Michel… - … Opinion in Structural …, 2021 - Elsevier
… natural proteins? This general question has been explored by analyzing the evolution of
different protein folds, for which the TIM barrel … of protein stability, folding, function and evolution. …
different protein folds, for which the TIM barrel … of protein stability, folding, function and evolution. …
Extension of a de novo TIM barrel with a rationally designed secondary structure element
JG Wiese, S Shanmugaratnam, B Höcker - Protein Science, 2021 - Wiley Online Library
… Nonetheless, we were able to insert a new element into the TIM barrel without disrupting its
structural integrity or stability. The newly inserted 3 10 helix appears to fit even more snugly …
structural integrity or stability. The newly inserted 3 10 helix appears to fit even more snugly …
Frustration and folding of a TIM barrel protein
… Although the kinetic species are conserved, the evolution of the sequences over time has
resulted in alternative locations for the cores of stability in the TIM barrel architecture. …
resulted in alternative locations for the cores of stability in the TIM barrel architecture. …
[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
… functions and its ubiquity in different types of enzymes, the TIM barrel represents a suitable
scaffold for protein … -fold symmetric TIM barrel was described: the sTIM11 protein. Considering …
scaffold for protein … -fold symmetric TIM barrel was described: the sTIM11 protein. Considering …
A conserved folding nucleus sculpts the free energy landscape of bacterial and archaeal orthologs from a divergent TIM barrel family
R Jain, K Muneeruddin, J Anderson… - Proceedings of the …, 2021 - National Acad Sciences
… of TIM barrel proteins. We conclude that the folding mechanism of the IGPS TIM barrel, including
the structures of … core of stability around which adjacent elements of structure condense. …
the structures of … core of stability around which adjacent elements of structure condense. …
Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion
SJ Caldwell, IC Haydon, N Piperidou… - Proceedings of the …, 2020 - National Acad Sciences
… , we have created a homodimeric protein with a TIM barrel base and a dimeric FD lid … to
enzyme function. In this work, the TIM barrel component of the highly stable TFD scaffold was …
enzyme function. In this work, the TIM barrel component of the highly stable TFD scaffold was …
Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase
G Gamiz-Arco, LI Gutierrez-Rus, VA Risso… - Nature …, 2021 - nature.com
… the proteins encoded by the most probabilistic sequences at nodes N72, N73, and N125. While
the three proteins were active and stable… over time. We therefore selected the resurrected …
the three proteins were active and stable… over time. We therefore selected the resurrected …
Hydrogen–deuterium exchange within adenosine deaminase, a TIM barrel hydrolase, identifies networks for thermal activation of catalysis
S Gao, EJ Thompson, SL Barrow… - Journal of the …, 2020 - ACS Publications
… This work applies the methodology to one of the ubiquitous TIM barrel proteins. … Enzyme
stability assays were performed to confirm that the enzyme remained fully active under the …
stability assays were performed to confirm that the enzyme remained fully active under the …
[HTML][HTML] Building better barrels–β-barrel biogenesis and insertion in bacteria and mitochondria
KA Diederichs, SK Buchanan, I Botos - Journal of molecular biology, 2021 - Elsevier
… Based on the new SAM complex structures, we propose that the mitochondrial β-barrel …
.60, 61 The first five proteins form a very stable core complex, while Tom70 and Tom20 readily …
.60, 61 The first five proteins form a very stable core complex, while Tom70 and Tom20 readily …
Transmembrane β-barrel proteins of bacteria: from structure to function
… structure of “classical” bacterial β-barrel proteins in more detail and describe how the proteins
… Heat-modifiability can also be used to study structural stability of β-barrels by sampling the …
… Heat-modifiability can also be used to study structural stability of β-barrels by sampling the …