The complex role of sequence and structure in the stability and function of the TIM barrel proteins

YH Chan - 2017 - repository.escholarship.umassmed …
Sequence divergence of orthologous proteins enables adaptation to a plethora of
environmental stresses and promotes evolution of novel functions. As one of the most …

Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints

YH Chan, SV Venev, KB Zeldovich… - Nature …, 2017 - nature.com
Sequence divergence of orthologous proteins enables adaptation to environmental stresses
and promotes evolution of novel functions. Limits on evolution imposed by constraints on …

Stepwise introduction of stabilizing mutations reveals nonlinear additive effects in de novo TIM barrels

JS Koch, S Romero‐Romero, B Höcker - Protein Science, 2024 - Wiley Online Library
Over the past decades, the TIM‐barrel fold has served as a model system for the exploration
of how changes in protein sequences affect their structural, stability, and functional …

[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 …

Alternative splice variants in TIM barrel proteins from human genome correlate with the structural and evolutionary modularity of this versatile protein fold

A Ochoa-Leyva, G Montero-Morán, G Saab-Rincón… - Plos one, 2013 - journals.plos.org
After the surprisingly low number of genes identified in the human genome, alternative
splicing emerged as a major mechanism to generate protein diversity in higher eukaryotes …

[HTML][HTML] De novo design of a highly stable ovoid TIM barrel: Unlocking pocket shape towards functional design

E ChuAlexander, R EguchiRaphael - BioDesign Research, 2022 - spj.science.org
The ability to finely control the structure of protein folds is an important prerequisite to
functional protein design. The TIM barrel fold is an important target for these efforts as it is …

Diversifying de novo TIM barrels by hallucination

J Beck, S Shanmugaratnam, B Höcker - Protein Science, 2024 - Wiley Online Library
De novo protein design expands the protein universe by creating new sequences to
accomplish tailor‐made enzymes in the future. A promising topology to implement diverse …

De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy

PS Huang, K Feldmeier, F Parmeggiani… - Nature chemical …, 2016 - nature.com
Despite efforts for over 25 years, de novo protein design has not succeeded in achieving the
TIM-barrel fold. Here we describe the computational design of four-fold symmetrical (β/α) 8 …

TIM Barrels 2.0–Stabilizing and Diversifying a De Novo Designed Protein

S Kordes - 2023 - epub.uni-bayreuth.de
The TIM barrel is one of the oldest and most ubiquitous protein folds and is often referred to
as the most successful in nature, due to its capability to host a diverse set of functions. This …

Learning to Design Protein Structure and Sequence

AE Chu - 2023 - search.proquest.com
The ability to finely control the structure of protein folds is an important prerequisite to
functional protein design. The TIM barrel fold is an important target for these efforts as it is …