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
The amino acid sequences of proteins have evolved over billions of years, preserving their
structures and functions while responding to evolutionary forces. Are there conserved …
structures and functions while responding to evolutionary forces. Are there conserved …
Mapping the structure of folding cores in TIM barrel proteins by hydrogen exchange mass spectrometry: the roles of motif and sequence for the indole-3-glycerol …
Z Gu, JA Zitzewitz, CR Matthews - Journal of molecular biology, 2007 - Elsevier
To test the roles of motif and amino acid sequence in the folding mechanisms of TIM barrel
proteins, hydrogen-deuterium exchange was used to explore the structure of the stable …
proteins, hydrogen-deuterium exchange was used to explore the structure of the stable …
Topology and sequence in the folding of a TIM barrel protein: Global analysis highlights partitioning between transient off-pathway and stable on-pathway folding …
WR Forsyth, O Bilsel, Z Gu, CR Matthews - Journal of molecular biology, 2007 - Elsevier
The relative contributions of chain topology and amino acid sequence in directing the folding
of a (βα) 8 TIM barrel protein of unknown function encoded by the Bacillus subtilis iolI gene …
of a (βα) 8 TIM barrel protein of unknown function encoded by the Bacillus subtilis iolI gene …
The TIM barrel architecture facilitated the early evolution of protein-mediated metabolism
AD Goldman, JT Beatty, LF Landweber - Journal of molecular evolution, 2016 - Springer
The triosephosphate isomerase (TIM) barrel protein fold is a structurally repetitive
architecture that is present in approximately 10% of all enzymes. It is generally assumed that …
architecture that is present in approximately 10% of all enzymes. It is generally assumed that …
Frustration and folding of a TIM barrel protein
Triosephosphate isomerase (TIM) barrel proteins have not only a conserved architecture
that supports a myriad of enzymatic functions, but also a conserved folding mechanism that …
that supports a myriad of enzymatic functions, but also a conserved folding mechanism that …
Structural analysis of kinetic folding intermediates for a TIM barrel protein, indole-3-glycerol phosphate synthase, by hydrogen exchange mass spectrometry and Gō …
Z Gu, MK Rao, WR Forsyth, JM Finke… - Journal of molecular …, 2007 - Elsevier
The structures of partially folded states appearing during the folding of a (βα) 8 TIM barrel
protein, the indole-3-glycerol phosphate synthase from Sulfolobus solfataricus (sIGPS), was …
protein, the indole-3-glycerol phosphate synthase from Sulfolobus solfataricus (sIGPS), was …
βα-Hairpin clamps brace βαβ modules and can make substantive contributions to the stability of TIM barrel proteins
X Yang, SV Kathuria, R Vadrevu, CR Matthews - PLoS One, 2009 - journals.plos.org
Non-local hydrogen bonding interactions between main chain amide hydrogen atoms and
polar side chain acceptors that bracket consecutive βα or αβ elements of secondary …
polar side chain acceptors that bracket consecutive βα or αβ elements of secondary …
Similarity in shape dictates signature intrinsic dynamics despite no functional conservation in TIM barrel enzymes
The conservation of the intrinsic dynamics of proteins emerges as we attempt to understand
the relationship between sequence, structure and functional conservation. We characterise …
the relationship between sequence, structure and functional conservation. We characterise …
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-barrel fold. Here we describe the computational design of four-fold symmetrical (β/α) 8 …
Diversity in αβ and βα Loop Connections in TIM Barrel Proteins: Implications for Stability and Design of the Fold
RV Kadumuri, R Vadrevu - Interdisciplinary Sciences: Computational Life …, 2018 - Springer
Abstract The (βα) 8/TIM barrel is one of the most common folds of known protein structures
facilitating diverse catalytic functions. The fold is formed by the repetition of the basic βαβ …
facilitating diverse catalytic functions. The fold is formed by the repetition of the basic βαβ …