The Stability Landscape of de novo TIM Barrels Explored by a Modular Design Approach

Autor: Sina Kordes, Miguel Costas, Yasel Guerra, Cinthya Tapia, David Baker, Eréndira Rojas-Ortega, Daniel-Adriano Silva Manzano, Birte Höcker, D. Alejandro Fernández-Velasco, Sergio Romero-Romero, Sooruban Shanmugaratnam, Adela Rodríguez-Romero
Jazyk: angličtina
Rok vydání: 2021
Předmět:
Models
Molecular
Protein Conformation
alpha-Helical
Protein Folding
Melting temperature
Stability (learning theory)
Computational biology
stability landscape
ΔΔGint
Gibbs free energy of coupling
Evolution
Molecular
03 medical and health sciences
0302 clinical medicine
Protein stability
Structural Biology
(β/α)8-barrel
TIM barrel
de novo protein design
Tm
midpoint of thermal unfolding
Molecular Biology
non-additive effects
030304 developmental biology
ComputingMethodologies_COMPUTERGRAPHICS
0303 health sciences
GdnHCl
guanidinium chloride
CD
Circular Dichroism
Chemistry
business.industry
Protein Stability
DSC
Differential Scanning Calorimetry
Temperature
Proteins
protein folding and stability
A
area under the stability curve
Modular design
Folding (chemistry)
Barrel
Eact
activation energy
ΔH85°C
change in enthalpy extrapolated at 85 °C
Epistasis
Protein Conformation
beta-Strand
business
Hydrophobic and Hydrophilic Interactions
030217 neurology & neurosurgery
IF
Intrinsic Fluorescence
Research Article
Zdroj: Journal of Molecular Biology
ISSN: 1089-8638
0022-2836
Popis: Graphical abstract
Highlights • The TIM barrel is a versatile fold to understand structure-stability relationships. • A collection of de novo TIM barrels with improved hydrophobic cores was designed. • DeNovoTIMs are reversible in chemical and thermal unfolding, which is uncommon in TIM barrels. • Epistatic effects play a central role in DeNovoTIMs stabilization. • DeNovoTIMs navigate a previously uncharted region of the stability landscape.
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 manipulating protein stability provide crucial information on the molecular determinants that modulate structure and stability, and expand the applications of de novo proteins. Since the (β/⍺)8-barrel or TIM-barrel fold is one of the most common functional scaffolds, in this work we designed a collection of stable de novo TIM barrels (DeNovoTIMs), using a computational fixed-backbone and modular approach based on improved hydrophobic packing of sTIM11, the first validated de novo TIM barrel, and subjected them to a thorough folding analysis. DeNovoTIMs navigate a region of the stability landscape previously uncharted by natural TIM barrels, with variations spanning 60 degrees in melting temperature and 22 kcal per mol in conformational stability throughout the designs. Significant non-additive or epistatic effects were observed when stabilizing mutations from different regions of the barrel were combined. The molecular basis of epistasis in DeNovoTIMs appears to be related to the extension of the hydrophobic cores. This study is an important step towards the fine-tuned modulation of protein stability by design.
Databáze: OpenAIRE
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