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Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics

DOI: 10.1016/j.csbj.2020.06.021 DOI Help

Authors: Petra Babkova (Masaryk University; St. Anne's University Hospital Brno) , Zuzana Dunajova (Masaryk University) , Radka Chaloupkova (Masaryk University) , Jiri Damborsky (Masaryk University; St. Anne's University Hospital Brno) , David Bednar (Masaryk University; St. Anne's University Hospital Brno) , Martin Marek (Masaryk University)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Computational And Structural Biotechnology Journal

State: Published (Approved)
Published: June 2020
Diamond Proposal Number(s): 11175

Open Access Open Access

Abstract: Ancestral sequence reconstruction is a powerful method for inferring ancestors of modern enzymes and for studying structure-function relationships of enzymes. We have previously applied this approach to haloalkane dehalogenases (HLDs) from the subfamily HLD-II and obtained thermodynamically highly stabilized enzymes (ΔTm up to 24°C), showing improved catalytic properties. Here we combined crystallographic structural analysis and computational molecular dynamics simulations to gain insight into the mechanisms by which ancestral HLDs became more robust enzymes with novel catalytic properties. Reconstructed ancestors exhibited similar structure topology as their descendants with the exception of a few loop deviations. Strikingly, molecular dynamics simulations revealed restricted conformational dynamics of ancestral enzymes, which prefer a single state, in contrast to modern enzymes adopting two different conformational states. The restricted dynamics can potentially be linked to their exceptional stabilization. The study provides molecular insights into protein stabilization due to ancestral sequence reconstruction, which is becoming a widely used approach for obtaining robust protein catalysts.

Journal Keywords: Enzymehaloalkane dehalogenase; ancestral sequence reconstruction; thermostability; X-ray crystallography; protein simulations; conformational flexibility; protein design

Diamond Keywords: Enzymes

Subject Areas: Biology and Bio-materials, Chemistry

Instruments: I03-Macromolecular Crystallography

Added On: 23/06/2020 15:57


Discipline Tags:

Biochemistry Catalysis Chemistry Structural biology Biophysics Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX)