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Zeballos N, Comino N, Andrés-Sanz D, Santiago-Arcos J, Azkargorta M, Elortza F, Diamanti E, López-Gallego F. Region-Directed Enzyme Immobilization through Engineering Protein Surface with Histidine Clusters. ACS APPLIED MATERIALS & INTERFACES 2024; 16:833-846. [PMID: 38135284 PMCID: PMC10788835 DOI: 10.1021/acsami.3c15993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Enzyme immobilization is a key enabling technology for a myriad of industrial applications, yet immobilization science is still too empirical to reach highly active and robust heterogeneous biocatalysts through a general approach. Conventional protein immobilization methods lack control over how enzymes are oriented on solid carriers, resulting in negative conformational changes that drive enzyme deactivation. Site-selective enzyme immobilization through peptide tags and protein domains addresses the orientation issue, but this approach limits the possible orientations to the N- and C-termini of the target enzyme. In this work, we engineer the surface of two model dehydrogenases to introduce histidine clusters into flexible regions not involved in catalysis, through which immobilization is driven. By varying the position and the histidine density of the clusters, we create a small library of enzyme variants to be immobilized on different carriers functionalized with different densities of various metal chelates (Co2+, Cu2+, Ni2+, and Fe3+). We first demonstrate that His-clusters can be as efficient as the conventional His-tags in immobilizing enzymes, recovering even more activity and gaining stability against some denaturing agents. Furthermore, we find that the enzyme orientation as well as the type and density of the metal chelates affect the immobilization parameters (immobilization yield and recovered activity) and the stability of the immobilized enzymes. According to proteomic studies, His-clusters enable a different enzyme orientation as compared to His-tag. Finally, these oriented heterogeneous biocatalysts are implemented in batch reactions, demonstrating that the stability achieved by an optimized orientation translates into increased operational stability.
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Affiliation(s)
- Nicoll Zeballos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Natalia Comino
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Daniel Andrés-Sanz
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Javier Santiago-Arcos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Mikel Azkargorta
- Center
for Cooperative Research in Biology (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 800 Bld, 48160 Derio, Bizkaia, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Felix Elortza
- Center
for Cooperative Research in Biology (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 800 Bld, 48160 Derio, Bizkaia, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Eleftheria Diamanti
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Fernando López-Gallego
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
- Ikerbasque,
Basque Foundation for Science, 48013 Bilbao, Spain
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Abellanas-Perez P, Carballares D, Rocha-Martin J, Fernandez-Lafuente R. The effects of the chemical modification on immobilized lipase features are affected by the enzyme crowding in the support. Biotechnol Prog 2024; 40:e3394. [PMID: 37828788 DOI: 10.1002/btpr.3394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/07/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
In this article, we have analyzed the interactions between enzyme crowding on a given support and its chemical modification (ethylenediamine modification via the carbodiimide route and picryl sulfonic (TNBS) modification of the primary amino groups) on the enzyme activity and stability. Lipase from Thermomyces lanuginosus (TLL) and lipase B from Candida antarctica (CALB) were immobilized on octyl-agarose beads at two very different enzyme loadings, one of them exceeding the capacity of the support, one well under this capacity. Chemical modifications of the highly loaded and lowly loaded biocatalysts gave very different results in terms of activity and stability, which could increase or decrease enzyme activity depending on the enzyme support loading. For example, both lowly loaded biocatalysts increased their activity after modification while the effect was the opposite for the highly loaded biocatalysts. Additionally, the modification with TNBS of highly loaded CALB biocatalyst increased its stability while decrease the activity.
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Affiliation(s)
| | - Diego Carballares
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, Madrid, Spain
| | - Javier Rocha-Martin
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
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Yang Z, Huang Z, Wu Q, Tang X, Huang Z. Cold-Adapted Proteases: An Efficient and Energy-Saving Biocatalyst. Int J Mol Sci 2023; 24:ijms24108532. [PMID: 37239878 DOI: 10.3390/ijms24108532] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/30/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
The modern biotechnology industry has a demand for macromolecules that can function in extreme environments. One example is cold-adapted proteases, possessing advantages such as maintaining high catalytic efficiency at low temperature and low energy input during production and inactivation. Meanwhile, cold-adapted proteases are characterised by sustainability, environmental protection, and energy conservation; therefore, they hold significant economic and ecological value regarding resource utilisation and the global biogeochemical cycle. Recently, the development and application of cold-adapted proteases have gained gaining increasing attention; however, their applications potential has not yet been fully developed, which has seriously restricted the promotion and application of cold-adapted proteases in the industry. This article introduces the source, related enzymology characteristics, cold resistance mechanism, and the structure-function relationship of cold-adapted proteases in detail. This is in addition to discussing related biotechnologies to improve stability, emphasise application potential in clinical medical research, and the constraints of the further developing of cold-adapted proteases. This article provides a reference for future research and the development of cold-adapted proteases.
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Affiliation(s)
- Zhengfeng Yang
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650000, China
| | - Zhendi Huang
- School of Life Sciences, Yunnan Normal University, Kunming 650000, China
| | - Qian Wu
- School of Life Sciences, Yunnan Normal University, Kunming 650000, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming 650000, China
| | - Xianghua Tang
- School of Life Sciences, Yunnan Normal University, Kunming 650000, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming 650000, China
| | - Zunxi Huang
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming 650000, China
- School of Life Sciences, Yunnan Normal University, Kunming 650000, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming 650000, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650000, China
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Roda S, Terholsen H, Meyer JRH, Cañellas-Solé A, Guallar V, Bornscheuer U, Kazemi M. AsiteDesign: a Semirational Algorithm for an Automated Enzyme Design. J Phys Chem B 2023; 127:2661-2670. [PMID: 36944360 PMCID: PMC10068746 DOI: 10.1021/acs.jpcb.2c07091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
With advances in protein structure predictions, the number of available high-quality structures has increased dramatically. In light of these advances, structure-based enzyme engineering is expected to become increasingly important for optimizing biocatalysts for industrial processes. Here, we present AsiteDesign, a Monte Carlo-based protocol for structure-based engineering of active sites. AsiteDesign provides a framework for introducing new catalytic residues in a given binding pocket to either create a new catalytic activity or alter the existing one. AsiteDesign is implemented using pyRosetta and incorporates enhanced sampling techniques to efficiently explore the search space. The protocol was tested by designing an alternative catalytic triad in the active site of Pseudomonas fluorescens esterase (PFE). The designed variant was experimentally verified to be active, demonstrating that AsiteDesign can find alternative catalytic triads. Additionally, the AsiteDesign protocol was employed to enhance the hydrolysis of a bulky chiral substrate (1-phenyl-2-pentyl acetate) by PFE. The experimental verification of the designed variants demonstrated that F158L/F198A and F125A/F158L mutations increased the hydrolysis of 1-phenyl-2-pentyl acetate from 8.9 to 66.7 and 23.4%, respectively, and reversed the enantioselectivity of the enzyme from (R) to (S)-enantiopreference, with 32 and 55% enantiomeric excess (ee), respectively.
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Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell, 1-3, Barcelona 08034, Spain
| | - Henrik Terholsen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Jule Ruth Heike Meyer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Albert Cañellas-Solé
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell, 1-3, Barcelona 08034, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell, 1-3, Barcelona 08034, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, 23, Barcelona 08010, Spain
| | - Uwe Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Masoud Kazemi
- Barcelona Supercomputing Center (BSC), Plaça d'Eusebi Güell, 1-3, Barcelona 08034, Spain
- Biomatter Designs, Žirmu̅n̨ g. 139A, Vilnius 09120, Lithuania
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