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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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2
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Abstract
Metalloproteins play diverse and critical functions in all living systems, and their dysfunctional forms are closely related to many human diseases. The development of methods that enable comprehensive mapping of metalloproteome is of great interest to help elucidate crucial roles of metalloproteins in both physiology and pathology, as well as to discover new metalloproteins. We herein briefly review recent progress in the field of metalloproteomics and provide future outlooks.
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Affiliation(s)
- Xin Zeng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yao Cheng
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing 100871, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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3
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Wang MS, Hoegler KJ, Hecht MH. Unevolved De Novo Proteins Have Innate Tendencies to Bind Transition Metals. Life (Basel) 2019; 9:E8. [PMID: 30634485 PMCID: PMC6463171 DOI: 10.3390/life9010008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/31/2018] [Accepted: 01/04/2019] [Indexed: 11/16/2022] Open
Abstract
Life as we know it would not exist without the ability of protein sequences to bind metal ions. Transition metals, in particular, play essential roles in a wide range of structural and catalytic functions. The ubiquitous occurrence of metalloproteins in all organisms leads one to ask whether metal binding is an evolved trait that occurred only rarely in ancestral sequences, or alternatively, whether it is an innate property of amino acid sequences, occurring frequently in unevolved sequence space. To address this question, we studied 52 proteins from a combinatorial library of novel sequences designed to fold into 4-helix bundles. Although these sequences were neither designed nor evolved to bind metals, the majority of them have innate tendencies to bind the transition metals copper, cobalt, and zinc with high nanomolar to low-micromolar affinity.
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Affiliation(s)
- Michael S Wang
- Department of Chemistry, Princeton University, Princeton, NJ 08540, USA.
| | - Kenric J Hoegler
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA.
| | - Michael H Hecht
- Department of Chemistry, Princeton University, Princeton, NJ 08540, USA.
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Sharifa Zaithun B, Emilia A, Mohamed Ibrahim Mohamed T, Karen Anne C, Mohd Basyaruddin AR. Histidine-based copper tetrapeptides as enantioselective catalysts for aldol reactions. RSC Adv 2018; 8:34004-34011. [PMID: 35548802 PMCID: PMC9086720 DOI: 10.1039/c8ra06814c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/18/2018] [Indexed: 12/18/2022] Open
Abstract
Copper(ii)-peptides are widely used as industrial catalysts such as in the aerobic oxidation of organic molecules, formation of new C–H bonds and in the azide–alkyne cycloaddition reaction. The length of peptides and the effect of adding copper metal into peptides were questioned in their field of applications. Five novel histidine-based tetrapeptides with the sequences HAAD (P1), HAFD (P2), HAVD (P3), AGHD (P4) and PGHD (P5) were synthesized using the solid phase peptide scheme and analysed with high performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) with percentage purities as high as 99.5%. All the peptides were positively charged (+1) and the molecular weight calculated from m/z values of MS results coincided with the theoretical molecular weight of the peptides. Copper(ii)-peptides derived from these peptides and copper(ii) acetate monohydrate (CuP1–CuP5) in a 1 : 2 ratio was synthesised, purified and characterised by ultraviolet-visible spectroscopy (UV-Vis), ultraviolet-fluorescence spectroscopy (fluorescence) and fourier transform infrared spectroscopy (FTIR), circular dichroism spectroscopy (CD) and optical rotation polarimetry. It provided the necessary information on the secondary structure and the successful binding of copper(ii) to the specific amino acids, hence leading to the putative geometry of copper(ii)-peptides and the difference in the chirality of amino acids, peptides and copper(ii)-peptides. The catalytic activities of the synthesised complexes were evaluated. CuP1 & CuP3 catalysed both the asymmetric aldol reactions with high enantioselectivity of p-nitrobenzaldehyde with cyclohexanone (% ee = 87.3 & 80.3, respectively) and of p-anisaldehyde with cyclohexanone (% ee = 95.5 & 90.9, respectively). P5 with the sequence H2N-PGHD-CONH.![]()
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Affiliation(s)
- Begum Sharifa Zaithun
- Integrated Chemical BioPhysics Research, Faculty of Science, Universiti Putra Malaysia 43400 UPM Serdang Selangor Malaysia
| | - AbdulMalek Emilia
- Integrated Chemical BioPhysics Research, Faculty of Science, Universiti Putra Malaysia 43400 UPM Serdang Selangor Malaysia.,Department of Chemistry, Faculty of Science, Universiti Putra Malaysia 43400 UPM Serdang Selangor Malaysia
| | | | - Crouse Karen Anne
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia 43400 UPM Serdang Selangor Malaysia
| | - Abdul Rahman Mohd Basyaruddin
- Integrated Chemical BioPhysics Research, Faculty of Science, Universiti Putra Malaysia 43400 UPM Serdang Selangor Malaysia.,Department of Chemistry, Faculty of Science, Universiti Putra Malaysia 43400 UPM Serdang Selangor Malaysia
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5
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Martin EM, Kondrat FDL, Stewart AJ, Scrivens JH, Sadler PJ, Blindauer CA. Native electrospray mass spectrometry approaches to probe the interaction between zinc and an anti-angiogenic peptide from histidine-rich glycoprotein. Sci Rep 2018; 8:8646. [PMID: 29872214 PMCID: PMC5988744 DOI: 10.1038/s41598-018-26924-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/17/2018] [Indexed: 12/11/2022] Open
Abstract
Zinc modulates the biological function of histidine-rich glycoprotein (HRG) through binding to its His-rich region (HRR). The Zn2+-binding properties of a 35 amino-acid biologically-active peptide mimic of the HRR, HRGP330, were investigated using dissociative mass spectrometry approaches in addition to travelling-wave ion mobility mass spectrometry (TWIM-MS). Native mass spectrometry confirmed zinc binding to HRGP330; however, broadening of the 1H NMR resonances upon addition of Zn2+ ions precluded the attainment of structural information. A complementary approach employing TWIM-MS indicated that HRGP330 has a more compact structure in the presence of Zn2+ ions. Top-down MS/MS data supported a metal-binding-induced conformational change, as fewer fragments were observed for Zn2+-bound HRGP330. Zn2+-bound fragments of both N-terminal and C-terminal ends of the peptide were identified from collision-induced dissociation (CID) and electron transfer dissociation/proton transfer reaction (ETD/PTR) experiments, suggesting that multiple binding sites exist within this region of HRG. The combination of mass spectrometry and NMR approaches provides new insight into the highly dynamic interaction between zinc and this His-rich peptide.
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Affiliation(s)
- Esther M Martin
- Department of Chemistry, University of Warwick, Coventry, UK
- Medimmune, Cambridge, UK
| | - Frances D L Kondrat
- School of Life Sciences, University of Warwick, Coventry, UK
- Immunocore Ltd, Abingdon, UK
| | - Alan J Stewart
- School of Medicine, University of St Andrews, St Andrews, UK
| | - James H Scrivens
- School of Life Sciences, University of Warwick, Coventry, UK
- School of Science, Engineering and Design, Teeside University, Middlesbrough, UK
| | - Peter J Sadler
- Department of Chemistry, University of Warwick, Coventry, UK
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7
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Urease inactivation by an unusual GroES chaperonin. Sci China Chem 2014. [DOI: 10.1007/s11426-014-5088-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Rowinska-Zyrek M, Zakrzewska-Czerwinska J, Zawilak-Pawlik A, Kozlowski H. Ni2+chemistry in pathogens – a possible target for eradication. Dalton Trans 2014; 43:8976-89. [DOI: 10.1039/c4dt00421c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nickel homeostasis inHelicobacter pyloriand potential histidine-rich binding sites from various bacterial and fungal pathogens are discussed.
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Affiliation(s)
| | - Jolanta Zakrzewska-Czerwinska
- Faculty of Biotechnology
- University of Wroclaw
- 50-383 Wroclaw, Poland
- Institute of Immunology and Experimental Therapy
- Polish Academy of Sciences
| | - Anna Zawilak-Pawlik
- Institute of Immunology and Experimental Therapy
- Polish Academy of Sciences
- Department of Microbiology
- 53-114 Wrocław, Poland
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Grasso G, Magrì A, Bellia F, Pietropaolo A, La Mendola D, Rizzarelli E. The copper(II) and zinc(II) coordination mode of HExxH and HxxEH motif in small peptides: the role of carboxylate location and hydrogen bonding network. J Inorg Biochem 2013; 130:92-102. [PMID: 24184693 DOI: 10.1016/j.jinorgbio.2013.09.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/30/2013] [Accepted: 09/30/2013] [Indexed: 10/26/2022]
Abstract
Copper(II) and zinc(II) complexes with two hexapeptides encompassing HExxH and HxxEH motif were characterized by means of a combined experimental and theoretical approach. Parallel tempering and density functional theory (DFT) investigations show the presence of different hydrogen bonding networks between the copper(II) and zinc(II) complexes with the two peptides, suggesting a significant contribution of these non-covalent interactions to the stability constant values. The glutamate carboxylate group has a direct role in metal ion binding. The location of this amino acid along the sequence of the investigated peptides is critical to determine thermodynamic and spectroscopic features of the copper(II) complex species, whereas is less relevant in the zinc(II) complexes formation. Electrospray ionization mass spectrometry (ESI-MS) characterization of the zinc(II) complex species show that in the [ZnH-2L] two deprotonated amide nitrogen atoms are involved in the metal coordination environment, an uncommon behavior in zinc(II) complexes for multi-histidine ligands.
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Affiliation(s)
- Giuseppe Grasso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, 95125 Catania, Italy
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Cheng T, Xia W, Wang P, Huang F, Wang J, Sun H. Histidine-rich proteins in prokaryotes: metal homeostasis and environmental habitat-related occurrence. Metallomics 2013; 5:1423-9. [DOI: 10.1039/c3mt00059a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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