1
|
Borghesani V, Zastrow ML, Tolbert AE, Deb A, Penner-Hahn JE, Pecoraro VL. Co(II) Substitution Enhances the Esterase Activity of a de Novo Designed Zn(II) Carbonic Anhydrase. Chemistry 2024; 30:e202304367. [PMID: 38377169 PMCID: PMC11045307 DOI: 10.1002/chem.202304367] [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: 12/29/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 02/22/2024]
Abstract
Carbonic Anhydrases (CAs) have been a target for de novo protein designers due to the simplicity of the active site and rapid rate of the reaction. The first reported mimic contained a Zn(II) bound to three histidine imidazole nitrogens and an exogenous water molecule, hence closely mimicking the native enzymes' first coordination sphere. Co(II) has served as an alternative metal to interrogate CAs due to its d7 electronic configuration for more detailed solution characterization. We present here the Co(II) substituted [Co(II)(H2O/OH-)]N(TRIL2WL23H)3 n+ that behaves similarly to native Co(II) substituted human-CAs. Like the Zn(II) analogue, the cobalt-derivative at slightly basic pH is incapable of hydrolyzing p-nitrophenylacetate (pNPA); however, as the pH is increased a significant activity develops, which at pH values above 10 eventually yields a catalytic efficiency that exceeds that of the [Zn(II)(OH-)]N(TRIL2WL23H)3 + peptide complex. X-ray absorption analysis is consistent with an octahedral species at pH 7.5 that converts to a 5-coordinate species by pH 11. UV-vis spectroscopy can monitor this transition, giving a pKa for the conversion of 10.3. We assign this conversion to the formation of a 5-coordinate Co(II)(Nimid)3(OH)(H2O) species. The pH dependent kinetic analysis indicates the maximal rate (kcat), and thus the catalytic efficiency (kcat/Km), follow the same pH profile as the spectroscopic conversion to the pentacoordinate species. This correlation suggests that the chemically irreversible ester hydrolysis corresponds to the rate determining process.
Collapse
Affiliation(s)
- Valentina Borghesani
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI-48109-1055, United States
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle, Scienze 11A, 43124, Parma, Italy
| | - Melissa L Zastrow
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI-48109-1055, United States
- Department of Chemistry, University of Houston, 3585 Cullen Blvd, Houston, TX-77204, United States
| | - Audrey E Tolbert
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI-48109-1055, United States
| | - Aniruddha Deb
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI-48109-1055, United States
| | - James E Penner-Hahn
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI-48109-1055, United States
| | - Vincent L Pecoraro
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI-48109-1055, United States
| |
Collapse
|
2
|
Pham TL, Conde González MR, Fazliev S, Kishore A, Comba P, Thomas F. Relationship of Thermostability and Binding Affinity in Metal-binding WW-Domain Minireceptors. Chembiochem 2024; 25:e202300715. [PMID: 38127995 DOI: 10.1002/cbic.202300715] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023]
Abstract
The design of metallo-miniproteins advances our understanding of the structural and functional roles of metals in proteins. We recently designed a metal-binding WW domain, WW-CA-Nle, which displays three histidine residues on its surface for coordination of divalent metals Ni(II), Zn(II) and Cu(II). However, WW-CA-Nle is a molten globule in the apo state and thus showed only moderate binding affinities with Kd values in the μM regime. In this report, we hypothesize that improved thermal stability of the apo state of the metal binding WW-domain scaffold should lead to improved preorganization of the metal-binding site and consequently to higher metal-binding affinities. By redesigning WW-CA-Nle, we obtained WW-CA variants, WW-CA-min and WW-CA-ANG, which were fully folded in the apo states and displayed moderate to excellent thermostabilities in the apo and holo states. We were able to show that the improved thermal stabilities led to improved metal binding, which was reflected in Kd values that were at least one order of magnitude lower compared to WW-CA-Nle. EPR spectroscopy and ITC measurements revealed a better defined and predisposed metal binding site in WW-CA-ANG.
Collapse
Affiliation(s)
- Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Marcos R Conde González
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Max Planck School Matter to Life
| | - Sunnatullo Fazliev
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Max Planck School Matter to Life
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Agi Kishore
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Max Planck School Matter to Life
- Institute of Inorganic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Peter Comba
- Institute of Inorganic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| |
Collapse
|
3
|
Stingley KJ, Carpenter BA, Kean KM, Waters ML. Mismatched covalent and noncovalent templating leads to large coiled coil-templated macrocycles. Chem Sci 2023; 14:4935-4944. [PMID: 37181761 PMCID: PMC10171189 DOI: 10.1039/d3sc00231d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/02/2023] [Indexed: 04/05/2023] Open
Abstract
Herein we describe the use of dynamic combinatorial chemistry to self-assemble complex coiled coil motifs. We amide-coupled a series of peptides designed to form homodimeric coiled coils with 3,5-dithiobenzoic acid (B) at the N-terminus and then allowed each B-peptide to undergo disulfide exchange. In the absence of peptide, monomer B forms cyclic trimers and tetramers, and thus we expected that addition of the peptide to monomer B would shift the equilibrium towards the tetramer to maximize coiled coil formation. Unexpectedly, we found that internal templation of the B-peptide through coiled coil formation shifts the equilibrium towards larger macrocycles up to 13 B-peptide subunits, with a preference for 4, 7, and 10-membered macrocycles. These macrocyclic assemblies display greater helicity and thermal stability relative to intermolecular coiled coil homodimer controls. The preference for large macrocycles is driven by the strength of the coiled coil, as increasing the coiled coil affinity increases the fraction of larger macrocycles. This system represents a new approach towards the development of complex peptide and protein assemblies.
Collapse
Affiliation(s)
- Kyla J Stingley
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
| | - Benjamin A Carpenter
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
| | - Kelsey M Kean
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
| | - Marcey L Waters
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
| |
Collapse
|
4
|
Lau ECHT, Åhlén M, Cheung O, Ganin AY, Smith DGE, Yiu HHP. Gold-iron oxide (Au/Fe3O4) magnetic nanoparticles as the nanoplatform for binding of bioactive molecules through self-assembly. Front Mol Biosci 2023; 10:1143190. [PMID: 37051321 PMCID: PMC10083301 DOI: 10.3389/fmolb.2023.1143190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/15/2023] [Indexed: 03/28/2023] Open
Abstract
Nanomedicine plays a crucial role in the development of next-generation therapies. The use of nanoparticles as drug delivery platforms has become a major area of research in nanotechnology. To be effective, these nanoparticles must interact with desired drug molecules and release them at targeted sites. The design of these “nanoplatforms” typically includes a functional core, an organic coating with functional groups for drug binding, and the drugs or bioactive molecules themselves. However, by exploiting the coordination chemistry between organic molecules and transition metal centers, the self-assembly of drugs onto the nanoplatform surfaces can bypass the need for an organic coating, simplifying the materials synthesis process. In this perspective, we use gold-iron oxide nanoplatforms as examples and outline the prospects and challenges of using self-assembly to prepare drug-nanoparticle constructs. Through a case study on the binding of insulin on Au-dotted Fe3O4 nanoparticles, we demonstrate how a self-assembly system can be developed. This method can also be adapted to other combinations of transition metals, with the potential for scaling up. Furthermore, the self-assembly method can also be considered as a greener alternative to traditional methods, reducing the use of chemicals and solvents. In light of the current climate of environmental awareness, this shift towards sustainability in the pharmaceutical industry would be welcomed.
Collapse
Affiliation(s)
- Elizabeth C. H. T. Lau
- Institute of Chemical Science, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, United Kingdom
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Michelle Åhlén
- Division of Nanotechnology and Functional Materials, Department of Material Sciences and Engineering, Uppsala University, Uppsala, Sweden
| | - Ocean Cheung
- Division of Nanotechnology and Functional Materials, Department of Material Sciences and Engineering, Uppsala University, Uppsala, Sweden
| | - Alexey Y. Ganin
- School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | - David G. E. Smith
- Institute of Biological Chemistry, Biophysics and Bioengineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, United Kingdom
| | - Humphrey H. P. Yiu
- Institute of Chemical Science, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, United Kingdom
- *Correspondence: Humphrey H. P. Yiu,
| |
Collapse
|
5
|
Bragança PMS, Carepo MSP, Pauleta SR, Pinter TBJ, Elia M, Cordas CM, Moura I, Pecoraro VL, Moura JJG. Incorporation of a molybdenum atom in a Rubredoxin-type Centre of a de novo-designed α 3DIV-L21C three-helical bundle peptide. J Inorg Biochem 2023; 240:112096. [PMID: 36603242 PMCID: PMC11232944 DOI: 10.1016/j.jinorgbio.2022.112096] [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: 09/29/2022] [Revised: 11/17/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022]
Abstract
The rational design and functionalization of small, simple, and stable peptides scaffolds is an attractive avenue to mimic catalytic metal-centres of complex proteins, relevant for the design of metalloenzymes with environmental, biotechnological and health impacts. The de novo designed α3DIV-L21C framework has a rubredoxin-like metal binding site and was used in this work to incorporate a Mo-atom. Thermostability studies using differential scanning calorimetry showed an increase of 4 °C in the melting temperature of the Mo-α3DIV-L21C when compared to the apo-α3DIV-L21C. Circular dichroism in the visible and far-UV regions corroborated these results showing that Mo incorporation provides stability to the peptide even though there were almost no differences observed in the secondary structure. A formal reduction potential of ∼ -408 mV vs. NHE, pH 7.6 was determined. Combining electrochemical results, EPR and UV-visible data we discuss the oxidation state of the molybdenum centre in Mo-α3DIV-L21C and propose that is mainly in a Mo (VI) oxidation state.
Collapse
Affiliation(s)
- Pedro M S Bragança
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Microbial Stress Lab, UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Marta S P Carepo
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Escola de Psicologia e Ciências da Vida, Departamento de Ciências da Vida, Universidade Lusófona de Humanidades e Tecnologias, Campo Grande, 1749-024 Lisboa, Portugal.
| | - Sofia R Pauleta
- Microbial Stress Lab, UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Tyler B J Pinter
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Maddalena Elia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Cristina M Cordas
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Isabel Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Vincent L Pecoraro
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - José J G Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.
| |
Collapse
|
6
|
Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
Collapse
Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | |
Collapse
|
7
|
Aupič J, Lapenta F, Strmšek Ž, Merljak E, Plaper T, Jerala R. Metal ion-regulated assembly of designed modular protein cages. SCIENCE ADVANCES 2022; 8:eabm8243. [PMID: 35714197 PMCID: PMC9205593 DOI: 10.1126/sciadv.abm8243] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Coiled-coil (CC) dimers are versatile, customizable building modules for the design of diverse protein architectures unknown in nature. Incorporation of dynamic self-assembly, regulated by a selected chemical signal, represents an important challenge in the construction of functional polypeptide nanostructures. Here, we engineered metal binding sites to render an orthogonal set of CC heterodimers Zn(II)-responsive as a generally applicable principle. The designed peptides assemble into CC heterodimers only in the presence of Zn(II) ions, reversibly dissociate by metal ion sequestration, and additionally act as pH switches, with low pH triggering disassembly. The developed Zn(II)-responsive CC set is used to construct programmable folding of CC-based nanostructures, from protein triangles to a two-chain bipyramidal protein cage that closes and opens depending on the metal ion. This demonstrates that dynamic self-assembly can be designed into CC-based protein cages by incorporation of metal ion-responsive CC building modules that act as conformational switches and that could also be used in other contexts.
Collapse
Affiliation(s)
- Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Estera Merljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, SI-1000 Ljubljana, Slovenia
| | - Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, SI-1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
8
|
Tanaka T, Kuroiwa K. Supramolecular Hybrids from Cyanometallate Complexes and Diblock Copolypeptide Amphiphiles in Water. Molecules 2022; 27:3262. [PMID: 35630738 PMCID: PMC9143414 DOI: 10.3390/molecules27103262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/20/2022] Open
Abstract
The self-assembly of discrete cyanometallates has attracted significant interest due to the potential of these materials to undergo soft metallophilic interactions as well as their optical properties. Diblock copolypeptide amphiphiles have also been investigated concerning their capacity for self-assembly into morphologies such as nanostructures. The present work combined these two concepts by examining supramolecular hybrids comprising cyanometallates with diblock copolypeptide amphiphiles in aqueous solutions. Discrete cyanometallates such as [Au(CN)2]-, [Ag(CN)2]-, and [Pt(CN)4]2- dispersed at the molecular level in water cannot interact with each other at low concentrations. However, the results of this work demonstrate that the addition of diblock copolypeptide amphiphiles such as poly-(L-lysine)-block-(L-cysteine) (Lysm-b-Cysn) to solutions of these complexes induces the supramolecular assembly of the discrete cyanometallates, resulting in photoluminescence originating from multinuclear complexes with metal-metal interactions. Electron microscopy images confirmed the formation of nanostructures of several hundred nanometers in size that grew to form advanced nanoarchitectures, including those resembling the original nanostructures. This concept of combining diblock copolypeptide amphiphiles with discrete cyanometallates allows the design of flexible and functional supramolecular hybrid systems in water.
Collapse
Affiliation(s)
| | - Keita Kuroiwa
- Department of Nanoscience, Faculty of Engineering, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan;
| |
Collapse
|
9
|
Steiner M, Reiher M. Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis. Top Catal 2022; 65:6-39. [PMID: 35185305 PMCID: PMC8816766 DOI: 10.1007/s11244-021-01543-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/11/2022]
Abstract
Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis on a par with experimental research in the field. Several advantages of this approach are key to catalysis: (i) automation allows one to consider orders of magnitude more structures in a systematic and open-ended fashion than what would be accessible by manual inspection. Eventually, full resolution in terms of structural varieties and conformations as well as with respect to the type and number of potentially important elementary reaction steps (including decomposition reactions that determine turnover numbers) may be achieved. (ii) Fast electronic structure methods with uncertainty quantification warrant high efficiency and reliability in order to not only deliver results quickly, but also to allow for predictive work. (iii) A high degree of autonomy reduces the amount of manual human work, processing errors, and human bias. Although being inherently unbiased, it is still steerable with respect to specific regions of an emerging network and with respect to the addition of new reactant species. This allows for a high fidelity of the formalization of some catalytic process and for surprising in silico discoveries. In this work, we first review the state of the art in computational catalysis to embed autonomous explorations into the general field from which it draws its ingredients. We then elaborate on the specific conceptual issues that arise in the context of autonomous computational procedures, some of which we discuss at an example catalytic system.
Collapse
Affiliation(s)
- Miguel Steiner
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| |
Collapse
|
10
|
Huang XL. What are the inorganic nanozymes? Artificial or inorganic enzymes! NEW J CHEM 2022. [DOI: 10.1039/d2nj02088b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The research on inorganic nanozymes remains very active since the first paper on the “intrinsic peroxidase-like properties of ferromagnetic nanoparticles” was published in Nature Nanotechnology in 2007. However, there is...
Collapse
|
11
|
Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
Collapse
Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| |
Collapse
|
12
|
Pachisia S, Gupta R. Supramolecular catalysis: the role of H-bonding interactions in substrate orientation and activation. Dalton Trans 2021; 50:14951-14966. [PMID: 34617524 DOI: 10.1039/d1dt02131a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen bonding plays significant roles in various biological processes during substrate orientation and binding and therefore assists in assorted organic transformations. However, replicating the intricate selection of hydrogen bonds, as observed in nature, in synthetic complexes has met with only limited success. Despite this fact, recent times have seen the emergence of several notable examples where hydrogen bonds have been introduced in synthetic complexes. A few such examples have also illustrated the substantial role played by the hydrogen bonds in influencing and often controlling the catalytic outcome. This perspective presents selected examples illustrating the significance of hydrogen bonds offered by the coordination and the organometallic complexes that aid in providing the desired orientation to a substrate adjacent to a catalytic metal center and remarkably assisting in the catalysis.
Collapse
Affiliation(s)
- Sanya Pachisia
- Department of Chemistry, University of Delhi, Delhi - 110007, India.
| | - Rajeev Gupta
- Department of Chemistry, University of Delhi, Delhi - 110007, India.
| |
Collapse
|
13
|
Unravelling the Structure of the Tetrahedral Metal-Binding Site in METP3 through an Experimental and Computational Approach. Molecules 2021; 26:molecules26175221. [PMID: 34500655 PMCID: PMC8434281 DOI: 10.3390/molecules26175221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022] Open
Abstract
Understanding the structural determinants for metal ion coordination in metalloproteins is a fundamental issue for designing metal binding sites with predetermined geometry and activity. In order to achieve this, we report in this paper the design, synthesis and metal binding properties of METP3, a homodimer made up of a small peptide, which self assembles in the presence of tetrahedrally coordinating metal ions. METP3 was obtained through a redesign approach, starting from the previously developed METP molecule. The undecapeptide sequence of METP, which dimerizes to house a Cys4 tetrahedral binding site, was redesigned in order to accommodate a Cys2His2 site. The binding properties of METP3 were determined toward different metal ions. Successful assembly of METP3 with Co(II), Zn(II) and Cd(II), in the expected 2:1 stoichiometry and tetrahedral geometry was proven by UV-visible spectroscopy. CD measurements on both the free and metal-bound forms revealed that the metal coordination drives the peptide chain to fold into a turned conformation. Finally, NMR data of the Zn(II)-METP3 complex, together with a retrostructural analysis of the Cys-X-X-His motif in metalloproteins, allowed us to define the model structure. All the results establish the suitability of the short METP sequence for accommodating tetrahedral metal binding sites, regardless of the first coordination ligands.
Collapse
|
14
|
Lella M, Mahalakshmi R. De novo
design of metal‐binding cleft in a
Trp‐Trp
stapled thermostable β‐hairpin peptide. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Muralikrishna Lella
- Molecular Biophysics Laboratory, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| |
Collapse
|
15
|
Nguyen H, Kleingardner J. Identifying metal binding amino acids based on backbone geometries as a tool for metalloprotein engineering. Protein Sci 2021; 30:1247-1257. [PMID: 33829594 DOI: 10.1002/pro.4074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 01/03/2023]
Abstract
Metal cofactors within proteins perform a versatile set of essential cellular functions. In order to take advantage of the diverse functionality of metalloproteins, researchers have been working to design or modify metal binding sites in proteins to rationally tune the function or activity of the metal cofactor. This study has performed an analysis on the backbone atom geometries of metal-binding amino acids among 10 different metal binding sites within the entire protein data bank. A set of 13 geometric parameters (features) was identified that is capable of predicting the presence of a metal cofactor in the protein structure with overall accuracies of up to 97% given only the relative positions of their backbone atoms. The decision tree machine-learning algorithm used can quickly analyze an entire protein structure for the presence of sets of primary metal coordination spheres upon mutagenesis, independent of their original amino acid identities. The methodology was designed for application in the field of metalloprotein engineering. A cluster analysis using the data set was also performed and demonstrated that the features chosen are useful for identifying clusters of structurally similar metal-binding sites.
Collapse
Affiliation(s)
- Hoang Nguyen
- Department of Computer Science, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Jesse Kleingardner
- Department of Chemistry and Biochemistry, Messiah University, Mechanicsburg, Pennsylvania, USA
| |
Collapse
|
16
|
Koebke KJ, Kühl T, Lojou E, Demeler B, Schoepp-Cothenet B, Iranzo O, Pecoraro VL, Ivancich A. The pH-Induced Selectivity Between Cysteine or Histidine Coordinated Heme in an Artificial α-Helical Metalloprotein. Angew Chem Int Ed Engl 2020; 60:3974-3978. [PMID: 33215801 DOI: 10.1002/anie.202012673] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/19/2020] [Indexed: 11/09/2022]
Abstract
De Novo metalloprotein design assesses the relationship between metal active site architecture and catalytic reactivity. Herein, we use an α-helical scaffold to control the iron coordination geometry when a heme cofactor is allowed to bind to either histidine or cysteine ligands, within a single artificial protein. Consequently, we uncovered a reversible pH-induced switch of the heme axial ligation within this simplified scaffold. Characterization of the specific heme coordination modes was done by using UV/Vis and Electron Paramagnetic Resonance spectroscopies. The penta- or hexa-coordinate thiolate heme (9≤pH≤11) and the penta-coordinate imidazole heme (6≤pH≤8.5) reproduces well the heme ligation in chloroperoxidases or cyt P450 monooxygenases and peroxidases, respectively. The stability of heme coordination upon ferric/ferrous redox cycling is a crucial property of the construct. At basic pHs, the thiolate mini-heme protein can catalyze O2 reduction when adsorbed onto a pyrolytic graphite electrode.
Collapse
Affiliation(s)
- Karl J Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Toni Kühl
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
| | - Elisabeth Lojou
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Barbara Schoepp-Cothenet
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
| | - Olga Iranzo
- Institut des Sciences Moléculaires de Marseille (iSm2), Centrale Marseille, Aix-Marseille Univ., CNRS, Marseille, France
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Anabella Ivancich
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
| |
Collapse
|
17
|
Koebke KJ, Kühl T, Lojou E, Demeler B, Schoepp‐Cothenet B, Iranzo O, Pecoraro VL, Ivancich A. The pH‐Induced Selectivity Between Cysteine or Histidine Coordinated Heme in an Artificial α‐Helical Metalloprotein. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Karl J. Koebke
- Department of Chemistry University of Michigan Ann Arbor MI 48109 USA
| | - Toni Kühl
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
| | - Elisabeth Lojou
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
| | - Borries Demeler
- Department of Chemistry and Biochemistry University of Lethbridge Lethbridge AB T1K 3M4 Canada
| | - Barbara Schoepp‐Cothenet
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
| | - Olga Iranzo
- Institut des Sciences Moléculaires de Marseille (iSm2) Centrale Marseille Aix-Marseille Univ. CNRS Marseille France
| | | | - Anabella Ivancich
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
| |
Collapse
|
18
|
Lancellotti L, Borsari M, Bellei M, Bonifacio A, Bortolotti CA, Di Rocco G, Ranieri A, Sola M, Battistuzzi G. Urea-induced denaturation of immobilized yeast iso-1 cytochrome c: Role of Met80 and Tyr67 in the thermodynamics of unfolding and promotion of pseudoperoxidase and nitrite reductase activities. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2020.137237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
19
|
Protein-caged zinc porphyrin as a carbonic anhydrase mimic for carbon dioxide capture. Sci Rep 2020; 10:19581. [PMID: 33177642 PMCID: PMC7659338 DOI: 10.1038/s41598-020-76482-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 10/16/2020] [Indexed: 11/29/2022] Open
Abstract
Zinc tetraphenylporphyrin (Zn-TPP) solubilized by GroEL protein cage was prepared as a supramolecular mimic of carbonic anhydrase (CA) for CO2 capture. It is shown that the soluble Zn-TPP-GroEL complex can be formed easily by detergent dialysis. The Zn-TPP/GroEL binding ratio was found to increase with their dialysis ratio until reaching the maximum of about 30 porphyrins per protein cage. Moreover, the complex showed hydrase activity that catalyzes the CO2 hydration in HCO3− and H+. It is further seen that the catalytic activity of Zn-TPP-GroEL was about one-half of that of a bovine CA at 25 °C. On the other hand, as the temperature was increased to 60 °C close to an industrial CO2 absorption temperature, the natural enzyme lost function while Zn-TPP-GroEL exhibited better catalytic performance indicative of a higher thermal stability. Finally, we demonstrate that the GroEL-solubilized Zn-TPP is able to accelerate the precipitation of CO2 in the form of CaCO3 and has better long-term performance than the bovine CA. Thus a new type of nano-caged system mimicking natural CAs for potential applications in carbon capture has been established.
Collapse
|
20
|
Curtis RW, Chmielewski J. A comparison of the collagen triple helix and
coiled‐coil
peptide building blocks on metal
ion‐mediated
supramolecular assembly. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Ryan W. Curtis
- Department of Chemistry Purdue University West Lafayette Indiana USA
| | - Jean Chmielewski
- Department of Chemistry Purdue University West Lafayette Indiana USA
| |
Collapse
|
21
|
Mancini JA, Pike DH, Tyryshkin AM, Haramaty L, Wang MS, Poudel S, Hecht M, Nanda V. Design of a Fe 4 S 4 cluster into the core of a de novo four-helix bundle. Biotechnol Appl Biochem 2020; 67:574-585. [PMID: 32770861 DOI: 10.1002/bab.2003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022]
Abstract
We explore the capacity of the de novo protein, S824, to incorporate a multinuclear iron-sulfur cluster within the core of a single-chain four-helix bundle. This topology has a high intrinsic designability because sequences are constrained largely by the pattern of hydrophobic and hydrophilic amino acids, thereby allowing for the extensive substitution of individual side chains. Libraries of novel proteins based on these constraints have surprising functional potential and have been shown to complement the deletion of essential genes in E. coli. Our structure-based design of four first-shell cysteine ligands, one per helix, in S824 resulted in successful incorporation of a cubane Fe4 S4 cluster into the protein core. A number of challenges were encountered during the design and characterization process, including nonspecific metal-induced aggregation and the presence of competing metal-cluster stoichiometries. The introduction of buried iron-sulfur clusters into the helical bundle is an initial step toward converting libraries of designed structures into functional de novo proteins with catalytic or electron-transfer functionalities.
Collapse
Affiliation(s)
- Joshua A Mancini
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Douglas H Pike
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Alexei M Tyryshkin
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Liti Haramaty
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Michael S Wang
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Saroj Poudel
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Michael Hecht
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Vikas Nanda
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School and the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| |
Collapse
|
22
|
Hishikawa Y, Maity B, Ito N, Abe S, Lu D, Ueno T. Design of Multinuclear Gold Binding Site at the Two-fold Symmetric Interface of the Ferritin Cage. CHEM LETT 2020. [DOI: 10.1246/cl.200217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yuki Hishikawa
- Department of Chemical Engineering, Tsinghua University, 30 Shuangqing Rd, Haidian District, Beijing 100-084, P. R. China
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Basudev Maity
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Nozomi Ito
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Diannan Lu
- Department of Chemical Engineering, Tsinghua University, 30 Shuangqing Rd, Haidian District, Beijing 100-084, P. R. China
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| |
Collapse
|
23
|
Zambrano G, Chino M, Renzi E, Di Girolamo R, Maglio O, Pavone V, Lombardi A, Nastri F. Clickable artificial heme-peroxidases for the development of functional nanomaterials. Biotechnol Appl Biochem 2020; 67:549-562. [PMID: 33463759 DOI: 10.1002/bab.1969] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/06/2020] [Indexed: 11/08/2022]
Abstract
Artificial metalloenzymes as catalysts are promising candidates for their use in different technologies, such as bioremediation, biomass transformation, or biosensing. Despite this, their practical exploitation is still at an early stage. Immobilized natural enzymes have been proposed to enhance their applicability. Immobilization may offer several advantages: (i) catalyst reuse; (ii) easy separation of the enzyme from the reaction medium; (iii) better tolerance to harsh temperature and pH conditions. Here, we report an easy immobilization procedure of an artificial peroxidase on different surfaces, by means of click chemistry. FeMC6*a, a recently developed peroxidase mimic, has been functionalized with a pegylated aza-dibenzocyclooctyne to afford a "clickable" biocatalyst, namely FeMC6*a-PEG4@DBCO, which easily reacts with azide-functionalized molecules and/or nanomaterials to afford functional bioconjugates. The clicked biocatalyst retains its structural and, to some extent, its functional behaviors, thus housing high potential for biotechnological applications.
Collapse
Affiliation(s)
- Gerardo Zambrano
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
| | - Emilia Renzi
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
| | - Rocco Di Girolamo
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy.,Istituto di Biostrutture e Bioimmagini, CNR, Napoli, Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
| |
Collapse
|
24
|
Laureanti JA, Ginovska B, Buchko GW, Schenter GK, Hebert M, Zadvornyy OA, Peters JW, Shaw WJ. A Positive Charge in the Outer Coordination Sphere of an Artificial Enzyme Increases CO2 Hydrogenation. Organometallics 2020. [DOI: 10.1021/acs.organomet.9b00843] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph A. Laureanti
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Bojana Ginovska
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, United States
| | - Gregory K. Schenter
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Margaret Hebert
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Oleg A. Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - John W. Peters
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Wendy J. Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| |
Collapse
|
25
|
Tolbert AE, Ervin CS, Ruckthong L, Paul TJ, Jayasinghe-Arachchige VM, Neupane KP, Stuckey JA, Prabhakar R, Pecoraro VL. Heteromeric three-stranded coiled coils designed using a Pb(II)(Cys) 3 template mediated strategy. Nat Chem 2020; 12:405-411. [PMID: 32123337 DOI: 10.1038/s41557-020-0423-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 01/19/2020] [Indexed: 11/09/2022]
Abstract
Three-stranded coiled coils are peptide structures constructed from amphipathic heptad repeats. Here we show that it is possible to form pure heterotrimeric three-stranded coiled coils by combining three distinct characteristics: (1) a cysteine sulfur layer for metal coordination, (2) a thiophilic, trigonal pyramidal metalloid (Pb(II)) that binds to these sulfurs and (3) an adjacent layer of reduced steric bulk generating a cavity where water can hydrogen bond to the cysteine sulfur atoms. Cysteine substitution in an a site yields Pb(II)A2B heterotrimers, while d sites provide pure Pb(II)C2D or Pb(II)CD2 scaffolds. Altering the metal from Pb(II) to Hg(II) or shifting the relative position of the sterically less demanding layer removes heterotrimer specificity. Because only two of the eight or ten hydrophobic layers are perturbed, catalytic sites can be introduced at other regions of the scaffold. A Zn(II)(histidine)3(H2O) centre can be incorporated at a remote location without perturbing the heterotrimer selectivity, suggesting a unique strategy to prepare dissymmetric catalytic sites within self-assembling de novo-designed proteins.
Collapse
Affiliation(s)
- Audrey E Tolbert
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Leela Ruckthong
- Department of Chemistry, Faculty of Science, King Mongkut's University of Technology, Thonburi (KMUTT), Bangkok, Thailand
| | - Thomas J Paul
- Department of Chemistry, University of Miami, Coral Gables, FL, USA
| | | | - Kosh P Neupane
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA. .,Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
26
|
Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
Collapse
|
27
|
Mathieu E, Tolbert AE, Koebke KJ, Tard C, Iranzo O, Penner-Hahn JE, Policar C, Pecoraro V. Rational De Novo Design of a Cu Metalloenzyme for Superoxide Dismutation. Chemistry 2020; 26:249-258. [PMID: 31710732 PMCID: PMC6944188 DOI: 10.1002/chem.201903808] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/04/2019] [Indexed: 01/16/2023]
Abstract
Superoxide dismutases (SODs) are highly efficient enzymes for superoxide dismutation and the first line of defense against oxidative stress. These metalloproteins contain a redox-active metal ion in their active site (Mn, Cu, Fe, Ni) with a tightly controlled reduction potential found in a close range around the optimal value of 0.36 V versus the normal hydrogen electrode (NHE). Rationally designed proteins with well-defined three-dimensional structures offer new opportunities for obtaining functional SOD mimics. Here, we explore four different copper-binding scaffolds: H3 (His3 ), H4 (His4 ), H2 DH (His3 Asp with two His and one Asp in the same plane) and H3 D (His3 Asp with three His in the same plane) by using the scaffold of the de novo protein GRα3 D. EPR and XAS analysis of the resulting copper complexes demonstrates that they are good CuII -bound structural mimics of Cu-only SODs. Furthermore, all the complexes exhibit SOD activity, though three orders of magnitude slower than the native enzyme, making them the first de novo copper SOD mimics.
Collapse
Affiliation(s)
- Emilie Mathieu
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
- These authors contributed equally to this work
| | - Audrey E. Tolbert
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
- These authors contributed equally to this work
| | - Karl J. Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
| | - Cédric Tard
- LCM, CNRS, Ecole Polytechnique, IP Paris, F-91128 Palaiseau, France
| | - Olga Iranzo
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | - Clotilde Policar
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Vincent Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103
| |
Collapse
|
28
|
Engineering Metalloprotein Functions in Designed and Native Scaffolds. Trends Biochem Sci 2019; 44:1022-1040. [DOI: 10.1016/j.tibs.2019.06.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
|
29
|
Aoki S, Kikuchi C, Kitagawa Y, Hasegawa Y, Sonoike S, Saga Y, Hatanaka M. Evaluation of Zn
2+
Coordination Structures in Chiral Zn
2+
Complexes Based on Shape Measurement Factors: Relationships between Activity and the Coordination Structure. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201900934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shin Aoki
- Faculty of Pharmaceutical Sciences Tokyo University of Science 2641 Yamazaki 278‐8510 Noda Chiba Japan
- Research Institute for Science and Technology Tokyo University of Science 2641 Yamazaki 278‐8510 Noda Chiba Japan
| | - Chiharu Kikuchi
- Faculty of Pharmaceutical Sciences Tokyo University of Science 2641 Yamazaki 278‐8510 Noda Chiba Japan
| | - Yuichi Kitagawa
- Faculty of Engineering and Graduate School of Engineering Hokkaido University Kita‐13 Jo. Nishi‐8 Chome 060‐8628 Sapporo Hokkaido Japan
| | - Yasuchika Hasegawa
- Faculty of Engineering and Graduate School of Engineering Hokkaido University Kita‐13 Jo. Nishi‐8 Chome 060‐8628 Sapporo Hokkaido Japan
| | - Shotaro Sonoike
- Faculty of Pharmaceutical Sciences Tokyo University of Science 2641 Yamazaki 278‐8510 Noda Chiba Japan
- Chugai Pharmaceutical Co., Ltd. 2‐1–1‐Nihonbashi Muromachi, Cyuo‐ku 103‐8324 Tokyo Japan
| | - Yutaka Saga
- Faculty of Pharmaceutical Sciences Tokyo University of Science 2641 Yamazaki 278‐8510 Noda Chiba Japan
| | - Miho Hatanaka
- Institute for Research Initiatives Division for Research Strategy Graduate School of Science and Technology, and Nara Institute of Science and Technology 8916‐5 Takayama‐cho, Ikoma‐shi 630‐0192 Nara Japan
| |
Collapse
|
30
|
Koebke KJ, Pecoraro VL. Noncoded Amino Acids in de Novo Metalloprotein Design: Controlling Coordination Number and Catalysis. Acc Chem Res 2019; 52:1160-1167. [PMID: 30933479 DOI: 10.1021/acs.accounts.9b00032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The relationship between structure and function has long been one of the major points of investigation in Biophysics. Understanding how much, or how little, of a protein's often complicated structure is necessary for its function can lead to directed therapeutic strategies and would allow one to design proteins for specific desired functions. Studying protein function by de novo design builds the functionality from the ground up in a completely unrelated and noncoded protein scaffold. Our lab has used this strategy to study heavy and transition metal binding within the TRI family of three stranded coiled coil (3SCC) constructs to understand coordination geometry and metalloenzyme catalytic control within a protein environment. These peptides contain hydrophobic layers within the interior of the 3SCC, which one can mutate to metal binding residues to create a minimal metal binding site, while solid phase synthesis allows our lab to easily incorporate a number of noncoded amino acids including d enantiomers of binding or secondary coordination sphere amino acids, penicillamine, or methylated versions of histidine. Our studies of Cd(II) binding to Cys3 environments have determined, largely through the use of 113Cd NMR and 111mCd PAC, that the coordination environment around a heavy metal can be controlled by incorporating noncoded amino acids in either the primary or secondary coordination spheres. We found mutating the metal binding amino acids to l-Pen can enforce trigonal Cd(II)S3 geometry exclusively compared to the mixed coordination determined for l-Cys coordination. The same result can be achieved with secondary sphere mutations as well by incorporating d-Leu above a Cys3. We hypothesize this latter effect is due to the increased steric packing above the metal binding site that occurs when the l-Leu oriented toward the N-terminus of the scaffold is mutated to d-Leu and oriented toward the C-terminus. Mutating the layer below Cys3 to d-Leu instead formed a mixed 4- and 5-coordinate Cd(II)S3(H2O) and Cd(II)S3(H2O)2 construct as steric bulk was decreased below the metal binding site. We have also applied noncoded amino acids to metalloenzyme systems by incorporating His residues that are methylated at the δ- or ε-nitrogen to enforce Cu(I) ligation to the opposite open nitrogen of His and found a 2 orders of magnitude increased catalytic efficiency for nitrite reductase activity with ε-nitrogen coordination compared to δ-nitrogen. These results exemplify the ability to tune coordination environment and catalytic efficiency within a de novo scaffold as well as the utility of noncoded amino acids to increase the chemist's toolbox. By furthering our understanding of metalloprotein design one could envision, through our use of amino acids not normally available to nature, that protein design laboratories will soon be capable of outperforming the native systems previously used as their benchmark of successful design. The ability to design proteins at this level would have far reaching and exciting benefits within various fields including medical and industrial applications.
Collapse
Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
| |
Collapse
|
31
|
Baskin M, Zhu H, Qu ZW, Chill JH, Grimme S, Maayan G. Folding of unstructured peptoids and formation of hetero-bimetallic peptoid complexes upon side-chain-to-metal coordination. Chem Sci 2019; 10:620-632. [PMID: 30713653 PMCID: PMC6334629 DOI: 10.1039/c8sc03616k] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/16/2018] [Indexed: 01/05/2023] Open
Abstract
Helices are key structural features in biopolymers, enabling a variety of biological functions. Mimicking these secondary structure motifs has wide potential in the development of biomimetic materials. Peptoids, N-substituted glycine oligomers, are an important class of peptide mimics that can adopt polyproline type helices if the majority of their sequence consists of chiral bulky pendent groups. Such side-chains are structure inducers but they have no functional value. We present here the inclusion of several metal-binding groups in one peptoid oligomer as a new platform towards the development of functional helical peptoids. Thus, we describe the coordination of two metal ions to unstructured peptoids incorporating four 8-hydroxyquinoline (HQ) ligands at fixed positions as two (HQ, HQ) metal binding sites, and a mixture of chiral benzyl and alkyl substituents in varied positions along the peptoid backbone. For the first time, we demonstrate by circular dichroism spectroscopy, solution NMR techniques and high-level DFT calculations that some of these unstructured peptoids can fold upon metal binding to form helical structures. Replacing one HQ ligand with a terpyridine (Terpy) ligand resulted in unique sequences that can selectively coordinate Cu2+ to the (Terpy, HQ) and Zn2+ (or Co2+) to the (HQ, HQ) sites from a solution mixture containing Cu2+ and Zn2+ (or Co2+) ions. Interestingly, the binding of Cu2+ to the (Terpy, HQ) site in one of these peptoids can initiate a conformational change that in turn facilitates the coordination of Zn2+ (or Co2+) ions to the (HQ, HQ) site, demonstrating a unique example of positive allosteric cooperativity in peptide mimics.
Collapse
Affiliation(s)
- Maria Baskin
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Technion City , Hailfa 32000 , Israel .
| | - Hui Zhu
- Mulliken Center for Theoretical Chemistry , Rheinische Friedrich-Wilhelms-Universität Bonn , Beringstrasse 4 , 53115 Bonn , Germany
| | - Zheng-Wang Qu
- Mulliken Center for Theoretical Chemistry , Rheinische Friedrich-Wilhelms-Universität Bonn , Beringstrasse 4 , 53115 Bonn , Germany
| | - Jordan H Chill
- Department of Chemistry , Bar-Ilan University , Ramat Gan 52900 , Israel
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry , Rheinische Friedrich-Wilhelms-Universität Bonn , Beringstrasse 4 , 53115 Bonn , Germany
| | - Galia Maayan
- Schulich Faculty of Chemistry , Technion - Israel Institute of Technology , Technion City , Hailfa 32000 , Israel .
| |
Collapse
|
32
|
Rai J, Basumatary B, Bhandary S, Murugavel M, Sankar J. A tris-(manganese(iii))corrole–porphyrin–corrole triad: synthesis, characterization and catalytic epoxidation. Dalton Trans 2019; 48:7394-7402. [DOI: 10.1039/c9dt00965e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A homotrimetallic manganese(iii) corrole–porphyrin–corrole triad has been synthesized and structurally characterized.
Collapse
Affiliation(s)
- Jyoti Rai
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal-462066
- India
| | - Biju Basumatary
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal-462066
- India
| | - Subhrajyoti Bhandary
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal-462066
- India
| | - Muthuchamy Murugavel
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal-462066
- India
| | - Jeyaraman Sankar
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal-462066
- India
| |
Collapse
|
33
|
Wuo MG, Hong SH, Singh A, Arora PS. Synthetic Control of Tertiary Helical Structures in Short Peptides. J Am Chem Soc 2018; 140:16284-16290. [PMID: 30395711 DOI: 10.1021/jacs.8b10082] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Helical secondary and tertiary motifs are commonly observed as binding epitopes in natural and engineered protein scaffolds. While several strategies have been described to constrain α-helices or reproduce their binding attributes in synthetic mimics, general strategies to mimic tertiary helical motifs remain in their infancy. We recently described a synthetic strategy to develop helical dimers ( J. Am. Chem. Soc. 2015, 137, 11618-11621). We found that replacement of an interhelical salt bridge with a covalent bond can stabilize antiparallel motifs in short sequences. Here we show that the approach can be generalized to obtain antiparallel and parallel dimers as well as trimer motifs. Helical stabilization requires judiciously designed cross-linkers as well as optimal interhelical hydrophobic packing. We anticipate that these mimics would afford new classes of modulators of biological function.
Collapse
Affiliation(s)
- Michael G Wuo
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Seong Ho Hong
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Arunima Singh
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Paramjit S Arora
- Department of Chemistry , New York University , New York , New York 10003 , United States
| |
Collapse
|
34
|
Aupič J, Lapenta F, Jerala R. SwitCCh: Metal-Site Design for Controlling the Assembly of a Coiled-Coil Homodimer. Chembiochem 2018; 19:2453-2457. [PMID: 30260542 DOI: 10.1002/cbic.201800578] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Indexed: 11/09/2022]
Abstract
Conformational change of proteins in response to chemical or physical signals is the underlying principle of many regulatory and transport mechanisms in biological systems. The ability to design proteins the conformational state of which can be precisely and reversibly controlled would facilitate the development of molecular machines tailored for specific applications. Here we explore metal-binding site design to engineer a peptide-based conformational switch called SwitCCh that assembles into a homodimeric coiled-coil in response to the addition of ZnII ions or low pH. Addition of ZnII promoted formation of a parallel homodimer with an increase in thermal stability by more than 30 °C. The peptide could be reversibly cycled between the coiled-coil and random conformation. Furthermore, the SwitCCh peptide was orthogonal to the previously developed coiled-coil dimer set, indicating it could be used for regulated self-assembly of coiled-coil based nanostructures and materials.
Collapse
Affiliation(s)
- Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.,Doctoral Study Programme in Chemical Sciences, University of Ljubljana, Večna pot 113, 1000, Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.,Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Kongresni trg 12, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg OF 13, 1000, Ljubljana, Slovenia
| |
Collapse
|
35
|
Affiliation(s)
- Valerie Vaissier Welborn
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, California 94720, United States
| |
Collapse
|
36
|
Koebke KJ, Ruckthong L, Meagher JL, Mathieu E, Harland J, Deb A, Lehnert N, Policar C, Tard C, Penner-Hahn JE, Stuckey JA, Pecoraro VL. Clarifying the Copper Coordination Environment in a de Novo Designed Red Copper Protein. Inorg Chem 2018; 57:12291-12302. [PMID: 30226758 PMCID: PMC6183058 DOI: 10.1021/acs.inorgchem.8b01989] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cupredoxins are copper-dependent electron-transfer proteins that can be categorized as blue, purple, green, and red depending on the spectroscopic properties of the Cu(II) bound forms. Interestingly, despite significantly different first coordination spheres and nuclearity, all cupredoxins share a common Greek Key β-sheet fold. We have previously reported the design of a red copper protein within a completely distinct three-helical bundle protein, α3DChC2. (1) While this design demonstrated that a β-barrel fold was not requisite to recapitulate the properties of a native cupredoxin center, the parent peptide α3D was not sufficiently stable to allow further study through additional mutations. Here we present the design of an elongated protein GRANDα3D (GRα3D) with Δ Gu = -11.4 kcal/mol compared to the original design's -5.1 kcal/mol. Diffraction quality crystals were grown of GRα3D (a first for an α3D peptide) and solved to a resolution of 1.34 Å. Examination of this structure suggested that Glu41 might interact with the Cu in our previously reported red copper protein. The previous bis(histidine)(cysteine) site (GRα3DChC2) was designed into this new scaffold and a series of variant constructs were made to explore this hypothesis. Mutation studies around Glu41 not only prove the proposed interaction, but also enabled tuning of the constructs' hyperfine coupling constant from 160 to 127 × 10-4 cm-1. X-ray absorption spectroscopy analysis is consistent with these hyperfine coupling differences being the result of variant 4p mixing related to coordination geometry changes. These studies not only prove that an Glu41-Cu interaction leads to the α3DChC2 construct's red copper protein like spectral properties, but also exemplify the exact control one can have in a de novo construct to tune the properties of an electron-transfer Cu site.
Collapse
Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Leela Ruckthong
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer L. Meagher
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Emilie Mathieu
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Jill Harland
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Clotilde Policar
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Cédric Tard
- LCM, CNRS, Ecole Polytechnique, Université Paris-Saclay, 91128 Palaiseau Cedex, France
| | - James E. Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jeanne A. Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
37
|
Alcala-Torano R, Walther M, Sommer DJ, Park CK, Ghirlanda G. Rational design of a hexameric protein assembly stabilized by metal chelation. Biopolymers 2018; 109:e23233. [PMID: 30191549 DOI: 10.1002/bip.23233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/15/2018] [Accepted: 07/05/2018] [Indexed: 12/27/2022]
Abstract
Protein-based self-assembled nanostructures hold tremendous promise as smart materials. One strategy to control the assembly of individual protein modules takes advantage of the directionality and high affinity bonding afforded by metal chelation. Here, we describe the use of 2,2'-bipyridine units (Bpy) as side chains to template the assembly of large structures (MW approx. 35 000 Da) in a metal-dependent manner. The structures are trimers of independently folded 3-helix bundles, and are held together by 2 Me(Bpy)3 complexes. The assemblies are stable to thermal denaturation, and are more than 90% helical at 90°C. Circular dichroism spectroscopy shows that one of the 2 possible (Bpy)3 enantiomers is favored over the other. Because of the sequence pliability of the starting peptides, these constructs could find use to organize functional groups at controlled positions within a supramolecular assembly.
Collapse
Affiliation(s)
| | - Mathieu Walther
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | - Dayn J Sommer
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | - Chad K Park
- Department of Biochemistry, University of Arizona, Tucson, Arizona
| | | |
Collapse
|
38
|
Koebke KJ, Pecoraro VL. Development of de Novo Copper Nitrite Reductases: Where We Are and Where We Need To Go. ACS Catal 2018; 8:8046-8057. [PMID: 30294504 DOI: 10.1021/acscatal.8b02153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of redox-active metalloprotein catalysts is a challenging objective of de novo protein design. Within this Perspective we detail our efforts to create a redox-active Cu nitrite reductase (NiR) by incorporating Cu into the hydrophobic interior of well-defined three-stranded coiled coils (3SCCs). The scaffold contains three histidine residues that provide a layer of three nitrogen donors that mimic the type 2 catalytic site of NiR. We have found that this strategy successfully produces an active and stable CuNiR model that functions for over 1000 turnovers. Spectroscopic evidence indicates that the Cu(I) site has a lower coordination number in comparison to the enzyme, whereas the Cu(II) geometry may more faithfully reproduce the NiR type 2 center. Mutations at the helical interface successfully produce a hydrogen bond between an interfacial Glu residue and the Culigating His residue, which allows for the tuning of the redox potential over a 100 mV range. We successfully created constructs with as much as a 120-fold improvement from the original design by modifying the steric bulk above or below the Cu binding site. These systems are now the most active water-soluble and stable artificial NiR catalysts yet produced. Several avenues for improving the catalytic efficiency of later designs are detailed within this Perspective, including adjustment of their resting oxidation state, the use of asymmetric scaffolds to allow for single amino acid mutation within the second coordination sphere, and the design of hydrogen-bonding networks to tune residue orientation and electronics. Through these studies the TRI-H system has given insight into the difficulties that arise in creating a de novo redox active enzyme. Work to improve upon this model will provide strategies by which redox-active de novo enzymes may be tuned and detail how native enzymes accomplish catalytic efficiencies through proton gated redox catalysis.
Collapse
Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
| |
Collapse
|
39
|
Espinoza-Cara A, Zitare U, Alvarez-Paggi D, Klinke S, Otero LH, Murgida DH, Vila AJ. Engineering a bifunctional copper site in the cupredoxin fold by loop-directed mutagenesis. Chem Sci 2018; 9:6692-6702. [PMID: 30310603 PMCID: PMC6115626 DOI: 10.1039/c8sc01444b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/27/2018] [Indexed: 12/30/2022] Open
Abstract
Copper sites in proteins are designed to perform either electron transfer or redox catalysis. Type 1 and CuA sites are electron transfer hubs bound to a rigid protein fold that prevents binding of exogenous ligands and side reactions. Here we report the engineering of two Type 1 sites by loop-directed mutagenesis within a CuA scaffold with unique electronic structures and functional features. A copper-thioether axial bond shorter than the copper-thiolate bond is responsible for the electronic structure features, in contrast to all other natural or chimeric sites where the copper thiolate bond is short. These sites display highly unusual features, such as: (1) a high reduction potential despite a strong interaction with the axial ligand, which we attribute to changes in the hydrogen bond network and (2) the ability to bind exogenous ligands such as imidazole and azide. This strategy widens the possibility of using natural protein scaffolds with functional features not present in nature.
Collapse
Affiliation(s)
- Andrés Espinoza-Cara
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Rosario , Argentina .
- Área Biofísica , Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Ulises Zitare
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
| | - Damián Alvarez-Paggi
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
| | - Daniel H Murgida
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Rosario , Argentina .
- Área Biofísica , Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
| |
Collapse
|
40
|
Sipka G, Kis M, Maróti P. Characterization of mercury(II)-induced inhibition of photochemistry in the reaction center of photosynthetic bacteria. PHOTOSYNTHESIS RESEARCH 2018; 136:379-392. [PMID: 29285578 DOI: 10.1007/s11120-017-0474-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
Mercuric contamination of aqueous cultures results in impairment of viability of photosynthetic bacteria primarily by inhibition of the photochemistry of the reaction center (RC) protein. Isolated reaction centers (RCs) from Rhodobacter sphaeroides were exposed to Hg2+ ions up to saturation concentration (~ 103 [Hg2+]/[RC]) and the gradual time- and concentration-dependent loss of the photochemical activity was monitored. The vast majority of Hg2+ ions (about 500 [Hg2+]/[RC]) had low affinity for the RC [binding constant Kb ~ 5 mM-1] and only a few (~ 1 [Hg2+]/[RC]) exhibited strong binding (Kb ~ 50 μM-1). Neither type of binding site had specific and harmful effects on the photochemistry of the RC. The primary charge separation was preserved even at saturation mercury(II) concentration, but essential further steps of stabilization and utilization were blocked already in the 5 < [Hg2+]/[RC] < 50 range whose locations were revealed. (1) The proton gate at the cytoplasmic site had the highest affinity for Hg2+ binding (Kb ~ 0.2 μM-1) and blocked the proton uptake. (2) Reduced affinity (Kb ~ 0.05 μM-1) was measured for the mercury(II)-binding site close to the secondary quinone that resulted in inhibition of the interquinone electron transfer. (3) A similar affinity was observed close to the bacteriochlorophyll dimer causing slight energetic changes as evidenced by a ~ 30 nm blue shift of the red absorption band, a 47 meV increase in the redox midpoint potential, and a ~ 20 meV drop in free energy gap of the primary charge pair. The primary quinone was not perturbed upon mercury(II) treatment. Although the Hg2+ ions attack the RC in large number, the exertion of the harmful effect on photochemistry is not through mass action but rather a couple of well-defined targets. Bound to these sites, the Hg2+ ions can destroy H-bond structures, inhibit protein dynamics, block conformational gating mechanisms, and modify electrostatic profiles essential for electron and proton transfer.
Collapse
Affiliation(s)
- Gábor Sipka
- Department of Medical Physics, University of Szeged, Rerrich Béla tér 1, Szeged, 6720, Hungary
- Department of Plant Biology, Hungarian Academy of Science, Biological Research Centre, Szeged, Hungary
| | - Mariann Kis
- Department of Medical Physics, University of Szeged, Rerrich Béla tér 1, Szeged, 6720, Hungary
| | - Péter Maróti
- Department of Medical Physics, University of Szeged, Rerrich Béla tér 1, Szeged, 6720, Hungary.
| |
Collapse
|
41
|
Heme redox potentials hold the key to reactivity differences between nitric oxide reductase and heme-copper oxidase. Proc Natl Acad Sci U S A 2018; 115:6195-6200. [PMID: 29802230 DOI: 10.1073/pnas.1720298115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite high structural homology between NO reductases (NORs) and heme-copper oxidases (HCOs), factors governing their reaction specificity remain to be understood. Using a myoglobin-based model of NOR (FeBMb) and tuning its heme redox potentials (E°') to cover the native NOR range, through manipulating hydrogen bonding to the proximal histidine ligand and replacing heme b with monoformyl (MF-) or diformyl (DF-) hemes, we herein demonstrate that the E°' holds the key to reactivity differences between NOR and HCO. Detailed electrochemical, kinetic, and vibrational spectroscopic studies, in tandem with density functional theory calculations, demonstrate a strong influence of heme E°' on NO reduction. Decreasing E°' from +148 to -130 mV significantly impacts electronic properties of the NOR mimics, resulting in 180- and 633-fold enhancements in NO association and heme-nitrosyl decay rates, respectively. Our results indicate that NORs exhibit finely tuned E°' that maximizes their enzymatic efficiency and helps achieve a balance between opposite factors: fast NO binding and decay of dinitrosyl species facilitated by low E°' and fast electron transfer facilitated by high E°'. Only when E°' is optimally tuned in FeBMb(MF-heme) for NO binding, heme-nitrosyl decay, and electron transfer does the protein achieve multiple (>35) turnovers, previously not achieved by synthetic or enzyme-based NOR models. This also explains a long-standing question in bioenergetics of selective cross-reactivity in HCOs. Only HCOs with heme E°' in a similar range as NORs (between -59 and 200 mV) exhibit NOR reactivity. Thus, our work demonstrates efficient tuning of E°' in various metalloproteins for their optimal functionality.
Collapse
|
42
|
Ségaud N, Drienovská I, Chen J, Browne WR, Roelfes G. Artificial Metalloproteins for Binding and Stabilization of a Semiquinone Radical. Inorg Chem 2018; 56:13293-13299. [PMID: 29027794 PMCID: PMC5676253 DOI: 10.1021/acs.inorgchem.7b02073] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
The interaction of a number of first-row
transition-metal ions with a 2,2′-bipyridyl alanine (bpyA)
unit incorporated into the lactococcal multidrug resistance regulator
(LmrR) scaffold is reported. The composition of the active site is
shown to influence binding affinities. In the case of Fe(II), we demonstrate
the need of additional ligating residues, in particular those containing
carboxylate groups, in the vicinity of the binding site. Moreover,
stabilization of di-tert-butylsemiquinone radical
(DTB-SQ) in water was achieved by binding to the designed
metalloproteins, which resulted in the radical being shielded from
the aqueous environment. This allowed the first characterization of
the radical semiquinone in water by resonance Raman spectroscopy. A coordination study of first-row transition-metal ions to bipyridine
alanine (bpyA) incorporated into the lactococcal multidrug resistance
regulator (LmrR) scaffold is reported. The designed metalloproteins
were shown to bind and stabilize the di-tert-butylsemiquinone
radical (DTB-SQ) in water, allowing for the first resonance
Raman characterization of this radical species in water.
Collapse
Affiliation(s)
- Nathalie Ségaud
- Stratingh Institute for Chemistry, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ivana Drienovská
- Stratingh Institute for Chemistry, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Juan Chen
- Stratingh Institute for Chemistry, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Wesley R Browne
- Stratingh Institute for Chemistry, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
43
|
Matsuo T, Kono T, Shobu I, Ishida M, Gonda K, Hirota S. Global Structural Flexibility of Metalloproteins Regulates Reactivity of Transition Metal Ion in the Protein Core: An Experimental Study Using Thiol-subtilisin as a Model Protein. Chemistry 2018; 24:2767-2775. [DOI: 10.1002/chem.201705920] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Takashi Matsuo
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Takamasa Kono
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Isamu Shobu
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Masaya Ishida
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Katsuya Gonda
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| | - Shun Hirota
- Graduate School of Materials Science; Nara Institute of Science and Technology (NAIST); 8916-5 Takayama-cho Ikoma Nara 630-0192 Japan
| |
Collapse
|
44
|
Rapson TD, Liu JW, Sriskantha A, Musameh M, Dunn CJ, Church JS, Woodhead A, Warden AC, Riley MJ, Harmer JR, Noble CJ, Sutherland TD. Design of silk proteins with increased heme binding capacity and fabrication of silk-heme materials. J Inorg Biochem 2017; 177:219-227. [DOI: 10.1016/j.jinorgbio.2017.08.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/14/2017] [Accepted: 08/30/2017] [Indexed: 01/12/2023]
|
45
|
Seoudi RS, Mechler A. Design Principles of Peptide Based Self-Assembled Nanomaterials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1030:51-94. [DOI: 10.1007/978-3-319-66095-0_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
46
|
Schwizer F, Okamoto Y, Heinisch T, Gu Y, Pellizzoni MM, Lebrun V, Reuter R, Köhler V, Lewis JC, Ward TR. Artificial Metalloenzymes: Reaction Scope and Optimization Strategies. Chem Rev 2017; 118:142-231. [PMID: 28714313 DOI: 10.1021/acs.chemrev.7b00014] [Citation(s) in RCA: 490] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The incorporation of a synthetic, catalytically competent metallocofactor into a protein scaffold to generate an artificial metalloenzyme (ArM) has been explored since the late 1970's. Progress in the ensuing years was limited by the tools available for both organometallic synthesis and protein engineering. Advances in both of these areas, combined with increased appreciation of the potential benefits of combining attractive features of both homogeneous catalysis and enzymatic catalysis, led to a resurgence of interest in ArMs starting in the early 2000's. Perhaps the most intriguing of potential ArM properties is their ability to endow homogeneous catalysts with a genetic memory. Indeed, incorporating a homogeneous catalyst into a genetically encoded scaffold offers the opportunity to improve ArM performance by directed evolution. This capability could, in turn, lead to improvements in ArM efficiency similar to those obtained for natural enzymes, providing systems suitable for practical applications and greater insight into the role of second coordination sphere interactions in organometallic catalysis. Since its renaissance in the early 2000's, different aspects of artificial metalloenzymes have been extensively reviewed and highlighted. Our intent is to provide a comprehensive overview of all work in the field up to December 2016, organized according to reaction class. Because of the wide range of non-natural reactions catalyzed by ArMs, this was done using a functional-group transformation classification. The review begins with a summary of the proteins and the anchoring strategies used to date for the creation of ArMs, followed by a historical perspective. Then follows a summary of the reactions catalyzed by ArMs and a concluding critical outlook. This analysis allows for comparison of similar reactions catalyzed by ArMs constructed using different metallocofactor anchoring strategies, cofactors, protein scaffolds, and mutagenesis strategies. These data will be used to construct a searchable Web site on ArMs that will be updated regularly by the authors.
Collapse
Affiliation(s)
- Fabian Schwizer
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yasunori Okamoto
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Tillmann Heinisch
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yifan Gu
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Michela M Pellizzoni
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Vincent Lebrun
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Raphael Reuter
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Valentin Köhler
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Jared C Lewis
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Thomas R Ward
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| |
Collapse
|
47
|
Ruckthong L, Peacock AFA, Pascoe CE, Hemmingsen L, Stuckey JA, Pecoraro VL. d-Cysteine Ligands Control Metal Geometries within De Novo Designed Three-Stranded Coiled Coils. Chemistry 2017; 23:8232-8243. [PMID: 28384393 DOI: 10.1002/chem.201700660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Indexed: 12/31/2022]
Abstract
Although metal ion binding to naturally occurring l-amino acid proteins is well documented, understanding the impact of the opposite chirality (d-)amino acids on the structure and stereochemistry of metals is in its infancy. We examine the effect of a d-configuration cysteine within a designed l-amino acid three-stranded coiled coil in order to enforce a precise coordination number on a metal center. The d chirality does not alter the native fold, but the side-chain re-orientation modifies the sterics of the metal binding pocket. l-Cys side chains within the coiled-coil structure have previously been shown to rotate substantially from their preferred positions in the apo structure to create a binding site for a tetra-coordinate metal ion. However, here we show by X-ray crystallography that d-Cys side chains are preorganized within a suitable geometry to bind such a ligand. This is confirmed by comparison of the structure of ZnII Cl(CSL16D C)32- to the published structure of ZnII (H2 O)(GRAND-CSL12AL16L C)3- . Moreover, spectroscopic analysis indicates that the CdII geometry observed by using l-Cys ligands (a mixture of three- and four-coordinate CdII ) is altered to a single four-coordinate species when d-Cys is present. This work opens a new avenue for the control of the metal site environment in man-made proteins, by simply altering the binding ligand with its mirror-imaged d configuration. Thus, the use of non-coded amino acids in the coordination sphere of a metal promises to be a powerful tool for controlling the properties of future metalloproteins.
Collapse
Affiliation(s)
- Leela Ruckthong
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Present address: Department Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bang Mod, ThungKhru, Bangkok, 10140, Thailand
| | - Anna F A Peacock
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Present address: School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Cherilyn E Pascoe
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Lars Hemmingsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| |
Collapse
|
48
|
Bhagi-Damodaran A, Kahle M, Shi Y, Zhang Y, Ädelroth P, Lu Y. Insights Into How Heme Reduction Potentials Modulate Enzymatic Activities of a Myoglobin-based Functional Oxidase. Angew Chem Int Ed Engl 2017; 56:6622-6626. [PMID: 28470988 DOI: 10.1002/anie.201701916] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Indexed: 01/01/2023]
Abstract
Heme-copper oxidase (HCO) is a class of respiratory enzymes that use a heme-copper center to catalyze O2 reduction to H2 O. While heme reduction potential (E°') of different HCO types has been found to vary >500 mV, its impact on HCO activity remains poorly understood. Here, we use a set of myoglobin-based functional HCO models to investigate the mechanism by which heme E°' modulates oxidase activity. Rapid stopped-flow kinetic measurements show that increasing heme E°' by ca. 210 mV results in increases in electron transfer (ET) rates by 30-fold, rate of O2 binding by 12-fold, O2 dissociation by 35-fold, while decreasing O2 affinity by 3-fold. Theoretical calculations reveal that E°' modulation has significant implications on electronic charge of both heme iron and O2 , resulting in increased O2 dissociation and reduced O2 affinity at high E°' values. Overall, this work suggests that fine-tuning E°' in HCOs and other heme enzymes can modulate their substrate affinity, ET rate and enzymatic activity.
Collapse
Affiliation(s)
- Ambika Bhagi-Damodaran
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Maximilian Kahle
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691, Stockholm, Sweden
| | - Yelu Shi
- Department of Biomedical Engineering, Chemistry and Biological Sciences, Stevens Institute of Technology, Hoboken, New Jersey, NY, 07030, USA
| | - Yong Zhang
- Department of Biomedical Engineering, Chemistry and Biological Sciences, Stevens Institute of Technology, Hoboken, New Jersey, NY, 07030, USA
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691, Stockholm, Sweden
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
49
|
Bhagi‐Damodaran A, Kahle M, Shi Y, Zhang Y, Ädelroth P, Lu Y. Insights Into How Heme Reduction Potentials Modulate Enzymatic Activities of a Myoglobin‐based Functional Oxidase. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Maximilian Kahle
- Department of Biochemistry and Biophysics Arrhenius Laboratories for Natural Sciences Stockholm University SE-10691 Stockholm Sweden
| | - Yelu Shi
- Department of Biomedical Engineering, Chemistry and Biological Sciences Stevens Institute of Technology Hoboken, New Jersey NY 07030 USA
| | - Yong Zhang
- Department of Biomedical Engineering, Chemistry and Biological Sciences Stevens Institute of Technology Hoboken, New Jersey NY 07030 USA
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics Arrhenius Laboratories for Natural Sciences Stockholm University SE-10691 Stockholm Sweden
| | - Yi Lu
- Department of Chemistry University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| |
Collapse
|
50
|
Cangelosi V, Ruckthong L, Pecoraro VL. Lead(II) Binding in Natural and Artificial Proteins. Met Ions Life Sci 2017; 17:/books/9783110434330/9783110434330-010/9783110434330-010.xml. [PMID: 28731303 PMCID: PMC5771651 DOI: 10.1515/9783110434330-010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
This article describes recent attempts to understand the biological chemistry of lead using a synthetic biology approach. Lead binds to a variety of different biomolecules ranging from enzymes to regulatory and signaling proteins to bone matrix. We have focused on the interactions of this element in thiolate-rich sites that are found in metalloregulatory proteins such as Pbr, Znt, and CadC and in enzymes such as δ-aminolevulinic acid dehydratase (ALAD). In these proteins, Pb(II) is often found as a homoleptic and hemidirectic Pb(II)(SR)3- complex. Using first principles of biophysics, we have developed relatively short peptides that can associate into three-stranded coiled coils (3SCCs), in which a cysteine group is incorporated into the hydrophobic core to generate a (cysteine)3 binding site. We describe how lead may be sequestered into these sites, the characteristic spectral features may be observed for such systems and we provide crystallographic insight on metal binding. The Pb(II)(SR)3- that is revealed within these α-helical assemblies forms a trigonal pyramidal structure (having an endo orientation) with distinct conformations than are also found in natural proteins (having an exo conformation). This structural insight, combined with 207Pb NMR spectroscopy, suggests that while Pb(II) prefers hemidirected Pb(II)(SR)3- scaffolds regardless of the protein fold, the way this is achieved within α-helical systems is different than in β-sheet or loop regions of proteins. These interactions between metal coordination preference and protein structural preference undoubtedly are exploited in natural systems to allow for protein conformation changes that define function. Thus, using a design approach that separates the numerous factors that lead to stable natural proteins allows us to extract fundamental concepts on how metals behave in biological systems.
Collapse
|