1
|
Wei Y, Li P. Theoretical insights into the reduction of Azurin metal site with unnatural amino acid substitutions. J Inorg Biochem 2024; 259:112651. [PMID: 38968926 DOI: 10.1016/j.jinorgbio.2024.112651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024]
Abstract
Copper-containing proteins play crucial roles in biological systems. Azurin is a copper-containing protein which has a Type 1 copper site that facilitates electron transfer in the cytochrome chain. Previous research has highlighted the significant impact of mutations in the axial Met121 of the copper site on the reduction potential. However, the mechanism of this regulation has not been fully established. In this study, we employed theoretical modeling to investigate the reduction of the Type 1 copper site, focusing on how unnatural amino acid substitutions at Met121 influence its behavior. Our findings demonstrated a strong linear correlation between electrostatic interactions and the reduction potential of the copper site, which indicates that the perturbation of the reduction potential is primarily influenced by electrostatic interactions between the metal ion and the ligating atom. Furthermore, we found that CF/π and CF…H interactions could induce subtle changes in geometry and hence impact the electronic properties of the systems under study. In addition, our calculations suggest the coordination mode and ion-ligand distance could significantly impact the reduction potential of a copper site. Overall, this study offers valuable insights into the structural and electronic properties of the Type 1 copper site, which could potentially guide the design of future artificial catalysts.
Collapse
Affiliation(s)
- Yang Wei
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, United States
| | - Pengfei Li
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, United States.
| |
Collapse
|
2
|
Mammoser CC, LeMasters BE, Edwards SG, McRae EM, Mullins MH, Wang Y, Garcia NM, Edmonds KA, Giedroc DP, Thielges MC. The structure of plastocyanin tunes the midpoint potential by restricting axial ligation of the reduced copper ion. Commun Chem 2023; 6:175. [PMID: 37612467 PMCID: PMC10447441 DOI: 10.1038/s42004-023-00977-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023] Open
Abstract
Blue copper proteins are models for illustrating how proteins tune metal properties. Nevertheless, the mechanisms by which the protein controls the metal site remain to be fully elucidated. A hindrance is that the closed shell Cu(I) site is inaccessible to most spectroscopic analyses. Carbon deuterium (C-D) bonds used as vibrational probes afford nonperturbative, selective characterization of the key cysteine and methionine copper ligands in both redox states. The structural integrity of Nostoc plastocyanin was perturbed by disrupting potential hydrogen bonds between loops of the cupredoxin fold via mutagenesis (S9A, N33A, N34A), variably raising the midpoint potential. The C-D vibrations show little change to suggest substantial alteration to the Cu(II) coordination in the oxidized state or in the Cu(I) interaction with the cysteine ligand. They rather indicate, along with visible and NMR spectroscopy, that the methionine ligand distinctly interacts more strongly with the Cu(I) ion, in line with the increases in midpoint potential. Here we show that the protein structure determines the redox properties by restricting the interaction between the methionine ligand and Cu(I) in the reduced state.
Collapse
Affiliation(s)
- Claire C Mammoser
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Brynn E LeMasters
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Sydney G Edwards
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Emma M McRae
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - M Hunter Mullins
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yiqi Wang
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Nicholas M Garcia
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53726, USA
| | - Katherine A Edmonds
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - David P Giedroc
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Megan C Thielges
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA.
| |
Collapse
|
3
|
Singha A, Sekretareva A, Tao L, Lim H, Ha Y, Braun A, Jones SM, Hedman B, Hodgson KO, Britt RD, Kosman DJ, Solomon EI. Tuning the Type 1 Reduction Potential of Multicopper Oxidases: Uncoupling the Effects of Electrostatics and H-Bonding to Histidine Ligands. J Am Chem Soc 2023. [PMID: 37294874 PMCID: PMC10392966 DOI: 10.1021/jacs.3c03241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In multicopper oxidases (MCOs), the type 1 (T1) Cu accepts electrons from the substrate and transfers these to the trinuclear Cu cluster (TNC) where O2 is reduced to H2O. The T1 potential in MCOs varies from 340 to 780 mV, a range not explained by the existing literature. This study focused on the ∼350 mV difference in potential of the T1 center in Fet3p and Trametes versicolor laccase (TvL) that have the same 2His1Cys ligand set. A range of spectroscopies performed on the oxidized and reduced T1 sites in these MCOs shows that they have equivalent geometric and electronic structures. However, the two His ligands of the T1 Cu in Fet3p are H-bonded to carboxylate residues, while in TvL they are H-bonded to noncharged groups. Electron spin echo envelope modulation spectroscopy shows that there are significant differences in the second-sphere H-bonding interactions in the two T1 centers. Redox titrations on type 2-depleted derivatives of Fet3p and its D409A and E185A variants reveal that the two carboxylates (D409 and E185) lower the T1 potential by 110 and 255-285 mV, respectively. Density functional theory calculations uncouple the effects of the charge of the carboxylates and their difference in H-bonding interactions with the His ligands on the T1 potential, indicating 90-150 mV for anionic charge and ∼100 mV for a strong H-bond. Finally, this study provides an explanation for the generally low potentials of metallooxidases relative to the wide range of potentials of the organic oxidases in terms of different oxidized states of their TNCs involved in catalytic turnover.
Collapse
Affiliation(s)
- Asmita Singha
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Alina Sekretareva
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Lizhi Tao
- Department of Chemistry, University of California at Davis, Davis, California 95616, United States
| | - Hyeongtaek Lim
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yang Ha
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Augustin Braun
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephen M Jones
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - R David Britt
- Department of Chemistry, University of California at Davis, Davis, California 95616, United States
| | - Daniel J Kosman
- Department of Biochemistry, The University at Buffalo, Buffalo, New York 14214, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| |
Collapse
|
4
|
Mitra S, Ainavarapu SRK, Dasgupta J. Long-Range Charge Delocalization Mediates the Ultrafast Ligand-to-Metal Charge Transfer Dynamics at the Cu 2+-Active Site in Azurin. J Phys Chem B 2022; 126:5390-5399. [PMID: 35797135 DOI: 10.1021/acs.jpcb.2c01427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The blue color metalloprotein in azurin has traditionally been attributed to the intense cysteine-to-Cu2+ ligand-to-metal charge transfer transition centered at 628 nm. Although resonance Raman measurements of the Cu2+ active site have implied that the LMCT transition electronically couples to the protein scaffold well beyond its primary metal-ligand coordination shell, the structural extent of this electronic coupling and visualization of the protein-mediated charge transfer dynamics have remained elusive. Here, using femtosecond broadband transient absorption and impulsive Raman spectroscopy, we provide direct evidence for a rapid relaxation between two distinct charge transfer states, having different spatial delocalization, within ∼300 fs followed by recombination of charges in subpicosecond time scales. We invoke the formation of a protein-centered radical cation, possibly Trp48 or a Phe residue, within 100 fs substantiating the long-range electronic coupling for the first time beyond the traditional copper active site. The Raman spectra of the excited CT state show the presence of protein-centric vibrations along with the vibrational modes assigned to the copper active site. Our results demonstrate a large delocalization length scale of the initially populated CT state, thereby highlighting the possibility of exploiting azurin photochemistry for energy conversion techniques.
Collapse
Affiliation(s)
- Soumyajit Mitra
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | | | - Jyotishman Dasgupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| |
Collapse
|
5
|
Abstract
Some oxidoreductase enzymes use redox-active tyrosine, tryptophan, cysteine, and/or glycine residues as one-electron, high-potential redox (radical) cofactors. Amino-acid radical cofactors typically perform one of four tasks-they work in concert with a metallocofactor to carry out a multielectron redox process, serve as storage sites for oxidizing equivalents, activate the substrate molecules, or move oxidizing equivalents over long distances. It is challenging to experimentally resolve the thermodynamic and kinetic redox properties of a single-amino-acid residue. The inherently reactive and highly oxidizing properties of amino-acid radicals increase the experimental barriers further still. This review describes a family of stable and well-structured model proteins that was made specifically to study tyrosine and tryptophan oxidation-reduction. The so-called α3X model protein system was combined with very-high-potential protein film voltammetry, transient absorption spectroscopy, and theoretical methods to gain a comprehensive description of the thermodynamic and kinetic properties of protein tyrosine and tryptophan radicals.
Collapse
Affiliation(s)
- Cecilia Tommos
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA;
| |
Collapse
|
6
|
Yu Y, Marshall NM, Garner DK, Nilges MJ, Lu Y. Tuning reduction potentials of type 1 copper center in azurin by replacing a histidine ligand with its isostructural analogues. J Inorg Biochem 2022; 234:111863. [DOI: 10.1016/j.jinorgbio.2022.111863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 05/02/2022] [Accepted: 05/08/2022] [Indexed: 11/16/2022]
|
7
|
Fedoretz-Maxwell BP, Shin CH, MacNeil GA, Worrall LJ, Park R, Strynadka NCJ, Walsby CJ, Warren JJ. The Impact of Second Coordination Sphere Methionine-Aromatic Interactions in Copper Proteins. Inorg Chem 2022; 61:5563-5571. [DOI: 10.1021/acs.inorgchem.2c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brooklyn P. Fedoretz-Maxwell
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Catherine H. Shin
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Gregory A. MacNeil
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Liam J. Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Rachel Park
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Charles J. Walsby
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Jeffrey J. Warren
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| |
Collapse
|
8
|
Gibbs CA, Fedoretz-Maxwell BP, Warren JJ. On the roles of methionine and the importance of its microenvironments in redox metalloproteins. Dalton Trans 2022; 51:4976-4985. [PMID: 35253809 DOI: 10.1039/d1dt04387k] [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 amino acid residue methionine (Met) is commonly thought of as a ligand in redox metalloproteins, for example in cytochromes c and in blue copper proteins. However, the roles of Met can go beyond a simple ligand. The thioether functional group of Met allows it to be considered as a hydrophobic residue as well as one that is capable of weak dipolar interactions. In addition, the lone pairs on sulphur allow Met to interact with other groups, inluding the aforementioned metal ions. Because of its properties, Met can play diverse roles in metal coordination, fine tuning of redox reactions, or supporting protein structures. These roles are strongly influenced by the nature of the surrounding medium. Herein, we describe several common interactions between Met and surrounding aromatic amino acids and how they affect the physical properties of both copper and iron metalloproteins. While the importance of interactions between Met and other groups is established in biological systems, less is known about their roles in redox metalloproteins and our view is that this is an area that is ready for greater attention.
Collapse
Affiliation(s)
- Curtis A Gibbs
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby BC V5A 1S6, Canada.
| | | | - Jeffrey J Warren
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby BC V5A 1S6, Canada.
| |
Collapse
|
9
|
Electrochemical Characterization of an Engineered Red Copper Protein Featuring an Unprecedented Entropic Control of the Reduction Potential. Bioelectrochemistry 2022; 146:108095. [DOI: 10.1016/j.bioelechem.2022.108095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 12/12/2022]
|
10
|
Zovo K, Pupart H, Van Wieren A, Gillilan RE, Huang Q, Majumdar S, Lukk T. Substitution of the Methionine Axial Ligand of the T1 Copper for the Fungal-like Phenylalanine Ligand (M298F) Causes Local Structural Perturbations that Lead to Thermal Instability and Reduced Catalytic Efficiency of the Small Laccase from Streptomyces coelicolor A3(2). ACS OMEGA 2022; 7:6184-6194. [PMID: 35224382 PMCID: PMC8867573 DOI: 10.1021/acsomega.1c06668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Many industrial processes operate at elevated temperatures or within broad pH and salinity ranges. However, the utilization of enzymes to carry out biocatalysis in such processes is often impractical or even impossible. Laccases (EC 1.10.3.2), which constitute a large family of multicopper oxidases, have long been used in the industrial setting. Although fungal laccases are in many respects considered superior to their bacterial counterparts, the bacterial laccases have been receiving greater attention recently. Albeit lower in redox potential than fungal laccases, bacterial laccases are commonly thermally more stable, act within broader pH ranges, do not contain posttranslational modifications, and could therefore serve as a high potential scaffold for directed evolution for the production of enzymes with enhanced properties. Several examples focusing on the axial ligand mutations of the T1 copper site have been published in the past. However, structural evidence on the local and global changes induced by those mutations have thus far been of computational nature only. In this study, we set out to structurally and kinetically characterize a few of the most commonly reported axial ligand mutations of a bacterial small laccase (SLAC) from Streptomyces coelicolor. While one of the mutations (Met to Leu) equips the enzyme with better thermal stability, the other (Met to Phe) induces an opposite effect. These mutations cause local structural rearrangement of the T1 site as demonstrated by X-ray crystallography. Our analysis confirms past findings that for SLACs, single point mutations that change the identity of the axial ligand of the T1 copper are not enough to provide a substantial increase in the catalytic efficiency but can in some cases have a detrimental effect on the enzyme's thermal stability parameters instead.
Collapse
Affiliation(s)
- Kairit Zovo
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Hegne Pupart
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| | - Arie Van Wieren
- Department
of Chemistry, Biochemistry, Physics and Engineering, Indiana University of Pennsylvania, Indiana, Pennsylvania 15705, United States
| | - Richard E. Gillilan
- MacCHESS
(Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, New York 14850, United
States
| | - Qingqiu Huang
- MacCHESS
(Macromolecular Diffraction Facility at CHESS), Cornell University, 161 Synchrotron Drive, Ithaca, New York 14850, United
States
| | - Sudipta Majumdar
- Department
of Chemistry, Biochemistry, Physics and Engineering, Indiana University of Pennsylvania, Indiana, Pennsylvania 15705, United States
| | - Tiit Lukk
- Department
of Chemistry and Biotechnology, Tallinn
University of Technology, Akadeemia tee 15, Tallinn 12618, Estonia
| |
Collapse
|
11
|
González PJ, Rivas MG, Ferroni FM, Rizzi AC, Brondino CD. Electron transfer pathways and spin–spin interactions in Mo- and Cu-containing oxidoreductases. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
12
|
Di Rocco G, Battistuzzi G, Borsari M, Bortolotti CA, Ranieri A, Sola M. The enthalpic and entropic terms of the reduction potential of metalloproteins: Determinants and interplay. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
13
|
Naowarojna N, Cheng R, Lopez J, Wong C, Qiao L, Liu P. Chemical modifications of proteins and their applications in metalloenzyme studies. Synth Syst Biotechnol 2021; 6:32-49. [PMID: 33665390 PMCID: PMC7897936 DOI: 10.1016/j.synbio.2021.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/14/2020] [Accepted: 01/03/2021] [Indexed: 12/21/2022] Open
Abstract
Protein chemical modifications are important tools for elucidating chemical and biological functions of proteins. Several strategies have been developed to implement these modifications, including enzymatic tailoring reactions, unnatural amino acid incorporation using the expanded genetic codes, and recognition-driven transformations. These technologies have been applied in metalloenzyme studies, specifically in dissecting their mechanisms, improving their enzymatic activities, and creating artificial enzymes with non-natural activities. Herein, we summarize some of the recent efforts in these areas with an emphasis on a few metalloenzyme case studies.
Collapse
Affiliation(s)
| | | | - Juan Lopez
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
| | - Christina Wong
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
| | - Lu Qiao
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA, 02215, United States
| |
Collapse
|
14
|
Szuster J, Zitare UA, Castro MA, Leguto AJ, Morgada MN, Vila AJ, Murgida DH. Cu A-based chimeric T1 copper sites allow for independent modulation of reorganization energy and reduction potential. Chem Sci 2020; 11:6193-6201. [PMID: 32953013 PMCID: PMC7480511 DOI: 10.1039/d0sc01620a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/01/2020] [Indexed: 01/19/2023] Open
Abstract
Attaining rational modulation of thermodynamic and kinetic redox parameters of metalloproteins is a key milestone towards the (re)design of proteins with new or improved redox functions. Here we report that implantation of ligand loops from natural T1 proteins into the scaffold of a CuA protein leads to a series of distorted T1-like sites that allow for independent modulation of reduction potentials (E°') and electron transfer reorganization energies (λ). On the one hand E°' values could be fine-tuned over 120 mV without affecting λ. On the other, λ values could be modulated by more than a factor of two while affecting E°' only by a few millivolts. These results are in sharp contrast to previous studies that used T1 cupredoxin folds, thus highlighting the importance of the protein scaffold in determining such parameters.
Collapse
Affiliation(s)
- Jonathan Szuster
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Ulises A Zitare
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - María A Castro
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| | - Alcides J Leguto
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Argentina
- Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Daniel H Murgida
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE, CONICET-UBA) , Argentina .
- Departamento de Química Inorgánica, Analítica y Química-Física , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Buenos Aires , Argentina
| |
Collapse
|
15
|
Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
Collapse
Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
| |
Collapse
|
16
|
Alwan KB, Welch EF, Blackburn NJ. Catalytic M Center of Copper Monooxygenases Probed by Rational Design. Effects of Selenomethionine and Histidine Substitution on Structure and Reactivity. Biochemistry 2019; 58:4436-4446. [PMID: 31626532 DOI: 10.1021/acs.biochem.9b00823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The M centers of the mononuclear monooxygenases peptidylglycine monooxygenase (PHM) and dopamine β-monooxygenase bind and activate dioxygen en route to substrate hydroxylation. Recently, we reported the rational design of a protein-based model in which the CusF metallochaperone was repurposed via a His to Met mutation to act as a structural and spectroscopic biomimic. The PHM M site exhibits a number of unusual attributes, including a His2Met ligand set, a fluxional Cu(I)-S(Met) bond, tight binding of exogenous ligands CO and N3-, and complete coupling of oxygen reduction to substrate hydroxylation even at extremely low turnover rates. In particular, mutation of the Met ligand to His completely eliminates the catalytic activity despite the propensity of CuI-His3 centers to bind and activate dioxygen in other metalloenzyme systems. Here, we further develop the CusF-based model to explore methionine variants in which Met is replaced by selenomethionine (SeM) and histidine. We examine the effects on coordinate structure and exogenous ligand binding via X-ray absorption spectroscopy and electron paramagnetic resonance and probe the consequences of mutations on redox chemistry via studies of the reduction by ascorbate and oxidation via molecular oxygen. The M-site model is three-coordinate in the Cu(I) state and binds CO to form a four-coordinate carbonyl. In the oxidized forms, the coordination changes to tetragonal five-coordinate with a long axial Met ligand that like the enzymes is undetectable at either the Cu or Se K edges. The EXAFS data at the Se K edge of the SeM variant provide unique information about the nature of the Cu-methionine bond that is likewise weak and fluxional. Kinetic studies document the sluggish reactivity of the Cu(I) complexes with molecular oxygen and rapid rates of reduction of the Cu(II) complexes by ascorbate, indicating a remarkable stability of the Cu(I) state in all three derivatives. The results show little difference between the Met ligand and its SeM and His congeners and suggest that the Met contributes to catalysis in ways that are more complex than simple perturbation of the redox chemistry. Overall, the results stimulate a critical re-examination of the canonical reaction mechanisms of the mononuclear copper monooxygenases.
Collapse
Affiliation(s)
- Katherine B Alwan
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Evan F Welch
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| | - Ninian J Blackburn
- Department of Chemical Physiology and Biochemistry , Oregon Health & Sciences University , Portland , Oregon 97239 , United States
| |
Collapse
|
17
|
Mirts EN, Bhagi-Damodaran A, Lu Y. Understanding and Modulating Metalloenzymes with Unnatural Amino Acids, Non-Native Metal Ions, and Non-Native Metallocofactors. Acc Chem Res 2019; 52:935-944. [PMID: 30912643 DOI: 10.1021/acs.accounts.9b00011] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Metalloproteins set the gold standard for performing important functions, including catalyzing demanding reactions under mild conditions. Designing artificial metalloenzymes (ArMs) to catalyze abiological reactions has been a major endeavor for many years, but most ArM activities are far below those of native enzymes, making them unsuitable for most pratical applications. A critical step to advance the field is to fundamentally understand what it takes to not only confer but also fine-tune ArM activities so they match those of native enzymes. Indeed, only once we can freely modulate ArM activity to rival (or surpass!) natural enzymes can the potential of ArMs be fully realized. A key to unlocking ArM potential is the observation that one metal primary coordination sphere can display a range of functions and levels of activity, leading to the realization that secondary coordination sphere (SCS) interactions are critically important. However, SCS interactions are numerous, long-range, and weak, making them very difficult to reproduce in ArMs. Furthermore, natural enzymes are tied to a small set of biologically available functional moieties from canonical amino acids and physiologically available metal ions and metallocofactors, severely limiting the chemical space available to probe and tune ArMs. In this Account, we summarize the use of unnatural amino acids (UAAs) and non-native metal ions and metallocofactors by our group and our collaborators to probe and modulate ArM functions. We incorporated isostructural UAAs in a type 1 copper (T1Cu) protein azurin to provide conclusive evidence that axial ligand hydrophobicity is a major determinant of T1Cu redunction potential ( E°'). Closely related work from other groups are also discussed. We also probed the role of protein backbone interactions that cannot be altered by standard mutagenesis by replacing the peptide bond with an ester linkage. We used insight gained from these studies to tune the E°' of azurin across the entire physiological range, the broadest range ever achieved in a single metalloprotein. Introducing UAA analogues of Tyr into ArM models of heme-copper oxidase (HCO) revealed a linear relationship between p Ka, E°', and activity. We also substituted non-native hemes and non-native metal ions for their native equivalents in these models to resolve several issues that were intractable in native HCOs and the closely related nitric oxide reductases, such as their roles in modulating substrate affinity, electron transfer rate, and activity. We incorporated abiological cofactors such as ferrocene and Mn(salen) into azurin and myoglobin, respectively, to stabilize these inorganic and organometallic compounds in water, confer abiological functions, tune their E°' and activity through SCS interactions, and show that the approach to metallocofactor anchoring and orientation can tune enantioselectivity and alter function. Replacing Cu in azurin with non-native Fe or Ni can impart novel activities, such as superoxide reduction and C-C bond formation. While progress was made, we have identified only a small fraction of the interactions that can be generally applied to ArMs to fine-tune their functions. Because SCS interactions are subtle and heavily interconnected, it has been difficult to characterize their effects quantitatively. It is vital to develop spectroscopic and computational techniques to detect and quantify their effects in both resting states and catalytic intermediates.
Collapse
Affiliation(s)
- Evan N. Mirts
- Department of Chemistry and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi-Damodaran
- Department of Chemistry and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
18
|
Mousa R, Notis Dardashti R, Metanis N. Selen und Selenocystein in der Proteinchemie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706876] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Reem Mousa
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| | - Rebecca Notis Dardashti
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| | - Norman Metanis
- The Institute of Chemistry; The Hebrew University of Jerusalem; Edmond J. Safra, Givat Ram Jerusalem 91904 Israel
| |
Collapse
|
19
|
Mousa R, Notis Dardashti R, Metanis N. Selenium and Selenocysteine in Protein Chemistry. Angew Chem Int Ed Engl 2017; 56:15818-15827. [PMID: 28857389 DOI: 10.1002/anie.201706876] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Indexed: 01/22/2023]
Abstract
Selenocysteine, the selenium-containing analogue of cysteine, is the twenty-first proteinogenic amino acid. Since its discovery almost fifty years ago, it has been exploited in unnatural systems even more often than in natural systems. Selenocysteine chemistry has attracted the attention of many chemists in the field of chemical biology owing to its high reactivity and resulting potential for various applications such as chemical modification, chemical protein (semi)synthesis, and protein folding, to name a few. In this Minireview, we will focus on the chemistry of selenium and selenocysteine and their utility in protein chemistry.
Collapse
Affiliation(s)
- Reem Mousa
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
| | - Rebecca Notis Dardashti
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
| | - Norman Metanis
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra, Givat Ram, Jerusalem, 91904, Israel
| |
Collapse
|
20
|
Fowler NJ, Blanford CF, Warwicker J, de Visser SP. Prediction of Reduction Potentials of Copper Proteins with Continuum Electrostatics and Density Functional Theory. Chemistry 2017; 23:15436-15445. [PMID: 28815759 PMCID: PMC5698706 DOI: 10.1002/chem.201702901] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Indexed: 12/20/2022]
Abstract
Blue copper proteins, such as azurin, show dramatic changes in Cu2+/Cu+ reduction potential upon mutation over the full physiological range. Hence, they have important functions in electron transfer and oxidation chemistry and have applications in industrial biotechnology. The details of what determines these reduction potential changes upon mutation are still unclear. Moreover, it has been difficult to model and predict the reduction potential of azurin mutants and currently no unique procedure or workflow pattern exists. Furthermore, high‐level computational methods can be accurate but are too time consuming for practical use. In this work, a novel approach for calculating reduction potentials of azurin mutants is shown, based on a combination of continuum electrostatics, density functional theory and empirical hydrophobicity factors. Our method accurately reproduces experimental reduction potential changes of 30 mutants with respect to wildtype within experimental error and highlights the factors contributing to the reduction potential change. Finally, reduction potentials are predicted for a series of 124 new mutants that have not yet been investigated experimentally. Several mutants are identified that are located well over 10 Å from the copper center that change the reduction potential by more than 85 mV. The work shows that secondary coordination sphere mutations mostly lead to long‐range electrostatic changes and hence can be modeled accurately with continuum electrostatics.
Collapse
Affiliation(s)
- Nicholas J Fowler
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Christopher F Blanford
- Manchester Institute of Biotechnology and School of Materials, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Jim Warwicker
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| |
Collapse
|
21
|
Manesis AC, O'Connor MJ, Schneider CR, Shafaat HS. Multielectron Chemistry within a Model Nickel Metalloprotein: Mechanistic Implications for Acetyl-CoA Synthase. J Am Chem Soc 2017; 139:10328-10338. [PMID: 28675928 DOI: 10.1021/jacs.7b03892] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The acetyl coenzyme A synthase (ACS) enzyme plays a central role in the metabolism of anaerobic bacteria and archaea, catalyzing the reversible synthesis of acetyl-CoA from CO and a methyl group through a series of nickel-based organometallic intermediates. Owing to the extreme complexity of the native enzyme systems, the mechanism by which this catalysis occurs remains poorly understood. In this work, we have developed a protein-based model for the NiP center of acetyl coenzyme A synthase using a nickel-substituted azurin protein (NiAz). NiAz is the first model nickel protein system capable of accessing three (NiI/NiII/NiIII) distinct oxidation states within a physiological potential range in aqueous solution, a critical feature for achieving organometallic ACS activity, and binds CO and -CH3 groups with biologically relevant affinity. Characterization of the NiI-CO species through spectroscopic and computational techniques reveals fundamentally similar features between the model NiAz system and the native ACS enzyme, highlighting the potential for related reactivity in this model protein. This work provides insight into the enzymatic process, with implications toward engineering biological catalysts for organometallic processes.
Collapse
Affiliation(s)
- Anastasia C Manesis
- The Ohio State University , 100 West 18th Avenue, Newman & Wolfrom Laboratory of Chemistry, Columbus, Ohio 43210, United States
| | - Matthew J O'Connor
- The Ohio State University , 100 West 18th Avenue, Newman & Wolfrom Laboratory of Chemistry, Columbus, Ohio 43210, United States
| | - Camille R Schneider
- The Ohio State University , 100 West 18th Avenue, Newman & Wolfrom Laboratory of Chemistry, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- The Ohio State University , 100 West 18th Avenue, Newman & Wolfrom Laboratory of Chemistry, Columbus, Ohio 43210, United States
| |
Collapse
|
22
|
Yamaguchi T, Nihei Y, Sutherland DEK, Stillman MJ, Kohzuma T. Stabilization of protein structure through π-π interaction in the second coordination sphere of pseudoazurin. Protein Sci 2017; 26:1921-1931. [PMID: 28691165 DOI: 10.1002/pro.3226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/01/2017] [Accepted: 07/04/2017] [Indexed: 11/11/2022]
Abstract
Noncovalent, weak interactions in the second coordination sphere of the copper active site of Pseudoazurin (PAz) from Achromobacter cycloclastes were examined using a series of Met16X variants. In this study, the differences in protein stability due to the changes in the nature of the 16th amino acid (Met, Phe, Val, Ile) were investigated by electrospray ionization mass spectrometry (ESI-MS) and far-UV circular dichroism (CD) as a result of acid denaturation. The percentage of native states (folded holo forms) of Met16Phe variants was estimated to be 75% at pH 2.9 although the wild-type (WT), Met16Val and Met16Ile PAz, became completely unfolded. The high stability under acidic conditions is correlated with the result of the active site being stabilized by the aromatic substitution of the Met16 residue. The π-π interaction in the second coordination sphere makes a significant contribution to the stability of active site and the protein matrix.
Collapse
Affiliation(s)
- Takahide Yamaguchi
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | - Yuko Nihei
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | - Duncan E K Sutherland
- Department of Biology, The University of Western Ontario, London, Ontario, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Martin J Stillman
- Department of Biology, The University of Western Ontario, London, Ontario, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Takamitsu Kohzuma
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| |
Collapse
|
23
|
Alvarez-Paggi D, Zitare UA, Szuster J, Morgada MN, Leguto AJ, Vila AJ, Murgida DH. Tuning of Enthalpic/Entropic Parameters of a Protein Redox Center through Manipulation of the Electronic Partition Function. J Am Chem Soc 2017; 139:9803-9806. [PMID: 28662578 DOI: 10.1021/jacs.7b05199] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Manipulation of the partition function (Q) of the redox center CuA from cytochrome c oxidase is attained by tuning the accessibility of a low lying alternative electronic ground state and by perturbation of the electrostatic potential through point mutations, loop engineering and pH variation. We report clear correlations of the entropic and enthalpic contributions to redox potentials with Q and with the identity and hydrophobicity of the weak axial ligand, respectively.
Collapse
Affiliation(s)
- Damian Alvarez-Paggi
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET ,1428 Buenos Aires, Argentina
| | - Ulises A Zitare
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET ,1428 Buenos Aires, Argentina
| | - Jonathan Szuster
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET ,1428 Buenos Aires, Argentina
| | - Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and CONICET , 2000 Rosario, Argentina
| | - Alcides J Leguto
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and CONICET , 2000 Rosario, Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and CONICET , 2000 Rosario, Argentina
| | - Daniel H Murgida
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET ,1428 Buenos Aires, Argentina
| |
Collapse
|
24
|
Roger M, Sciara G, Biaso F, Lojou E, Wang X, Bauzan M, Giudici-Orticoni MT, Vila AJ, Ilbert M. Impact of copper ligand mutations on a cupredoxin with a green copper center. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:351-359. [DOI: 10.1016/j.bbabio.2017.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 11/26/2022]
|
25
|
Yu Y, Petrik ID, Chacón KN, Hosseinzadeh P, Chen H, Blackburn NJ, Lu Y. Effect of circular permutation on the structure and function of type 1 blue copper center in azurin. Protein Sci 2017; 26:218-226. [PMID: 27759897 PMCID: PMC5275729 DOI: 10.1002/pro.3071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022]
Abstract
Type 1 copper (T1Cu) proteins are electron transfer (ET) proteins involved in many important biological processes. While the effects of changing primary and secondary coordination spheres in the T1Cu ET function have been extensively studied, few report has explored the effect of the overall protein structural perturbation on active site configuration or reduction potential of the protein, even though the protein scaffold has been proposed to play a critical role in enforcing the entatic or "rack-induced" state for ET functions. We herein report circular permutation of azurin by linking the N- and C-termini and creating new termini in the loops between 1st and 2nd β strands or between 3rd and 4th β strands. Characterization by electronic absorption, electron paramagnetic spectroscopies, as well as crystallography and cyclic voltammetry revealed that, while the overall structure and the primary coordination sphere of the circular permutated azurins remain the same as those of native azurin, their reduction potentials increased by 18 and 124 mV over that of WTAz. Such increases in reduction potentials can be attributed to subtle differences in the hydrogen-bonding network in secondary coordination sphere around the T1Cu center.
Collapse
Affiliation(s)
- Yang Yu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjin300308China
| | - Igor D. Petrik
- Department of Chemistry, University of Illinois at Urbana‐ChampaignUrbanaIllinois61801
| | | | - Parisa Hosseinzadeh
- Department of BiochemistryUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois61801
| | - Honghui Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjin300308China
- Tianjin University of Science and TechnologyTianjin300457China
| | - Ninian J. Blackburn
- Institute of Environmental Health, Oregon Health and Science UniversityPortlandOregon97239
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana‐ChampaignUrbanaIllinois61801
- Department of BiochemistryUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois61801
| |
Collapse
|
26
|
Hu C, Yu Y, Wang J. Improving artificial metalloenzymes' activity by optimizing electron transfer. Chem Commun (Camb) 2017; 53:4173-4186. [DOI: 10.1039/c6cc09921a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This feature article discusses the strategies to optimize electron transfer efficiency, towards enhancing the activity of artificial metalloenzymes.
Collapse
Affiliation(s)
- Cheng Hu
- Laboratory of RNA Biology
- Institute of Biophysics
- Chinese Academy of Sciences
- Chaoyang District
- China
| | - Yang Yu
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
- China
| | - Jiangyun Wang
- Laboratory of RNA Biology
- Institute of Biophysics
- Chinese Academy of Sciences
- Chaoyang District
- China
| |
Collapse
|
27
|
Biosynthetic approach to modeling and understanding metalloproteins using unnatural amino acids. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0343-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
28
|
Clark KM, Tian S, van der Donk WA, Lu Y. Probing the role of the backbone carbonyl interaction with the Cu A center in azurin by replacing the peptide bond with an ester linkage. Chem Commun (Camb) 2016; 53:224-227. [PMID: 27918029 PMCID: PMC5253137 DOI: 10.1039/c6cc07274g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The role of a backbone carbonyl interaction with an engineered CuA center in azurin was investigated by developing a method of synthesis and incorporation of a depsipeptide where one of the amide bonds in azurin is replaced by an ester bond using expressed protein ligation. Studies by electronic absorption and electron paramagnetic resonance spectroscopic techniques indicate that, while the substitution does not significantly alter the geometry of the site, it weakens the axial interaction to the CuA center and strengthens the Cu-Cu bond, as evidenced by the blue shift of the near-IR absorption that has been assigned to the Cu-Cu ψ → ψ* transition. Interestingly, the changes in the electronic structure from the replacement did not result in a change in the reduction potential of the CuA center, suggesting that the diamond core structure of Cu2SCys2 is resistant to variations in axial interactions.
Collapse
Affiliation(s)
- Kevin M Clark
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue Urbana, IL 61801, USA.
| | - Shiliang Tian
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue Urbana, IL 61801, USA. and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue Urbana, IL 61801, USA
| | - Yi Lu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue Urbana, IL 61801, USA. and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue Urbana, IL 61801, USA
| |
Collapse
|
29
|
Nastri F, Chino M, Maglio O, Bhagi-Damodaran A, Lu Y, Lombardi A. Design and engineering of artificial oxygen-activating metalloenzymes. Chem Soc Rev 2016; 45:5020-54. [PMID: 27341693 PMCID: PMC5021598 DOI: 10.1039/c5cs00923e] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many efforts are being made in the design and engineering of metalloenzymes with catalytic properties fulfilling the needs of practical applications. Progress in this field has recently been accelerated by advances in computational, molecular and structural biology. This review article focuses on the recent examples of oxygen-activating metalloenzymes, developed through the strategies of de novo design, miniaturization processes and protein redesign. Considerable progress in these diverse design approaches has produced many metal-containing biocatalysts able to adopt the functions of native enzymes or even novel functions beyond those found in Nature.
Collapse
Affiliation(s)
- Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
- IBB, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Illinois at Urbana-Champaign, A322 CLSL, 600 South Mathews Avenue, Urbana, IL 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, A322 CLSL, 600 South Mathews Avenue, Urbana, IL 61801
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| |
Collapse
|
30
|
Hosseinzadeh P, Tian S, Marshall NM, Hemp J, Mullen T, Nilges MJ, Gao YG, Robinson H, Stahl DA, Gennis RB, Lu Y. A Purple Cupredoxin from Nitrosopumilus maritimus Containing a Mononuclear Type 1 Copper Center with an Open Binding Site. J Am Chem Soc 2016; 138:6324-7. [DOI: 10.1021/jacs.5b13128] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Howard Robinson
- Biology
Department, Brookhaven National Laboratory, Upton, New York 11973-5000, United States
| | - David A. Stahl
- Department
of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195, United States
| | | | | |
Collapse
|
31
|
Hosseinzadeh P, Lu Y. Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:557-581. [PMID: 26301482 PMCID: PMC4761536 DOI: 10.1016/j.bbabio.2015.08.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022]
Abstract
Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.
Collapse
Affiliation(s)
- Parisa Hosseinzadeh
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry and Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews St., Urbana, IL, 61801, USA.
| |
Collapse
|
32
|
Yamaguchi T, Yano J, Yachandra VK, Nihei Y, Togashi H, Szilagyi RK, Kohzuma T. The Allosteric Regulation of Axial/Rhombic Population in a “Type 1” Copper Site: Multi-Edge X-ray Absorption Spectroscopic and Density Functional Studies of Pseudoazurin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20150225] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory
| | | | - Yuko Nihei
- Institute of Applied Beam Science, Ibaraki University
| | | | | | | |
Collapse
|
33
|
Lewis JC. Metallopeptide catalysts and artificial metalloenzymes containing unnatural amino acids. Curr Opin Chem Biol 2015; 25:27-35. [PMID: 25545848 PMCID: PMC4380757 DOI: 10.1016/j.cbpa.2014.12.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/03/2014] [Accepted: 12/11/2014] [Indexed: 01/24/2023]
Abstract
Metallopeptide catalysts and artificial metalloenzymes built from peptide scaffolds and catalytically active metal centers possess a number of exciting properties that could be exploited for selective catalysis. Control over metal catalyst secondary coordination spheres, compatibility with library based methods for optimization and evolution, and biocompatibility stand out in this regard. A wide range of unnatural amino acids (UAAs) have been incorporated into peptide and protein scaffolds using several distinct methods, and the resulting UAAs containing scaffolds can be used to create novel hybrid metal-peptide catalysts. Promising levels of selectivity have been demonstrated for several hybrid catalysts, and these provide a strong impetus and important lessons for the design of and optimization of hybrid catalysts.
Collapse
Affiliation(s)
- Jared C Lewis
- University of Chicago, Department of Chemistry, 5735 South Ellis Avenue, Chicago, IL 60637, United States.
| |
Collapse
|
34
|
Farver O, Hosseinzadeh P, Marshall NM, Wherland S, Lu Y, Pecht I. Long-Range Electron Transfer in Engineered Azurins Exhibits Marcus Inverted Region Behavior. J Phys Chem Lett 2015; 6:100-105. [PMID: 26263097 DOI: 10.1021/jz5022685] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The Marcus theory of electron transfer (ET) predicts that while the ET rate constants increase with rising driving force until it equals a reaction's reorganization energy, at higher driving force the ET rate decreases, having reached the Marcus inverted region. While experimental evidence of the inverted region has been reported for organic and inorganic ET reactions as well as for proteins conjugated with ancillary redox moieties, evidence of the inverted region in a "protein-only" system has remained elusive. We herein provide such evidence in a series of nonderivatized proteins. These results may facilitate the design of ET centers for future applications such as advanced energy conversions.
Collapse
Affiliation(s)
- Ole Farver
- †Department of Analytical and Bioinorganic Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark
| | | | | | - Scot Wherland
- ∥Department of Chemistry, Washington State University, PO Box 644630, Pullman, Washington 99164, United States
| | | | - Israel Pecht
- §Department of Immunology, Weizmann Institute of Science, Wolfson Building, Rehovot 76100, Israel
| |
Collapse
|
35
|
Marchi-Delapierre C, Rondot L, Cavazza C, Ménage S. Oxidation Catalysis by Rationally Designed Artificial Metalloenzymes. Isr J Chem 2014. [DOI: 10.1002/ijch.201400110] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|
36
|
Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 559] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
37
|
Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | |
Collapse
|
38
|
Clark KM, Yu Y, van der Donk WA, Blackburn N, Lu Y. Modulating the Copper-Sulfur Interaction in Type 1 Blue Copper Azurin by Replacing Cys112 with Nonproteinogenic Homocysteine. Inorg Chem Front 2014; 1:153-158. [PMID: 24707355 PMCID: PMC3972132 DOI: 10.1039/c3qi00096f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Cu-SCys interaction is known to play a dominant role in defining the type 1 (T1) blue copper center with respect to both its electronic structure and electron transfer function. Despite this importance, its role has yet to be probed by mutagenesis studies without dramatic change of its T1 copper character. We herein report replacement of the conserved Cys112 in azurin with the nonproteinogenic amino acid homocysteine. Based on electronic absorption, electron paramagnetic resonance, and extended x-ray absorption fine structural spectroscopic studies, this variant displays typical type 1 copper site features. Surprisingly, instead of increasing the strength of the Cu-sulfur interaction by the introduction of the extra methylene group, the Cys112Hcy azurin showed a decrease in the covalent interaction between SHcy and Cu(II) when compared with the WT SCys-Cu(II) interaction. This is likely due to geometric adjustment of the center that resulted in the copper ion moving out of the trigonal plane defined by two histidines and one Hcy and closer to Met121. These structural changes resulted in an increase of reduction potential by 35 mV, consistent with lower Cu-S covalency. These results suggest that the Cu-SCys interaction is close to being optimal in native blue copper protein. It also demonstrates the power of using nonproteinogenic amino acids in addressing important issues in bioinorganic chemistry.
Collapse
Affiliation(s)
- Kevin M Clark
- University of Illinois-Urbana, Department of Biochemistry, Urbana, IL61801; USA
| | - Yang Yu
- University of Illinois-Urbana. Center for Biophysics and Computational Biology, Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- University of Illinois-Urbana, Department of Biochemistry, Urbana, IL61801; USA
- University of Illinois-Urbana. Center for Biophysics and Computational Biology, Urbana, IL 61801, USA
- University of Illinois-Urbana. Department of Chemistry, Urbana, IL 61801, USA
- Howard Hughes Medical Institute, Urbana, IL 61801, USA
| | - Ninian Blackburn
- Oregon Health & Sciences University, Institute of Environmental Health, Beaverton, OR 97006, USA
| | - Yi Lu
- University of Illinois-Urbana, Department of Biochemistry, Urbana, IL61801; USA
- University of Illinois-Urbana. Center for Biophysics and Computational Biology, Urbana, IL 61801, USA
- University of Illinois-Urbana. Department of Chemistry, Urbana, IL 61801, USA
| |
Collapse
|
39
|
Isomorphic deactivation of a Pseudomonas aeruginosa oxidoreductase: The crystal structure of Ag(I) metallated azurin at 1.7 Å. J Inorg Biochem 2013; 128:11-6. [PMID: 23911566 DOI: 10.1016/j.jinorgbio.2013.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 07/05/2013] [Accepted: 07/08/2013] [Indexed: 11/21/2022]
Abstract
Multiple biophysical methods demonstrate that silver effectively metallates Pseudomonas aeruginosa apo-azurin in solution. X-ray crystallography of the silver-modified protein reveals that silver binds to azurin at the traditional copper mediated active site with nearly identical geometry. Cyclic voltammetry indicates that the silver adduct is redox inert. Our results suggest that a potential mechanism for the microbial toxicity of silver is the deactivation of copper oxidoreductases by the effective binding and structural mimicry by silver without the corresponding function.
Collapse
|
40
|
Wilson TD, Yu Y, Lu Y. Understanding copper-thiolate containing electron transfer centers by incorporation of unnatural amino acids and the CuA center into the type 1 copper protein azurin. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.06.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
41
|
Prabhulkar S, Tian H, Wang X, Zhu JJ, Li CZ. Engineered proteins: redox properties and their applications. Antioxid Redox Signal 2012; 17:1796-822. [PMID: 22435347 PMCID: PMC3474195 DOI: 10.1089/ars.2011.4001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Revised: 03/20/2012] [Accepted: 03/21/2012] [Indexed: 10/28/2022]
Abstract
Oxidoreductases and metalloproteins, representing more than one third of all known proteins, serve as significant catalysts for numerous biological processes that involve electron transfers such as photosynthesis, respiration, metabolism, and molecular signaling. The functional properties of the oxidoreductases/metalloproteins are determined by the nature of their redox centers. Protein engineering is a powerful approach that is used to incorporate biological and abiological redox cofactors as well as novel enzymes and redox proteins with predictable structures and desirable functions for important biological and chemical applications. The methods of protein engineering, mainly rational design, directed evolution, protein surface modifications, and domain shuffling, have allowed the creation and study of a number of redox proteins. This review presents a selection of engineered redox proteins achieved through these methods, resulting in a manipulation in redox potentials, an increase in electron-transfer efficiency, and an expansion of native proteins by de novo design. Such engineered/modified redox proteins with desired properties have led to a broad spectrum of practical applications, ranging from biosensors, biofuel cells, to pharmaceuticals and hybrid catalysis. Glucose biosensors are one of the most successful products in enzyme electrochemistry, with reconstituted glucose oxidase achieving effective electrical communication with the sensor electrode; direct electron-transfer-type biofuel cells are developed to avoid thermodynamic loss and mediator leakage; and fusion proteins of P450s and redox partners make the biocatalytic generation of drug metabolites possible. In summary, this review includes the properties and applications of the engineered redox proteins as well as their significance and great potential in the exploration of bioelectrochemical sensing devices.
Collapse
Affiliation(s)
- Shradha Prabhulkar
- Nanobioengineering/Bioelectronics Laboratory, Department of Biomedical Engineering, Florida International University, Miami, Florida
| | - Hui Tian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Xiaotang Wang
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Jun-Jie Zhu
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Chen-Zhong Li
- Nanobioengineering/Bioelectronics Laboratory, Department of Biomedical Engineering, Florida International University, Miami, Florida
| |
Collapse
|
42
|
McLaughlin MP, Retegan M, Bill E, Payne TM, Shafaat HS, Peña S, Sudhamsu J, Ensign AA, Crane BR, Neese F, Holland PL. Azurin as a protein scaffold for a low-coordinate nonheme iron site with a small-molecule binding pocket. J Am Chem Soc 2012; 134:19746-57. [PMID: 23167247 PMCID: PMC3515693 DOI: 10.1021/ja308346b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The apoprotein of Pseudomonas aeruginosa azurin binds iron(II) to give a 1:1 complex, which has been characterized by electronic absorption, Mössbauer, and NMR spectroscopies, as well as X-ray crystallography and quantum-chemical computations. Despite potential competition by water and other coordinating residues, iron(II) binds tightly to the low-coordinate site. The iron(II) complex does not react with chemical redox agents to undergo oxidation or reduction. Spectroscopically calibrated quantum-chemical computations show that the complex has high-spin iron(II) in a pseudotetrahedral coordination environment, which features interactions with side chains of two histidines and a cysteine as well as the C═O of Gly45. In the (5)A(1) ground state, the d(z(2)) orbital is doubly occupied. Mutation of Met121 to Ala leaves the metal site in a similar environment but creates a pocket for reversible binding of small anions to the iron(II) center. Specifically, azide forms a high-spin iron(II) complex and cyanide forms a low-spin iron(II) complex.
Collapse
Affiliation(s)
| | - Marius Retegan
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Thomas M. Payne
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Hannah S. Shafaat
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Salvador Peña
- Department of Chemistry, University of Rochester, Rochester, New York 14618
| | - Jawahar Sudhamsu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Amy A. Ensign
- Department of Chemistry, University of Rochester, Rochester, New York 14618
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Patrick L. Holland
- Department of Chemistry, University of Rochester, Rochester, New York 14618
| |
Collapse
|
43
|
Hadt RG, Sun N, Marshall NM, Hodgson KO, Hedman B, Lu Y, Solomon EI. Spectroscopic and DFT studies of second-sphere variants of the type 1 copper site in azurin: covalent and nonlocal electrostatic contributions to reduction potentials. J Am Chem Soc 2012; 134:16701-16. [PMID: 22985400 PMCID: PMC3506006 DOI: 10.1021/ja306438n] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reduction potentials (E(0)) of type 1 (T1) or blue copper (BC) sites in proteins and enzymes with identical first coordination spheres around the redox active copper ion can vary by ~400 mV. Here, we use a combination of low-temperature electronic absorption and magnetic circular dichroism, electron paramagnetic resonance, resonance Raman, and S K-edge X-ray absorption spectroscopies to investigate a series of second-sphere variants--F114P, N47S, and F114N in Pseudomonas aeruginosa azurin--which modulate hydrogen bonding to and protein-derived dipoles nearby the Cu-S(Cys) bond. Density functional theory calculations correlated to the experimental data allow for the fractionation of the contributions to tuning E(0) into covalent and nonlocal electrostatic components. These are found to be significant, comparable in magnitude, and additive for active H-bonds, while passive H-bonds are mostly nonlocal electrostatic in nature. For dipoles, these terms can be additive to or oppose one another. This study provides a methodology for uncoupling covalency from nonlocal electrostatics, which, when coupled to X-ray crystallographic data, distinguishes specific local interactions from more long-range protein/active interactions, while affording further insight into the second-sphere mechanisms available to the protein to tune the E(0) of electron-transfer sites in biology.
Collapse
Affiliation(s)
- Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Ning Sun
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Nicholas M. Marshall
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Yi Lu
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| |
Collapse
|
44
|
Warren JJ, Lancaster KM, Richards JH, Gray HB. Inner- and outer-sphere metal coordination in blue copper proteins. J Inorg Biochem 2012; 115:119-26. [PMID: 22658756 PMCID: PMC3434318 DOI: 10.1016/j.jinorgbio.2012.05.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 04/30/2012] [Accepted: 05/01/2012] [Indexed: 10/28/2022]
Abstract
Blue copper proteins (BCPs) comprise classic cases of Nature's profound control over the electronic structures and chemical reactivity of transition metal ions. Early studies of BCPs focused on their inner coordination spheres, that is, residues that directly coordinate Cu. Equally important are the electronic and geometric perturbations to these ligands provided by the outer coordination sphere. In this tribute to Hans Freeman, we review investigations that have advanced the understanding of how inner-sphere and outer-sphere coordination affects biological Cu properties.
Collapse
Affiliation(s)
- Jeffrey J Warren
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | | |
Collapse
|
45
|
Chacón KN, Blackburn NJ. Stable Cu(II) and Cu(I) mononuclear intermediates in the assembly of the CuA center of Thermus thermophilus cytochrome oxidase. J Am Chem Soc 2012; 134:16401-12. [PMID: 22946616 DOI: 10.1021/ja307276z] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CuA is a dinuclear mixed-valence center located in subunit 2 of the ba(3)-type cytochrome oxidase from Thermus thermophilus. The assembly of this site within the periplasmic membrane is believed to be mediated by the copper chaperones Sco and/or PCuAC, but the biological mechanisms are still poorly understood, thereby stimulating interest in the mechanisms of CuA formation from inorganic ions. The formulation of the CuA center as an electron-delocalized Cu(1.5)-Cu(1.5) system implicates both Cu(II) and Cu(I) states in the metalation process. In earlier work we showed that selenomethionine (SeM) substitution of the coordinated M160 residue provided a ligand-directed probe for studying the copper coordination environment via the Se XAS signal, which was particularly useful for interrogating the Cu(I) states where other spectroscopic probes are absent. In the present study we have investigated the formation of mixed-valence CuA and its M160SeM derivative by stopped-flow UV-vis, EPR, and XAS at both Cu and Se edges, while the formation of fully reduced di-Cu(I) CuA has been studied by XAS alone. Our results establish the presence of previously undetected mononuclear intermediates and show important differences from the metalation reactions of purple CuA azurin. XAS spectroscopy at Cu and Se edges has allowed us to extend mechanistic inferences to formation of the di-Cu(I) state which may be more relevant to biological CuA assembly. In particular, we find that T. thermophilus CuA assembles more rapidly than reported for other CuA systems and that the dominant intermediate along the pathway to mixed-valence is a new green species with λ(max) = 460 nm. This intermediate has been isolated in a homogeneous state and shown to be a mononuclear Cu(II)-(His)(Cys)(2) species with no observable Cu(II)-(Met) interaction. Reduction with dithionite generates its Cu(I) homologue which is again mononuclear but now shows a strong interaction with the Met160 thioether. The results are discussed within the framework of the "coupled distortion" model for Cu(II) thiolates and their relevance to biological metalation reactions of the CuA center.
Collapse
Affiliation(s)
- Kelly N Chacón
- Institute of Environmental Health, Oregon Health and Sciences University, Beaverton, Oregon 97006, USA
| | | |
Collapse
|
46
|
A theoretical investigation of the functional role of the axial methionine ligand of the Cu(A) site in cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1314-27. [PMID: 21745457 DOI: 10.1016/j.bbabio.2011.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/29/2011] [Accepted: 06/22/2011] [Indexed: 11/20/2022]
Abstract
The functional roles of the amino acid residues of the Cu(A) site in bovine cytochrome c oxidase (CcO) were investigated by utilizing hybrid quantum mechanics (QM)/molecular mechanics (MM) calculations. The energy levels of the molecular orbitals (MOs) involving Cu d(zx) orbitals unexpectedly increased, as compared with those found previously with a simplified model system lacking the axial Met residue (i.e., Cu(2)S(2)N(2)). This elevation of MO energies stemmed from the formation of the anti-bonding orbitals, which are generated by hybridization between the d(zx) orbitals of Cu ions and the p-orbitals of the S and O atoms of the axial ligands. To clarify the roles of the axial Met ligand, the inner-sphere reorganization energies of the Cu(A) site were computed, with the Met residue assigned to either the QM or MM region. The reorganization energy slightly increased when the Met residue was excluded from the QM region. The existing experimental data and the present structural modeling study also suggested that the axial Met residue moderately increased the redox potential of the Cu(A) site. Thus, the role of the Met may be to regulate the electron transfer rate through the fine modulation of the electronic structure of the Cu(A) "platform", created by two Cys/His residues coordinated to the Cu ions. This regulation would provide the optimum redox potential/reorganization energy of the Cu(A) site, and thereby facilitate the subsequent cooperative reactions, such as the proton pump and the enzymatic activity, of CcO. This article is part of a Special Issue entitled: Allosteric cooperativity in respiratory proteins.
Collapse
|
47
|
Hong G, Ivnitski DM, Johnson GR, Atanassov P, Pachter R. Design parameters for tuning the type 1 Cu multicopper oxidase redox potential: insight from a combination of first principles and empirical molecular dynamics simulations. J Am Chem Soc 2011; 133:4802-9. [PMID: 21388209 DOI: 10.1021/ja105586q] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The redox potentials and reorganization energies of the type 1 (T1) Cu site in four multicopper oxidases were calculated by combining first principles density functional theory (QM) and QM/MM molecular dynamics (MD) simulations. The model enzymes selected included the laccase from Trametes versicolor, the laccase-like enzyme isolated from Bacillus subtilis, CueO required for copper homeostasis in Escherichia coli, and the small laccase (SLAC) from Streptomyces coelicolor. The results demonstrated good agreement with experimental data and provided insight into the parameters that influence the T1 redox potential. Effects of the immediate T1 Cu site environment, including the His(N(δ))-Cys(S)-His(N(δ)) and the axial coordinating amino acid, as well as the proximate H(N)(backbone)-S(Cys) hydrogen bond, were discerned. Furthermore, effects of the protein backbone and side-chains, as well as of the aqueous solvent, were studied by QM/MM molecular dynamics (MD) simulations, providing an understanding of influences beyond the T1 Cu coordination sphere. Suggestions were made regarding an increase of the T1 redox potential in SLAC, i.e., of Met198 and Thr232 in addition to the axial amino acid Met298. Finally, the results of this work presented a framework for understanding parameters that influence the Type 1 Cu MCO redox potential, useful for an ever-growing range of laccase-based applications.
Collapse
Affiliation(s)
- Gongyi Hong
- Air Force Research Laboratory, Materials & Manufacturing Directorate, Wright-Patterson Air Force Base, Ohio 45433, USA
| | | | | | | | | |
Collapse
|
48
|
Choi M, Davidson VL. Cupredoxins--a study of how proteins may evolve to use metals for bioenergetic processes. Metallomics 2011; 3:140-51. [PMID: 21258692 DOI: 10.1039/c0mt00061b] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cupredoxins are small proteins that contain type I copper centers, which are ubiquitous in nature. They function as electron transfer shuttles between proteins. This review of the structure and properties of native cupredoxins, and those modified by site-directed mutagenesis, illustrates how these proteins may have evolved to specifically bind copper, develop recognition sites for specific redox partners, tune redox potential for a particular function, and allow for efficient electron transfer through the protein matrix. This is relevant to the general understanding of the roles of metals in energy metabolism, respiration and photosynthesis.
Collapse
Affiliation(s)
- Moonsung Choi
- Department of Biochemistry, University of Mississippi Medical Center, 2500 N. State St., Jackson, MS 39216-4505, USA
| | | |
Collapse
|
49
|
Lancaster KM, Sproules S, Palmer JH, Richards JH, Gray HB. Outer-sphere effects on reduction potentials of copper sites in proteins: the curious case of high potential type 2 C112D/M121E Pseudomonas aeruginosa azurin. J Am Chem Soc 2011; 132:14590-5. [PMID: 20879734 DOI: 10.1021/ja105731x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Redox and spectroscopic (electronic absorption, multifrequency electron paramagnetic resonance (EPR), and X-ray absorption) properties together with X-ray crystal structures are reported for the type 2 Cu(II) C112D/M121E variant of Pseudomonas aeruginosa azurin. The results suggest that Cu(II) is constrained from interaction with the proximal glutamate; this structural frustration implies a "rack" mechanism for the 290 mV (vs NHE) reduction potential measured at neutral pH. At high pH (∼9), hydrogen bonding in the outer coordination sphere is perturbed to allow axial glutamate ligation to Cu(II), with a decrease in potential to 119 mV. These results highlight the role played by outer-sphere interactions, and the structural constraints they impose, in determining the redox behavior of transition metal protein cofactors.
Collapse
Affiliation(s)
- Kyle M Lancaster
- Beckman Institute, California Institute of Technology, Pasadena, California 91125, USA.
| | | | | | | | | |
Collapse
|
50
|
Biological Outer-Sphere Coordination. MOLECULAR ELECTRONIC STRUCTURES OF TRANSITION METAL COMPLEXES I 2011. [DOI: 10.1007/430_2011_49] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|