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Das D, Ainavarapu SRK. Protein engineering using circular permutation - structure, function, stability, and applications. FEBS J 2024. [PMID: 38676939 DOI: 10.1111/febs.17146] [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: 10/12/2023] [Revised: 03/13/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024]
Abstract
Protein engineering is important for creating novel variants from natural proteins, enabling a wide range of applications. Approaches such as rational design and directed evolution are routinely used to make new protein variants. Computational tools like de novo design can introduce new protein folds. Expanding the amino acid repertoire to include unnatural amino acids with non-canonical side chains in vitro by native chemical ligation and in vivo via codon expansion methods broadens sequence and structural possibilities. Circular permutation (CP) is an invaluable approach to redesigning a protein by rearranging the amino acid sequence, where the connectivity of the secondary structural elements is altered without changing the overall structure of the protein. Artificial CP proteins (CPs) are employed in various applications such as biocatalysis, sensing of small molecules by fluorescence, genome editing, ligand-binding protein switches, and optogenetic engineering. Many studies have shown that CP can lead to either reduced or enhanced stability or catalytic efficiency. The effects of CP on a protein's energy landscape cannot be predicted a priori. Thus, it is important to understand how CP can affect the thermodynamic and kinetic stability of a protein. In this review, we discuss the discovery and advancement of techniques to create protein CP, and existing reviews on CP. We delve into the plethora of biological applications for designed CP proteins. We subsequently discuss the experimental and computational reports on the effects of CP on the thermodynamic and kinetic stabilities of proteins of various topologies. An understanding of the various aspects of CP will allow the reader to design robust CP proteins for their specific purposes.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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2
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Mydy LS, Hungerford J, Chigumba DN, Konwerski JR, Jantzi SC, Wang D, Smith JL, Kersten RD. An intramolecular macrocyclase in plant ribosomal peptide biosynthesis. Nat Chem Biol 2024; 20:530-540. [PMID: 38355722 PMCID: PMC11049724 DOI: 10.1038/s41589-024-01552-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
The biosynthetic dogma of ribosomally synthesized and posttranslationally modified peptides (RiPP) involves enzymatic intermolecular modification of core peptide motifs in precursor peptides. The plant-specific BURP-domain protein family, named after their four founding members, includes autocatalytic peptide cyclases involved in the biosynthesis of side-chain-macrocyclic plant RiPPs. Here we show that AhyBURP, a representative of the founding Unknown Seed Protein-type BURP-domain subfamily, catalyzes intramolecular macrocyclizations of its core peptide during the sequential biosynthesis of monocyclic lyciumin I via glycine-tryptophan crosslinking and bicyclic legumenin via glutamine-tyrosine crosslinking. X-ray crystallography of AhyBURP reveals the BURP-domain fold with two type II copper centers derived from a conserved stapled-disulfide and His motif. We show the macrocyclization of lyciumin-C(sp3)-N-bond formation followed by legumenin-C(sp3)-O-bond formation requires dioxygen and radical involvement based on enzyme assays in anoxic conditions and isotopic labeling. Our study expands enzymatic intramolecular modifications beyond catalytic moiety and chromophore biogenesis to RiPP biosynthesis.
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Affiliation(s)
- Lisa S Mydy
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Jordan Hungerford
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Desnor N Chigumba
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Sarah C Jantzi
- Plasma Chemistry Laboratory, Center for Applied Isotope Studies, University of Georgia, Athens, GA, USA
| | - Di Wang
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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3
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Joy A, Biswas R. Significance of the Disulfide Bridge in the Structure and Stability of Metalloprotein Azurin. J Phys Chem B 2024; 128:973-984. [PMID: 38236012 DOI: 10.1021/acs.jpcb.3c07089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Metalloproteins make up a class of proteins that incorporate metal ions into their structures, enabling them to perform essential functions in biological systems, such as catalysis and electron transport. Azurin is one such metalloprotein with copper cofactor, having a β-barrel structure with exceptional thermal stability. The copper metal ion is coordinated at one end of the β-barrel structure, and there is a disulfide bond at the opposite end. In this study, we explore the effect of this disulfide bond in the high thermal stability of azurin by analyzing both the native S-S bonded and S-S nonbonded (S-S open) forms using temperature replica exchange molecular dynamics (REMD). Similar to experimental observations, we find a 35 K decrease in denaturation temperature for S-S open azurin compared to that of the native holo form (420 K). As observed in the case of native holo azurin, the unfolding process of the S-S open form also started with disruptions of the α-helix. The free energy surfaces of the unfolding process revealed that the denaturation event of the S-S open form progresses through different sets of conformational ensembles. Subsequently, we compared the stabilities of individual β-sheet strands of both the S-S bonded and the S-S nonbonded forms of azurin. Further, we examined the contacts between individual residues for the central structures from the free energy surfaces of the S-S nonbonded form. The microscopic origin of the lowering in the denaturation temperature is further supplemented by thermodynamic analysis.
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Affiliation(s)
- Albin Joy
- Department of Chemistry, Indian Institute of Technology Tirupati, Yerpedu, Tirupati, Andhra Pradesh, India 517619
| | - Rajib Biswas
- Department of Chemistry, Indian Institute of Technology Tirupati, Yerpedu, Tirupati, Andhra Pradesh, India 517619
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4
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Roger M, Leone P, Blackburn NJ, Horrell S, Chicano TM, Biaso F, Giudici-Orticoni MT, Abriata LA, Hura GL, Hough MA, Sciara G, Ilbert M. Beyond the coupled distortion model: structural analysis of the single domain cupredoxin AcoP, a green mononuclear copper centre with original features. Dalton Trans 2024; 53:1794-1808. [PMID: 38170898 PMCID: PMC10804444 DOI: 10.1039/d3dt03372d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
Cupredoxins are widely occurring copper-binding proteins with a typical Greek-key beta barrel fold. They are generally described as electron carriers that rely on a T1 copper centre coordinated by four ligands provided by the folded polypeptide. The discovery of novel cupredoxins demonstrates the high diversity of this family, with variations in terms of copper-binding ligands, copper centre geometry, redox potential, as well as biological function. AcoP is a periplasmic cupredoxin belonging to the iron respiratory chain of the acidophilic bacterium Acidithiobacillus ferrooxidans. AcoP presents original features, including high resistance to acidic pH and a constrained green-type copper centre of high redox potential. To understand the unique properties of AcoP, we undertook structural and biophysical characterization of wild-type AcoP and of two Cu-ligand mutants (H166A and M171A). The crystallographic structures, including native reduced AcoP at 1.65 Å resolution, unveil a typical cupredoxin fold. The presence of extended loops, never observed in previously characterized cupredoxins, might account for the interaction of AcoP with physiological partners. The Cu-ligand distances, determined by both X-ray diffraction and EXAFS, show that the AcoP metal centre seems to present both T1 and T1.5 features, in turn suggesting that AcoP might not fit well to the coupled distortion model. The crystal structures of two AcoP mutants confirm that the active centre of AcoP is highly constrained. Comparative analysis with other cupredoxins of known structures, suggests that in AcoP the second coordination sphere might be an important determinant of active centre rigidity due to the presence of an extensive hydrogen bond network. Finally, we show that other cupredoxins do not perfectly follow the coupled distortion model as well, raising the suspicion that further alternative models to describe copper centre geometries need to be developed, while the importance of rack-induced contributions should not be underestimated.
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Affiliation(s)
- Magali Roger
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Philippe Leone
- CNRS, Aix-Marseille University, Laboratoire d'Ingénierie des Systèmes Macromoléculaires, LISM UMR7255, 13009 Marseille, France
| | - Ninian J Blackburn
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Sam Horrell
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Tadeo Moreno Chicano
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Frédéric Biaso
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Marie-Thérèse Giudici-Orticoni
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling and Protein Purification and Structure Core Facility, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Giuliano Sciara
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
- Aix Marseille Univ, INRAE, BBF UMR1163, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Marianne Ilbert
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
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Wang JX, Vilbert AC, Cui C, Mirts EN, Williams LH, Kim W, Jessie Zhang Y, Lu Y. Increasing Reduction Potentials of Type 1 Copper Center and Catalytic Efficiency of Small Laccase from Streptomyces coelicolor through Secondary Coordination Sphere Mutations. Angew Chem Int Ed Engl 2023; 62:e202314019. [PMID: 37926680 PMCID: PMC10842694 DOI: 10.1002/anie.202314019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
The key to type 1 copper (T1Cu) function lies in the fine tuning of the CuII/I reduction potential (E°'T1Cu ) to match those of its redox partners, enabling efficient electron transfer in a wide range of biological systems. While the secondary coordination sphere (SCS) effects have been used to tune E°'T1Cu in azurin over a wide range, these principles are yet to be generalized to other T1Cu-containing proteins to tune catalytic properties. To this end, we have examined the effects of Y229F, V290N and S292F mutations around the T1Cu of small laccase (SLAC) from Streptomyces coelicolor to match the high E°'T1Cu of fungal laccases. Using ultraviolet-visible absorption and electron paramagnetic resonance spectroscopies, together with X-ray crystallography and redox titrations, we have probed the influence of SCS mutations on the T1Cu and corresponding E°'T1Cu . While minimal and small E°'T1Cu increases are observed in Y229F- and S292F-SLAC, the V290N mutant exhibits a major E°'T1Cu increase. Moreover, the influence of these mutations on E°'T1Cu is additive, culminating in a triple mutant Y229F/V290N/S292F-SLAC with the highest E°'T1Cu of 556 mV vs. SHE reported to date. Further activity assays indicate that all mutants retain oxygen reduction reaction activity, and display improved catalytic efficiencies (kcat /KM ) relative to WT-SLAC.
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Affiliation(s)
- Jing-Xiang Wang
- Department of Chemistry, The University of Texas at Austin, 105 East 24th Street, Austin, TX 78712, USA
| | - Avery C Vilbert
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA
| | - Chang Cui
- Department of Chemistry, The University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, IL 61801, USA
| | - Evan N Mirts
- Department of Chemistry, The University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, IL 61801, USA
| | - Lucas H Williams
- Department of Molecular Biosciences, The University of Texas at Austin, 100 East 24th St., Austin, TX 78712, USA
| | - Wantae Kim
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Austin, TX 78712, USA
| | - Y Jessie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, 100 East 24th St., Austin, TX 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, 100 East 24th St., Austin, TX 78712, USA
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, 105 East 24th Street, Austin, TX 78712, USA
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, USA
- Department of Chemistry, The University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, IL 61801, USA
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 East Dean Keeton Street, Austin, TX 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, 100 East 24th St., Austin, TX 78712, USA
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6
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Das D, Ainavarapu SRK. Circular permutation at azurin's active site slows down its folding. J Biol Inorg Chem 2023; 28:737-749. [PMID: 37957357 DOI: 10.1007/s00775-023-02023-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Circular permutation (CP) is a technique by which the primary sequence of a protein is rearranged to create new termini. The connectivity of the protein is altered but the overall protein structure generally remains unperturbed. Understanding the effect of CP can help design robust proteins for numerous applications such as in genetic engineering, optoelectronics, and improving catalytic activity. Studies on different protein topologies showed that CP usually affects protein stability as well as unfolding rates. Though a significant number of proteins contain metals or other cofactors, reports of metalloprotein CPs are rare. Thus, we chose a bacterial metalloprotein, azurin, and its CP within the metal-binding site (cpF114). We studied the stabilities, folding, and unfolding rates of apo- and Zn2+-bound CP azurin using fluorescence and circular dichroism. The introduced CP had destabilizing effects on the protein. Also, the folding of the Zn2+-CP protein was much slower than that of the Zn2+-WT or apo-protein. We compared this study to our previously reported azurin-cpN42, where we had observed an equilibrium and kinetic intermediate. cpF114 exhibits an apparent two-state equilibrium unfolding but has an off-pathway kinetic intermediate. Our study hinted at CP as a method to modify the energy landscape of proteins to alter their folding pathways. WT azurin, being a faster folder, may have evolved to optimize the folding rate of metal-bound protein compared to its CPs, albeit all of them have the same structure and function. Our study underscores that protein sequence and protein termini positions are crucial for metalloproteins. TOC Figure. (Top) Zn2+-azurin WT structure (PDB code: 1E67) and 2-D topology diagram of Zn2+-cpF114 azurin. (Bottom) Cartoon diagram representing folding (red arrows) and unfolding (blue arrows) of apo- and Zn2+- WT and cpF114 azurins. The width of the arrows represents the rate of the corresponding processes.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai, 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai, 400005, India.
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7
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Liu Y, Harnden KA, Van Stappen C, Dikanov SA, Lu Y. A designed Copper Histidine-brace enzyme for oxidative depolymerization of polysaccharides as a model of lytic polysaccharide monooxygenase. Proc Natl Acad Sci U S A 2023; 120:e2308286120. [PMID: 37844252 PMCID: PMC10614608 DOI: 10.1073/pnas.2308286120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/03/2023] [Indexed: 10/18/2023] Open
Abstract
The "Histidine-brace" (His-brace) copper-binding site, composed of Cu(His)2 with a backbone amine, is found in metalloproteins with diverse functions. A primary example is lytic polysaccharide monooxygenase (LPMO), a class of enzymes that catalyze the oxidative depolymerization of polysaccharides, providing not only an energy source for native microorganisms but also a route to more effective industrial biomass conversion. Despite its importance, how the Cu His-brace site performs this unique and challenging oxidative depolymerization reaction remains to be understood. To answer this question, we have designed a biosynthetic model of LPMO by incorporating the Cu His-brace motif into azurin, an electron transfer protein. Spectroscopic studies, including ultraviolet-visible (UV-Vis) absorption and electron paramagnetic resonance, confirm copper binding at the designed His-brace site. Moreover, the designed protein is catalytically active towards both cellulose and starch, the native substrates of LPMO, generating degraded oligosaccharides with multiturnovers by C1 oxidation. It also performs oxidative cleavage of the model substrate 4-nitrophenyl-D-glucopyranoside, achieving a turnover number ~9% of that of a native LPMO assayed under identical conditions. This work presents a rationally designed artificial metalloenzyme that acts as a structural and functional mimic of LPMO, which provides a promising system for understanding the role of the Cu His-brace site in LPMO activity and potential application in polysaccharide degradation.
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Affiliation(s)
- Yiwei Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Texas at Austin, Austin, TX78712
| | - Kevin A. Harnden
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, Austin, TX78712
| | - Sergei A. Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Texas at Austin, Austin, TX78712
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8
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López-Ortiz M, Zamora RA, Giannotti MI, Gorostiza P. The Protein Matrix of Plastocyanin Supports Long-Distance Charge Transport with Photosystem I and the Copper Ion Regulates Its Spatial Span and Conductance. ACS NANO 2023; 17:20334-20344. [PMID: 37797170 DOI: 10.1021/acsnano.3c06390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Charge exchange is the fundamental process that sustains cellular respiration and photosynthesis by shuttling electrons in a cascade of electron transfer (ET) steps between redox cofactors. While intraprotein charge exchange is well characterized in protein complexes bearing multiple redox sites, interprotein processes are less understood due to the lack of suitable experimental approaches and the dynamic nature of the interactions. Proteins constrained between electrodes are known to support electron transport (ETp) through the protein matrix even without redox cofactors, as the charges housed by the redox sites in ET are furnished by the electrodes. However, it is unknown whether protein ETp mechanisms apply to the interprotein medium present under physiological conditions. We study interprotein charge exchange between plant photosystem I (PSI) and its soluble redox partner plastocyanin (Pc) and address the role of the Pc copper center. Using electrochemical scanning tunneling spectroscopy (ECSTS) current-distance and blinking measurements, we quantify the spatial span of charge exchange between individual Pc/PSI pairs and ETp through transient Pc/PSI complexes. Pc devoid of the redox center (Pcapo) can exchange charge with PSI at longer distances than with the copper ion (Pcholo). Conductance bursts associated with Pcapo/PSI complex formation are higher than in Pcholo/PSI. Thus, copper ions are not required for long-distance Pc/PSI ETp but regulate its spatial span and conductance. Our results suggest that the redox center that carries the charge in Pc is not necessary to exchange it in interprotein ET through the aqueous solution and question the canonical view of tight complex binding between redox protein partners.
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Affiliation(s)
- Manuel López-Ortiz
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- CIBER-BBN, ISCIII, Barcelona 08028, Spain
| | - Ricardo A Zamora
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- CIBER-BBN, ISCIII, Barcelona 08028, Spain
| | - Marina I Giannotti
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- CIBER-BBN, ISCIII, Barcelona 08028, Spain
- Department of Materials Science and Physical Chemistry, University of Barcelona, Martí i Franquès 1-11, Barcelona 08028, Spain
| | - Pau Gorostiza
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- CIBER-BBN, ISCIII, Barcelona 08028, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
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9
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Van Stappen C, Dai H, Jose A, Tian S, Solomon EI, Lu Y. Primary and Secondary Coordination Sphere Effects on the Structure and Function of S-Nitrosylating Azurin. J Am Chem Soc 2023; 145:20610-20623. [PMID: 37696009 PMCID: PMC10539042 DOI: 10.1021/jacs.3c07399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Much progress has been made in understanding the roles of the secondary coordination sphere (SCS) in tuning redox potentials of metalloproteins. In contrast, the impact of SCS on reactivity is much less understood. A primary example is how copper proteins can promote S-nitrosylation (SNO), which is one of the most important dynamic post-translational modifications, and is crucial in regulating nitric oxide storage and transportation. Specifically, the factors that instill CuII with S-nitrosylating capabilities and modulate activity are not well understood. To address this issue, we investigated the influence of the primary and secondary coordination sphere on CuII-catalyzed S-nitrosylation by developing a series of azurin variants with varying catalytic capabilities. We have employed a multidimensional approach involving electronic absorption, S and Cu K-edge XAS, EPR, and resonance Raman spectroscopies together with QM/MM computational analysis to examine the relationships between structure and molecular mechanism in this reaction. Our findings have revealed that kinetic competency is correlated with three balancing factors, namely Cu-S bond strength, Cu spin localization, and relative S(ps) vs S(pp) contributions to the ground state. Together, these results support a reaction pathway that proceeds through the attack of the Cu-S bond rather than electrophilic addition to CuII or radical attack of SCys. The insights gained from this work provide not only a deeper understanding of SNO in biology but also a basis for designing artificial and tunable SNO enzymes to regulate NO and prevent diseases due to SNO dysregulation.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 E 24th St., Austin, Texas 78712, United States
| | - Huiguang Dai
- Department of Chemistry, University of Texas at Austin, 105 E 24th St., Austin, Texas 78712, United States
- Department of Chemistry, University of Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Anex Jose
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Shiliang Tian
- Department of Chemistry, University of Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 E 24th St., Austin, Texas 78712, United States
- Department of Chemistry, University of Urbana-Champaign, Champaign, Illinois 61801, United States
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10
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Abstract
Metal cofactors are critical centers for different biochemical processes of metalloproteins, and often, this metal coordination renders additional structural stability. In this study, we explore the additional stability conferred by the copper ion on azurin by analyzing both the apo and holo forms using temperature replica exchange molecular dynamics (REMD) data. We find a 14 K decrease in denaturation temperature for apo (406 K) azurin relative to that of holo (420 K), indicating a copper ion-induced additional thermal stability for holo azurin. The unfolding of apo azurin begins with the melting of α-helix and β-sheet V, similar to that of holo form. β-Sheets IV, VII, and VIII are comparatively more stable than other β-strands and melt at higher temperatures. Similar to holo azurin, the strong hydrophobic interactions among the apolar residues in the protein core is the key factor that renders high stability to apo protein as well. We construct free energy surfaces at different temperatures to capture the major conformations along the unfolding basins of the protein. Using contact maps from different basins we show the changes in the interaction between different residues along the unfolding pathway. Furthermore, we compare the Cα root-mean-square fluctuations (Cα-RMSF) and B-factor of all residues of apo and holo forms to understand the flexibility of different regions. The concerted displacement of α-helix and β-sheets V and VI from the protein core is another distinction we observe for apo compared to the holo form, where β-sheet VI was relatively stable.
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Affiliation(s)
- Albin Joy
- Department of Chemistry, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
| | - Rajib Biswas
- Department of Chemistry and Center for Atomic, Molecular and Optical Sciences & Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
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11
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Kontkanen OV, Biriukov D, Futera Z. Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin. Phys Chem Chem Phys 2023; 25:12479-12489. [PMID: 37097130 DOI: 10.1039/d3cp00197k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
As the field of nanoelectronics based on biomolecules such as peptides and proteins rapidly grows, there is a need for robust computational methods able to reliably predict charge transfer properties at bio/metallic interfaces. Traditionally, hybrid quantum-mechanical/molecular-mechanical techniques are employed for systems where the electron hopping transfer mechanism is applicable to determine physical parameters controlling the thermodynamics and kinetics of charge transfer processes. However, these approaches are limited by a relatively high computational cost when extensive sampling of a configurational space is required, like in the case of soft biomatter. For these applications, semi-empirical approaches such as the perturbed matrix method (PMM) have been developed and successfully used to study charge-transfer processes in biomolecules. Here, we explore the performance of PMM on prototypical redox-active protein azurin in various environments, from solution to vacuum interfaces with gold surfaces and protein junction. We systematically benchmarked the robustness and convergence of the method with respect to the quantum-centre size, size of the Hamiltonian, number of samples, and level of theory. We show that PMM can adequately capture all the trends associated with the structural and electronic changes related to azurin oxidation at bio/metallic interfaces.
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Affiliation(s)
- Outi Vilhelmiina Kontkanen
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
| | - Denys Biriukov
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Zdenek Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
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12
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Kircheva N, Angelova S, Dobrev S, Petkova V, Nikolova V, Dudev T. Cu +/Ag + Competition in Type I Copper Proteins (T1Cu). Biomolecules 2023; 13:biom13040681. [PMID: 37189429 DOI: 10.3390/biom13040681] [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: 03/30/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Due to the similarity in the basic coordination behavior of their mono-charged cations, silver biochemistry is known to be linked to that of copper in biological systems. Still, Cu+/2+ is an essential micronutrient in many organisms, while no known biological process requires silver. In human cells, copper regulation and trafficking is strictly controlled by complex systems including many cytosolic copper chaperones, whereas some bacteria exploit the so-called "blue copper" proteins. Therefore, evaluating the controlling factors of the competition between these two metal cations is of enormous interest. By employing the tools of computational chemistry, we aim to delineate the extent to which Ag+ might be able to compete with the endogenous copper in its Type I (T1Cu) proteins, and where and if, alternatively, it is handled uniquely. The effect of the surrounding media (dielectric constant) and the type, number, and composition of amino acid residues are taken into account when modelling the reactions in the present study. The obtained results clearly indicate the susceptibility of the T1Cu proteins to a silver attack due to the favorable composition and geometry of the metal-binding centers, along with the similarity between the Ag+/Cu+-containing structures. Furthermore, by exploring intriguing questions of both metals' coordination chemistry, an important background for understanding the metabolism and biotransformation of silver in organisms is provided.
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Affiliation(s)
- Nikoleta Kircheva
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Silvia Angelova
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Stefan Dobrev
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Vladislava Petkova
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Valya Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164 Sofia, Bulgaria
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164 Sofia, Bulgaria
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13
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Papp E, Vattay G, Romero-Muñiz C, Zotti LA, Fereiro JA, Sheves M, Cahen D. Experimental Data Confirm Carrier-Cascade Model for Solid-State Conductance across Proteins. J Phys Chem B 2023; 127:1728-1734. [PMID: 36790863 DOI: 10.1021/acs.jpcb.2c07946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The finding that electronic conductance across ultrathin protein films between metallic electrodes remains nearly constant from room temperature to just a few degrees Kelvin has posed a challenge. We show that a model based on a generalized Landauer formula explains the nearly constant conductance and predicts an Arrhenius-like dependence for low temperatures. A critical aspect of the model is that the relevant activation energy for conductance is either the difference between the HOMO and HOMO-1 or the LUMO+1 and LUMO energies instead of the HOMO-LUMO gap of the proteins. Analysis of experimental data confirms the Arrhenius-like law and allows us to extract the activation energies. We then calculate the energy differences with advanced DFT methods for proteins used in the experiments. Our main result is that the experimental and theoretical activation energies for these three different proteins and three differently prepared solid-state junctions match nearly perfectly, implying the mechanism's validity.
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Affiliation(s)
- Eszter Papp
- Department of Physics of Complex Systems, Eötvös Loránd University, Egyetem tér 1-3., H-1053 Budapest, Hungary
| | - Gábor Vattay
- Department of Physics of Complex Systems, Eötvös Loránd University, Egyetem tér 1-3., H-1053 Budapest, Hungary
| | - Carlos Romero-Muñiz
- Departamento de Física Aplicada I, Universidad de Sevilla, E-41012 Seville, Spain
| | - Linda A Zotti
- Departamento de Física Teórica de la Materia Condensada and IFIMAC, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Jerry A Fereiro
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram - 695551 Kerala, India
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - David Cahen
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 76100 Rehovot, Israel
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14
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Structural Analyses of the Multicopper Site of CopG Support a Role as a Redox Enzyme. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1414:97-121. [PMID: 36637718 DOI: 10.1007/5584_2022_753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Metal ions can be both essential components of cells as well as potential toxins if present in excess. Organisms utilize a variety of protein systems to maintain the concentration of metal ions within the appropriate range for cellular function, and to avoid concentrations where cellular damage can occur. In bacteria, numerous proteins contribute to copper homeostasis, including copper transporters, chelators, and redox enzymes. The genes that encode these proteins are often found in clusters, thus providing modular components that work together to achieve homeostasis. A better understanding of how these components function and cooperate to achieve metal ion resistance is needed, given the extensive use of metal ions, including copper, as broad-spectrum biocides in a variety of clinical and environmental settings. The copG gene is a common component of such copper resistance clusters, but its contribution to copper resistance is not well understood. In this review the available information about the CopG protein encoded by this gene is summarized. Comparison of the recent structure to diverse copper-containing metallochaperones, metalloenzymes, and electron transfer proteins suggests that CopG is a redox enzyme that uses multiple copper ions as active site redox cofactors to act on additional copper ion substrates. Mechanisms for both oxidase and reductase activity are proposed, and the biological advantages that these activities can contribute in conjunction with existing systems are described.
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15
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Choi JK, Naffouje SA, Goto M, Wang J, Christov K, Rademacher DJ, Green A, Stecenko AA, Chakrabarty AM, Das Gupta TK, Yamada T. Cross-talk between cancer and Pseudomonas aeruginosa mediates tumor suppression. Commun Biol 2023; 6:16. [PMID: 36609683 PMCID: PMC9823004 DOI: 10.1038/s42003-022-04395-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023] Open
Abstract
Microorganisms living at many sites in the human body compose a complex and dynamic community. Accumulating evidence suggests a significant role for microorganisms in cancer, and therapies that incorporate bacteria have been tried in various types of cancer. We previously demonstrated that cupredoxin azurin secreted by the opportunistic pathogen Pseudomonas aeruginosa, enters human cancer cells and induces apoptotic death1-4. However, the physiological interactions between P. aeruginosa and humans and their role in tumor homeostasis are largely unknown. Here, we show that P. aeruginosa upregulated azurin secretion in response to increasing numbers of and proximity to cancer cells. Conversely, cancer cells upregulated aldolase A secretion in response to increasing proximity to P. aeruginosa, which also correlated with enhanced P. aeruginosa adherence to cancer cells. Additionally, we show that cancer patients had detectable P. aeruginosa and azurin in their tumors and exhibited increased overall survival when they did, and that azurin administration reduced tumor growth in transgenic mice. Our results suggest host-bacterial symbiotic mutualism acting as a diverse adjunct to the host defense system via inter-kingdom communication mediated by the evolutionarily conserved proteins azurin and human aldolase A. This improved understanding of the symbiotic relationship of bacteria with humans indicates the potential contribution to tumor homeostasis.
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Affiliation(s)
- Juliana K Choi
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA.,Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Samer A Naffouje
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA.,General Surgery, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Masahide Goto
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - Jing Wang
- Department of Mathematics, Statistics and Computer Science, University of Illinois College of Liberal Arts and Sciences, Chicago, IL, 60607, USA
| | - Konstantin Christov
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - David J Rademacher
- Department of Microbiology and Immunology and Core Imaging Facility, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Albert Green
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - Arlene A Stecenko
- Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ananda M Chakrabarty
- Department of Microbiology & Immunology, University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - Tapas K Das Gupta
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA.
| | - Tohru Yamada
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL, 60612, USA. .,Richard & Loan Hill Department of Biomedical Engineering, University of Illinois College of Engineering, Chicago, IL, 60607, USA.
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16
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Avagyan S, Makhatadze GI. Volumetric Properties of the Transition State Ensemble for Protein Folding. J Phys Chem B 2022; 126:7615-7620. [PMID: 36150186 DOI: 10.1021/acs.jpcb.2c05437] [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
Understanding how high hydrostatic pressure affects biomacromolecular interaction is important for deciphering the molecular mechanisms by which organisms adapt to live at the bottom of the ocean. The relative effect of hydrostatic pressure on the rates of folding/unfolding reactions is defined by the volumetric properties of the transition state ensemble relative to the folded and unfolded states. All-atom structure-based molecular dynamics simulations combined with quantitative computational protocol to compute volumes from three-dimensional coordinates allow volumetric mapping of protein folding landscape. This, is turn, provides qualitative understanding of the effects of hydrostatic pressure on energy landscape of proteins. The computational results for six different proteins are directly benchmark against experimental data and show an excellent agreement. Both experiments and computation show that the transition-state ensemble volume appears to be in-between the folded and unfolded state volumes, and thus the hydrostatic pressure accelerates protein unfolding.
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Affiliation(s)
- Samvel Avagyan
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - George I Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Department on Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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17
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Guo J, Fisher OS. Orchestrating copper binding: structure and variations on the cupredoxin fold. J Biol Inorg Chem 2022; 27:529-540. [PMID: 35994119 DOI: 10.1007/s00775-022-01955-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/07/2022] [Indexed: 11/26/2022]
Abstract
A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was originally identified in Type 1 "blue copper" centers but has since proven to be a common domain architecture within an increasingly large and diverse group of copper binding domains. The cupredoxin fold has a number of qualities that make it ideal for coordinating Cu ions for purposes including electron transfer, enzyme catalysis, assembly of other copper sites, and copper sequestration. The structural core does not undergo major conformational changes upon metal binding, but variations within the coordination environment of the metal site confer a range of Cu-binding affinities, reduction potentials, and spectroscopic properties. Here, we discuss these proteins from a structural perspective, examining how variations within the overall cupredoxin fold and metal binding sites are linked to distinct spectroscopic properties and biological functions. Expanding far beyond the blue copper proteins, cupredoxin domains are used by a growing number of proteins and enzymes as a means of binding copper ions, with many more likely remaining to be identified.
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Affiliation(s)
- Jing Guo
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Oriana S Fisher
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA.
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18
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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19
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Sarhangi SM, Matyushov DV. Anomalously Small Reorganization Energy of the Half Redox Reaction of Azurin. J Phys Chem B 2022; 126:3000-3011. [DOI: 10.1021/acs.jpcb.2c00338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Setare M. Sarhangi
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, United States
| | - Dmitry V. Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, United States
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20
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Kontkanen OV, Biriukov D, Futera Z. Reorganization Free Energy of Copper Proteins in Solution, in Vacuum, and on Metal Surfaces. J Chem Phys 2022; 156:175101. [DOI: 10.1063/5.0085141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Metalloproteins, known to efficiently transfer electronic charge in biological systems, recently found their utilization in nanobiotechnological devices where the protein is placed into direct contact with metal surfaces. The feasibility of oxidation/reduction of the protein redox sites is affected by the reorganization free energies, one of the key parameters determining the transfer rates. While their values have been measured and computed for proteins in their native environments, i.e., in aqueous solution, the reorganization free energies of dry proteins or proteins adsorbed to metal surfaces remain unknown. Here, we investigate the redox properties of blue copper protein azurin, a prototypical redox-active metalloprotein previously probed by various experimental techniques both in solution and on metal/vacuum interfaces. We used a hybrid QM/MM computational technique based on DFT to explore protein dynamics, flexibility, and corresponding reorganization free energies in aqueous solution, vacuum, and on vacuum gold interfaces. Somewhat surprisingly, the reorganization free energy only slightly decreases when azurin is dried because the loss of the hydration shell leads to larger flexibility of the protein near its redox site. At the vacuum gold surfaces, the energetics of the structure relaxation depends on the adsorption geometry, however, significant reduction of the reorganization free energy was not observed. These findings have important consequences for the charge transport mechanism in vacuum devices, showing that the free energy barriers for protein oxidation remain significant even under ultra-high vacuum conditions.
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Affiliation(s)
| | - Denys Biriukov
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences, Czech Republic
| | - Zdenek Futera
- University of South Bohemia in Ceske Budejovice Faculty of Science, Czech Republic
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21
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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
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22
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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.
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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.
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23
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Joy A, Biswas R. Molecular Insight into the High Thermal Stability of Metalloprotein Azurin. J Phys Chem B 2022; 126:2496-2506. [PMID: 35324174 DOI: 10.1021/acs.jpcb.2c00622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate the events characterizing the steps of the unfolding pathway of blue copper metalloprotein azurin using replica exchange molecular dynamics (REMD). Our studies show that the unfolding of azurin begins with the melting of α-helix and β-sheets II and V. This is followed by the melting of other β-sheets and the exposure of hydrophobic protein core to the solvent, resulting in disruptions of its tertiary structure. Free energy surfaces constructed at different temperatures portray different basins that signify the stability of different melted structures in the unfolding process. The contact maps at different temperatures reveal that the strong hydrophobic interaction within the core of the protein is the vital force that renders high stability to this protein. Analysis of the individual β-sheets by looking into their amino acid sequence shows that β-sheets with charged side chains on the surface melt fast compared to others. The β-barrel of azurin is able to dynamically rearrange, and it helps the protein to preserve its hydrophobic core, holding back the native topology from melting fast. B-factor analysis shows that residues of β-sheets III, IV, and VII deviate less from their initial structure at the transition temperature.
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Affiliation(s)
- Albin Joy
- Department of Chemistry, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
| | - Rajib Biswas
- Department of Chemistry and Center for Atomic, Molecular and Optical Sciences & Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
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24
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Chen X, Chen M, Wolynes PG, Wittung-Stafshede P, Gray HB. Frustration Dynamics and Electron-Transfer Reorganization Energies in Wild-Type and Mutant Azurins. J Am Chem Soc 2022; 144:4178-4185. [PMID: 35171591 PMCID: PMC8915257 DOI: 10.1021/jacs.1c13454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Long-range electron
tunneling through metalloproteins is facilitated
by evolutionary tuning of donor–acceptor electronic couplings,
formal electrochemical potentials, and active-site reorganization
energies. Although the minimal frustration of the folding landscape
enables this tuning, residual frustration in the vicinity of the metallocofactor
can allow conformational fluctuations required for protein function.
We show here that the constrained copper site in wild-type azurin
is governed by an intricate pattern of minimally frustrated local
and distant interactions that together enable rapid electron flow
to and from the protein. In contrast, sluggish electron transfer reactions
(unfavorable reorganization energies) of active-site azurin variants
are attributable to increased frustration near to as well as distant
from the copper site, along with an exaggerated oxidation-state dependence
of both minimally and highly frustrated interaction patterns.
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Affiliation(s)
- Xun Chen
- Center for Theoretical Biological Physics, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Mingchen Chen
- Center for Theoretical Biological Physics, Houston, Texas 77005, United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States.,Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Harry B Gray
- Beckman Institute and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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25
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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]
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26
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Das D, Ainavarapu SRK. Azurin-Derived Peptides: Comparison of Nickel- and Copper-Binding Properties. Inorg Chem 2021; 60:9720-9726. [PMID: 34137603 DOI: 10.1021/acs.inorgchem.1c01007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metalloproteins are an important class of proteins involved in metal uptake, transport, and electron-transfer reactions. Mimicking the active sites of these proteins through miniaturization is an active area of research with applications in biotechnology and medicine. Azurin is a 128-residue copper-binding cupredoxin protein involved in electron-transfer reactions. Previous studies have reported on the copper-binding-induced spectroscopic and structural properties of peptide loops (11 and 13 residues) from azurin. These azurin peptides exhibited novel stoichiometries. However, the underlying mechanism of fluorescence quenching upon copper binding remains to be understood, whether it is due to electron transfer, energy transfer, or both. Here, we report nickel-binding-associated spectroscopic and structural properties of the azurin peptides. They develop a β-turn upon nickel binding as seen in circular dichroism and exhibit electronic transitions centered at 270 and 450 nm. Unlike copper, which exhibited 1:1 and 1:2 peptide:metal stoichiometries, nickel exhibited only a 1:1 stoichiometry. Tryptophan-containing peptides showed fluorescence quenching upon nickel binding, which is due to electron transfer. These results further suggest that the quenching in copper-bound peptides is also due to electron transfer, which could not be ascertained in previous studies. Overall, azurin peptides provide a platform for studying metal-induced structural and spectroscopic properties using transition-metal ions.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
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27
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Schulz C, van Gastel M, Pantazis DA, Neese F. Converged Structural and Spectroscopic Properties for Refined QM/MM Models of Azurin. Inorg Chem 2021; 60:7399-7412. [PMID: 33939922 PMCID: PMC8154437 DOI: 10.1021/acs.inorgchem.1c00640] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 12/27/2022]
Abstract
Blue copper proteins continue to challenge experiment and theory with their electronic structure and spectroscopic properties that respond sensitively to the coordination environment of the copper ion. In this work, we report state-of-the art electronic structure studies for geometric and spectroscopic properties of the archetypal "Type I" copper protein azurin in its Cu(II) state. A hybrid quantum mechanics/molecular mechanics (QM/MM) approach is used, employing both density functional theory (DFT) and coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) methods for the QM region, the latter method making use of the domain-based local pair natural orbital (DLPNO) approach. Models of increasing QM size are employed to investigate the convergence of critical geometric parameters. It is shown that convergence is slow and that a large QM region is critical for reproducing the short experimental Cu-SCys112 distance. The study of structural convergence is followed by investigation of spectroscopic parameters using both DFT and DLPNO-CC methods and comparing these to the experimental spectrum using simulations. The results allow us to examine for the first time the distribution of spin densities and hyperfine coupling constants at the coupled cluster level, leading us to revisit the experimental assignment of the 33S hyperfine splitting. The wavefunction-based approach to obtain spin-dependent properties of open-shell systems demonstrated here for the case of azurin is transferable and applicable to a large array of bioinorganic systems.
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Affiliation(s)
- Christine
E. Schulz
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Maurice van Gastel
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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28
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Balogh RK, Németh E, Jones NC, Hoffmann SV, Jancsó A, Gyurcsik B. A study on the secondary structure of the metalloregulatory protein CueR: effect of pH, metal ions and DNA. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:491-500. [PMID: 33907862 DOI: 10.1007/s00249-021-01539-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/13/2021] [Accepted: 04/14/2021] [Indexed: 11/30/2022]
Abstract
The response of CueR towards environmental changes in solution was investigated. CueR is a bacterial metal ion selective transcriptional metalloregulator protein, which controls the concentration of copper ions in the cell. Although several articles have been devoted to the discussion of the structural and functional features of this protein, CueR has not previously been extensively characterized in solution. Here, we studied the effect of change in pH, temperature, and the presence of specific or non-specific binding partners on the secondary structure of CueR with circular dichroism (CD) spectroscopy. A rather peculiar reversible pH-dependent secondary structure transformation was observed, elucidated and supplemented with pKa estimation by PROPKA and CpHMD simulations suggesting an important role of His(76) and His(94) in this process. CD experiments revealed that the presence of DNA prevents this structural switch, suggesting that DNA locks CueR in the α-helical-rich form. In contrast to the non-cognate metal ions HgII, CdII and ZnII, the presence of the cognate AgI ion affects the secondary structure of CueR, most probably by stabilizing the metal ion and DNA-binding domains of the protein.
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Affiliation(s)
- Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary.,Institute of Enzymology, Genome Stability Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest, 1117, Hungary
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000, Aarhus C, Denmark
| | - Søren Vrønning Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000, Aarhus C, Denmark
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary.
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29
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The Role of Metal Ions in the Electron Transport through Azurin-Based Junctions. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11093732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We studied the coherent electron transport through metal–protein–metal junctions based on a blue copper azurin, in which the copper ion was replaced by three different metal ions (Co, Ni and Zn). Our results show that neither the protein structure nor the transmission at the Fermi level change significantly upon metal replacement. The discrepancy with previous experimental observations suggests that the transport mechanism taking place in these types of junctions is probably not fully coherent.
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30
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Bizzarri AR, Cannistraro S. Toward Cancer Diagnostics of the Tumor Suppressor p53 by Surface Enhanced Raman Spectroscopy. SENSORS (BASEL, SWITZERLAND) 2020; 20:s20247153. [PMID: 33327383 PMCID: PMC7764831 DOI: 10.3390/s20247153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 05/10/2023]
Abstract
The tumor suppressor p53 protein plays a crucial role in many biological processes. The presence of abnormal concentrations of wild-type p53, or some of its mutants, can be indicative of a pathological cancer state. p53 represents therefore a valuable biomarker for tumor screening approaches and development of suitable biosensors for its detection deserves a high interest in early diagnostics. Here, we revisit our experimental approaches, combining Surface Enhanced Raman Spectroscopy (SERS) and nanotechnological materials, for ultrasensitive detection of wild-type and mutated p53, in the perspective to develop biosensors to be used in clinical diagnostics. The Raman marker is provided by a small molecule (4-ATP) acting as a bridge between gold nanoparticles (NPs) and a protein biomolecule. The Azurin copper protein and specific antibodies of p53 were used as a capture element for p53 (wild-type and its mutants). The developed approaches allowed us to reach a detection level of p53 down to 10-17 M in both buffer and serum. The implementation of the method in a biosensor device, together with some possible developments are discussed.
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31
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Huang F, Shu Q, Qin Z, Tian J, Su Z, Huang Y, Gao M. Anticancer Actions of Azurin and Its Derived Peptide p28. Protein J 2020; 39:182-189. [PMID: 32180097 DOI: 10.1007/s10930-020-09891-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cancers are a great threat to humans. In cancer therapy, surgical removal of the tumor combined with radiotherapy and chemotherapy is the most routine treatment procedure and usually the most effective. However, radiotherapy and chemotherapy drugs that kill cancer cells efficiently also kill normal cells, thus exhibiting large side effects. Cancer-targeted drugs, which aim to specifically recognize proteins or signaling pathways associated with tumor proliferation and migration, have achieved marked progress in recent years. Azurin is a copper-containing redox protein secreted by Pseudomonas aeruginosa. Azurin and its derived peptide p28 preferentially enter a variety of cancer cells and induce apoptosis or cell cycle arrest. Mechanistic studies revealed that azurin and p28 target the p53 and receptor tyrosine kinase signaling pathways as well as other pathways. Two phase I trials of p28 have been carried out, with findings that p28 is safe and exhibits anticancer activity in both adult and pediatric patients. In this review paper, we provide an up-to-date summary of progress on the anticancer mechanisms and therapeutic strategies for azurin and p28.
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Affiliation(s)
- Fan Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, 430068, Hubei, China.,Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Qianhui Shu
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, 430068, Hubei, China.,Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Zhaojie Qin
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, 430068, Hubei, China.,Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Jianglin Tian
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, 430068, Hubei, China.,Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, 430068, Hubei, China.,Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, 430068, Hubei, China.,Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Meng Gao
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, 430068, Hubei, China. .,Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China.
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32
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Raber HF, Heerde T, El Din SN, Flaig C, Hilgers F, Bitzenhofer N, Jäger KE, Drepper T, Gottschalk KE, Bodenberger NE, Weil T, Kubiczek DH, Rosenau F. Azulitox—A Pseudomonas aeruginosa P28-Derived Cancer-Cell-Specific Protein Photosensitizer. Biomacromolecules 2020; 21:5067-5076. [DOI: 10.1021/acs.biomac.0c01216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Heinz Fabian Raber
- Institute for Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Thomas Heerde
- Institute for Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Suzanne Nour El Din
- Institute for Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Carolin Flaig
- Institute for Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Institute for Experimental Physics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426 Jülich, Germany
| | - Nora Bitzenhofer
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426 Jülich, Germany
| | - Karl-Erich Jäger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426 Jülich, Germany
- Institute of Bio- and Geosciences (IBG-1: Biotechnology) Forschungszentrum Jülich, Stetternicher Forst, 52426 Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich, Stetternicher Forst, 52426 Jülich, Germany
| | - Kay-Eberhard Gottschalk
- Institute for Experimental Physics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | | | - Tanja Weil
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany
| | - Dennis Horst Kubiczek
- Institute for Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Frank Rosenau
- Institute for Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany
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33
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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.
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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
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34
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Crittenden CM, Novelli ET, Mehaffey MR, Xu GN, Giles DH, Fies WA, Dalby KN, Webb LJ, Brodbelt JS. Structural Evaluation of Protein/Metal Complexes via Native Electrospray Ultraviolet Photodissociation Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1140-1150. [PMID: 32275426 PMCID: PMC7386362 DOI: 10.1021/jasms.0c00066] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ultraviolet photodissociation (UVPD) has emerged as a promising tool to characterize proteins with regard to not only their primary sequences and post-translational modifications, but also their tertiary structures. In this study, three metal-binding proteins, Staphylococcal nuclease, azurin, and calmodulin, are used to demonstrate the use of UVPD to elucidate metal-binding regions via comparisons between the fragmentation patterns of apo (metal-free) and holo (metal-bound) proteins. The binding of staphylococcal nuclease to calcium was evaluated, in addition to a series of lanthanide(III) ions which are expected to bind in a similar manner as calcium. On the basis of comparative analysis of the UVPD spectra, the binding region for calcium and the lanthanide ions was determined to extend from residues 40-50, aligning with the known crystal structure. Similar analysis was performed for both azurin (interrogating copper and silver binding) and calmodulin (four calcium binding sites). This work demonstrates the utility of UVPD methods for determining and analyzing the metal binding sites of a variety of classes of proteins.
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Affiliation(s)
| | - Elisa T Novelli
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - M Rachel Mehaffey
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Gulan N Xu
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - David H Giles
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Whitney A Fies
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712, United States
- Graduate Program in Cell and Molecular Biology, University of Texas, Austin, Texas 78712, United States
| | - Lauren J Webb
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
- Institute for Cell and Molecular Biology, University of Texas, Austin, Texas 78712, United States
- Texas Materials Institute, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
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35
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Ortega M, Vilhena JG, Zotti LA, Díez-Pérez I, Cuevas JC, Pérez R. Tuning Structure and Dynamics of Blue Copper Azurin Junctions via Single Amino-Acid Mutations. Biomolecules 2019; 9:biom9100611. [PMID: 31618974 PMCID: PMC6843909 DOI: 10.3390/biom9100611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/02/2019] [Accepted: 10/09/2019] [Indexed: 12/15/2022] Open
Abstract
In the growing field of biomolecular electronics, blue-copper Azurin stands out as one of the most widely studied protein in single-molecule contacts. Interestingly, despite the paramount importance of the structure/dynamics of molecular contacts in their transport properties, these factors remain largely unexplored from the theoretical point of view in the context of single Azurin junctions. Here we address this issue using all-atom Molecular Dynamics (MD) of Pseudomonas Aeruginosa Azurin adsorbed to a Au(111) substrate. In particular, we focus on the structure and dynamics of the free/adsorbed protein and how these properties are altered upon single-point mutations. The results revealed that wild-type Azurin adsorbs on Au(111) along two well defined configurations: one tethered via cysteine groups and the other via the hydrophobic pocket surrounding the Cu 2 + . Surprisingly, our simulations revealed that single amino-acid mutations gave rise to a quenching of protein vibrations ultimately resulting in its overall stiffening. Given the role of amino-acid vibrations and reorientation in the dehydration process at the protein-water-substrate interface, we suggest that this might have an effect on the adsorption process of the mutant, giving rise to new adsorption configurations.
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Affiliation(s)
- Maria Ortega
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - J G Vilhena
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland.
| | - Linda A Zotti
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Ismael Díez-Pérez
- Department of Chemistry, Faculty of Natural & Mathematical Sciences, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK.
| | - Juan Carlos Cuevas
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
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36
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Romero-Muñiz C, Ortega M, Vilhena JG, Diéz-Pérez I, Cuevas JC, Pérez R, Zotti LA. Mechanical Deformation and Electronic Structure of a Blue Copper Azurin in a Solid-State Junction. Biomolecules 2019; 9:biom9090506. [PMID: 31546917 PMCID: PMC6769874 DOI: 10.3390/biom9090506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/14/2019] [Accepted: 09/16/2019] [Indexed: 01/26/2023] Open
Abstract
Protein-based electronics is an emerging field which has attracted considerable attention over the past decade. Here, we present a theoretical study of the formation and electronic structure of a metal-protein-metal junction based on the blue-copper azurin from pseudomonas aeruginosa. We focus on the case in which the protein is adsorbed on a gold surface and is contacted, at the opposite side, to an STM (Scanning Tunneling Microscopy) tip by spontaneous attachment. This has been simulated through a combination of molecular dynamics and density functional theory. We find that the attachment to the tip induces structural changes in the protein which, however, do not affect the overall electronic properties of the protein. Indeed, only changes in certain residues are observed, whereas the electronic structure of the Cu-centered complex remains unaltered, as does the total density of states of the whole protein.
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Affiliation(s)
- Carlos Romero-Muñiz
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - María Ortega
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - J G Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland.
| | - Ismael Diéz-Pérez
- Department of Chemistry, Faculty of Natural & Mathematical Sciences, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK.
| | - Juan Carlos Cuevas
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Linda A Zotti
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
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37
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Abstract
Copper is a redox-active transition metal ion required for the function of many essential human proteins. For biosynthesis of proteins coordinating copper, the metal may bind before, during or after folding of the polypeptide. If the metal binds to unfolded or partially folded structures of the protein, such coordination may modulate the folding reaction. The molecular understanding of how copper is incorporated into proteins requires descriptions of chemical, thermodynamic, kinetic and structural parameters involved in the formation of protein-metal complexes. Because free copper ions are toxic, living systems have elaborate copper-transport systems that include particular proteins that facilitate efficient and specific delivery of copper ions to target proteins. Therefore, these pathways become an integral part of copper protein folding in vivo. This review summarizes biophysical-molecular in vitro work assessing the role of copper in folding and stability of copper-binding proteins as well as protein-protein copper exchange reactions between human copper transport proteins. We also describe some recent findings about the participation of copper ions and copper proteins in protein misfolding and aggregation reactions in vitro.
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38
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Mukhopadhyay BP. Putative role of conserved water molecules in the hydration and inter-domain recognition of mono nuclear copper centers in O2-bound human ceruloplasmin: A comparative study between X-ray and MD simulated structures. Bioinformation 2019; 15:402-411. [PMID: 31312077 PMCID: PMC6614124 DOI: 10.6026/97320630015402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/02/2019] [Indexed: 11/23/2022] Open
Abstract
Human Ceruloplasmin (hCP) is an unique multicopper oxidase which involves in different biological functions e.g., iron metabolism, copper transportation, biogenic amine oxidation ,and its malfunction causes Wilson's and Menkes diseases. MD- simulation studies of O2- bound solvated structure have revealed the role of several conserved/ semi-conserved water molecules in the hydration of type-I copper centers and their involvement to recognition dynamics of these metal centers. In O2- bound structure, hydration potentiality of CuRS (Cu1106) type-I copper center is observed to be unique, where two water molecules (W1-W2) are interacting with the metal sites, which was not found in X-ray structures of hCP. Generally, in the interdomain recognition of CuCys-His to CuRS, CuRS to CuPR and CuPR to CuCys-His centers, the copper bound His-residue of one domain interacts with the Glu-residue of other complementary domain through conserved/ semi-conserved (W3 to W5) water- mediated hydrogen bonds (Cu-His...W...Glu), however direct salt-bridge (Cu-His...Glu) interaction were observed in the X- ray structures. The MD- simulated and X- ray structures have indicated some possibilities on the Cu-His...W...Glu ↔ Cu-His...Glu transition during the interdomain recognition of type-I copper centers, which may have some importance in biology and chemistry of ceruloplasmin.
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Affiliation(s)
- Bishnu P. Mukhopadhyay
- Department of Chemistry National Institute of Technology-Durgapur, West Bengal, Durgapur - 713209, India
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39
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Wilder LM, Fies WA, Rabin C, Webb LJ, Crooks RM. Conjugation of an α-Helical Peptide to the Surface of Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:3363-3371. [PMID: 30802061 DOI: 10.1021/acs.langmuir.9b00075] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We are interested in functionalizing gold nanoparticles (AuNPs) with proteins using a biomimetic approach in which an intermediate peptide "glue" directs the orientation of a protein relative to the AuNP surface. The first step toward this goal is described in the present article. Specifically, we show that ∼5 nm AuNPs can be functionalized with a mixed self-assembled monolayer (SAM) consisting of oligo(ethylene glycol) alkanethiols terminated with either hydroxyl or azide groups, and that the resulting materials are stable and soluble in water. The azide groups on the surface of the AuNPs can be subsequently linked to alkyne-functionalized peptides via a copper-catalyzed azide-alkyne cycloaddition (click) reaction. Analysis of the resulting material by Fourier transform infrared and circular dichroism spectroscopy demonstrates that the peptide is covalently linked to the SAM and that it exists in an α-helical conformation. In addition to our intended purpose of using these highly structured, biomimetic materials to orient proteins, they may also be useful for applications involving interactions between nanoparticles and cells.
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Affiliation(s)
- Logan M Wilder
- Department of Chemistry and Texas Materials Institute , The University of Texas at Austin , 105 E. 24th Street, Stop A5300 , Austin , Texas 78712-1224 , United States
| | - Whitney A Fies
- Department of Chemistry and Texas Materials Institute , The University of Texas at Austin , 105 E. 24th Street, Stop A5300 , Austin , Texas 78712-1224 , United States
| | - Charlie Rabin
- Department of Chemistry and Texas Materials Institute , The University of Texas at Austin , 105 E. 24th Street, Stop A5300 , Austin , Texas 78712-1224 , United States
| | - Lauren J Webb
- Department of Chemistry and Texas Materials Institute , The University of Texas at Austin , 105 E. 24th Street, Stop A5300 , Austin , Texas 78712-1224 , United States
| | - Richard M Crooks
- Department of Chemistry and Texas Materials Institute , The University of Texas at Austin , 105 E. 24th Street, Stop A5300 , Austin , Texas 78712-1224 , United States
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40
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Devlin T, Hofman CR, Acevedo ZPV, Kohler KR, Tao L, Britt RD, Hoke KR, Hunsicker-Wang LM. DEPC modification of the Cu A protein from Thermus thermophilus. J Biol Inorg Chem 2018; 24:117-135. [PMID: 30523412 DOI: 10.1007/s00775-018-1632-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/28/2018] [Indexed: 11/28/2022]
Abstract
The CuA center is the initial electron acceptor in cytochrome c oxidase, and it consists of two copper ions bridged by two cysteines and ligated by two histidines, a methionine, and a carbonyl in the peptide backbone of a nearby glutamine. The two ligating histidines are of particular interest as they may influence the electronic and redox properties of the metal center. To test for the presence of reactive ligating histidines, a portion of cytochrome c oxidase from the bacteria Thermus thermophilus that contains the CuA site (the TtCuA protein) was treated with the chemical modifier diethyl pyrocarbonate (DEPC) and the reaction followed through UV-visible, circular dichroism, and electron paramagnetic resonance spectroscopies at pH 5.0-9.0. A mutant protein (H40A/H117A) with the non-ligating histidines removed was similarly tested. Introduction of an electron-withdrawing DEPC-modification onto the ligating histidine 157 of TtCuA increased the reduction potential by over 70 mV, as assessed by cyclic voltammetry. Results from both proteins indicate that DEPC reacts with one of the two ligating histidines, modification of a ligating histidine raises the reduction potential of the CuA site, and formation of the DEPC adduct is reversible at room temperature. The existence of the reactive ligating histidine suggests that this residue may play a role in modulating the electronic and redox properties of TtCuA through kinetically-controlled proton exchange with the solvent. Lack of reactivity by the metalloproteins Sco and azurin, both of which contain a mononuclear copper center, indicate that reactivity toward DEPC is not a characteristic of all ligating histidines.
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Affiliation(s)
- Taylor Devlin
- Department of Chemistry, Trinity University, San Antonio, TX, 78212-7200, USA
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA
| | - Cristina R Hofman
- Department of Chemistry, Trinity University, San Antonio, TX, 78212-7200, USA
| | - Zachary P V Acevedo
- Department of Chemistry, Trinity University, San Antonio, TX, 78212-7200, USA
| | - Kelsey R Kohler
- Department of Chemistry, Trinity University, San Antonio, TX, 78212-7200, USA
| | - Lizhi Tao
- Department of Chemistry, University of California at Davis, Davis, CA, 95616, USA
| | - R David Britt
- Department of Chemistry, University of California at Davis, Davis, CA, 95616, USA
| | - Kevin R Hoke
- Department of Chemistry and Biochemistry, Berry College, Mount Berry, GA, 30149, USA
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41
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Madrid-Úsuga D, Melo-Luna CA, Insuasty A, Ortiz A, Reina JH. Optical and Electronic Properties of Molecular Systems Derived from Rhodanine. J Phys Chem A 2018; 122:8469-8476. [PMID: 30350632 DOI: 10.1021/acs.jpca.8b08265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Push-pull functional compounds consisting of dicyanorhodanine derivatives have attracted a lot of interest because their optical, electronic, and charge transport properties make them useful as building blocks for organic photovoltaic implementations. The analysis of the frontier molecular orbitals shows that the vertical transitions of electronic absorption are characterized as intramolecular charge transfer; furthermore, we show that the analyzed compounds exhibit bathochromic displacements when comparing the presence (or absence) of solvent as an interacting medium. In comparison with materials defined by their energy of reorganization of electrons (holes) as electron (hole) transporters, we find a transport hierarchy whereby the molecule ( Z)-2-(1,1-dicyanomethylene)-5-[(4-dimethylamino)benzylidene]-1,3-thiazol-4 is better at transporting holes than molecule ( Z)-2-(1,1-dicyanomethylene)-5-(tetrathiafulvalene-2-ylidene)-1,3-thiazol-4.
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Affiliation(s)
- Duvalier Madrid-Úsuga
- Centre for Bioinformatics and Photonics-CIBioFi , Universidad del Valle , Calle 13 No. 100-00, Edificio E20, No. 1069, Cali 760032 , Colombia.,Department of Physics , Universidad del Valle , 760032 Cali , Colombia
| | - Carlos A Melo-Luna
- Centre for Bioinformatics and Photonics-CIBioFi , Universidad del Valle , Calle 13 No. 100-00, Edificio E20, No. 1069, Cali 760032 , Colombia.,Department of Physics , Universidad del Valle , 760032 Cali , Colombia
| | - Alberto Insuasty
- Department of Chemistry and Biology , Universidad del Norte , Km 5 via Puerto Colombia , 081007 Barranquilla , Colombia
| | - Alejandro Ortiz
- Centre for Bioinformatics and Photonics-CIBioFi , Universidad del Valle , Calle 13 No. 100-00, Edificio E20, No. 1069, Cali 760032 , Colombia.,Department of Chemistry , Universidad del Valle , 760032 Cali , Colombia
| | - John H Reina
- Centre for Bioinformatics and Photonics-CIBioFi , Universidad del Valle , Calle 13 No. 100-00, Edificio E20, No. 1069, Cali 760032 , Colombia.,Department of Physics , Universidad del Valle , 760032 Cali , Colombia
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42
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Shen L, Zeng X, Hu H, Hu X, Yang W. Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants. J Chem Theory Comput 2018; 14:4948-4957. [PMID: 30040901 DOI: 10.1021/acs.jctc.8b00403] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Understanding the regulation mechanism and molecular determinants of the reduction potential of metalloprotein is a major challenge. An ab initio quantum mechanical/molecular mechanical (QM/MM) method combining the minimum free energy path (MFEP) and fractional number of electron (FNE) approaches has been developed in our group to simulate the redox processes of large systems. The FNE scheme provides an efficient unique description for the redox process, while the MFEP method provides improved conformational sampling on complex environments such as protein in the QM/MM calculations. The reduction potentials of wild-type and seven mutants of azurin, a type 1 copper metalloprotein, were simulated with the QM/MM-MFEP+FNE approach in this paper. A range of 350 mV for the variations of the reduction potentials of these azurin proteins was reproduced faithfully with relative errors around 20 mV. The correlation between structural interactions and reduction potentials observed in simulations provides in-depth insight into the regulation of reduction potentials, which potentially can also be very useful to the engineering of metalloprotein-based electrocatalysts in artificial photosynthesis. The excellent accuracy and efficiency of the QM/MM-MFEP+FNE approach demonstrate the potential for simulations of many electron transfer processes in condensed phases and biochemical systems.
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Affiliation(s)
- Lin Shen
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Xiancheng Zeng
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Hao Hu
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Xiangqian Hu
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Weitao Yang
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
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43
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Planchestainer M, Segaud N, Shanmugam M, McMaster J, Paradisi F, Albrecht M. Carbene in Cupredoxin Protein Scaffolds: Replacement of a Histidine Ligand in the Active Site Substantially Alters Copper Redox Properties. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
| | - Nathalie Segaud
- Department of Chemistry & BiochemistryUniversität Bern Freiestrasse 3 3012 Bern Switzerland
| | - Muralidharan Shanmugam
- Manchester Institute of BiotechnologyUniversity of Manchester 131 Princess St Manchester M1 7DN UK
| | - Jonathan McMaster
- School of ChemistryUniversity of Nottingham University Park Nottingham NG7 2RD UK
| | - Francesca Paradisi
- School of ChemistryUniversity of Nottingham University Park Nottingham NG7 2RD UK
| | - Martin Albrecht
- Department of Chemistry & BiochemistryUniversität Bern Freiestrasse 3 3012 Bern Switzerland
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44
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Planchestainer M, Segaud N, Shanmugam M, McMaster J, Paradisi F, Albrecht M. Carbene in Cupredoxin Protein Scaffolds: Replacement of a Histidine Ligand in the Active Site Substantially Alters Copper Redox Properties. Angew Chem Int Ed Engl 2018; 57:10677-10682. [DOI: 10.1002/anie.201807168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Indexed: 01/17/2023]
Affiliation(s)
| | - Nathalie Segaud
- Department of Chemistry & BiochemistryUniversität Bern Freiestrasse 3 3012 Bern Switzerland
| | - Muralidharan Shanmugam
- Manchester Institute of BiotechnologyUniversity of Manchester 131 Princess St Manchester M1 7DN UK
| | - Jonathan McMaster
- School of ChemistryUniversity of Nottingham University Park Nottingham NG7 2RD UK
| | - Francesca Paradisi
- School of ChemistryUniversity of Nottingham University Park Nottingham NG7 2RD UK
| | - Martin Albrecht
- Department of Chemistry & BiochemistryUniversität Bern Freiestrasse 3 3012 Bern Switzerland
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45
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Wherland S, Pecht I. Radiation chemists look at damage in redox proteins induced by X-rays. Proteins 2018; 86:817-826. [DOI: 10.1002/prot.25521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/26/2018] [Accepted: 04/25/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Scot Wherland
- Department of Chemistry; Washington State University; Pullman Washington
| | - Israel Pecht
- Department of Immunology; The Weizmann Institute of Science; Rehovot 76100 Israel
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46
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Lopez AJ, Martínez L. Parametric models to compute tryptophan fluorescence wavelengths from classical protein simulations. J Comput Chem 2018; 39:1249-1258. [PMID: 29484676 DOI: 10.1002/jcc.25188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/22/2017] [Accepted: 01/28/2018] [Indexed: 12/21/2022]
Abstract
Fluorescence spectroscopy is an important method to study protein conformational dynamics and solvation structures. Tryptophan (Trp) residues are the most important and practical intrinsic probes for protein fluorescence due to the variability of their fluorescence wavelengths: Trp residues emit in wavelengths ranging from 308 to 360 nm depending on the local molecular environment. Fluorescence involves electronic transitions, thus its computational modeling is a challenging task. We show that it is possible to predict the wavelength of emission of a Trp residue from classical molecular dynamics simulations by computing the solvent-accessible surface area or the electrostatic interaction between the indole group and the rest of the system. Linear parametric models are obtained to predict the maximum emission wavelengths with standard errors of the order 5 nm. In a set of 19 proteins with emission wavelengths ranging from 308 to 352 nm, the best model predicts the maximum wavelength of emission with a standard error of 4.89 nm and a quadratic Pearson correlation coefficient of 0.81. These models can be used for the interpretation of fluorescence spectra of proteins with multiple Trp residues, or for which local Trp environmental variability exists and can be probed by classical molecular dynamics simulations. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Alvaro J Lopez
- Institute of Chemistry and Center for Computational Engineering & Sciences, University of Campinas, Campinas, SP, Brazil
| | - Leandro Martínez
- Institute of Chemistry and Center for Computational Engineering & Sciences, University of Campinas, Campinas, SP, Brazil
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47
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Kozak JJ, Gray HB, Garza-López RA. Relaxation of structural constraints during Amicyanin unfolding. J Inorg Biochem 2018; 179:135-145. [PMID: 29222970 PMCID: PMC7222854 DOI: 10.1016/j.jinorgbio.2017.11.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/28/2017] [Accepted: 11/17/2017] [Indexed: 11/21/2022]
Abstract
We study the thermal unfolding of amicyanin by quantifying the resiliency of the native state to structural perturbations. Three signatures characterizing stages of unfolding are identified. The first signature, lateral extension of the polypeptide chain, is calculated directly from the reported crystallographic data. Two other signatures, the radial displacement of each residue from Cu(II) and the angular spread in the chain as the protein unfolds, are calculated using crystallographic data in concert with a geometrical model we introduced previously (J.J. Kozak, H. B. Gray, R. A. Garza-López, J. Inorg. Biochem. 155(2016) 44-55). Particular attention is paid to the resiliency of the two beta sheets in amicyanin. The resiliency of residues in the near neighborhood of the Cu center to destabilization provides information on the persistence of the entatic state. Similarly, examining the resiliency of residues intercalated between structured regions (beta sheets, the alpha helix) provides a basis for identifying a "hydrophobic core." A principal focus of our study is to compare results obtained using our geometrical model with the experimental results (C. La Rosa, D. Milardi, D. M. Grasso, M. P. Verbeet, G. W. Canters, L. Sportelli, R. Guzzi, Eur. Biophy. J.30(8),(2002) 559-570) on the denaturation of amicyanin, and we show that our results support a classical model proposed by these authors.
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Affiliation(s)
- John J Kozak
- DePaul University, 243 South Wabash Ave., Chicago, IL 60604-6116, United States
| | - Harry B Gray
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, United States
| | - Roberto A Garza-López
- Department of Chemistry, Seaver Chemistry Laboratory, Pomona College, Claremont, CA 91711, United States.
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48
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Differences in the mechanical unfolding pathways of apo- and copper-bound azurins. Sci Rep 2018; 8:1989. [PMID: 29386517 PMCID: PMC5792602 DOI: 10.1038/s41598-018-19755-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/30/2017] [Indexed: 01/20/2023] Open
Abstract
Metalloproteins carry out diverse biological functions including metal transport, electron transfer, and catalysis. At present, the influence of metal cofactors on metalloprotein stability is not well understood. Here, we report the mechanical stability and unfolding pathway of azurin, a cupredoxin family protein with β-barrel topology and type I copper-binding centre. Single-molecule force spectroscopy (SMFS) experiments reveal 2-state and 3-state unfolding pathways for apo-azurin. The intermediate in the 3-state pathway occurs at an unfolding contour length of 7.5 nm from the native state. Steered molecular dynamics (SMD) simulations show that apo-azurin unfolds via a first transition state (TS) where β2Β–β8 and β7–β8 strand pairs rupture to form the intermediate, which subsequently unfolds by the collective rupture of remaining strands. SMFS experiments on holo-azurin exhibit an additional 4-state pathway besides the 2-state and 3-state pathways. The unfolding contour length leading to the first intermediate is 6.7 nm suggesting a sequestration of ~1 nm polypeptide chain length by the copper. SMD simulations reveal atomistic details of the copper sequestration and predict a combined β4–β7 pair and copper coordination sphere rupture to create the third TS in the 4-state pathway. Our systematic studies provide detailed mechanistic insights on modulation of protein mechanical properties by metal-cofactors.
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49
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Andreoni A, Sen S, Hagedoorn PL, Buma WJ, Aartsma TJ, Canters GW. Fluorescence Correlation Spectroscopy of Labeled Azurin Reveals Photoinduced Electron Transfer between Label and Cu Center. Chemistry 2018; 24:646-654. [PMID: 29064125 DOI: 10.1002/chem.201703733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Indexed: 11/06/2022]
Abstract
Fluorescent labeling of biomacromolecules enjoys increasing popularity for structural, mechanistic, and microscopic investigations. Its success hinges on the ability of the dye to alternate between bright and dark states. Förster resonance energy transfer (FRET) is an important source of fluorescence modulation. Photo-induced electron transfer (PET) may occur as well, but is often considered only when donor and acceptor are in van der Waals contact. In this study, PET is shown between a label and redox centers in oxidoreductases, which may occur over large distances. In the small blue copper protein azurin, labeled with ATTO655, PET is observed when the label is at 18.5 Å, but not when it is at 29.1 Å from the Cu. For CuII , PET from label to Cu occurs at a rate of (4.8±0.3)×104 s-1 and back at (0.7±0.1)×103 s-1 . With CuI the numbers are (3.3±0.7)×106 s-1 and (1.0±0.1)×104 s-1 . Reorganization energies and electronic coupling elements are in the range of 0.8-1.2 eV and 0.02-0.5 cm-1 , respectively. These data are compatible with electron transfer (ET) along a through-bond pathway although transient complex formation followed by ET cannot be ruled out. The outcome of this study is a useful guideline for experimental designs in which oxidoreductases are labelled with fluorescent dyes, with particular attention to single molecule investigations. The labelling position for FRET can be optimized to avoid reactions like PET by evaluating the structure and thermodynamics of protein and label.
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Affiliation(s)
- Alessio Andreoni
- Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, 2333CC, Leiden, The Netherlands.,Present address: National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Saptaswa Sen
- Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, 2333CC, Leiden, The Netherlands.,Present address: AlbaNova University Center, Department of Applied Physics, KTH-Royal Institute of, Technology, 10691, Stockholm, Sweden
| | - Peter-Leon Hagedoorn
- TU Delft, Applied Sciences, Biotechnology, Building 58, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Wybren J Buma
- Van't Hoff Institute for Molecular Sciences, Science Park 904, P.O. Box 94157, 1090 GD, Amsterdam, The Netherlands
| | - Thijs J Aartsma
- Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, 2333CC, Leiden, The Netherlands
| | - Gerard W Canters
- Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, 2333CC, Leiden, The Netherlands
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50
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Panda SS, Katz HE, Tovar JD. Solid-state electrical applications of protein and peptide based nanomaterials. Chem Soc Rev 2018; 47:3640-3658. [DOI: 10.1039/c7cs00817a] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review summarizes recent advancements in electrical properties and applications of natural proteins and mutated variants, synthetic oligopeptides and peptide–π conjugates.
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Affiliation(s)
- Sayak Subhra Panda
- Department of Chemistry
- Krieger School of Arts and Sciences
- Johns Hopkins University
- Baltimore
- USA
| | - Howard E. Katz
- Department of Chemistry
- Krieger School of Arts and Sciences
- Johns Hopkins University
- Baltimore
- USA
| | - John D. Tovar
- Department of Chemistry
- Krieger School of Arts and Sciences
- Johns Hopkins University
- Baltimore
- USA
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