1
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Ru X, Crane BR, Zhang P, Beratan DN. Why Do Most Aromatics Fail to Support Hole Hopping in the Cytochrome c Peroxidase-Cytochrome c Complex? J Phys Chem B 2021; 125:7763-7773. [PMID: 34235935 DOI: 10.1021/acs.jpcb.1c05064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron transport through aromatic species (especially tryptophan and tyrosine) plays a central role in water splitting, redox signaling, oxidative damage protection, and bioenergetics. The cytochrome c peroxidase (CcP)-cytochrome c (Cc) complex (CcP:Cc) is used widely to study interprotein electron transfer (ET) mechanisms. Tryptophan 191 (Trp191) of CcP supports hole hopping charge recombination in the CcP:Cc complex. Experimental studies find that when Trp191 is substituted by tyrosine, phenylalanine, or redox-active aniline derivatives bound in the W191G cavity, enzymatic activity and charge recombination rates both decrease. Theoretical analysis of these CcP:Cc complexes finds that the ET kinetics depend strongly on the chemistry of the modified Trp site. The computed electronic couplings in the W191F and W191G species are orders of magnitude smaller than in the native protein, due largely to the absence of a hopping intermediate and the large tunneling distance. Small molecules bound in the W191G cavity are weakly coupled electronically to the Cc heme, and the structural disorder of the guest molecule in the binding pocket may contribute further to the lack of enzymatic activity. The couplings in W191Y are not substantially weakened compared to the native species, but the redox potential difference for tyrosine vs tryptophan oxidation accounts for the slower rate in the Tyr mutant. Thus, theoretical analysis explains why only the native Trp supports rapid hole hopping in the CcP:Cc complex. Favorable free energies and electronic couplings are essential for establishing an efficient hole hopping relay in this protein-protein complex.
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Affiliation(s)
- Xuyan Ru
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States.,Department of Physics, Duke University, Durham, North Carolina 27708, United States
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2
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Roda S, Robles-Martín A, Xiang R, Kazemi M, Guallar V. Structural-Based Modeling in Protein Engineering. A Must Do. J Phys Chem B 2021; 125:6491-6500. [PMID: 34106727 DOI: 10.1021/acs.jpcb.1c02545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biotechnological solutions will be a key aspect in our immediate future society, where optimized enzymatic processes through enzyme engineering might be an important solution for waste transformation, clean energy production, biodegradable materials, and green chemistry, for example. Here we advocate the importance of structural-based bioinformatics and molecular modeling tools in such developments. We summarize our recent experiences indicating a great prediction/success ratio, and we suggest that an early in silico phase should be performed in enzyme engineering studies. Moreover, we demonstrate the potential of a new technique combining Rosetta and PELE, which could provide a faster and more automated procedure, an essential aspect for a broader use.
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Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | | | - Ruite Xiang
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Masoud Kazemi
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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3
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de Eugenio LI, Peces-Pérez R, Linde D, Prieto A, Barriuso J, Ruiz-Dueñas FJ, Martínez MJ. Characterization of a Dye-Decolorizing Peroxidase from Irpex lacteus Expressed in Escherichia coli: An Enzyme with Wide Substrate Specificity Able to Transform Lignosulfonates. J Fungi (Basel) 2021; 7:325. [PMID: 33922393 PMCID: PMC8145141 DOI: 10.3390/jof7050325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
A dye-decolorizing peroxidase (DyP) from Irpex lacteus was cloned and heterologously expressed as inclusion bodies in Escherichia coli. The protein was purified in one chromatographic step after its in vitro activation. It was active on ABTS, 2,6-dimethoxyphenol (DMP), and anthraquinoid and azo dyes as reported for other fungal DyPs, but it was also able to oxidize Mn2+ (as manganese peroxidases and versatile peroxidases) and veratryl alcohol (VA) (as lignin peroxidases and versatile peroxidases). This corroborated that I. lacteus DyPs are the only enzymes able to oxidize high redox potential dyes, VA and Mn+2. Phylogenetic analysis grouped this enzyme with other type D-DyPs from basidiomycetes. In addition to its interest for dye decolorization, the results of the transformation of softwood and hardwood lignosulfonates suggest a putative biological role of this enzyme in the degradation of phenolic lignin.
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Affiliation(s)
| | | | | | | | | | | | - María Jesús Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (L.I.d.E.); (R.P.-P.); (D.L.); (A.P.); (J.B.); (F.J.R.-D.)
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4
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Yee EF, Dzikovski B, Crane BR. Tuning Radical Relay Residues by Proton Management Rescues Protein Electron Hopping. J Am Chem Soc 2019; 141:17571-17587. [PMID: 31603693 DOI: 10.1021/jacs.9b05715] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Transient tyrosine and tryptophan radicals play key roles in the electron transfer (ET) reactions of photosystem (PS) II, ribonucleotide reductase (RNR), photolyase, and many other proteins. However, Tyr and Trp are not functionally interchangeable, and the factors controlling their reactivity are often unclear. Cytochrome c peroxidase (CcP) employs a Trp191•+ radical to oxidize reduced cytochrome c (Cc). Although a Tyr191 replacement also forms a stable radical, it does not support rapid ET from Cc. Here we probe the redox properties of CcP Y191 by non-natural amino acid substitution, altering the ET driving force and manipulating the protic environment of Y191. Higher potential fluorotyrosine residues increase ET rates marginally, but only addition of a hydrogen bond donor to Tyr191• (via Leu232His or Glu) substantially alters activity by increasing the ET rate by nearly 30-fold. ESR and ESEEM spectroscopies, crystallography, and pH-dependent ET kinetics provide strong evidence for hydrogen bond formation to Y191• by His232/Glu232. Rate measurements and rapid freeze quench ESR spectroscopy further reveal differences in radical propagation and Cc oxidation that support an increased Y191• formal potential of ∼200 mV in the presence of E232. Hence, Y191 inactivity results from a potential drop owing to Y191•+ deprotonation. Incorporation of a well-positioned base to accept and donate back a hydrogen bond upshifts the Tyr• potential into a range where it can effectively oxidize Cc. These findings have implications for the YZ/YD radicals of PS II, hole-hopping in RNR and cryptochrome, and engineering proteins for long-range ET reactions.
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Affiliation(s)
- Estella F Yee
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States.,National Biomedical Center for Advanced ESR Technologies (ACERT) , Cornell University , Ithaca , New York 14850 , United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
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5
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Garcia-Borràs M, Houk KN, Jiménez-Osés G. Computational Design of Protein Function. COMPUTATIONAL TOOLS FOR CHEMICAL BIOLOGY 2017. [DOI: 10.1039/9781788010139-00087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The computational design of enzymes is a tremendous challenge for both chemistry and biochemistry. The ability to design stable and functional biocatalysts that could operate under different conditions to perform chemical reactions without precedent in nature, allowing the large-scale production of chemicals à la carte, would revolutionise both synthetic, pharmacologic and materials chemistry. Despite the great advances achieved, this highly multidisciplinary area of research is still in its infancy. This chapter describes the ‘inside-out’ protocol for computational enzyme design and both the achievements and limitations of the current technology are highlighted. Furthermore, molecular dynamics simulations have proved to be invaluable in the enzyme design process, constituting an important tool for discovering elusive catalytically relevant conformations of the engineered or designed enzyme. As a complement to the ‘inside-out’ design protocol, different examples where hybrid QM/MM approaches have been directly applied to discover beneficial mutations in rational computational enzyme design are described.
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Affiliation(s)
- Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California Los Angeles California CA 90095-1569 USA
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles California CA 90095-1569 USA
| | - Gonzalo Jiménez-Osés
- Departamento de Química, Centro de Investigación en Síntesis Química Universidad de La Rioja 26006 Logroño La Rioja Spain
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6
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Masone D, Uhart M, Bustos DM. On the role of residue phosphorylation in 14-3-3 partners: AANAT as a case study. Sci Rep 2017; 7:46114. [PMID: 28387381 PMCID: PMC5384239 DOI: 10.1038/srep46114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/08/2017] [Indexed: 01/14/2023] Open
Abstract
Twenty years ago, a novel concept in protein structural biology was discovered: the intrinsically disordered regions (IDRs). These regions remain largely unstructured under native conditions and the more are studied, more properties are attributed to them. Possibly, one of the most important is their ability to conform a new type of protein-protein interaction. Besides the classical domain-to-domain interactions, IDRs follow a 'fly-casting' model including 'induced folding'. Unfortunately, it is only possible to experimentally explore initial and final states. However, the complete movie of conformational changes of protein regions and their characterization can be addressed by in silico experiments. Here, we simulate the binding of two proteins to describe how the phosphorylation of a single residue modulates the entire process. 14-3-3 protein family is considered a master regulator of phosphorylated proteins and from a modern point-of-view, protein phosphorylation is a three component system, with writers (kinases), erasers (phosphatases) and readers. This later biological role is attributed to the 14-3-3 protein family. Our molecular dynamics results show that phosphorylation of the key residue Thr31 in a partner of 14-3-3, the aralkylamine N-acetyltransferase, releases the fly-casting mechanism during binding. On the other hand, the non-phosphorylation of the same residue traps the proteins, systematically and repeatedly driving the simulations into wrong protein-protein conformations.
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Affiliation(s)
- Diego Masone
- Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
| | - Marina Uhart
- Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina
| | - Diego M. Bustos
- Instituto de Histología y Embriología (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CC56, Universidad Nacional de Cuyo (UNCuyo), 5500, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
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7
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Payne TM, Yee EF, Dzikovski B, Crane BR. Constraints on the Radical Cation Center of Cytochrome c Peroxidase for Electron Transfer from Cytochrome c. Biochemistry 2016; 55:4807-22. [PMID: 27499202 PMCID: PMC5689384 DOI: 10.1021/acs.biochem.6b00262] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The tryptophan 191 cation radical of cytochrome c peroxidase (CcP) compound I (Cpd I) mediates long-range electron transfer (ET) to cytochrome c (Cc). Here we test the effects of chemical substitution at position 191. CcP W191Y forms a stable tyrosyl radical upon reaction with peroxide and produces spectral properties similar to those of Cpd I but has low reactivity toward reduced Cc. CcP W191G and W191F variants also have low activity, as do redox ligands that bind within the W191G cavity. Crystal structures of complexes between Cc and CcP W191X (X = Y, F, or G), as well as W191G with four bound ligands reveal similar 1:1 association modes and heme pocket conformations. The ligands display structural disorder in the pocket and do not hydrogen bond to Asp235, as does Trp191. Well-ordered Tyr191 directs its hydroxyl group toward the porphyrin ring, with no basic residue in the range of interaction. CcP W191X (X = Y, F, or G) variants substituted with zinc-porphyrin (ZnP) undergo photoinduced ET with Cc(III). Their slow charge recombination kinetics that result from loss of the radical center allow resolution of difference spectra for the charge-separated state [ZnP(+), Cc(II)]. The change from a phenyl moiety at position 191 in W191F to a water-filled cavity in W191G produces effects on ET rates much weaker than the effects of the change from Trp to Phe. Low net reactivity of W191Y toward Cc(II) derives either from the inability of ZnP(+) or the Fe-CcP ferryl to oxidize Tyr or from the low potential of the resulting neutral Tyr radical.
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Affiliation(s)
- Thomas M. Payne
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States
| | - Estella F. Yee
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States,National Biomedical Center for Advanced ESR Technologies (ACERT), Cornell University, Ithaca 14850, USA
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States,To whom correspondence should be addressed , Tel (607) 254-8634 (B.R.C)
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8
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Cabeza de Vaca I, Acebes S, Guallar V. Ecoupling server: A tool to compute and analyze electronic couplings. J Comput Chem 2016; 37:1740-5. [DOI: 10.1002/jcc.24392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Israel Cabeza de Vaca
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Life Science Department, Electronic and Atomic Modeling Group; Nexus II, C/Jordi Girona, 29 Barcelona 08034 Spain
- Department of Chemistry; Yale University; New Haven Connecticut 06520-8107
| | - Sandra Acebes
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Life Science Department, Electronic and Atomic Modeling Group; Nexus II, C/Jordi Girona, 29 Barcelona 08034 Spain
| | - Victor Guallar
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Life Science Department, Electronic and Atomic Modeling Group; Nexus II, C/Jordi Girona, 29 Barcelona 08034 Spain
- Institució Catalana De Recerca I Estudis Avançats (ICREA); Barcelona Spain
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9
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Acebes S, Fernandez-Fueyo E, Monza E, Lucas MF, Almendral D, Ruiz-Dueñas FJ, Lund H, Martinez AT, Guallar V. Rational Enzyme Engineering Through Biophysical and Biochemical Modeling. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00028] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Sandra Acebes
- Joint BSC-CRG-IRB
Research Program in Computational Biology, Barcelona Supercomputing
Center, Jordi Girona 29, E-08034 Barcelona, Spain
| | - Elena Fernandez-Fueyo
- Centro de Investigaciones
Biológicas, CSIC, Ramiro de
Maeztu 9, E-28040 Madrid, Spain
| | - Emanuele Monza
- Joint BSC-CRG-IRB
Research Program in Computational Biology, Barcelona Supercomputing
Center, Jordi Girona 29, E-08034 Barcelona, Spain
| | - M. Fatima Lucas
- Joint BSC-CRG-IRB
Research Program in Computational Biology, Barcelona Supercomputing
Center, Jordi Girona 29, E-08034 Barcelona, Spain
- Anaxomics Biotech, Balmes 89, 08008 Barcelona, Spain
| | - David Almendral
- Centro de Investigaciones
Biológicas, CSIC, Ramiro de
Maeztu 9, E-28040 Madrid, Spain
| | | | - Henrik Lund
- Novozymes A/S, Krogshoejvej 36, DK-2880 Bagsvaerd, Denmark
| | - Angel T. Martinez
- Centro de Investigaciones
Biológicas, CSIC, Ramiro de
Maeztu 9, E-28040 Madrid, Spain
| | - Victor Guallar
- Joint BSC-CRG-IRB
Research Program in Computational Biology, Barcelona Supercomputing
Center, Jordi Girona 29, E-08034 Barcelona, Spain
- ICREA, Passeig Lluís Companys 23, E-08010 Barcelona, Spain
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10
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A theoretical multiscale treatment of protein-protein electron transfer: The ferredoxin/ferredoxin-NADP(+) reductase and flavodoxin/ferredoxin-NADP(+) reductase systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1530-8. [PMID: 26385068 DOI: 10.1016/j.bbabio.2015.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 11/21/2022]
Abstract
In the photosynthetic electron transfer (ET) chain, two electrons transfer from photosystem I to the flavin-dependent ferredoxin-NADP(+) reductase (FNR) via two sequential independent ferredoxin (Fd) electron carriers. In some algae and cyanobacteria (as Anabaena), under low iron conditions, flavodoxin (Fld) replaces Fd as single electron carrier. Extensive mutational studies have characterized the protein-protein interaction in FNR/Fd and FNR/Fld complexes. Interestingly, even though Fd and Fld share the interaction site on FNR, individual residues on FNR do not participate to the same extent in the interaction with each of the protein partners, pointing to different electron transfer mechanisms. Despite of extensive mutational studies, only FNR/Fd X-ray structures from Anabaena and maize have been solved; structural data for FNR/Fld remains elusive. Here, we present a multiscale modelling approach including coarse-grained and all-atom protein-protein docking, the QM/MM e-Pathway analysis and electronic coupling calculations, allowing for a molecular and electronic comprehensive analysis of the ET process in both complexes. Our results, consistent with experimental mutational data, reveal the ET in FNR/Fd proceeding through a bridge-mediated mechanism in a dominant protein-protein complex, where transfer of the electron is facilitated by Fd loop-residues 40-49. In FNR/Fld, however, we observe a direct transfer between redox cofactors and less complex specificity than in Fd; more than one orientation in the encounter complex can be efficient in ET.
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11
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Giannotti MI, Cabeza de Vaca I, Artés JM, Sanz F, Guallar V, Gorostiza P. Direct Measurement of the Nanomechanical Stability of a Redox Protein Active Site and Its Dependence upon Metal Binding. J Phys Chem B 2015; 119:12050-8. [DOI: 10.1021/acs.jpcb.5b06382] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marina I. Giannotti
- Networking Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid 28029, Spain
- Physical
Chemistry Department, Universitat de Barcelona, Barcelona 08028, Spain
- Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac 15-21, Barcelona 08028, Spain
| | - Israel Cabeza de Vaca
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain
| | - Juan M. Artés
- Physical
Chemistry Department, Universitat de Barcelona, Barcelona 08028, Spain
- Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac 15-21, Barcelona 08028, Spain
| | - Fausto Sanz
- Networking Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid 28029, Spain
- Physical
Chemistry Department, Universitat de Barcelona, Barcelona 08028, Spain
- Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac 15-21, Barcelona 08028, Spain
| | - Victor Guallar
- Joint
BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Pau Gorostiza
- Networking Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid 28029, Spain
- Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac 15-21, Barcelona 08028, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
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12
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Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study. Biochem J 2015; 466:253-62. [PMID: 25495127 PMCID: PMC4357238 DOI: 10.1042/bj20141211] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Dye-decolorizing peroxidase (DyP) of Auricularia auricula-judae has been expressed in Escherichia coli as a representative of a new DyP family, and subjected to mutagenic, spectroscopic, crystallographic and computational studies. The crystal structure of DyP shows a buried haem cofactor, and surface tryptophan and tyrosine residues potentially involved in long-range electron transfer from bulky dyes. Simulations using PELE (Protein Energy Landscape Exploration) software provided several binding-energy optima for the anthraquinone-type RB19 (Reactive Blue 19) near the above aromatic residues and the haem access-channel. Subsequent QM/MM (quantum mechanics/molecular mechanics) calculations showed a higher tendency of Trp-377 than other exposed haem-neighbouring residues to harbour a catalytic protein radical, and identified the electron-transfer pathway. The existence of such a radical in H₂O₂-activated DyP was shown by low-temperature EPR, being identified as a mixed tryptophanyl/tyrosyl radical in multifrequency experiments. The signal was dominated by the Trp-377 neutral radical contribution, which disappeared in the W377S variant, and included a tyrosyl contribution assigned to Tyr-337 after analysing the W377S spectra. Kinetics of substrate oxidation by DyP suggests the existence of high- and low-turnover sites. The high-turnover site for oxidation of RB19 (k(cat) > 200 s⁻¹) and other DyP substrates was assigned to Trp-377 since it was absent from the W377S variant. The low-turnover site/s (RB19 k(cat) ~20 s⁻¹) could correspond to the haem access-channel, since activity was decreased when the haem channel was occluded by the G169L mutation. If a tyrosine residue is also involved, it will be different from Tyr-337 since all activities are largely unaffected in the Y337S variant.
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13
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Monza E, Lucas MF, Camarero S, Alejaldre LC, Martínez AT, Guallar V. Insights into Laccase Engineering from Molecular Simulations: Toward a Binding-Focused Strategy. J Phys Chem Lett 2015; 6:1447-1453. [PMID: 26263150 DOI: 10.1021/acs.jpclett.5b00225] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Understanding the molecular determinants of enzyme performance is of primary importance for the rational design of ad hoc mutants. A novel approach, which combines efficient conformational sampling and quick reactivity scoring, is used here to shed light on how substrate oxidation was improved during the directed evolution experiment of a fungal laccase (from Pycnoporus cinnabarinus), an industrially relevant class of oxidoreductases. It is found that the enhanced activity of the evolved enzyme is mainly the result of substrate arrangement in the active site, with no important change in the redox potential of the T1 copper. Mutations at the active site shift the binding mode into a more buried substrate position and provide a more favorable electrostatic environment for substrate oxidation. As a consequence, engineering the binding event seems to be a viable way to in silico evolution of oxidoreductases.
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Affiliation(s)
- Emanuele Monza
- †Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
| | - M Fatima Lucas
- †Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Susana Camarero
- ‡Centro de Investigacion Biológica, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Lorea C Alejaldre
- ‡Centro de Investigacion Biológica, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Angel T Martínez
- ‡Centro de Investigacion Biológica, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Victor Guallar
- †Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
- §Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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14
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Winkler JR, Gray HB. Could tyrosine and tryptophan serve multiple roles in biological redox processes? PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2015; 373:rsta.2014.0178. [PMID: 25666062 PMCID: PMC4342971 DOI: 10.1098/rsta.2014.0178] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Single-step electron tunnelling reactions can transport charges over distances of 15-20 Åin proteins. Longer-range transfer requires multi-step tunnelling processes along redox chains, often referred to as hopping. Long-range hopping via oxidized radicals of tryptophan and tyrosine, which has been identified in several natural enzymes, has been demonstrated in artificial constructs of the blue copper protein azurin. Tryptophan and tyrosine serve as hopping way stations in high-potential charge transport processes. It may be no coincidence that these two residues occur with greater-than-average frequency in O(2)- and H(2)O(2)-reactive enzymes. We suggest that appropriately placed tyrosine and/or tryptophan residues prevent damage from high-potential reactive intermediates by reduction followed by transfer of the oxidizing equivalent to less harmful sites or out of the protein altogether.
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Affiliation(s)
- Jay R Winkler
- Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Harry B Gray
- Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
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Beratan DN, Liu C, Migliore A, Polizzi NF, Skourtis SS, Zhang P, Zhang Y. Charge transfer in dynamical biosystems, or the treachery of (static) images. Acc Chem Res 2015; 48:474-81. [PMID: 25307316 PMCID: PMC4333612 DOI: 10.1021/ar500271d] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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The image is not the thing. Just as a pipe rendered
in an oil painting cannot be smoked, quantum mechanical coupling pathways
rendered on LCDs do not convey electrons. The aim of this Account
is to examine some of our recent discoveries regarding biological
electron transfer (ET) and transport mechanisms that emerge when one
moves beyond treacherous static views to dynamical frameworks. Studies over the last two decades introduced both atomistic detail
and macromolecule dynamics to the description of biological ET. The
first model to move beyond the structureless square-barrier tunneling
description is the Pathway model, which predicts how protein secondary
motifs and folding-induced through-bond and through-space tunneling
gaps influence kinetics. Explicit electronic structure theory is applied
routinely now to elucidate ET mechanisms, to capture pathway interferences,
and to treat redox cofactor electronic structure effects. Importantly,
structural sampling of proteins provides an understanding of how dynamics
may change the mechanisms of biological ET, as ET rates are exponentially
sensitive to structure. Does protein motion average out tunneling
pathways? Do conformational fluctuations gate biological ET? Are transient
multistate resonances produced by energy gap fluctuations? These questions
are becoming accessible as the static view of biological ET recedes
and dynamical viewpoints take center stage. This Account introduces
ET reactions at the core of bioenergetics, summarizes our team’s
progress toward arriving at an atomistic-level description, examines
how thermal fluctuations influence ET, presents metrics that characterize
dynamical effects on ET, and discusses applications in very long (micrometer
scale) bacterial nanowires. The persistence of structural effects
on the ET rates in the face of thermal fluctuations is considered.
Finally, the flickering resonance (FR) view of charge transfer is
presented to examine how fluctuations control low-barrier transport
among multiple groups in van der Waals contact. FR produces exponential
distance dependence in the absence of tunneling; the exponential character
emerges from the probability of matching multiple vibronically broadened
electronic energies within a tolerance defined by the rms coupling
among interacting groups. FR thus produces band like coherent transport
on the nanometer length scale, enabled by conformational fluctuations.
Taken as a whole, the emerging context for ET in dynamical biomolecules
provides a robust framework to design and interpret the inner workings
of bioenergetics from the molecular to the cellular scale and beyond,
with applications in biomedicine, biocatalysis, and energy science.
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Linde D, Ruiz-Dueñas FJ, Fernández-Fueyo E, Guallar V, Hammel KE, Pogni R, Martínez AT. Basidiomycete DyPs: Genomic diversity, structural-functional aspects, reaction mechanism and environmental significance. Arch Biochem Biophys 2015; 574:66-74. [PMID: 25637654 DOI: 10.1016/j.abb.2015.01.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 11/26/2022]
Abstract
The first enzyme with dye-decolorizing peroxidase (DyP) activity was described in 1999 from an arthroconidial culture of the fungus Bjerkandera adusta. However, the first DyP sequence had been deposited three years before, as a peroxidase gene from a culture of an unidentified fungus of the family Polyporaceae (probably Irpex lacteus). Since the first description, fewer than ten basidiomycete DyPs have been purified and characterized, but a large number of sequences are available from genomes. DyPs share a general fold and heme location with chlorite dismutases and other DyP-type related proteins (such as Escherichia coli EfeB), forming the CDE superfamily. Taking into account the lack of an evolutionary relationship with the catalase-peroxidase superfamily, the observed heme pocket similarities must be considered as a convergent type of evolution to provide similar reactivity to the enzyme cofactor. Studies on the Auricularia auricula-judae DyP showed that high-turnover oxidation of anthraquinone type and other DyP substrates occurs via long-range electron transfer from an exposed tryptophan (Trp377, conserved in most basidiomycete DyPs), whose catalytic radical was identified in the H2O2-activated enzyme. The existence of accessory oxidation sites in DyP is suggested by the residual activity observed after site-directed mutagenesis of the above tryptophan. DyP degradation of substituted anthraquinone dyes (such as Reactive Blue 5) most probably proceeds via typical one-electron peroxidase oxidations and product breakdown without a DyP-catalyzed hydrolase reaction. Although various DyPs are able to break down phenolic lignin model dimers, and basidiomycete DyPs also present marginal activity on nonphenolic dimers, a significant contribution to lignin degradation is unlikely because of the low activity on high redox-potential substrates.
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Affiliation(s)
- Dolores Linde
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | | | - Elena Fernández-Fueyo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Victor Guallar
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Kenneth E Hammel
- US Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI 53726, USA
| | - Rebecca Pogni
- Dept. Biotechnologies, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain.
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17
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Fernández-Fueyo E, Acebes S, Ruiz-Dueñas FJ, Martínez MJ, Romero A, Medrano FJ, Guallar V, Martínez AT. Structural implications of the C-terminal tail in the catalytic and stability properties of manganese peroxidases from ligninolytic fungi. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:3253-65. [PMID: 25478843 PMCID: PMC4257621 DOI: 10.1107/s1399004714022755] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/16/2014] [Indexed: 11/20/2022]
Abstract
The genome of Ceriporiopsis subvermispora includes 13 manganese peroxidase (MnP) genes representative of the three subfamilies described in ligninolytic fungi, which share an Mn(2+)-oxidation site and have varying lengths of the C-terminal tail. Short, long and extralong MnPs were heterologously expressed and biochemically characterized, and the first structure of an extralong MnP was solved. Its C-terminal tail surrounds the haem-propionate access channel, contributing to Mn(2+) oxidation by the internal propionate, but prevents the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS), which is only oxidized by short MnPs and by shortened-tail variants from site-directed mutagenesis. The tail, which is anchored by numerous contacts, not only affects the catalytic properties of long/extralong MnPs but is also associated with their high acidic stability. Cd(2+) binds at the Mn(2+)-oxidation site and competitively inhibits oxidation of both Mn(2+) and ABTS. Moreover, mutations blocking the haem-propionate channel prevent substrate oxidation. This agrees with molecular simulations that position ABTS at an electron-transfer distance from the haem propionates of an in silico shortened-tail form, while it cannot reach this position in the extralong MnP crystal structure. Only small differences exist between the long and the extralong MnPs, which do not justify their classification as two different subfamilies, but they significantly differ from the short MnPs, with the presence/absence of the C-terminal tail extension being implicated in these differences.
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Affiliation(s)
| | - Sandra Acebes
- Joint BSC–CRG–IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain
| | | | - María Jesús Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Antonio Romero
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - Victor Guallar
- Joint BSC–CRG–IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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18
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Heck A, Woiczikowski PB, Kubař T, Welke K, Niehaus T, Giese B, Skourtis S, Elstner M, Steinbrecher TB. Fragment Orbital Based Description of Charge Transfer in Peptides Including Backbone Orbitals. J Phys Chem B 2014; 118:4261-72. [DOI: 10.1021/jp408907g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Alexander Heck
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - P. Benjamin Woiczikowski
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Kai Welke
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Thomas Niehaus
- Department
of Physics, University of Regensburg, 93053 Regensburg, Germany
| | - Bernd Giese
- Department
of Chemistry, University of Fribourg, Chemin du Musee 9, CH-1700 Fribourg, Switzerland
| | - Spiros Skourtis
- Department
of Physics, University of Cyprus, PO Box 20537, Nicosia 1678, Cyprus
| | - Marcus Elstner
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Thomas B. Steinbrecher
- Department
for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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Vazquez-Duhalt R, Aguila SA, Arrocha AA, Ayala M. QM/MM Molecular Modeling and Marcus Theory in the Molecular Design of Electrodes for Enzymatic Fuel Cells. ChemElectroChem 2013. [DOI: 10.1002/celc.201300096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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20
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Saen-Oon S, Lucas MF, Guallar V. Electron transfer in proteins: theory, applications and future perspectives. Phys Chem Chem Phys 2013; 15:15271-85. [DOI: 10.1039/c3cp50484k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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