Perspectives in Bioinorganic Catalysis

A special issue of Catalysts (ISSN 2073-4344). This special issue belongs to the section "Biocatalysis".

Deadline for manuscript submissions: closed (15 January 2021) | Viewed by 24901

Special Issue Editor

Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
Interests: Biophysics; Bioinorganic Chemistry; Metalloenzymes; Biocatalysis; Functional Protein Dynamics; Computational Chemistry; Vibrational Spectroscopy; Ultrafast and Nonlinear Spectroscopy; Small Molecule Activation; Biohydrogen

Special Issue Information

Dear Colleagues,

Metalloenzymes are complex catalysts at the interface between the biological and inorganic world. Due to their intricate architectures and sophisticated base-metal active sites, these key players of the cellular metabolism continue to outperform most synthetic catalysts in terms of specificity, turnover rate, and sustainability. Consequently, understanding metalloenzymes on a molecular level is vital from fundamental, medical, and application perspectives.

Despite considerable research efforts, the fundamental principles of bioinorganic catalysis are still under debate, and mechanistic details are unexplored, speculated, or discussed controversially in many cases. Likewise, mapping out strategies for metalloenzyme engineering and the design of functional synthetic analogues remains a difficult task.

This special issue aims to tackle these challenges by addressing both fundamental and target-specific questions in metalloenzyme research together with methodological developments and new avenues for biotechnological utilization and bioinspired catalyst design.

Submissions are welcome as research papers, reviews, and perspective articles. Topics of interest include (but are not limited to):

  • Structural, electronic, and mechanistic aspects of metalloenzyme catalysis;
  • Experimental and theoretical techniques for studying metalloenzymes;
  • Fundamental principles of enzymatic catalysis, including non-classical aspects;
  • Inter- and intramolecular communication between metal sites;
  • Interactions between metals sites and the protein matrix;
  • Multiscale dynamics and mesoscopic properties of proteins;
  • Metalloenzyme engineering and biotechnological reaction cascades;
  • In vivo, operando, and time-resolved spectroscopy of metalloenzymes;
  • Synthetic approaches to bioinorganic catalysis, including bio-chemical hybrid strategies.

Dr. Marius Horch 
Guest Editor

Manuscript Submission Information

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Keywords

  • Biocatalysis
  • Bioinorganic Chemistry
  • Metalloenzymes
  • Biomimetic Chemistry
  • Bioinspired Chemistry
  • Computational Chemistry
  • Inorganic Spectroscopy
  • Biomolecular Spectroscopy
  • Catalytic Mechanisms
  • Structure–Function-Relationships

Published Papers (8 papers)

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Research

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20 pages, 2456 KiB  
Article
Understanding 2D-IR Spectra of Hydrogenases: A Descriptive and Predictive Computational Study
by Yvonne Rippers, Barbara Procacci, Neil T. Hunt and Marius Horch
Catalysts 2022, 12(9), 988; https://doi.org/10.3390/catal12090988 - 01 Sep 2022
Cited by 1 | Viewed by 1726
Abstract
[NiFe] hydrogenases are metalloenzymes that catalyze the reversible cleavage of dihydrogen (H2), a clean future fuel. Understanding the mechanism of these biocatalysts requires spectroscopic techniques that yield insights into the structure and dynamics of the [NiFe] active site. Due to [...] Read more.
[NiFe] hydrogenases are metalloenzymes that catalyze the reversible cleavage of dihydrogen (H2), a clean future fuel. Understanding the mechanism of these biocatalysts requires spectroscopic techniques that yield insights into the structure and dynamics of the [NiFe] active site. Due to the presence of CO and CN ligands at this cofactor, infrared (IR) spectroscopy represents an ideal technique for studying these aspects, but molecular information from linear IR absorption experiments is limited. More detailed insights can be obtained from ultrafast nonlinear IR techniques like IRpump-IRprobe and two-dimensional (2D-)IR spectroscopy. However, fully exploiting these advanced techniques requires an in-depth understanding of experimental observables and the encoded molecular information. To address this challenge, we present a descriptive and predictive computational approach for the simulation and analysis of static 2D-IR spectra of [NiFe] hydrogenases and similar organometallic systems. Accurate reproduction of experimental spectra from a first-coordination-sphere model suggests a decisive role of the [NiFe] core in shaping the enzymatic potential energy surface. We also reveal spectrally encoded molecular information that is not accessible by experiments, thereby helping to understand the catalytic role of the diatomic ligands, structural differences between [NiFe] intermediates, and possible energy transfer mechanisms. Our studies demonstrate the feasibility and benefits of computational spectroscopy in the 2D-IR investigation of hydrogenases, thereby further strengthening the potential of this nonlinear IR technique as a powerful research tool for the investigation of complex bioinorganic molecules. Full article
(This article belongs to the Special Issue Perspectives in Bioinorganic Catalysis)
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16 pages, 3320 KiB  
Article
The Amino Acids Motif -32GSSYN36- in the Catalytic Domain of E. coli Flavorubredoxin NO Reductase Is Essential for Its Activity
by Maria C. Martins, Susana F. Fernandes, Bruno A. Salgueiro, Jéssica C. Soares, Célia V. Romão, Cláudio M. Soares, Diana Lousa, Filipe Folgosa and Miguel Teixeira
Catalysts 2021, 11(8), 926; https://doi.org/10.3390/catal11080926 - 30 Jul 2021
Cited by 1 | Viewed by 2413
Abstract
Flavodiiron proteins (FDPs) are a family of modular and soluble enzymes endowed with nitric oxide and/or oxygen reductase activities, producing N2O or H2O, respectively. The FDP from Escherichia coli, which, apart from the two core domains, possesses a [...] Read more.
Flavodiiron proteins (FDPs) are a family of modular and soluble enzymes endowed with nitric oxide and/or oxygen reductase activities, producing N2O or H2O, respectively. The FDP from Escherichia coli, which, apart from the two core domains, possesses a rubredoxin-like domain at the C-terminus (therefore named flavorubredoxin (FlRd)), is a bona fide NO reductase, exhibiting O2 reducing activity that is approximately ten times lower than that for NO. Among the flavorubredoxins, there is a strictly conserved amino acids motif, -G[S,T]SYN-, close to the catalytic diiron center. To assess its role in FlRd’s activity, we designed several site-directed mutants, replacing the conserved residues with hydrophobic or anionic ones. The mutants, which maintained the general characteristics of the wild type enzyme, including cofactor content and integrity of the diiron center, revealed a decrease of their oxygen reductase activity, while the NO reductase activity—specifically, its physiological function—was almost completely abolished in some of the mutants. Molecular modeling of the mutant proteins pointed to subtle changes in the predicted structures that resulted in the reduction of the hydration of the regions around the conserved residues, as well as in the elimination of hydrogen bonds, which may affect proton transfer and/or product release. Full article
(This article belongs to the Special Issue Perspectives in Bioinorganic Catalysis)
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16 pages, 3806 KiB  
Article
Electronic and Structural Properties of the Double Cubane Iron-Sulfur Cluster
by Nadia Elghobashi-Meinhardt, Daria Tombolelli and Maria Andrea Mroginski
Catalysts 2021, 11(2), 245; https://doi.org/10.3390/catal11020245 - 12 Feb 2021
Cited by 5 | Viewed by 2499
Abstract
The double-cubane cluster (DCC) refers to an [Fe8S9] iron-sulfur complex that is otherwise only known to exist in nitrogenases. Containing a bridging µ2-S ligand, the DCC in the DCC-containing protein (DCCP) is covalently linked to the protein [...] Read more.
The double-cubane cluster (DCC) refers to an [Fe8S9] iron-sulfur complex that is otherwise only known to exist in nitrogenases. Containing a bridging µ2-S ligand, the DCC in the DCC-containing protein (DCCP) is covalently linked to the protein scaffold via six coordinating cysteine residues. In this study, the nature of spin coupling and the effect of spin states on the cluster’s geometry are investigated computationally. Using density functional theory (DFT) and a broken symmetry (BS) approach to study the electronic ground state of the system, we computed the exchange interaction between the spin-coupled spins of the four FeFe dimers contained in the DCC. This treatment yields results that are in excellent agreement with both computed and experimentally determined exchange parameters for analogously coupled di-iron complexes. Hybrid quantum mechanical (QM)/molecular mechanical (MM) geometry optimizations show that cubane cluster A closest to charged amino acid side chains (Arg312, Glu140, Lys146) is less compact than cluster B, indicating that electrons of the same spin in a charged environment seek maximum separation. Overall, this study provides the community with a fundamental reference for subsequent studies of DCCP, as well as for investigations of other [Fe8S9]-containing enzymes. Full article
(This article belongs to the Special Issue Perspectives in Bioinorganic Catalysis)
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19 pages, 6801 KiB  
Article
New Phosphorous-Based [FeFe]-Hydrogenase Models
by Florian Wittkamp, Esma Birsen Boydas, Michael Roemelt and Ulf-Peter Apfel
Catalysts 2020, 10(5), 522; https://doi.org/10.3390/catal10050522 - 08 May 2020
Cited by 6 | Viewed by 3474
Abstract
[FeFe]-hydrogenases have attracted research for more than twenty years as paragons for the design of new catalysts for the hydrogen evolution reaction (HER). The bridging dithiolate comprising a secondary amine as bridgehead is the key element for the reactivity of native [FeFe]-hydrogenases and [...] Read more.
[FeFe]-hydrogenases have attracted research for more than twenty years as paragons for the design of new catalysts for the hydrogen evolution reaction (HER). The bridging dithiolate comprising a secondary amine as bridgehead is the key element for the reactivity of native [FeFe]-hydrogenases and was therefore the midpoint of hundreds of biomimetic hydrogenase models. However, within those mimics, phosphorous is barely seen as a central element in the azadithiolato bridge despite being the direct heavier homologue of nitrogen. We herein synthesized three new phosphorous based [FeFe]-hydrogenase models by reacting dithiols (HSCH2)2P(O)R (R = Me, OEt, OPh) with Fe3(CO)12. All synthesized mimics show catalytic reactivity regarding HER and change their mechanisms depending on the strength of the used acid. In all presented mimics, the oxide is the center of reactivity, independent of the nature of the bridgehead. However, the phosphorous atom might be reduced by the methods we present herein to alter the reactivity of the model compounds towards protons and oxygen. Full article
(This article belongs to the Special Issue Perspectives in Bioinorganic Catalysis)
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Review

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51 pages, 3958 KiB  
Review
Bio-Inspired Molecular Catalysts for Water Oxidation
by Dan Xiao, Jennifer Gregg, K. V. Lakshmi and Peter J. Bonitatibus, Jr.
Catalysts 2021, 11(9), 1068; https://doi.org/10.3390/catal11091068 - 31 Aug 2021
Cited by 3 | Viewed by 4061
Abstract
The catalytic tetranuclear manganese-calcium-oxo cluster in the photosynthetic reaction center, photosystem II, provides an excellent blueprint for light-driven water oxidation in nature. The water oxidation reaction has attracted intense interest due to its potential as a renewable, clean, and environmentally benign source of [...] Read more.
The catalytic tetranuclear manganese-calcium-oxo cluster in the photosynthetic reaction center, photosystem II, provides an excellent blueprint for light-driven water oxidation in nature. The water oxidation reaction has attracted intense interest due to its potential as a renewable, clean, and environmentally benign source of energy production. Inspired by the oxygen-evolving complex of photosystem II, a large of number of highly innovative synthetic bio-inspired molecular catalysts are being developed that incorporate relatively cheap and abundant metals such as Mn, Fe, Co, Ni, and Cu, as well as Ru and Ir, in their design. In this review, we briefly discuss the historic milestones that have been achieved in the development of transition metal catalysts and focus on a detailed description of recent progress in the field. Full article
(This article belongs to the Special Issue Perspectives in Bioinorganic Catalysis)
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28 pages, 2993 KiB  
Review
A Beginner’s Guide to Thermodynamic Modelling of [FeFe] Hydrogenase
by James A. Birrell, Patricia Rodríguez-Maciá and Adrian Hery-Barranco
Catalysts 2021, 11(2), 238; https://doi.org/10.3390/catal11020238 - 11 Feb 2021
Cited by 2 | Viewed by 2548
Abstract
[FeFe] hydrogenases, which are considered the most active naturally occurring catalysts for hydrogen oxidation and proton reduction, are extensively studied as models to learn the important features for efficient H2 conversion catalysis. Using infrared spectroscopy as a selective probe, the redox behaviour [...] Read more.
[FeFe] hydrogenases, which are considered the most active naturally occurring catalysts for hydrogen oxidation and proton reduction, are extensively studied as models to learn the important features for efficient H2 conversion catalysis. Using infrared spectroscopy as a selective probe, the redox behaviour of the active site H-cluster is routinely modelled with thermodynamic schemes based on the Nernst equation for determining thermodynamic parameters, such as redox midpoint potentials and pKa values. Here, the thermodynamic models usually applied to [FeFe] hydrogenases are introduced and discussed in a pedagogic fashion and their applicability to additional metalloenzymes and molecular catalysts is also addressed. Full article
(This article belongs to the Special Issue Perspectives in Bioinorganic Catalysis)
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43 pages, 6348 KiB  
Review
Electrocatalysis by Heme Enzymes—Applications in Biosensing
by Lidia Zuccarello, Catarina Barbosa, Smilja Todorovic and Célia M. Silveira
Catalysts 2021, 11(2), 218; https://doi.org/10.3390/catal11020218 - 06 Feb 2021
Cited by 24 | Viewed by 3662
Abstract
Heme proteins take part in a number of fundamental biological processes, including oxygen transport and storage, electron transfer, catalysis and signal transduction. The redox chemistry of the heme iron and the biochemical diversity of heme proteins have led to the development of a [...] Read more.
Heme proteins take part in a number of fundamental biological processes, including oxygen transport and storage, electron transfer, catalysis and signal transduction. The redox chemistry of the heme iron and the biochemical diversity of heme proteins have led to the development of a plethora of biotechnological applications. This work focuses on biosensing devices based on heme proteins, in which they are electronically coupled to an electrode and their activity is determined through the measurement of catalytic currents in the presence of substrate, i.e., the target analyte of the biosensor. After an overview of the main concepts of amperometric biosensors, we address transduction schemes, protein immobilization strategies, and the performance of devices that explore reactions of heme biocatalysts, including peroxidase, cytochrome P450, catalase, nitrite reductase, cytochrome c oxidase, cytochrome c and derived microperoxidases, hemoglobin, and myoglobin. We further discuss how structural information about immobilized heme proteins can lead to rational design of biosensing devices, ensuring insights into their efficiency and long-term stability. Full article
(This article belongs to the Special Issue Perspectives in Bioinorganic Catalysis)
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Other

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22 pages, 8999 KiB  
Perspective
Construction of Synthetic Models for Nitrogenase-Relevant NifB Biogenesis Intermediates and Iron-Carbide-Sulfide Clusters
by Chris Joseph, John Patrick Shupp, Caitlyn R. Cobb and Michael J. Rose
Catalysts 2020, 10(11), 1317; https://doi.org/10.3390/catal10111317 - 13 Nov 2020
Cited by 4 | Viewed by 3254
Abstract
The family of nitrogenase enzymes catalyzes the reduction of atmospheric dinitrogen (N2) to ammonia under remarkably benign conditions of temperature, pressure, and pH. Therefore, the development of synthetic complexes or materials that can similarly perform this reaction is of critical interest. [...] Read more.
The family of nitrogenase enzymes catalyzes the reduction of atmospheric dinitrogen (N2) to ammonia under remarkably benign conditions of temperature, pressure, and pH. Therefore, the development of synthetic complexes or materials that can similarly perform this reaction is of critical interest. The primary obstacle for obtaining realistic synthetic models of the active site iron-sulfur-carbide cluster (e.g., FeMoco) is the incorporation of a truly inorganic carbide. This review summarizes the present state of knowledge regarding biological and chemical (synthetic) incorporation of carbide into iron-sulfur clusters. This includes the Nif cluster of proteins and associated biochemistry involved in the endogenous biogenesis of FeMoco. We focus on the chemical (synthetic) incorporation portion of our own efforts to incorporate and modify C1 units in iron/sulfur clusters. We also highlight recent contributions from other research groups in the area toward C1 and/or inorganic carbide insertion. Full article
(This article belongs to the Special Issue Perspectives in Bioinorganic Catalysis)
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