Subtopic Deep Dive
Fe-Only Hydrogenases
Research Guide
What is Fe-Only Hydrogenases?
Fe-only hydrogenases, also known as [FeFe]-hydrogenases, are iron-sulfur cluster-containing enzymes from anaerobic bacteria and algae that catalyze the reversible oxidation of H₂ at a unique H-cluster active site.
[FeFe]-hydrogenases feature a diiron subsite coordinated by CO, CN⁻ ligands, and a [4Fe-4S] cluster linked to additional iron-sulfur clusters for electron transfer (Peters, 1998). Over 100 structural and spectroscopic studies have elucidated their mechanisms, with key works including X-ray crystallography and FTIR analysis (Nicolet et al., 2001). These enzymes exhibit turnover frequencies exceeding 10,000 s⁻¹ under optimal conditions.
Why It Matters
Fe-only hydrogenases provide blueprints for synthetic catalysts mimicking their H-cluster for efficient H₂ production in renewable energy systems (McKone et al., 2013). Green algae expressing these enzymes offer biological H₂ sources coupled with solar energy conversion (Melis and Happe, 2001). Biomimetic designs inspired by Clostridium pasteurianum CpI achieve near-reversible potentials matching platinum catalysts (Peters, 1998). Genomic surveys confirm H₂ metabolism's ubiquity across microbial ecosystems, informing sustainable bioenergy strategies (Greening et al., 2015).
Key Research Challenges
H-cluster O₂ sensitivity
The H-cluster inactivates rapidly upon O₂ exposure despite buried active sites, limiting applications (Imlay, 2006). Spectroscopic studies show oxidative damage to Fe coordination (Nicolet et al., 2001). Engineering variants requires balancing catalytic speed with stability.
Maturation pathway complexity
Biosynthesis involves radical SAM enzymes for CN⁻ and CO ligation, with over 10 accessory proteins needed (Vignais et al., 2001). Heterologous expression in E. coli yields low active yields. Synthetic mimics struggle to replicate native assembly precision.
Electron transfer optimization
Proximal [4Fe-4S] clusters relay electrons, but coupling efficiency varies by organism (Peters, 1998). FTIR detects redox-state changes, yet long-range tunneling remains poorly modeled. Integrating into electrodes demands precise cluster spacing control.
Essential Papers
X-ray Crystal Structure of the Fe-Only Hydrogenase (CpI) from Clostridium pasteurianum to 1.8 Angstrom Resolution
John W. Peters · 1998 · 1.9K citations
A three-dimensional structure for the monomeric iron-containing hydrogenase (CpI) from Clostridium pasteurianum was determined to 1.8 angstrom resolution by x-ray crystallography using multiwavelen...
Molybdenum phosphide as an efficient electrocatalyst for the hydrogen evolution reaction
Peng Xiao, Mahasin Alam Sk, Larissa Thia et al. · 2014 · Energy & Environmental Science · 1.3K citations
The phosphorization of molybdenum leads to a good non-noble metal catalyst for the hydrogen evolution reaction in both acidic and alkaline conditions.
Classification and phylogeny of hydrogenases
Paulette M. Vignais, Bernard Billoud, Jacques Meyer · 2001 · FEMS Microbiology Reviews · 1.0K citations
Hydrogenases (H2ases) catalyze the reversible oxidation of molecular hydrogen and play a central role in microbial energy metabolism. Most of these enzymes are found in Archaea and Bacteria, but a ...
Crystallographic and FTIR Spectroscopic Evidence of Changes in Fe Coordination Upon Reduction of the Active Site of the Fe-Only Hydrogenase from<i>Desulfovibrio</i><i>d</i><i>esulfuricans</i>
Yvain Nicolet, António L. De Lacey, X. Vernède et al. · 2001 · Journal of the American Chemical Society · 777 citations
Fe-only hydrogenases, as well as their NiFe counterparts, display unusual intrinsic high-frequency IR bands that have been assigned to CO and CN(-) ligation to iron in their active sites. FTIR expe...
Earth-abundant hydrogen evolution electrocatalysts
James R. McKone, Smaranda C. Marinescu, Bruce S. Brunschwig et al. · 2013 · Chemical Science · 716 citations
Splitting water to hydrogen and oxygen is a promising approach for storing energy from intermittent renewables, such as solar power. Efficient, scalable solar-driven electrolysis devices require ac...
Iron‐sulphur clusters and the problem with oxygen
James A. Imlay · 2006 · Molecular Microbiology · 690 citations
Summary During the first billion years of life on the Earth, the environment was anaerobic. Iron and sulphur were plentiful, and they were recruited in the formation of iron‐sulphur (Fe‐S) clusters...
Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival
Chris Greening, Ambarish Biswas, Carlo R. Carere et al. · 2015 · The ISME Journal · 658 citations
Abstract Recent physiological and ecological studies have challenged the long-held belief that microbial metabolism of molecular hydrogen (H2) is a niche process. To gain a broader insight into the...
Reading Guide
Foundational Papers
Start with Peters (1998) for 1.8 Å CpI structure defining the H-cluster; follow with Vignais et al. (2001) for phylogenetic classification distinguishing FeFe from NiFe types; Nicolet et al. (2001) adds FTIR redox evidence.
Recent Advances
Greening et al. (2015) surveys H₂ metabolism distribution; Søndergaard et al. (2016) introduces HydDB for sequence analysis.
Core Methods
Multiwavelength anomalous dispersion phasing (Peters, 1998); FTIR spectroscopy of CO/CN ligands (Nicolet et al., 2001); genomic/metagenomic hydrogenase tracking (Greening et al., 2015).
How PapersFlow Helps You Research Fe-Only Hydrogenases
Discover & Search
Research Agent uses citationGraph on Peters (1998) to map 1854-citing works, revealing structural descendants like Nicolet et al. (2001), then findSimilarPapers expands to O₂ tolerance studies. exaSearch queries 'FeFe hydrogenase H-cluster mimics' across 250M+ OpenAlex papers, surfacing Greening et al. (2015) genomic data.
Analyze & Verify
Analysis Agent runs readPaperContent on Peters (1998) to extract H-cluster coordinates, verifies via CoVe against Nicolet et al. (2001) FTIR data, and uses runPythonAnalysis for matplotlib plots of Fe-Fe distances from PDB files. GRADE assigns A-level evidence to crystal structures, flagging B-level for unverified mimics.
Synthesize & Write
Synthesis Agent detects gaps in O₂-stable variants via contradiction flagging across Imlay (2006) and Vignais et al. (2001), then Writing Agent applies latexEditText for mechanism diagrams and latexSyncCitations to compile reviews. exportMermaid generates electron transfer pathway flowcharts from cluster phylogenies.
Use Cases
"Analyze H-cluster redox potentials from FTIR spectra in Desulfovibrio hydrogenase"
Research Agent → searchPapers('Nicolet 2001') → Analysis Agent → readPaperContent + runPythonAnalysis (pandas peak fitting on IR bands) → matplotlib plot of reduction states with statistical verification.
"Write LaTeX review on FeFe hydrogenase maturation with citations"
Synthesis Agent → gap detection on Vignais (2001) → Writing Agent → latexEditText (insert mechanisms) → latexSyncCitations (Vignais, Peters) → latexCompile → PDF with H-cluster figure.
"Find open-source code for hydrogenase structural modeling"
Research Agent → searchPapers('Peters 1998 CpI structure') → Code Discovery → paperExtractUrls → paperFindGithubRepo → githubRepoInspect → Python scripts for [4Fe-4S] simulations.
Automated Workflows
Deep Research workflow scans 50+ hydrogenase papers via citationGraph from Peters (1998), generating structured reports on H-cluster evolution with GRADE scores. DeepScan applies 7-step CoVe to verify O₂ damage mechanisms across Imlay (2006) and Nicolet et al. (2001). Theorizer hypothesizes improved electron relays by merging Greening et al. (2015) phylogenies with McKone (2013) electrocatalysts.
Frequently Asked Questions
What defines Fe-only hydrogenases?
Fe-only hydrogenases are [FeFe]-type enzymes with an H-cluster featuring a diiron site ligated by CO, CN⁻, and dithiomethylamine, linked to [4Fe-4S] clusters (Peters, 1998).
What are key methods for studying them?
X-ray crystallography resolves structures to 1.8 Å (Peters, 1998); FTIR detects CO/CN stretches shifting on reduction (Nicolet et al., 2001).
What are the most cited papers?
Peters (1998, 1854 citations) provides the CpI structure; Vignais et al. (2001, 1048 citations) classifies hydrogenase phylogeny.
What open problems exist?
Overcoming O₂ inactivation (Imlay, 2006); simplifying maturation for synthetic biology; optimizing biomimetic electrocatalysts (McKone et al., 2013).
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