Search NASA⌕ Search

SEARCH · Search NASA

Results for “metalloprotein”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
NASA NTRS2022

Overcoming Universal Restrictions on Metal Selectivity by Protein Design

Selective metal coordination is central to the functions of metalloproteins:1,2 each metalloprotein must pair with its cognate metallocofactor to fulfl its biological role3 . However, achieving metal selectivity solely through a three-dimensional protein structure is a great challenge, because there is a limited set of metal-coordinating amino acid functionalities and proteins are inherently fexible, which impedes steric selection of metals3,4 . Metal-binding afnities of natural proteins are primarily dictated by the electronic properties of metal ions and follow the Irving–Williams series5 (Mn2+ < Fe2+ < Co2+ < Ni2+ Zn2+) with few exceptions6,7 . Accordingly, metalloproteins overwhelmingly bind Cu2+ and Zn2+ in isolation, regardless of the nature of their active sites and their cognate metal ions1,3,8 . This led organisms to evolve complex homeostatic machinery and non-equilibrium strategies to achieve correct metal speciation1,3,8–10. Here we report an artifcial dimeric protein, (AB)2, that thermodynamically overcomes the Irving–Williams restrictions in vitro and in cells, favouring the binding of lower-Irving–Williams transition metals over Cu2+, the most dominant ion in the Irving–Williams series. Counter to the convention in molecular design of achieving specifcity through structural preorganization, (AB)2 was deliberately designed to be fexible. This fexibility enabled (AB)2 to adopt mutually exclusive, metal-dependent conformational states, which led to the discovery of structurally coupled coordination sites that disfavour Cu2+ ions by enforcing an unfavourable coordination geometry. Aside from highlighting fexibility as a valuable element in protein design, our results illustrate design principles for constructing selective metal sequestration agents.

Tae Su Choi↗
DOE OSTI2023

Impact of a Biological Chelator, Lanmodulin, on Minor Actinide Aqueous Speciation and Transport in the Environment

Minor actinides are major contributors to the long-term radiotoxicity of nuclear fuels and other radioactive wastes. Here in this context, understanding their interactions with natural chelators and minerals is key to evaluating their transport behavior in the environment. The lanmodulin family of metalloproteins is produced by ubiquitous bacteria and Methylorubrum extorquens lanmodulin (LanM) was recently identified as one of nature’s most selective chelators for trivalent f-elements. Herein, we investigated the behavior of neptunium, americium, and curium in the presence of LanM, carbonate ions, and common minerals (calcite, montmorillonite, quartz, and kaolinite). We show that LanM’s aqueous complexes with Am(III) and Cm(III) remain stable in carbonate-bicarbonate solutions. Furthermore, the sorption of Am(III) to these minerals is strongly impacted by LanM, while Np(V) sorption is not. With calcite, even a submicromolar concentration of LanM leads to a significant reduction in the Am(III) distribution coefficient (K d , from >10 4 to ~10 2 mL/g at pH 8.5), rendering it even more mobile than Np(V). Thus, LanM-type chelators can potentially increase the mobility of trivalent actinides and lanthanide fission products under environmentally relevant conditions. Monitoring biological chelators, including metalloproteins, and their biogenerators should therefore be considered during the evaluation of radioactive waste repository sites and the risk assessment of contaminated sites.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2026

Rational Design of Lanmodulin Variants for Size-Based Selectivity of Individual Rare Earth Elements

Rare earth elements (REEs) are essential to modern technologies, yet their high physical and chemical similarity makes separation of individual REEs difficult and environmentally taxing. Metalloproteins offer a promising alternative for selective REE binding, as they tend to have high metal ion affinity and specificity. Lanmodulin (LanM), in particular, has arisen as a potential candidate for REE separation as it exhibits picomolar affinity for elements in the REE family. Prior work has shown that the single point mutation D9N can shift LanM’s preference away from lanthanides toward actinides, motivating efforts to tune selectivity of LanM through targeted mutagenesis. Here, we tested the hypothesis that introducing selective aspartic acid to glutamic acid substitutions in the metal coordinating EF hands of LanM would impose steric constraints that would drive LanM affinity away from larger ions, such as La3+, to smaller ions, such as Y3+. To test this hypothesis, a combination of computational and experimental approaches were employed to evaluate the signal mutations LanM D5E and LanM D3E and the double mutants LanM D1ED5E and LanM D3ED9E. Surprisingly, increasing the number of mutations within the metal center did not enhance affinity for smaller REEs, or decrease affinity for larger ions. Only the single point mutation LanM D5E weakened La3+ binding by one order of magnitude relative to LanM wild type (WT), and pairing it with a second mutation to produce LanM D1ED5E drove La3+ affinity to be stronger than that seen for LanM WT. The D3E mutation alone prevented proper expression and folding, but paring it with D9E to produce LanM D3ED9E rescued expression and yielded La3+ affinities comparable to LanM WT. All variants that expressed (LanM D5E, LanM D1ED5E, LanM D3ED9E) displayed Y3+ affinities comparable to LanM WT. Overall, these results highlight the tunability of LanM’s metal-binding environment but also expose current limitations in predicting structural responses to point mutations within a protein sequence. This work establishes a foundation that can be used for refining computational and experimental strategies to engineer metalloproteins with tailored REE selectivity.

Close, Emily [Pacific Northwest National Laborator↗
DOE OSTI2020

Heterologous Expression and Engineering of the Nitrogenase Cofactor Biosynthesis Scaffold NifEN

NifEN plays a crucial role in the biosynthesis of nitrogenase, catalyzing the final step of cofactor maturation prior to delivering the cofactor to NifDK, the catalytic component of nitrogenase. The difficulty in expressing NifEN, a complex, heteromultimeric metalloprotein sharing structural/functional homology with NifDK, is a major challenge in the heterologous expression of nitrogenase. Herein, we report the expression and engineering of Azotobacter vinelandii NifEN in Escherichia coli. Biochemical and spectroscopic analyses demonstrate the integrity of the heterologously expressed NifEN in composition and functionality and, additionally, the ability of an engineered NifEN variant to mimic NifDK in retaining the matured cofactor at an analogous cofactor-binding site. This is an important step toward piecing together a viable pathway for the heterologous expression of nitrogenase and identifying variants for the mechanistic investigation of this enzyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Heterologous Expression and Engineering of the Nitrogenase Cofactor Biosynthesis Scaffold NifEN

Abstract NifEN plays a crucial role in the biosynthesis of nitrogenase, catalyzing the final step of cofactor maturation prior to delivering the cofactor to NifDK, the catalytic component of nitrogenase. The difficulty in expressing NifEN, a complex, heteromultimeric metalloprotein sharing structural/functional homology with NifDK, is a major challenge in the heterologous expression of nitrogenase. Herein, we report the expression and engineering of Azotobacter vinelandii NifEN in Escherichia coli . Biochemical and spectroscopic analyses demonstrate the integrity of the heterologously expressed NifEN in composition and functionality and, additionally, the ability of an engineered NifEN variant to mimic NifDK in retaining the matured cofactor at an analogous cofactor‐binding site. This is an important step toward piecing together a viable pathway for the heterologous expression of nitrogenase and identifying variants for the mechanistic investigation of this enzyme.

Solomon, Joseph B.↗
DOE OSTI2020

Special Issue on Nitrogenases and Homologous Systems

The nitrogenase superfamily comprises homologous enzyme systems that carry out fundamentally important processes, including the reduction of N 2 and CO, and the biosynthesis of bacteriochlorophyll and coenzyme F430. This special issue provides a cross-disciplinary overview of the ongoing research in this highly diverse and unique research area of metalloprotein biochemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Crystallography Reveals Metal‐Triggered Restructuring of β‐Hairpins

Abstract Metal binding to β‐sheets occurs in many metalloproteins and is also implicated in the pathology of Alzheimer's disease. De novo designed metallo‐β‐sheets have been pursued as models and mimics of these proteins. However, no crystal structures of canonical β‐sheet metallopeptides have yet been obtained, in stark contrast to many examples for ɑ‐helical metallopeptides, leading to a poor understanding for their chemistry. To address this, we have engineered tryptophan zippers, stable 12‐residue β‐sheet peptides, to bind Cu(II) ions and obtained crystal structures through single crystal X‐ray diffraction (SC‐XRD). We find that metal binding triggers several unexpected supramolecular assemblies that demonstrate the range of higher‐order structures available to metallo‐β‐sheets. Overall, these findings underscore the importance of crystallography in elucidating the rich structural landscape of metallo‐β‐sheet peptides.

Thuc Dang, Viet↗
DOE OSTI2023

Quantifying metal-binding specificity of Cc NikZ-II from Clostridium carboxidivorans in the presence of competing metal ions

Many proteins bind transition metal ions as cofactors to carry out their biological functions. Despite binding affinities for divalent transition metal ions being predominantly dictated by the Irving-Williams series for wild-type proteins, in vivo metal ion binding specificity is ensured by intracellular mechanisms that regulate free metal ion concentrations. However, a growing area of biotechnology research considers the use of metal-binding proteins in vitro to purify specific metal ions from wastewater, where specificity is dictated by the protein's metal binding affinities. A goal of metalloprotein engineering is to modulate these affinities to improve a protein's specificity towards a particular metal; however, the quantitative relationship between the affinities and the equilibrium metal-bound protein fractions depends on the underlying binding mechanisms. Here we demonstrate a high-throughput intrinsic tryptophan fluorescence quenching method to validate binding models in multi-metal solutions for CcNikZ-II, a nickel-binding protein from Clostridium carboxidivorans. Using our validated models, we quantify the relationship between binding affinity and specificity in different classes of metal-binding models for CcNikZ-II. In conclusion, we further illustrate the potential relevance of data-informed models to predicting engineering targets for improved specificity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

CAML: Commutative Algebra Machine Learning─A Case Study on Protein–Ligand Binding Affinity Prediction

Recently, Suwayyid and Wei introduced commutative algebra as an emerging paradigm for machine learning and data science. In this work, we propose commutative algebra machine learning (CAML) for the prediction of protein−ligand binding affinities. Specifically, we apply persistent Stanley−Reisner theory, a key concept in combinatorial commutative algebra, to the affinity predictions of protein−ligand binding and metalloprotein−ligand binding. We present three new algorithms, i.e., element-specific commutative algebra, category-specific commutative algebra, and commutative algebra on bipartite complexes, to tackle the complexity of data involved in (metallo) protein−ligand complexes. We show that the proposed CAML outperforms other state-of-theart methods in (metallo) protein−ligand binding affinity predictions, indicating the great potential of commutative algebra learning.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Assessing Metal Ion Assignment Accuracy in Protein Data Bank Models via Elemental Spectroscopy

Accurate representation of metal ions in macromolecular structures is critical for chemical interpretation, computational modeling, and machine-learning methods that rely on Protein Data Bank (PDB) entries. However, the elemental identity of metals modeled in crystallographic structures is often inferred indirectly and rarely validated experimentally. Here, we combine Particle Induced X-ray Emission (PIXE) and X-ray Fluorescence Spectroscopy (XRFS) to determine the elemental composition of protein samples used to generate 70 deposited metalloprotein crystal structures. By analyzing the original protein material employed for crystallization, but before the addition of crystallization buffer solutions, we assess whether the modeled metal ions in deposited structures are consistent with experimentally detectable elemental content. We find that in a majority of cases, the metals modeled in the corresponding PDB entries are inconsistent with the metals present in the protein samples before crystallization, or that additional metals are present but not represented in the structural models. Spectroscopic results were integrated with automated crystallographic validation metrics, including real-space Z-difference (RSZD) analysis and systematic rerefinement, to evaluate atomic-number mismatch at metal sites. PIXE and XRFS show strong agreement for dominant elemental signals and provide complementary, scalable approaches for identifying suspect metal assignments. This work does not address physiological or functional metalation but instead highlights a widespread data integrity issue in deposited macromolecular structures, PDB-wide. These results establish an experimentally corroborated link between elemental identity and crystallographic validation metrics, enabling the large-scale detection of chemically inconsistent annotations in structural databases used for computational modeling and machine learning.

Crystallization↗
DOE OSTI2023

Ten-Fold Solvent Kinetic Isotope Effect for the Nonradiative Relaxation of the Aqueous Ferrate(VI) Ion

Hypervalent iron intermediates have been invoked in the catalytic cycles of many metalloproteins, and thus, it is crucial to understand how the coupling between such species and their environment can impact their chemical and physical properties in such contexts. In this work, we take advantage of the solvent kinetic isotope effect (SKIE) to gain insight into the nonradiative deactivation of electronic excited states of the aqueous ferrate-(VI) ion. Here we observe an exceptionally large SKIE of 9.7 for the nanosecond-scale relaxation of the lowest energy triplet ligand field state to the ground state. Proton inventory studies demonstrate that a single solvent O-H bond is coupled to the ion during deactivation, likely due to the sparse vibrational structure of ferrate-(VI). Such a mechanism is consistent with that reported for the deactivation of f-f excited states of aqueous trivalent lanthanides, which exhibit comparably large SKIE values. This phenomenon is ascribed entirely to dissipation of energy into a higher overtone of a solvent acceptor mode, as any impact on the apparent relaxation rate due to a change in solvent viscosity is negligible.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Computing Reaction Kinetics with MC-PDFT–OPESf: Combining Multireference Electronic Structure Theory and Enhanced Sampling

Accurate rate constants are crucial for understanding and optimizing catalytic reactions mediated by enzymes, metalloproteins, and heterogeneous catalysts. These systems frequently present a dual computational challenge. Multiconfigurational reaction sites require multireference techniques for the accurate treatment of the electronic structure, and high activation barriers prevent efficient sampling of unbiased reactive transitions. In this work, we combine multiconfiguration pair-density functional theory (MC-PDFT) as an accurate and efficient multireference electronic structure method with on-the-fly probability-enhanced sampling flooding (OPESf) as an enhanced sampling method capable of accelerating reactive transitions. We demonstrate the approach on the Diels–Alder [4+2] cycloaddition between cis-butadiene and ethene as a reaction characterized by a large activation barrier and multireference character. MC-PDFT–OPESf provides reaction rates in agreement with experiments at a fraction of the computational cost required by conventional unbiased ab initio calculations. Here, we propose MC-PDFT–OPESf as an efficient approach for computing kinetics in strongly correlated molecular systems.

Chemical calculations↗
DOE OSTI2024

A Copper-Binding Peptide with Therapeutic Potential against Alzheimer′s Disease: From the Blood–Brain Barrier to Metal Competition

Alzheimer’s disease (AD) is the most common form of dementia worldwide. AD brains are characterized by the accumulation of amyloid-β peptides (Aβ) that bind Cu 2+ and have been associated with several neurotoxic mechanisms. Although the use of copper chelators to prevent the formation of Cu 2+ -Aβ complexes has been proposed as a therapeutic strategy, recent studies show that copper is an important neuromodulator that is essential for a neuroprotective mechanism mediated by Cu 2+ binding to the cellular prion protein (PrPC). Therefore, in addition to metal selectivity and blood–brain barrier (BBB) permeability, an emerging challenge for copper chelators is to prevent the formation of neurotoxic Cu 2+ -Aβ species without perturbing the neuroprotective Cu 2+ -PrPC interaction. Previously, we reported the design of a tetrapeptide (TP) that withdraws Cu 2+ from Aβ(1–16) and impacts the Cu 2+ -induced aggregation of Aβ(1–40). In this study, we improved the drug-like properties of TP in a BBB model, evaluated the metal selectivity of the optimized peptide (TP*), and tested its effect on Cu 2+ coordination to PrPC and proteins involved in copper trafficking, such as copper transporter 1 and albumin. Our results show that changing the stereochemistry of the first residue prevents TP degradation in the BBB model and coadministration of TP with a peptide that increases BBB permeability allows its passage through the BBB model. TP* is highly selective toward Cu 2+ in the presence of Zn 2+ ions, transfers Cu 2+ to copper-trafficking proteins, and forms a ternary TP*-Cu 2+ -PrP species that does not perturb the physiological conformation of PrP and displays only a minor impact in the neuroprotective Cu 2+ -dependent interaction of PrPC with the N-methyl-d-aspartate receptor. Overall, these results show that TP* displays desirable features for a copper chelator with therapeutic potential against AD. Moreover, this is the first study that explores the effect of a Cu 2+ chelator with therapeutic potential for AD on Cu 2+ coordination to PrPC (an emerging key player in AD pathology), integrating recent knowledge about metalloproteins involved in AD with the design of copper chelators against AD.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Random heteropolymers as enzyme mimics

Despite successes in replicating the primary–secondary–tertiary structure hierarchy of protein, it remains elusive to synthetically materialize protein functions that are deeply rooted in their chemical, structural and dynamic heterogeneities. We propose that for polymers with backbone chemistries different from that of proteins, programming spatial and temporal projections of sidechains at the segmental level can be effective in replicating protein behaviours; and leveraging the rotational freedom of polymer can mitigate deficiencies in monomeric sequence specificity and achieve behaviour uniformity at the ensemble level. Here, guided by the active site analysis of about 1,300 metalloproteins, we design random heteropolymers (RHPs) as enzyme mimics based on one-pot synthesis. We introduce key monomers as the equivalents of the functional residues of protein and statistically modulate the chemical characteristics of key monomer-containing segments, such as segmental hydrophobicity. The resultant RHPs form pseudo-active sites that provide key monomers with protein-like microenvironments, co-localize substrates with catalytic or cofactor-binding sidechains and catalyse reactions such as oxidation and cyclization of citronellal with isopulegol/menthoglycol selectivity. This RHP design led to enzyme-like materials that can retain catalytic activity under non-biological conditions, are compatible with scalable processing and have expanded substrate scope, including environmentally long-lasting antibiotic tetracycline.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Mechanisms and heterogeneity of in situ mineral processing by the marine nitrogen fixer Trichodesmium revealed by single-colony metaproteomics

The keystone marine nitrogen fixer Trichodesmium thrives in high-dust environments. While laboratory investigations have observed that Trichodesmium colonies can access the essential nutrient iron from dust particles, less clear are the biochemical strategies underlying particle–colony interactions in nature. Here we demonstrate that Trichodesmium colonies engage with mineral particles in the wild with distinct molecular responses. We encountered particle-laden Trichodesmium colonies at a sampling location in the Southern Caribbean Sea; microscopy and synchrotron-based imaging then demonstrated heterogeneous associations with iron oxide and iron-silicate minerals. Metaproteomic analysis of individual colonies by a new low-biomass approach revealed responses in biogeochemically relevant proteins including photosynthesis proteins and metalloproteins containing iron, nickel, copper, and zinc. The iron-storage protein ferritin was particularly enriched implying accumulation of mineral-derived iron, and multiple iron acquisition pathways including Fe(II), Fe(III), and Fe-siderophore transporters were engaged. While the particles provided key trace metals such as iron and nickel, there was also evidence that Trichodesmium was altering its strategy to confront increased superoxide production and metal exposure. Chemotaxis regulators also responded to mineral presence suggesting involvement in particle entrainment. These molecular responses are fundamental to Trichodesmium’s ecological success and global biogeochemical impact, and may contribute to the leaching of particulate trace metals with implications for global iron and carbon cycling.

Held, Noelle A.↗
DOE OSTI2023

Bivalent molecular mimicry by ADP protects metal redox state and promotes coenzyme B 12 repair

Control over transition metal redox state is essential for metalloprotein function and can be achieved via coordination chemistry and/or sequestration from bulk solvent. Human methylmalonyl-Coenzyme A (CoA) mutase (MCM) catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA using 5′-deoxyadenosylcobalamin (AdoCbl) as a metallocofactor. During catalysis, the occasional escape of the 5′-deoxyadenosine (dAdo) moiety leaves the cob(II)alamin intermediate stranded and prone to hyperoxidation to hydroxocobalamin, which is recalcitrant to repair. In this study, we have identified the use of bivalent molecular mimicry by ADP, coopting the 5′-deoxyadenosine and diphosphate moieties in the cofactor and substrate, respectively, to protect against cob(II)alamin overoxidation on MCM. Crystallographic and electron paramagnetic resonance (EPR) data reveal that ADP exerts control over the metal oxidation state by inducing a conformational change that seals off solvent access, rather than by switching five-coordinate cob(II)alamin to the more air stable four-coordinate state. Subsequent binding of methylmalonyl-CoA (or CoA) promotes cob(II)alamin off-loading from MCM to adenosyltransferase for repair. This study identifies an unconventional strategy for controlling metal redox state by an abundant metabolite to plug active site access, which is key to preserving and recycling a rare, but essential, metal cofactor.

Science & Technology - Other Topics↗
DOE OSTI2023

A designed Copper Histidine-brace enzyme for oxidative depolymerization of polysaccharides as a model of lytic polysaccharide monooxygenase

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.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗