-
Accounts of Chemical Research Feb 2019Nature puts to use only a small fraction of metal ions in the periodic table. Yet, when incorporated into protein scaffolds, this limited set of metal ions carry out...
Nature puts to use only a small fraction of metal ions in the periodic table. Yet, when incorporated into protein scaffolds, this limited set of metal ions carry out innumerable cellular functions and execute essential biochemical transformations such as photochemical HO oxidation, O or CO reduction, and N fixation, highlighting the outsized importance of metalloproteins in biology. Not surprisingly, elucidating the intricate interplay between metal ions and protein structures has been the focus of extensive structural and mechanistic scrutiny over the last several decades. As a result of such top-down efforts, we have gained a reasonably detailed understanding of how metal ions shape protein structures and how protein structures in turn influence metal reactivity. It is fair to say that we now have some idea-and in some cases, a good idea-about how most known metalloproteins function and we possess enough insight to quickly assess the modus operandi of newly discovered ones. However, translating this knowledge into an ability to construct functional metalloproteins from scratch represents a challenge at a whole different level: it is one thing to know how an automobile works; it is another to build one. In our quest to build new metalloproteins, we have taken an original approach in which folded, monomeric proteins are used as ligands or synthons for building supramolecular complexes through metal-mediated self-assembly (MDPSA, Metal-Directed Protein Self-Assembly). The interfaces in the resulting protein superstructures are subsequently tailored with covalent, noncovalent, or additional metal-coordination interactions for stabilization and incorporation of new functionalities (MeTIR, Metal Templated Interface Redesign). In an earlier Account, we had described the proof-of-principle studies for MDPSA and MeTIR, using a four-helix bundle, heme protein cytochrome cb (cyt cb), as a model building block. By the end of those studies, we were able to demonstrate that a tetrameric, Zn-directed cyt cb complex (Zn:M1) could be stabilized through computationally prescribed noncovalent interactions inserted into the nascent protein-protein interfaces. In this Account, we first describe the rationale and motivation for our particular metalloprotein engineering strategy and a brief summary of our earlier work. We then describe the next steps in the "evolution" of bioinorganic complexity on the Zn:M1 scaffold, namely, (a) the generation of a self-standing protein assembly that can stably and selectively bind metal ions, (b) the creation of reactive metal centers within the protein assembly, and (c) the coupling of metal coordination and reactivity to external stimuli through allosteric effects.
Topics: Catalytic Domain; Cytochrome b Group; Esterases; Metalloproteins; Point Mutation; Protein Conformation; Protein Engineering; Zinc; beta-Lactamases
PubMed: 30698941
DOI: 10.1021/acs.accounts.8b00617 -
Chembiochem : a European Journal of... Jun 2020The nitrogenase superfamily comprises homologous enzyme systems that carry out fundamentally important processes, including the reduction of N and CO, and the...
The nitrogenase superfamily comprises homologous enzyme systems that carry out fundamentally important processes, including the reduction of N 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.
Topics: Metalloproteins; Nitrogenase; Oxidation-Reduction
PubMed: 32426925
DOI: 10.1002/cbic.202000279 -
Small (Weinheim An Der Bergstrasse,... Nov 2020Photoimmunotherapy (PIT) has shown enormous potential in not only eliminating primary tumors, but also inhibiting abscopal tumor growth. However, the efficacy of PIT is...
Photoimmunotherapy (PIT) has shown enormous potential in not only eliminating primary tumors, but also inhibiting abscopal tumor growth. However, the efficacy of PIT is greatly limited by tumor hypoxia, which causes the attenuation of phototherapeutic efficacy and is a feature of the immunosuppressive tumor microenvironment (TME). In this study, one type of brand-new artificial metalloprotein nanoanalogues is developed via reasonable integration of a "phototherapy-enzymatic" RuO and a model antigen, ovalbumin (OVA) for enhanced PIT of cancers, namely, RuO -hybridized OVA nanoanalogues (RuO @OVA NAs). The RuO @OVA NAs exhibit remarkable photothermal/photodynamic capabilities under the near-infrared light irradiation. More importantly, the photoacoustic imaging and immunofluorescence staining confirm that RuO @OVA NAs can remarkably alleviate hypoxia via in situ catalysis of hydrogen peroxide overexpressed in the TME to produce oxygen (O ). This ushers a prospect of concurrently enhancing photodynamic therapy and reversing the immunosuppressive TME. Also, OVA, as a supplement to the immune stimulation induced by phototherapy, can activate immune responses. Finally, further combination with the cytotoxic T-lymphocyte-associated protein 4 checkpoint blockade is reported to effectively eliminate the primary tumor and inhibit distant tumor growth via the abscopal effect of antitumor immune responses, prolonging the survival.
Topics: Catalysis; Cell Line, Tumor; Metalloproteins; Oxygen; Phototherapy
PubMed: 33089606
DOI: 10.1002/smll.202004345 -
Current Opinion in Chemical Biology Feb 2011About one-third of all proteins are associated with a metal. Metalloproteomics is defined as the structural and functional characterization of metalloproteins on a... (Review)
Review
About one-third of all proteins are associated with a metal. Metalloproteomics is defined as the structural and functional characterization of metalloproteins on a genome-wide scale. The methodologies utilized in metalloproteomics, including both forward (bottom-up) and reverse (top-down) technologies, to provide information on the identity, quantity, and function of metalloproteins are discussed. Important techniques frequently employed in metalloproteomics include classical proteomic tools such as mass spectrometry and 2D gels, immobilized-metal affinity chromatography, bioinformatic sequence analysis and homology modeling, X-ray absorption spectroscopy and other synchrotron radiation based tools. Combinative applications of these techniques provide a powerful approach to understand the function of metalloproteins.
Topics: Animals; Computational Biology; Humans; Metalloproteins; Protein Conformation; Proteomics
PubMed: 21130021
DOI: 10.1016/j.cbpa.2010.11.004 -
FEMS Microbiology Letters Dec 2011The Tat pathway is a common protein translocation system that is found in the bacterial cytoplasmic membrane, as well as in the cyanobacterial and plant thylakoid... (Review)
Review
The Tat pathway is a common protein translocation system that is found in the bacterial cytoplasmic membrane, as well as in the cyanobacterial and plant thylakoid membranes. It is unusual in that the Tat pathway transports fully folded, often metal cofactor-containing proteins across these membranes. In bacteria, the Tat pathway plays an important role in the biosynthesis of noncytoplasmic metalloproteins. By compartmentalizing protein folding to the cytoplasm, the potentially aberrant binding of non-native metal ions to periplasmic proteins is avoided. To date, most of our understanding of Tat function has been obtained from studies using Escherichia coli as a model organism but cyanobacteria have an extra layer of complexity with proteins targeted to both the cytoplasmic and thylakoid membranes. We examine our current understanding of the Tat pathway in cyanobacteria and its role in metalloprotein biosynthesis.
Topics: Cyanobacteria; Membrane Transport Proteins; Metalloproteins; Metals; Protein Transport
PubMed: 22092855
DOI: 10.1111/j.1574-6968.2011.02391.x -
Molecules (Basel, Switzerland) Feb 2022Metalloproteins are a family of proteins characterized by metal ion binding, whereby the presence of these ions confers key catalytic and ligand-binding properties. Due... (Review)
Review
Metalloproteins are a family of proteins characterized by metal ion binding, whereby the presence of these ions confers key catalytic and ligand-binding properties. Due to their ubiquity among biological systems, researchers have made immense efforts to predict the structural and functional roles of metalloproteins. Ultimately, having a comprehensive understanding of metalloproteins will lead to tangible applications, such as designing potent inhibitors in drug discovery. Recently, there has been an acceleration in the number of studies applying machine learning to predict metalloprotein properties, primarily driven by the advent of more sophisticated machine learning algorithms. This review covers how machine learning tools have consolidated and expanded our comprehension of various aspects of metalloproteins (structure, function, stability, ligand-binding interactions, and inhibitors). Future avenues of exploration are also discussed.
Topics: Amino Acid Sequence; Binding Sites; Drug Design; Machine Learning; Metalloproteins; Models, Molecular; Protein Binding; Protein Stability; Proteolysis; Structure-Activity Relationship
PubMed: 35209064
DOI: 10.3390/molecules27041277 -
Journal of Inorganic Biochemistry Jan 2002Achieving a thorough explanation of the behavior of metal sites in the formation of native metalloprotein structures is an exciting challenge in the biochemistry of... (Review)
Review
Achieving a thorough explanation of the behavior of metal sites in the formation of native metalloprotein structures is an exciting challenge in the biochemistry of metallobiomacromolecules. This study presents a personal insight into the subject. It is proposed that a metal center and its exogenous ligand compose a template. A template may impose a clear stereochemical preference on the loose peptide chains, and organize them into natural stereospecificity via the metal-ligand interaction, a long-range and strong interaction. Therefore, the stable peptide conformation induced by the template effect surrounding a template polyhedron could be called a template-mediated structural motif (TMSM).
Topics: Animals; Binding Sites; Humans; Metalloproteins; Metals; Models, Molecular; Protein Conformation
PubMed: 11750028
DOI: 10.1016/s0162-0134(01)00337-3 -
The Journal of Biological Chemistry Mar 2018Copper is essential for most organisms as a cofactor for key enzymes involved in fundamental processes such as respiration and photosynthesis. However, copper also has... (Review)
Review
Copper is essential for most organisms as a cofactor for key enzymes involved in fundamental processes such as respiration and photosynthesis. However, copper also has toxic effects in cells, which is why eukaryotes and prokaryotes have evolved mechanisms for safe copper handling. A new family of bacterial proteins uses a Cys-rich four-helix bundle to safely store large quantities of Cu(I). The work leading to the discovery of these proteins, their properties and physiological functions, and how their presence potentially impacts the current views of bacterial copper handling and use are discussed in this review.
Topics: Bacteria; Bacterial Proteins; Copper; Metalloproteins
PubMed: 29414794
DOI: 10.1074/jbc.TM117.000180 -
Journal of Chromatography. A Aug 2022Metalloproteins play crucial and distinct roles in a variety of biological processes that rely heavily on the metal ions and various proteins. However, there is still a...
Metalloproteins play crucial and distinct roles in a variety of biological processes that rely heavily on the metal ions and various proteins. However, there is still a lack of method for rapid analysis of metalloproteins in complex samples, especially in salt-rich matrices. In this study, a sensitive method for separation and determination of metalloproteins in salt-rich matrices was developed based on the size exclusion chromatography coupled with inductively coupled plasma-mass spectrometry (SEC-ICP-MS), combining with the high matrix introduction (HMI) mode, which is quite essential for biological system. The separation conditions of the SEC-ICP-MS system were optimized by using four iodine labeled proteins with different molecular weights, including bovine serum albumin (BSA, 66.0 kDa), ovalbumin (OVA, 44.0 kDa), carbonic anhydrase (CA, 29.0 kDa) and ribonuclease A (RA, 13.7 kDa). After optimization, four iodine labeled proteins and iodine ions were successfully separated within 30 min by using 10 mmol/L HEPES and 40 mmol/L NaSO (pH=7.0) as mobile phase and a linear relationship between log molecular weight and retention time was established. The relative standard deviations (RSDs, n = 5) of the retention time and peak areas for the four iodine labeled proteins were in the range of 0.2-0.9% and 3.3-7.7%, respectively, suggesting good precision and repeatability. Then the proposed method was successfully applied to the rapid separation and detection of lead-binding proteins in real biological tissue samples.
Topics: Chromatography, Gel; Iodine; Mass Spectrometry; Metalloproteins; Metals
PubMed: 35830839
DOI: 10.1016/j.chroma.2022.463303 -
International Journal of Molecular... Jun 2023We present a Ni site model of acetyl coenzyme-A synthase (ACS) within a de novo-designed trimer peptide that self-assembles to produce a homoleptic Ni(Cys) binding...
We present a Ni site model of acetyl coenzyme-A synthase (ACS) within a de novo-designed trimer peptide that self-assembles to produce a homoleptic Ni(Cys) binding motif. Spectroscopic and kinetic studies of ligand binding demonstrate that Ni binding stabilizes the peptide assembly and produces a terminal Ni-CO complex. When the CO-bound state is reacted with a methyl donor, a new species is quickly produced with new spectral features. While the metal-bound CO is albeit unactivated, the presence of the methyl donor produces an activated metal-CO complex. Selective outer sphere steric modifications demonstrate that the physical properties of the ligand-bound states are altered differently depending on the location of the steric modification above or below the Ni site.
Topics: Metalloproteins; Acetyl Coenzyme A; Kinetics; Ligands; Nickel; Coordination Complexes; Nitric Oxide Synthase; Aldehyde Oxidoreductases
PubMed: 37373464
DOI: 10.3390/ijms241210317