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The Journal of Physical Chemistry. B Apr 2022We investigate the events characterizing the steps of the unfolding pathway of blue copper metalloprotein azurin using replica exchange molecular dynamics (REMD). Our...
We investigate the events characterizing the steps of the unfolding pathway of blue copper metalloprotein azurin using replica exchange molecular dynamics (REMD). Our studies show that the unfolding of azurin begins with the melting of α-helix and β-sheets II and V. This is followed by the melting of other β-sheets and the exposure of hydrophobic protein core to the solvent, resulting in disruptions of its tertiary structure. Free energy surfaces constructed at different temperatures portray different basins that signify the stability of different melted structures in the unfolding process. The contact maps at different temperatures reveal that the strong hydrophobic interaction within the core of the protein is the vital force that renders high stability to this protein. Analysis of the individual β-sheets by looking into their amino acid sequence shows that β-sheets with charged side chains on the surface melt fast compared to others. The β-barrel of azurin is able to dynamically rearrange, and it helps the protein to preserve its hydrophobic core, holding back the native topology from melting fast. B-factor analysis shows that residues of β-sheets III, IV, and VII deviate less from their initial structure at the transition temperature.
Topics: Azurin; Copper; Hydrophobic and Hydrophilic Interactions; Metalloproteins; Molecular Dynamics Simulation; Protein Folding
PubMed: 35324174
DOI: 10.1021/acs.jpcb.2c00622 -
Chemical Communications (Cambridge,... Jun 2022Herein we describe a designed protein building block whose self-assembly behaviour is dually gated by the redox state of disulphide bonds and the identity of exogenous...
Herein we describe a designed protein building block whose self-assembly behaviour is dually gated by the redox state of disulphide bonds and the identity of exogenous metal ions. This protein construct is shown - through extensive structural and biophysical characterization - to access five distinct oligomeric states, exemplifying how the complex interplay between hydrophobic, metal-ligand, and reversible covalent interactions could be harnessed to obtain multiple, responsive protein architectures from a single building block.
Topics: Hydrophobic and Hydrophilic Interactions; Ligands; Metalloproteins; Metals; Oxidation-Reduction
PubMed: 35642584
DOI: 10.1039/d2cc02440c -
Journal of Inorganic Biochemistry Jul 2023Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can...
Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene ("BMIE"), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu and Zn in bidentate (N) and tridentate (NS*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn, Cu, and Co. EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (HO/HO, tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. These features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.
Topics: Metalloproteins; Cysteine; Zinc; Metals; Peptide Hydrolases; Imidazoles; Sulfhydryl Compounds; Copper; Crystallography, X-Ray; Ligands
PubMed: 37030124
DOI: 10.1016/j.jinorgbio.2023.112206 -
Current Medicinal Chemistry 2019
Topics: Catalysis; Enzyme Inhibitors; Enzymes; Humans; Metalloproteins
PubMed: 31453777
DOI: 10.2174/092986732615190725122012 -
Quarterly Reviews of Biophysics 2004Metals are commonly found as natural constituents of proteins. Since many such metals can interact specifically with their corresponding unfolded proteins in vitro ,... (Review)
Review
Metals are commonly found as natural constituents of proteins. Since many such metals can interact specifically with their corresponding unfolded proteins in vitro , cofactor-binding prior to polypeptide folding may be a biological path to active metalloproteins. By interacting with the unfolded polypeptide, the metal may create local structure that initiates and directs the polypeptide-folding process. Here, we review recent literature that addresses the involvement of metals in protein-folding reactions in vitro . To date, the best characterized systems are simple one such as blue-copper proteins, heme-binding proteins, iron-sulfur-cluster proteins and synthetic metallopeptides. Taken together, the available data demonstrates that metals can play diverse roles: it is clear that many cofactors bind before polypeptide folding and influence the reaction; yet, some do not bind until a well-structured active site is formed. The significance of characterizing the effects of metals on protein conformational changes is underscored by the many human diseases that are directly linked to anomalous protein-metal interactions.
Topics: Biophysical Phenomena; Biophysics; Carrier Proteins; Hemeproteins; Iron-Sulfur Proteins; Metalloproteins; Models, Molecular; Protein Folding; Zinc Fingers
PubMed: 16194296
DOI: 10.1017/S003358350500404X -
Origins of Life and Evolution of the... Dec 2022Protein coordinated iron-sulfur clusters drive electron flow within metabolic pathways for organisms throughout the tree of life. It is not known how iron-sulfur...
Protein coordinated iron-sulfur clusters drive electron flow within metabolic pathways for organisms throughout the tree of life. It is not known how iron-sulfur clusters were first incorporated into proteins. Structural analogies to iron-sulfide minerals present on early Earth, suggest a connection in the evolution of both proteins and minerals. The availability of large protein and mineral crystallographic structure data sets, provides an opportunity to explore co-evolution of proteins and minerals on a large-scale using informatics approaches. However, quantitative comparisons are confounded by the infinite, repeating nature of the mineral lattice, in contrast to metal clusters in proteins, which are finite in size. We address this problem using the Niggli reduction to transform a mineral lattice to a finite, unique structure that when translated reproduces the crystal lattice. Protein and reduced mineral structures were represented as quotient graphs with the edges and nodes corresponding to bonds and atoms, respectively. We developed a graph theory-based method to calculate the maximum common connected edge subgraph (MCCES) between mineral and protein quotient graphs. MCCES can accommodate differences in structural volumes and easily allows additional chemical criteria to be considered when calculating similarity. To account for graph size differences, we use the Tversky similarity index. Using consistent criteria, we found little similarity between putative ancient iron-sulfur protein clusters and iron-sulfur mineral lattices, suggesting these metal sites are not as evolutionarily connected as once thought. We discuss possible evolutionary implications of these findings in addition to suggesting an alternative proxy, mineral surfaces, for better understanding the coevolution of the geosphere and biosphere.
Topics: Metalloproteins; Minerals; Iron-Sulfur Proteins; Sulfur; Iron
PubMed: 36383289
DOI: 10.1007/s11084-022-09630-x -
Physical Chemistry Chemical Physics :... Oct 2006This review is intended to account for the experimental and theoretical achievements obtained in a period of about 15 years on the investigation of the electron... (Review)
Review
This review is intended to account for the experimental and theoretical achievements obtained in a period of about 15 years on the investigation of the electron transport through single redox metalloproteins by scanning probe techniques. A highly focussed research effort has been deployed by the scientists active in this particular field towards measuring and interpreting electronic current signals flowing via blue copper, redox metalloproteins (e.g. azurin). The field has taken a remarkable advantage of the use of electrochemically assisted scanning tunnelling microscope (EC-STM) which has allowed to probe single molecule signals under full control of all the potential values involved in the experiments. This experimental activity has both triggered more comprehensive theoretical interpretations and has been, in its turn, stimulated by theoreticians to test always new predictions. The authors hope to have succeeded in providing the reader with a valuable appraisal of this fascinating field.
Topics: Electric Conductivity; Electrochemistry; Electrodes; Electron Transport; Metalloproteins; Microscopy, Scanning Probe; Models, Theoretical; Oxidation-Reduction; Sensitivity and Specificity
PubMed: 17001404
DOI: 10.1039/b607021c -
Advances in Experimental Medicine and... 2018Metallomics allows the integration of traditionally analytical studies with inorganic and biochemical studies. The study of metallomics in living organisms allows us to... (Review)
Review
Metallomics allows the integration of traditionally analytical studies with inorganic and biochemical studies. The study of metallomics in living organisms allows us to obtain information about how the metal ion is distributed and coordinated with proteins, the essentiality and/or toxicity, and the individual concentrations of metal species, thus contributing to elucidation of the physiological and functional aspects of these biomolecules. In this context, several lines of research have appeared in the literature with different terms and approaches. For example, metallomic, which deals with the characterization of the total metal/metalloid species present in an organism; metalloprotein, which deals with the characterization of the total elements present in a specific site of an organism (cellular behavior, protein, metalloprotein); and metallomic, which deals with a more in-depth study of metallome. In this area, information is sought on the interactions and functional connections of metal/metalloid species with genes, proteins, metabolites and other biomolecules of the organism and, therefore, the elucidation of the biological role exerted by the metal ions bound to the biomolecules. In this chapter, we will describe techniques used in animal studies.
Topics: Animals; Fish Proteins; Fishes; Metalloids; Metalloproteins; Metals
PubMed: 29884963
DOI: 10.1007/978-3-319-90143-5_5 -
Nature Aug 2009
Topics: Enzymes; Iron-Sulfur Proteins; Metalloproteins
PubMed: 19675640
DOI: 10.1038/460813a -
Molecules (Basel, Switzerland) Jul 2020Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a... (Review)
Review
Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life.
Topics: Animals; Binding Sites; Computational Biology; Eukaryota; Genomics; Humans; Metalloproteins; Prokaryotic Cells; Proteome; Trace Elements
PubMed: 32722260
DOI: 10.3390/molecules25153366