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Metal coordination is essential for structural/catalytic functions of metalloproteins that mediate a wide range of biological processes in living organisms. Advances in bioinformatics have significantly enhanced our understanding of metal-binding sites and their functional roles in metalloproteins. State-of-the-art computational models developed for metal-binding sites seamlessly integrate protein sequence and structural data to unravel the complexities of metal coordination environments. Our goal in this mini-review is to give an overview of these tools and highlight the current challenges (predicting dynamic metal-binding sites, determining functional metalation states, and designing intricate coordination networks) remaining in the predictive models of metal-binding sites. Addressing these challenges will not only deepen our knowledge of natural metalloproteins but also accelerate the development of artificial metalloproteins with novel and precisely engineered functionalities.
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http://dx.doi.org/10.1016/j.mocell.2025.100191 | DOI Listing |
Int J Biol Macromol
August 2025
Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Iran. Electronic address:
Metalloproteins, accounting for nearly half of all known proteins, are fundamental to biological processes and applications, including catalysis, electron transport and pharmaceutical engineering. Accurately predicting metal-binding sites is critical for elucidating molecular interactions and advancing innovations in the biotechnology and pharmaceutical industries. Traditional sequence- and structure-based prediction methods often struggle with the complexity and diversity of metalloprotein datasets.
View Article and Find Full Text PDFJ Inorg Biochem
December 2025
Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487-0336, USA. Electronic address:
Trivalent chromium has been shown to be transported in vivo from the bloodstream to the tissues via endocytosis by transferrin (Tf), the major iron transport protein in the blood. Recent in vitro studies using Cr(III)-Tf have shown that under physiologically relevant conditions, the binding of Cr(III) to Tf and the loss of Cr(III) from the Cr(III)-Tf/Tf receptor complex are rapid. However, the major form of transferrin in the bloodstream is monoferric Tf.
View Article and Find Full Text PDFChem Biol Interact
October 2025
University of Ljubljana, Faculty of Medicine, Institute of Biochemistry and Molecular Genetics, Vrazov trg 2, 1000, Ljubljana, Slovenia. Electronic address:
Paraoxonase 1 (PON1) is a metalloenzyme that requires calcium ions at both catalytic and structural binding sites to hydrolyze the substrates. The enzyme is efficiently inhibited by several metal ions, especially transition metals, which tend to bind non-specifically to oxygen, nitrogen, and sulfur ligands of amino acid residues on the PON1 surface. In contrast, several lanthanide ions can specifically replace isomorphous Ca ions from many protein binding sites, making them among the most potent metal inhibitors of PON1.
View Article and Find Full Text PDFIEEE Trans Comput Biol Bioinform
August 2025
This study presents an end-to-end deep learning framework for protein-to-metal-ion binding prediction, a critical task in understanding protein function, structural stability, and metal transport mechanisms. A binding site is a residue location in a protein sequence where a metal binds to a protein. Manual curation of metal binding sites is a tedious process involving mining through research articles, making it expensive, laborious, and time-consuming.
View Article and Find Full Text PDFWater Environ Res
August 2025
Department of Civil Engineering, Delhi Technological University, Delhi, India.
This study investigates the influence of pH and organic matter (OM) on the concentrations of potential toxic elements, that is, Fe, Mn, Cd, Cu, Cr, Ni, Pb, and Zn metals in the surface sediments of the Ganga River. The research explores the interaction between sediment properties and metal contamination in a 225-km stretch of the river in Uttar Pradesh, India, where industrial, agricultural, and domestic pollution contribute to heavy metal accumulation. Surface sediments act as reservoirs for these metals, influencing their mobility, bioavailability, and toxicity.
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