Computational approaches forde novodesign and redesign of metal-binding sites on proteins.
Metal ions play pivotal roles in protein structure, function and stability. The functional and structural diversity of proteins in nature expanded with the incorporation of metal ions or clusters in proteins. Approximately one-third of these proteins in the databases contain metal ions. Many biological and chemical processes in nature involve metal ion-binding proteins, aka metalloproteins. Many cellular reactions that underpin life require metalloproteins. Most of the remarkable, complex chemical transformations are catalysed by metalloenzymes. Realization of the importance of metal-binding sites in a variety of cellular events led to the advancement of various computational methods for their prediction and characterization. Furthermore, as structural and functional knowledgebase about metalloproteins is expanding with advances in computational and experimental fields, the focus of the research is now shifting towardsde novodesign and redesign of metalloproteins to extend nature's own diversity beyond its limits. In this review, we will focus on the computational toolbox for prediction of metal ion-binding sites,de novometalloprotein design and redesign. We will also give examples of tailor-made artificial metalloproteins designed with the computational toolbox.
Department of Statistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul, Turkey.
Gunseli Bayram
GB
Akcapinar
Department of Statistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul, Turkey Ugur.Sezerman@acibadem.edu.tr.
Osman Ugur
OU
Sezerman
D020816:Amino Acid Motifs; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D008667:Metalloproteins / Q000737:chemistry*; D008670:Metals / Q000737:chemistry*; D008958:Models, Molecular; D015202:Protein Engineering / Q000379:methods*
D008667:Metalloproteins; D008670:Metals
artificial metalloproteins; computational protein design; computational protein re-design; de novo design; metal binding sites