title: Cardiolipin Interactions with Proteins.
abstract: Cardiolipins (CL) represent unique phospholipids of bacteria and eukaryotic mitochondria with four acyl chains and two phosphate groups that have been implicated in numerous functions from energy metabolism to apoptosis. Many proteins are known to interact with CL, and several cocrystal structures of protein-CL complexes exist. In this work, we describe the collection of the first systematic and, to the best of our knowledge, the comprehensive gold standard data set of all known CL-binding proteins. There are 62 proteins in this data set, 21 of which have nonredundant crystal structures with bound CL molecules available. Using binding patch analysis of amino acid frequencies, secondary structures and loop supersecondary structures considering phosphate and acyl chain binding regions together and separately, we gained a detailed understanding of the general structural and dynamic features involved in CL binding to proteins. Exhaustive docking of CL to all known structures of proteins experimentally shown to interact with CL demonstrated the validity of the docking approach, and provides a rich source of information for experimentalists who may wish to validate predictions.
authors: Division of Metabolic and Vascular Health, Medical School, University of Warwick, Coventry, United Kingdom.
authors: Joan
authors: J
authors: Planas-Iglesias
authors: Division of Metabolic and Vascular Health, Medical School, University of Warwick, Coventry, United Kingdom.
authors: Himal
authors: H
authors: Dwarakanath
authors: Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania.
authors: Dariush
authors: D
authors: Mohammadyani
authors: Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania.
authors: Naveena
authors: N
authors: Yanamala
authors: Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania.
authors: Valerian E
authors: VE
authors: Kagan
authors: Division of Metabolic and Vascular Health, Medical School, University of Warwick, Coventry, United Kingdom; Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania. Electronic address: j.klein-seetharaman@warwick.ac.uk.
authors: Judith
authors: J
authors: Klein-Seetharaman
mesh_terms: D001665:Binding Sites; D002308:Cardiolipins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D062126:Databases, Chemical; D057927:Hydrophobic and Hydrophilic Interactions; D062105:Molecular Docking Simulation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*
chemical_list: D002308:Cardiolipins; D011506:Proteins