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Your search keyword '"Intermembrane space proteins"' showing total 3 results
Start Over Descriptor "Intermembrane space proteins" Topic mitochondria
3 results on '"Intermembrane space proteins"'

1. Predicting protein submitochondrial locations by incorporating the positional-specific physicochemical properties into Chou's general pseudo-amino acid compositions.

Author

Jiao YS and Du PF

Subjects
Amino Acid Sequence, Amino Acids chemistry, Animals, Chemical Phenomena, Computational Biology methods, Databases, Protein, Humans, Mitochondria chemistry, Mitochondria ultrastructure, Mitochondrial Membranes, Proteins chemistry, Mitochondria metabolism, Proteins metabolism, Proteomics methods
Abstract

Predicting protein submitochondrial locations has been studied for about ten years. A dozen of methods were developed in this regard. Although a mitochondrion has four submitochondrial compartments, all existing studies considered only three of them. The mitochondrial intermembrane space proteins were always excluded in these studies. However, there are over 50 mitochondrial intermembrane space proteins in the recent release of UniProt database. We think it is time to incorporate these proteins in predicting protein submitochondrial locations. We proposed the functional domain enrichment score, which can be used as an enhancement to our positional-specific physicochemical properties method. We constructed a high-quality working dataset from the UniProt database. This dataset contains proteins from all four submitochondrial locations. Proteins with multiple submitochondrial locations are also included. Our method achieved over 70% prediction accuracy for proteins with single location on this dataset. On the M3-317 benchmarking dataset, our method achieved comparable prediction performance to other state-of-the-art methods. Our results indicate that the intermembrane space proteins can be incorporated in predicting protein submitochondrial locations. By evaluating our method with the proteins that have multiple submitochondrial locations, we conclude that our method is capable of predicting multiple submitochondrial locations. This is the first report of ab initio methods that can identify intermembrane space proteins. This is also the first attempt to incorporate proteins with multiple submitochondrial locations. The benchmarking dataset can be obtained by emails to the corresponding author., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Published
2017
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2. MIA40 is an oxidoreductase that catalyzes oxidative protein folding in mitochondria

Author

Lucia Banci, Kostas Tokatlidis, Chiara Cefaro, Dionisia P. Sideris, Ivano Bertini, Nitsa Katrakili, Manuele Martinelli, Simone Ciofi-Baffoni, and Angelo Gallo

Subjects
Models, Molecular, Protein Folding, Protein Conformation, Mitochondrial intermembrane space, NMR STRUCTURE DETERMINATION, Molecular Sequence Data, education, Oxidative phosphorylation, Protein degradation, Mitochondrion, Biology, Thioredoxin fold, RELAY SYSTEM, Mitochondrial Membrane Transport Proteins, CYTOCHROME-C, Structural Biology, Oxidoreductase, Mitochondrial Precursor Protein Import Complex Proteins, IMPORT PATHWAY, Humans, Amino Acid Sequence, Nuclear Magnetic Resonance, Biomolecular, Molecular Biology, CHAPERONE, chemistry.chemical_classification, ERV1, Mitochondria, INTERMEMBRANE SPACE PROTEINS, DISULFIDE BOND FORMATION, RESPIRATORY-CHAIN, CHEMICAL-SHIFTS, Biochemistry, chemistry, Protein folding, Oxidation-Reduction, Sequence Alignment, Cysteine
Abstract

MIA40 has a key role in oxidative protein folding in the mitochondrial intermembrane space. We present the solution structure of human MIA40 and its mechanism as a catalyst of oxidative folding. MIA40 has a 66-residue folded domain made of an alpha-helical hairpin core stabilized by two structural disulfides and a rigid N-terminal lid, with a characteristic CPC motif that can donate its disulfide bond to substrates. The CPC active site is solvent-accessible and sits adjacent to a hydrophobic cleft. Its second cysteine (Cys55) is essential in vivo and is crucial for mixed disulfide formation with the substrate. The hydrophobic cleft functions as a substrate binding domain, and mutations of this domain are lethal in vivo and abrogate binding in vitro. MIA40 represents a thioredoxin-unrelated, minimal oxidoreductase, with a facile CPC redox active site that ensures its catalytic function in oxidative folding in mitochondria.

Published
2009
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3. Structural insight into the TRIAP1/PRELI-like domain family of mitochondrial phospholipid transfer complexes

Author

Stephen Matthews, James A. Garnett, Ernesto Yagüe, Thomas Langer, Heather Baldie, Peter Simpson, Xeni Miliara, Inmaculada Pérez-Dorado, Ferdos Abid Ali, Takashi Tatsuta, Medical Research Council (MRC), and Wellcome Trust

Subjects
CARDIOLIPIN, Biochemistry & Molecular Biology, Molecular Sequence Data, Mitochondrion, Biology, 0601 Biochemistry and Cell Biology, Crystallography, X-Ray, Endoplasmic Reticulum, Biochemistry, Protein Structure, Secondary, Mitochondrial Proteins, INTRAMITOCHONDRIAL TRANSPORT, chemistry.chemical_compound, Protein structure, Genetics, Cardiolipin, Humans, Amino Acid Sequence, Inner mitochondrial membrane, Molecular Biology, Phospholipids, Adaptor Proteins, Signal Transducing, PHOSPHATIDIC-ACID, Science & Technology, Binding Sites, IMPORT, Endoplasmic reticulum, Scientific Reports, Intracellular Signaling Peptides and Proteins, Membrane Proteins, Biological Transport, Cell Biology, Mitochondrial carrier, UPS1P, Cell biology, Mitochondria, Protein Structure, Tertiary, INTERMEMBRANE SPACE PROTEINS, chemistry, Membrane protein, Mitochondrial Membranes, Life Sciences & Biomedicine, Hydrophobic and Hydrophilic Interactions, Sequence Alignment, Function (biology), Developmental Biology, Molecular Chaperones
Abstract

The composition of the mitochondrial membrane is important for its architecture and proper function. Mitochondria depend on a tightly regulated supply of phospholipid via intra-mitochondrial synthesis and by direct import from the endoplasmic reticulum. The Ups1/PRELI-like family together with its mitochondrial chaperones (TRIAP1/Mdm35) represent a unique heterodimeric lipid transfer system that is evolutionary conserved from yeast to man. Work presented here provides new atomic resolution insight into the function of a human member of this system. Crystal structures of free TRIAP1 and the TRIAP1-SLMO1 complex reveal how the PRELI domain is chaperoned during import into the intermembrane mitochondrial space. The structural resemblance of PRELI-like domain of SLMO1 with that of mammalian phoshatidylinositol transfer proteins (PITPs) suggest that they share similar lipid transfer mechanisms, in which access to a buried phospholipid-binding cavity is regulated by conformationally adaptable loops. Synopsis The structures of TRIAP1 and its complex with SLMO1 reveal how the PRELI domain is chaperoned during mitochondrial import. Access to an internal phospholipid binding cavity is likely regulated by conformationally adaptable loops. Structures of TRIAP1 and the TRIAP1-SLMO1 complex were solved by X-ray crystallography. The PRELI-like domain of SLMO1 resembles that of mammalian phoshatidylinositol transfer proteins (PITPs). Mutagenesis experiments highlight the roles of an internal hydrophilic cavity and lipid exchange loops in phospholipid extraction. The structures of TRIAP1 and its complex with SLMO1 reveal how the PRELI domain is chaperoned during mitochondrial import. Access to an internal phospholipid binding cavity is likely regulated by conformationally adaptable loops.

Published
2015
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