Comparative analysis of membrane protein structure databases

Shimizu, Kentaro; Cao, Wei; Saad, Gull; Shoji, Michiru; Terada, Tohru

doi:10.1016/j.bbamem.2018.01.005

Cited by 38 publications

(39 citation statements)

References 39 publications

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“…Interactor Reference VDAC Tubulin, Desmin, Vimentin, plectin, hexokinase and creatine kinases, MtCK, ANT, cardiolipin [10,42,43] Acyl-dihydroxyacetone phosphate reductase Unclear [13] ADP/ATP carrier Previous suggested as dimer, and now convincedly proved as monomers [44] Phosphate carrier ATP synthase, mitochondrial peptidyl-prolyl cis-trans isomerase, NaStEP, Citrate synthase, isocitrate dehydrogenase and oxoglutarate dehydrogenase [25,[45][46][47] Pyruvate carrier Heterodimer [48,49] Tricarboxylate carrier Homodimer [50] Dicarboxylate carrier Homodimer [51] Oxoglutarate carrier Homodimer, BCL2 [52,53] Glutamate transporter Synaptic protein [54] Aspartate/glutamate carrier Homodimer [36,39,55] The association of mitochondrial transport proteins plays an important role in the movement of metabolites across the IMM. For example, although not a member of the MCF, the heteromeric complex of the mitochondrial pyruvate carrier (MPC) is strategically positioned at the intersection between glycolysis in the cytosol and OXPHOS in the mitochondria [48].…”

Section: Mitochondria Carriermentioning

confidence: 99%

On the Detection and Functional Significance of the Protein–Protein Interactions of Mitochondrial Transport Proteins

Zhang

Fernie

2020

Biomolecules

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Protein–protein assemblies are highly prevalent in all living cells. Considerable evidence has recently accumulated suggesting that particularly transient association/dissociation of proteins represent an important means of regulation of metabolism. This is true not only in the cytosol and organelle matrices, but also at membrane surfaces where, for example, receptor complexes, as well as those of key metabolic pathways, are common. Transporters also frequently come up in lists of interacting proteins, for example, binding proteins that catalyze the production of their substrates or that act as relays within signal transduction cascades. In this review, we provide an update of technologies that are used in the study of such interactions with mitochondrial transport proteins, highlighting the difficulties that arise in their use for membrane proteins and discussing our current understanding of the biological function of such interactions.

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Section: Mitochondria Carriermentioning

confidence: 99%

On the Detection and Functional Significance of the Protein–Protein Interactions of Mitochondrial Transport Proteins

Zhang

Fernie

2020

Biomolecules

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“…We avoid structural uncertainty by selecting only X-ray structures and by discarding entries with resolution >3.5 Å or polypeptide chains with large missing segments (>100 consecutive amino acids). While both the OPM and the PDBTM databases provide sets of embedded membrane proteins, the two databases are not entirely consistent with each other in coverage or annotation and each suffers from its specific drawbacks (Shimizu et al, 2018). Hence, we developed an automated procedure that takes both databases into consideration when building our dataset.…”

Section: A Uniform and Consistent Dataset Of Membrane Proteinsmentioning

confidence: 99%

“…We chose the OPM database (Lomize et al, 2012) as the primary source of information on which EncoMPASS is built for the following reasons: its entries are manually curated, which generally improves accuracy, the insertion of the membrane proteins in the model lipid bilayer is accurate (Shimizu et al, 2018), and it contains information on the transmembrane segments of each TM chain. Nevertheless, manual curation can, at times, produce errors, and thus, the corresponding structure is also downloaded from the PDB (Berman et al, 2000).…”

Section: Initial Structure Collectionmentioning

confidence: 99%

EncoMPASS: an Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry

Aleksandrova¹,

Sarti²,

Forrest³

2018

Preprint

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Highlights:-EncoMPASS relates and analyzes known structures of membrane proteins -Structure and sequence similarity is assessed through alignments and topology considerations, not clustering -Symmetry is detected based on CE-Symm and SymD using a multi-step procedure 2 SummaryProtein structure determination and prediction, active site detection, and protein sequence alignment techniques all exploit information about protein structure and structural relationships. For membrane proteins, however, there is no agreement among available online tools for highlighting and mapping such structural similarities. Moreover, no available resource provides a systematic overview of quaternary and internal symmetries, and their orientation with respect to the membrane, despite the fact that these properties can provide key insights into membrane protein function. To address these issues, we created the Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry (EncoMPASS), a database for relating integral membrane proteins of known structure from the points of view of sequence, structure, and symmetry. EncoMPASS is accessible at https://encompass.ninds.nih.gov and its contents can be easily downloaded. This allows the user not only to focus on specific systems, but also to study general properties of the structure and evolution of membrane proteins.3

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“…Obtaining high-quality crystals suitable for X-ray crystallography is still far from trivial. Solid-state NMR spectroscopy, and especially cryo-electron microscopy (cryo-EM), reaching near-atomic resolution, have become central tools to study membraneassociated protein complexes 5,6 . However, experimental conditions such as low expression profiles and/or high instability outside the native membrane still makes their structural characterization challenging 7 .…”

Section: Introductionmentioning

confidence: 99%

Integrative Modeling of Membrane-associated Protein Assemblies

Roel‐Touris

Jiménez‐García

Bonvin

2020

Preprint

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Historically, membrane protein systems have been considered as one of the most challenging systems to study with experimental structural biology techniques. Over the past years, increased number of experimental structures of membrane proteins have become available thanks in particular to advances in solid-state NMR spectroscopy and cryo-electron microscopy. This has opened the route to modeling the complexes that those membrane proteins form by methods such as docking. Most approaches developed to date are, however, not capable of incorporating the topological information provided by the membrane into the modeling process. Here, we present an integrative computational protocol for the modeling of membrane-associated protein assemblies, specifically complexes consisting of a membrane-embedded protein and a soluble partner. It combines efficient, artificial intelligence-based rigid-body docking by LightDock with a flexible final refinement with HADDOCK to remove potential clashes at the interface. We make use of an equilibrated coarse-grained lipid bilayer to represent the information encoded in the membrane in the form of artificial beads, which allows to target the docking towards the binding-competent regions. We demonstrate the performance of this membrane-driven protocol on eighteen membrane-associated complexes, whose interface lies between the membrane and either the cytosolic or periplasmic regions. In addition, we evaluate how different membrane definitions impact the performance of the docking protocol and provide a comparison, in terms of success rate, to another state-of-the-art docking software, ZDOCK. Finally, we discuss the quality of the generated models and propose possible future developments. Our membrane docking protocol should allow to shed light on the still rather dark fraction of the interactome consisting of membrane proteins.

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Comparative analysis of membrane protein structure databases

Cited by 38 publications

References 39 publications

On the Detection and Functional Significance of the Protein–Protein Interactions of Mitochondrial Transport Proteins

On the Detection and Functional Significance of the Protein–Protein Interactions of Mitochondrial Transport Proteins

EncoMPASS: an Encyclopedia of Membrane Proteins Analyzed by Structure and Symmetry

Integrative Modeling of Membrane-associated Protein Assemblies

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