Indian proteomics efforts and human proteome project

Sirdeshmukh, Ravi

doi:10.1016/j.jprot.2015.03.018

Cited by 5 publications

(2 citation statements)

References 8 publications

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“…However, experimental conditions such as low-expression profiles and/or high instability outside the native membrane still makes their structural characterization challenging 7 . Despite their large representation in the proteome (in human, nearly a quarter of the genome encodes for MPs 8 ), roughly only 1% of all deposited protein structures in the Protein Data Bank 9 (PDB) corresponds to MPs, with 1099 unique protein entries as of July 2020: https://blanco.biomol.uci.edu/mpstruc/ . Even less of those have been experimentally solved in complex with their counterpart(s).…”

Section: Introductionmentioning

confidence: 99%

Integrative modeling of membrane-associated protein assemblies

2020

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Membrane proteins are among the most challenging systems to study with experimental structural biology techniques. The increased number of deposited structures of membrane proteins has opened the route to modeling their complexes by methods such as docking. Here, we present an integrative computational protocol for the modeling of membrane-associated protein assemblies. The information encoded by the membrane is represented by artificial beads, which allow targeting of the docking toward the binding-competent regions. 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 demonstrate the performance of this protocol on eighteen membrane-associated complexes, whose interface lies between the membrane and either the cytosolic or periplasmic regions. In addition, we provide a comparison to another state-of-the-art docking software, ZDOCK. This protocol should shed light on the still dark fraction of the interactome consisting of membrane proteins.

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Section: Introductionmentioning

confidence: 99%

Integrative modeling of membrane-associated protein assemblies

2020

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“…However, experimental conditions such as low expression profiles and/or high instability outside the native membrane still makes their structural characterization challenging 7 . Despite their large representation in the proteome (in human, nearly a quarter of the genome encodes for MPs 8 ), roughly only 1% of all deposited protein structures in the Protein Data Bank 9 11 . Some rely on secondary structure or topology prediction and make use of either knowledge-based statistics or evolutionary information to generate 3D models 12,13 .…”

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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Gold nanomaterials and their potential use as cryo-electron tomography labels

Beales

Medalia

2022

Journal of Structural Biology

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Indian proteomics efforts and human proteome project

Cited by 5 publications

References 8 publications

Integrative modeling of membrane-associated protein assemblies

Integrative modeling of membrane-associated protein assemblies

Integrative Modeling of Membrane-associated Protein Assemblies

Gold nanomaterials and their potential use as cryo-electron tomography labels

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