M-ZDOCK: a grid-based approach for Cn symmetric multimer docking

Pierce, Brian G.; Tong, Weiwei; Weng, Zhiping

doi:10.1093/bioinformatics/bti229

Cited by 161 publications

(135 citation statements)

References 35 publications

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“…Next, we constructed trimeric models for the missing segments in the P5 structure. First, the monomeric N-terminal homology model was trimerized (see Materials and Methods) (32). Second, the two linker regions not resolved in the x-ray maps, namely the collagen-like region and the eight-glycine stretch, were both modeled by using a collagen structure as a template (PDB ID code 1CLG) (33).…”

Section: Resultsmentioning

confidence: 99%

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Tale of two spikes in bacteriophage PRD1

Huiskonen

Manole

Butcher

2007

Proc. Natl. Acad. Sci. U.S.A.

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Structural comparisons between bacteriophage PRD1 and adenovirus have revealed an evolutionary relationship that has contributed significantly to current ideas on virus phylogeny. However, the structural organization of the receptor-binding spike complex and how the different symmetry mismatches are mediated between the spike-complex proteins are not clear. We determined the architecture of the PRD1 spike complex by using electron microscopy and three-dimensional image reconstruction of a series of PRD1 mutants. We constructed an atomic model for the fulllength P5 spike protein by using comparative modeling. P5 was shown to be bound directly to the penton base protein P31. P5 and the receptor-binding protein P2 form two separate spikes, interacting with each other near the capsid shell. P5, with a tumor necrosis factor-like head domain, may have been responsible for host recognition before capture of the current receptor-binding protein P2.electron cryomicroscopy ͉ symmetry mismatch ͉ vertex ͉ virus

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Section: Resultsmentioning

confidence: 99%

“…The modeling of the P5 N-terminal fragment was carried out by using SWISS-MODEL (39). A P5 N-terminal trimer was generated from the monomer model by using M-ZDOCK (32). First, the monomer-monomer interface within the trimer was predicted.…”

Section: Methodsmentioning

confidence: 99%

Tale of two spikes in bacteriophage PRD1

Huiskonen

Manole

Butcher

2007

Proc. Natl. Acad. Sci. U.S.A.

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“…4C). Existing grid-based methods are limited to symmetric oligomers with point symmetries (29)(30)(31). To accommodate helical symmetries, we therefore based our grid-search on a previously proposed approach for efficient modeling of symmetric oligomers from NMR data for any given fixed symmetry (32).…”

Section: Resultsmentioning

confidence: 99%

Structure determination of helical filaments by solid-state NMR spectroscopy

Bardiaux

Ahmed

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVS CARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers.solid-state NMR | protein structure | grid search | MAVS | innate immunity

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“…38 Existing docking-based approaches are not complete, because they generate possible docked structures by sampling, and might miss conformations close to the native structure. This is evident from our tests on phospholamban, when we used several available dockingbased methods [21][22][23] to predict the complex structure from the subunit structure. A significant number of the models provided by these approaches satisfy none of the experimental intersubunit NOE restraints determined by Oxenoid and Chou.…”

Section: Introductionmentioning

confidence: 93%

“…[17][18][19][20] Docking-based methods are immediately applicable to homo-oligomers, by docking two subunits of the homo-oligomer. Pierce and Weng, 21 Duhovny et al, 22 and Comeau and Camacho 23 have all used docking-based approaches, followed by filtering based on symmetry and scoring by minimizing energy functions, to predict structures of homo-oligomers.…”

Section: Introductionmentioning

confidence: 99%

Structure determination of symmetric homo‐oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing

et al. 2006

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Structural studies of symmetric homo-oligomers provide mechanistic insights into their roles in essential biological processes, including cell signaling and cellular regulation. This paper presents a novel algorithm for homo-oligomeric structure determination, given the subunit structure, that is both complete, in that it evaluates all possible conformations, and data-driven, in that it evaluates conformations separately for consistency with experimental data and for quality of packing. Completeness ensures that the algorithm does not miss the native conformation, and being data-driven enables it to assess the structural precision possible from data alone. Our algorithm performs a branch-and-bound search in the symmetry configuration space, the space of symmetry axis parameters (positions and orientations) defining all possible C n homo-oligomeric complexes for a given subunit structure. It eliminates those symmetry axes inconsistent with intersubunit nuclear Overhauser effect (NOE) distance restraints and then identifies conformations representing any consistent, well-packed structure to within a user-defined similarity level.For the human phospholamban pentamer in dodecylphosphocholine micelles, using the structure of one subunit determined from a subset of the experimental NMR data, our algorithm identifies a diverse set of complex structures consistent with the nine intersubunit NOE restraints. The distribution of determined structures provides an objective characterization of structural uncertainty: backbone RMSD to the previously determined structure ranges from 1.07 to 8.85 Å , and variance in backbone atomic coordinates is an average of 12.32 Å 2 . Incorporating vdW packing reduces structural diversity to a maximum backbone RMSD of 6.24 Å and an average backbone variance of 6.80 Å 2 . By comparing data consistency and packing quality under different assumptions of oligomeric number, our algorithm identifies the pentamer as the most likely oligomeric state of phospholamban, demonstrating that it is possible to determine the oligomeric number directly from NMR data. Additional tests on a number of homo-oligomers, from dimer to heptamer, similarly demonstrate the power of our method to provide unbiased determination and evaluation of homo-oligomeric complex structures.

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M-ZDOCK: a grid-based approach for Cn symmetric multimer docking

Abstract: http://zlab.bu.edu/m-zdock.

Cited by 161 publications

References 35 publications

Tale of two spikes in bacteriophage PRD1

Tale of two spikes in bacteriophage PRD1

Structure determination of helical filaments by solid-state NMR spectroscopy

Structure determination of symmetric homo‐oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing

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