Concentration-based self-assembly of phycocyanin

Eisenberg, Ido; Harris, Daniel K.; Levi‐Kalisman, Yael; Yochelis, Shira; Shemesh, Asaf; Ben‐Nissan, Gili; Sharon, Michal; Raviv, Uri; Adir, Noam; Keren, Nir; Paltiel, Yossi

doi:10.1007/s11120-017-0406-7

Cited by 22 publications

(20 citation statements)

References 37 publications

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“…Recently, we have used D+ to analyze solution X-ray scattering data (Eisenberg et al, 2017;Asor et al, 2017;Ginsburg et al, 2017;Chung et al, 2017). In particular, we have analyzed solutions of SJW1660 flagellar filaments (Louzon et al, 2017).…”

Section: Resultsmentioning

confidence: 99%

D+: Software for High-Resolution Hierarchical Modeling of Solution X-Ray Scattering from Complex Structures

Ginsburg¹,

Ben-Nun²,

Asor³

et al. 2018

Preprint

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<div>In this paper, we present our new computer program, D+, which uses the reciprocal-grid (RG) algorithm to efficiently compute X-ray scattering curves from solutions of complex structures at high-resolution. Structures are defined in hierarchical trees in which subunits can be represented by geometric or atomic models. Repeating subunits can be docked into their assembly symmetries, describing their locations and orientations in space. The scattering amplitude of the entire structure can be calculated by computing the amplitudes of the basic subunits on 3D reciprocal-space grids, moving up in the hierarchy, calculating the RGs of the larger structures, and by repeating this process for all the leaves and nodes of the tree. For very large structures, a Hybrid method can be used to avoid numerical artifacts. In the Hybrid method, only grids of smaller subunits are summed and used as subunits in a direct computation of the scattering amplitude. D+ can accurately analyze both small- and wide-angle solution X-ray scattering data. We present how D+ applies the RG algorithm, accounts for rotations and translations of subunits, processes atomic models, accounts for the contribution of the solvent as well as the solvation layer of complex structures in a scalable manner, writes and accesses RGs, interpolates between grid points, computes numerical integrals, enables the use of scripts to define complicated structures, applies fitting algorithms, accounts for several coexisting uncorrelated populations, and accelerates computations using GPUs. D+ may also account for different X-ray energies to analyze anomalous solution X-ray scattering data. An accessory tool that can identify repeating subunits in a protein data bank (PDB) file of a complex structure is provided. The tool can compute the orientation and translation of repeating subunits needed for exploiting the advantages of the RG algorithm in D+. In addition, a python wrapper is also available, enabling more advanced computations and integration of D+ with other computational tools. Finally, we present a large number of tests and compare the results of D+ with other programs when possible and demonstrate the use of D+ to analyze solution scattering data from dynamic microtubule structures with different protofilament number. D+ and its source code are freely available (https://scholars.huji.ac.il/uriraviv/software/d-software) for academic users and developers. </div>

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Section: Resultsmentioning

confidence: 99%

D+: Software for High-Resolution Hierarchical Modeling of Solution X-Ray Scattering from Complex Structures

Ginsburg¹,

Ben-Nun²,

Asor³

et al. 2018

Preprint

Self Cite

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show abstract

“…More details are provided in the User's Manual (https://scholars.huji.ac.il/uriraviv/book/ users-manual). Eisenberg et al, 2017;Shemesh et al, 2018). To further validate and demonstrate the use of D+, we measured and analyzed the scattering curve from lysozyme and microtubule (MT) structures in solution.…”

Section: Program Modules and Workflowmentioning

confidence: 99%

“…Recently, we have used D+ to analyze various solution X-ray scattering data (Eisenberg et al, 2017;Asor et al, 2017Asor et al, , 2019Ginsburg et al, 2017;Chung et al, 2017;Shemesh et al, 2018). In particular, we have analyzed solutions of SJW1660 flagellar filaments (Louzon et al, 2017).…”

Section: Figurementioning

confidence: 99%

D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures

et al. 2019

Self Cite

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This paper presents the computer program D+ (https://scholars.huji.ac.il/ uriraviv/book/d-0), where the reciprocal-grid (RG) algorithm is implemented. D+ efficiently computes, at high-resolution, the X-ray scattering curves from complex structures that are isotropically distributed in random orientations in solution. Structures are defined in hierarchical trees in which subunits can be represented by geometric or atomic models. Repeating subunits can be docked into their assembly symmetries, describing their locations and orientations in space. The scattering amplitude of the entire structure can be calculated by computing the amplitudes of the basic subunits on 3D reciprocal-space grids, moving up in the hierarchy, calculating the RGs of the larger structures, and repeating this process for all the leaves and nodes of the tree. For very large structures (containing over 100 protein subunits), a hybrid method can be used to avoid numerical artifacts. In the hybrid method, only grids of smaller subunits are summed and used as subunits in a direct computation of the scattering amplitude. D+ can accurately analyze both small-and wide-angle solution X-ray scattering data. This article describes how D+ applies the RG algorithm, accounts for rotations and translations of subunits, processes atomic models, accounts for the contribution of the solvent as well as the solvation layer of complex structures in a scalable manner, writes and accesses RGs, interpolates between grid points, computes numerical integrals, enables the use of scripts to define complicated structures, applies fitting algorithms, accounts for several coexisting uncorrelated populations, and accelerates computations using GPUs. D+ may also account for different X-ray energies to analyze anomalous solution X-ray scattering data. An accessory tool that can identify repeating subunits in a Protein Data Bank file of a complex structure is provided. The tool can compute the orientation and translation of repeating subunits needed for exploiting the advantages of the RG algorithm in D+. A Python wrapper (https://scholars. huji.ac.il/uriraviv/book/python-api) is also available, enabling more advanced computations and integration of D+ with other computational tools. Finally, a large number of tests are presented. The results of D+ are compared with those of other programs when possible, and the use of D+ to analyze solution scattering data from dynamic microtubule structures with different protofilament number is demonstrated. D+ and its source code are freely available for academic users and developers (https://bitbucket.org/uriraviv/public-dplus/src/ master/).

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“…Additionally, with the introduction of the Orbitrap mass analyzer with extended mass range, very high mass resolution on proteins and protein complexes can now be achieved enabling even small post‐translational modifications, such as glycosylation and phosphorylation , to be uniquely resolved on proteins up to 150 kDa in size. Moreover, specific to photosynthetic complexes, native MS has recently offered new structural insights into the pigment‐protein complex, FMO and the phycobiliprotein, phycocyanin from Thermosynechococcus vulcanus .…”

Section: Introductionmentioning

confidence: 99%

Connecting color with assembly in the fluorescent B‐phycoerythrin protein complex

2017

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Phycoerythrin is the major light-harvesting pigment protein in red algae and is nowadays widely used as a fluorescent probe in biotechnological applications such as flow cytometry and immunofluorescence microscopy. In addition, it has had substantial economic impact due to its potential as a natural food colorant. However, knowledge on the precise molecular composition of phycoerythrin is limited. Here, we use a combination of high-resolution native mass spectrometry (MS) and fluorescence spectroscopy to characterize the assembly properties of the B-phycoerythrin protein complex from Porphyridium cruentum. Our data highlight the stabilizing role of the c subunit in the intact B-phycoerythrin protein complex. In addition, by native MS we monitor B-phycoerythrin (dis)assembly intermediates, providing insight into which species contribute to B-phycoerythrins color and the factors that give B-phycoerythrin its highly fluorescent properties. Together, the data provide significant insights into the structural properties of B-phycoerythrin which is beneficial for its use within the biotechnology industry.

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Concentration-based self-assembly of phycocyanin

Cited by 22 publications

References 37 publications

D+: Software for High-Resolution Hierarchical Modeling of Solution X-Ray Scattering from Complex Structures

D+: Software for High-Resolution Hierarchical Modeling of Solution X-Ray Scattering from Complex Structures

D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures

Connecting color with assembly in the fluorescent B‐phycoerythrin protein complex

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