Maximum-likelihood determination of anomalous substructures

Read, Randy J.; McCoy, Airlie J.

doi:10.1107/s2059798317013468

Cited by 4 publications

(2 citation statements)

References 36 publications

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“…In X-ray crystallography, structure determination of coiled-coil proteins has posed a long-standing challenge to the use of MR ( 22 , 43 , 59 ). MR is based on comparisons between the Patterson synthesis calculated from the model and the analogous synthesis generated from the diffraction data ( 43 ).…”

Section: Discussionmentioning

confidence: 99%

Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae

Hsieh

Smallwood

et al. 2023

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

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In many organs, small openings across capillary endothelial cells (ECs) allow the diffusion of low–molecular weight compounds and small proteins between the blood and tissue spaces. These openings contain a diaphragm composed of radially arranged fibers, and current evidence suggests that a single-span type II transmembrane protein, plasmalemma vesicle-associated protein-1 (PLVAP), constitutes these fibers. Here, we present the three-dimensional crystal structure of an 89-amino acid segment of the PLVAP extracellular domain (ECD) and show that it adopts a parallel dimeric alpha-helical coiled-coil configuration with five interchain disulfide bonds. The structure was solved using single-wavelength anomalous diffraction from sulfur-containing residues (sulfur SAD) to generate phase information. Biochemical and circular dichroism (CD) experiments show that a second PLVAP ECD segment also has a parallel dimeric alpha-helical configuration—presumably a coiled coil—held together with interchain disulfide bonds. Overall, ~2/3 of the ~390 amino acids within the PLVAP ECD adopt a helical configuration, as determined by CD. We also determined the sequence and epitope of MECA-32, an anti-PLVAP antibody. Taken together, these data lend strong support to the model of capillary diaphragms formulated by Tse and Stan in which approximately ten PLVAP dimers are arranged within each 60- to 80-nm-diameter opening like the spokes of a bicycle wheel. Passage of molecules through the wedge-shaped pores is presumably determined both by the length of PLVAP—i.e., the long dimension of the pore—and by the chemical properties of amino acid side chains and N-linked glycans on the solvent-accessible faces of PLVAP.

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Section: Discussionmentioning

confidence: 99%

Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae

Hsieh

Smallwood

et al. 2023

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

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“…CC 1/2 (ano) is independent of the standard deviation but requires unmerged data. Substructure location based on maximum-likelihood targets (Read & McCoy, 2018) does not require the data to be truncated because the maximum-likelihood function weights the data appropriately.…”

Section: Data Truncationmentioning

confidence: 99%

An introduction to experimental phasing of macromolecules illustrated bySHELX; new autotracing features

Usón

Sheldrick

2018

Acta Crystallogr D Struct Biol

176

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For the purpose of this article, experimental phasing is understood to mean the determination of macromolecular structures by exploiting small intensity differences of Friedel opposites and possibly of reflections measured at different wavelengths or for heavy-atom derivatives, without the use of specific structural models. TheSHELXprograms provide a robust and efficient route for routine structure solution by the SAD, MAD and related methods, but involve a number of simplifying assumptions that may limit their applicability in borderline cases. The substructure atoms (i.e.those with significant anomalous scattering) are first located by direct methods, and the experimental data are then used to estimate phase shifts that are added to the substructure phases to obtain starting phases for the native reflections. These are then improved by density modification and, if the resolution of the data and the type of structure permit, polyalanine tracing. A number of extensions to the tracing algorithm are discussed; these are designed to improve its performance at low resolution. Given native data to 2.5 Å resolution or better, a correlation coefficient greater than 25% between the structure factors calculated from such a trace and the native data is usually a good indication that the structure has been solved.

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IPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination

Ding¹,

Zhang²,

He³

et al. 2020

J Appl Crystallogr

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A new version (2.0) of the pipeline IPCAS (Iterative Protein Crystal structure Automatic Solution) has been released, in which the program OASIS performs direct-method single-wavelength anomalous diffraction/single isomorphous replacement phasing and direct-method-aided partial-structure extension. IPCAS incorporates the widely used packages CCP4 and PHENIX for locating heavy atoms, density modification, molecular replacement, model building and refinement. Important extensions to the previous version of IPCAS include a resolution screening method for non-crystallographic symmetry searching, an alternate model-building protocol for avoiding premature convergence and direct-method image processing for electron microscopy maps, including singleparticle cryo-EM maps. Moreover, a new graphical user interface is provided for controlling and real-time monitoring of the whole dual-space iterative process, which works as a plugin to CCP4i. Applications of the new IPCAS to difficult cases have yielded promising results, including 'direct-method phasing and fragment extension' from weak anomalous diffraction signal data and 'directmethod-aided partial-structure extension' from low-homology models.

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Maximum-likelihood determination of anomalous substructures

Cited by 4 publications

References 36 publications

Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae

Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae

An introduction to experimental phasing of macromolecules illustrated bySHELX; new autotracing features

IPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination

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