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Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM.

ABSTRACT: Understanding how structure and function meet to drive biological processes is progressively shifting the cryoEM field towards a more advanced analysis of macromolecular flexibility. Thanks to techniques such as single-particle analysis and electron tomography, it is possible to image a macromolecule in different states, information that can subsequently be extracted through advanced image-processing methods to build a richer approximation of a conformational landscape. However, the interoperability of all of these algorithms remains a challenging task that is left to users, preventing them from defining a single flexible workflow in which conformational information can be addressed by different algorithms. Therefore, in this work, a new framework integrated into Scipion is proposed called the Flexibility Hub. This framework automatically handles intercommunication between different heterogeneity software, simplifying the task of combining the software into workflows in which the quality and the amount of information extracted from flexibility analysis is maximized.

SUBMITTER: Herreros D

PROVIDER: S-EPMC10306064 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature

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Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM.

Herreros D D Krieger J M JM Fonseca Y Y Conesa P P Harastani M M Vuillemot R R Hamitouche I I Serrano Gutiérrez R R Gragera M M Melero R R Jonic S S Carazo J M JM Sorzano C O S COS

Acta crystallographica. Section D, Structural biology 20230616 Pt 7

Understanding how structure and function meet to drive biological processes is progressively shifting the cryoEM field towards a more advanced analysis of macromolecular flexibility. Thanks to techniques such as single-particle analysis and electron tomography, it is possible to image a macromolecule in different states, information that can subsequently be extracted through advanced image-processing methods to build a richer approximation of a conformational landscape. However, the interoperabi ...[more]

PMID: 37326585

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Project description:A dinucleating macrocycle, H(2)PIM, containing phenoxylimine metal-binding units has been prepared. Reaction of H(2)PIM with [Fe(2)(Mes)(4)] (Mes = 2,4,6-trimethylphenyl) and sterically hindered carboxylic acids, Ph(3)CCO(2)H or Ar(Tol)CO(2)H (2,6-bis(p-tolyl)benzoic acid), afforded complexes [Fe(2)(PIM)(Ph(3)CCO(2))(2)] (1) and [Fe(2)(PIM)(Ar(Tol)CO(2))(2)] (2), respectively. X-ray diffraction studies revealed that these diiron(II) complexes closely mimic the active site structures of the hydroxylase components of bacterial multicomponent monooxygenases (BMMs), particularly the syn disposition of the nitrogen donor atoms and the bridging μ-η(1)η(2) and μ-η(1)η(1) modes of the carboxylate ligands at the diiron(II) centers. Cyclic voltammograms of 1 and 2 displayed quasi-reversible redox couples at +16 and +108 mV vs ferrocene/ferrocenium, respectively. Treatment of 2 with silver perchlorate afforded a silver(I)/iron(III) heterodimetallic complex, [Fe(2)(μ-OH)(2)(ClO(4))(2)(PIM)(Ar(Tol)CO(2))Ag] (3), which was structurally and spectroscopically characterized. Complexes 1 and 2 both react rapidly with dioxygen. Oxygenation of 1 afforded a (μ-hydroxo)diiron(III) complex [Fe(2)(μ-OH)(PIM)(Ph(3)CCO(2))(3)] (4), a hexa(μ-hydroxo)tetrairon(III) complex [Fe(4)(μ-OH)(6)(PIM)(2)(Ph(3)CCO(2))(2)] (5), and an unidentified iron(III) species. Oxygenation of 2 exclusively formed di(carboxylato)diiron(III) compounds, a testimony to the role of the macrocylic ligand in preserving the dinuclear iron center under oxidizing conditions. X-ray crystallographic and (57)Fe Mössbauer spectroscopic investigations indicated that 2 reacts with dioxygen to give a mixture of (μ-oxo)diiron(III) [Fe(2)(μ-O)(PIM)(Ar(Tol)CO(2))(2)] (6) and di(μ-hydroxo)diiron(III) [Fe(2)(μ-OH)(2)(PIM)(Ar(Tol)CO(2))(2)] (7) units in the same crystal lattice. Compounds 6 and 7 spontaneously convert to a tetrairon(III) complex, [Fe(4)(μ-OH)(6)(PIM)(2)(Ar(Tol)CO(2))(2)] (8), when treated with excess H(2)O.

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Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM.

Publications

Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM.

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