Structural heterogeneity in a parent ground-state structure of AnPixJg2 revealed by theory and spectroscopy

Abstract

We investigated the red absorbing, dark stable state (Pr state) of the second GAF domain of the cyanobacteriochrome AnPixJ (AnPixJg2) by a molecular dynamics simulation of 1 μs duration. Our results reveal two distinct conformational isoforms of the chromophore, from which only one was known from crystallographic experiments. The interconversion between both isoforms is accompanied by alterations in the hydrogen bond pattern between the chromophore and the protein and the solvation structure of the chromophore binding pocket. The existence of sub-states in the Pr form of AnPixJg2 is supported by the results from experimental C MAS NMR spectroscopy. Our finding is consistent with the observation of structural heterogeneity in other cyanobacteriochromes and phytochromes.

Correlating structural and photochemical heterogeneity in cyanobacteriochrome NpR6012g4

“…Within the calculated ensemble of structures for the dark state, we observe multiple configurations for Trp655 and Asp657, two residues known to play key roles in chromophorylation and spectral tuning (15). Structural heterogeneity of the equivalent Trp residue in AnPixJg2 has been reported in a simulation, but the crystal structure of the AnPixJg2 dark state only contains the Trpin conformation (34,49). We also observe a horizontal configuration for the Asp657 side chain that ablates hydrogen bonding to the chromophore B-and C-rings.…”

“…W 655 V and W 655 A variants both exhibited spectrally heterogeneous 15Z dark states containing both red-and orange-absorbing populations, but W 655 H NpR6012g4 failed to bind chromophore(15). The equivalent Trp289 adopted multiple conformations in a microsecond simulation of the AnPixJg2 dark state(49), so this C…”

The Effective Conjugation Length Is Responsible for the Red/Green Spectral Tuning in the Cyanobacteriochrome Slr1393g3

“…Spectroscopic studies have been reported for several members of the red/green subfamily, i.e. : AnPixJg2, [9,[13][14][15]17,18,23,24] NpR6012g4, [12,16,30,[20][21][22][25][26][27][28][29] and Slr1393g3. [31][32][33][34] However, computational studies of the spectral tuning in this CBCR family and other related bilinbinding photoreceptors are rare [35][36][37][38] although the hybrid quantum mechanics/molecular mechanics (QM/MM) methodology has provided valuable insight into the spectral tuning of other photoreceptor protein families with isomerizable double bonds.…”

“…[31][32][33][34] However, computational studies of the spectral tuning in this CBCR family and other related bilinbinding photoreceptors are rare [35][36][37][38] although the hybrid quantum mechanics/molecular mechanics (QM/MM) methodology has provided valuable insight into the spectral tuning of other photoreceptor protein families with isomerizable double bonds. [19,[39][40][41] The simulations performed so far for CBCRs are either classical molecular dynamics of the protein [15,24] or excited state quantum chemical calculations on isolated chromophores. [21,36,[42][43][44][45][46] A computational approach to describe the spectral properties of phytochromes and CBCRs was impaired not only by the size and flexibility of the chromophore but also by a lack of sufficiently resolved crystal structures.…”

Die effektive Konjugationslänge ist für die spektrale Verschiebung im rot/grün schaltenden Cyanobakteriochrom Slr1393g3 verantwortlich

“…Spektroskopische Studien wurden für mehrere Mitglieder der rot/grün Unterfamilie veröffentlicht: AnPixJg2, NpR6012g4, und Slr1393g3, allerdings sind computergestützte Berechnungen zur Lage der Absorptionsmaxima in dieser CBCR‐Familie und in anderen verwandten Bilin‐bindenden Photorezeptoren kaum vorhanden, obwohl die hybride quantenmechanische/molekularmechanische Methodik wertvolle Einblicke in die Farbabstimmung von anderen Photorezeptor‐Proteinfamilien mit isomerisierbaren Doppelbindungen geliefert hat . Die Simulationen, die bislang für CBCRs durchgeführt wurden, verwenden entweder klassische Molekulardynamik für das Protein oder quantenchemische Berechnungen der angeregten Zustände des isolierten Chromophors . Ein rechnergestützter Zugang zur Beschreibung der spektralen Eigenschaften von Phytochromen und CBCRs wurde bisher nicht nur durch die Größe und Flexibilität des Chromophors erschwert, sondern auch auf Grund mangelnder Kristallstrukturen in hinreichender Auflösung.…”