The effective conjugation length is responsible for the red/green spectral tuning in the cyanobacteriochrome Slr1393g3

C Wiebeler, AG Rao, W Gaertner… - Angewandte Chemie …, 2019 - Wiley Online Library
The origin of the spectral shift from a red‐to a green‐absorbing form in a
cyanobacteriochrome, Slr1393g3, was identified by combined quantum …

Reversible disassembly-reassembly of C-phycocyanin in pressurization-depressurization cycles of high hydrostatic pressure

Y Li, Q Li, RE Gillilan, A Abbaspourrad - International Journal of Biological …, 2023 - Elsevier
Hydrostatic pressure can reversibly modulate protein-protein and protein-chromophore
interactions of C-phycocyanin (C-PC) from Spirulina platensis. Small-angle X-ray scattering …

Computational challenges in modeling of representative bioimaging proteins: GFP-like proteins, flavoproteins, and phytochromes

AV Nemukhin, BL Grigorenko… - The Journal of …, 2019 - ACS Publications
Remarkable success in engineering novel efficient biomarkers based on fluorescent and
photoactive proteins provokes a question of whether computational modeling of their …

Real-time tracking of phytochrome's orientational changes during Pr photoisomerization

Y Yang, M Linke, T Von Haimberger… - Journal of the …, 2012 - ACS Publications
Photoisomerization of a protein bound chromophore is the basis of the light sensing and
signaling responses of many photoreceptors. Z-to-E photoisomerization of the Pr Cph1Δ2 …

Protonation of the biliverdin IXα chromophore in the red and far-red photoactive states of a bacteriophytochrome

V Modi, S Donnini, G Groenhof… - The Journal of Physical …, 2019 - ACS Publications
The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from
Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this …

QM/MM benchmarking of cyanobacteriochrome Slr1393g3 absorption spectra

C Wiebeler, I Schapiro - Molecules, 2019 - mdpi.com
Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that are
promising candidates for biotechnological applications. Computational studies can …

Intrinsic structure and electronic spectrum of deprotonated biliverdin: cryogenic ion spectroscopy and ion mobility

W Zagorec-Marks, LG Dodson, P Weis… - Journal of the …, 2021 - ACS Publications
We investigated the structural and spectroscopic properties of singly deprotonated biliverdin
anions in vacuo, using a combination of cryogenic ion spectroscopy, ion mobility …

The structural changes in the signaling mechanism of bacteriophytochromes in solution revealed by a multiscale computational investigation

V Macaluso, G Salvadori, L Cupellini, B Mennucci - Chemical Science, 2021 - pubs.rsc.org
Phytochromes are red-light sensing proteins, with important light-regulatory roles in different
organisms, which are capturing an increasing interest in bioimaging and optogenetics. Upon …

Elucidating the role of structural fluctuations, and intermolecular and vibronic interactions in the spectroscopic response of a bacteriophytochrome

V Macaluso, L Cupellini, G Salvadori… - Physical Chemistry …, 2020 - pubs.rsc.org
We present the first comprehensive multiscale computational investigation of Resonance
Raman, absorption and Circular Dichroism spectra of the resting state of the Deinococcus …

Structural determinants of improved fluorescence in a family of bacteriophytochrome-based infrared fluorescent proteins: insights from continuum electrostatic …

M Feliks, C Lafaye, X Shu, A Royant, M Field - Biochemistry, 2016 - ACS Publications
Using X-ray crystallography, continuum electrostatic calculations, and molecular dynamics
simulations, we have studied the structure, protonation behavior, and dynamics of the …