3 research outputs found
Microsecond Deprotonation of Aspartic Acid and Response of the α/β Subdomain Precede C‑Terminal Signaling in the Blue Light Sensor Plant Cryptochrome
Plant cryptochromes are photosensory
receptors that regulate various
central aspects of plant growth and development. These receptors consist
of a photolyase homology region (PHR) carrying the oxidized flavin
adenine dinucleotide (FAD) cofactor, and a cryptochrome C-terminal
extension (CCT), which is essential for signaling. Absorption of blue/UVA
light leads to formation of the FAD neutral radical as the likely
signaling state, and ultimately activates the CCT. Little is known
about the signal transfer from the flavin to the CCT. Here, we investigated
the photoreaction of the PHR by time-resolved step-scan FT-IR spectroscopy
complemented by UV–vis spectroscopy. The first spectrum at
500 ns shows major contributions from the FAD anion radical, which
is demonstrated to then be protonated by aspartic acid 396 to the
neutral radical within 3.5 μs. The analysis revealed the existence
of three intermediates characterized by changes in secondary structure.
A marked loss of β-sheet structure is observed in the second
intermediate evolving with a time constant of 500 μs. This change
is accompanied by a conversion of a tyrosine residue, which is identified
as the formation of a tyrosine radical in the UV–vis. The only
β-sheet in the PHR is located within the α/β subdomain,
∼25 Å away from the flavin. This subdomain has been previously
attributed a role as a putative antenna binding site, but is now suggested
to have evolved to a component in the signaling of plant cryptochromes
by mediating the interaction with the CCT
Response of the Sensory Animal-like Cryptochrome aCRY to Blue and Red Light As Revealed by Infrared Difference Spectroscopy
Cryptochromes act as blue light sensors
in plants, insects, fungi,
and bacteria. Recently, an animal-like cryptochrome (aCRY) was identified
in the green alga <i>Chlamydomonas reinhardtii</i> by which
gene expression is altered in response to not only blue light but
also yellow and red light. This unique response of a flavoprotein <i>in vivo</i> has been attributed to the fact that the neutral
radical of the flavin chromophore acts as dark form of the sensor,
which absorbs in almost the entire visible spectral range (<680
nm). Here, we investigated light-induced processes in the protein
moiety of full-length aCRY by UV–vis and Fourier transform
infrared spectroscopy. Findings are compared to published results
on the homologous (6-4) photolyases, DNA repair enzymes. The oxidized
state of aCRY is converted to the neutral radical by blue light. The
recovery is strongly dependent on pH and might be catalyzed by a conserved
histidine of the (6-4)/clock cluster. The decay is independent of
oxygen concentration in contrast to that of other cryptochromes and
(6-4) photolyases. This blue light reaction of the oxidized flavin
is not accompanied by any detectable changes in secondary structure,
in agreement with a role <i>in vivo</i> of an unphysiological
preactivation. In contrast, the conversion by red light of the neutral
radical to the anionic fully reduced state proceeds with conformational
changes in turn elements, which most probably constitute a part of
the signaling process. These changes have not been detected in the
corresponding transition of (6-4) photolyase, which points to a decisive
difference between the sensor and the enzyme
Improved Precursor Characterization for Data-Dependent Mass Spectrometry
Modern
ion trap mass spectrometers are capable of collecting up
to 60 tandem MS (MS/MS) scans per second, in theory providing acquisition
speeds that can sample every eluting peptide precursor presented to
the MS system. In practice, however, the precursor sampling capacity
enabled by these ultrafast acquisition rates is often underutilized
due to a host of reasons (e.g., long injection times and wide analyzer
mass ranges). One often overlooked reason for this underutilization
is that the instrument exhausts all the peptide features it identifies
as suitable for MS/MS fragmentation. Highly abundant features can
prevent annotation of lower abundance precursor ions that occupy similar
mass-to-charge (<i>m</i>/<i>z</i>) space, which
ultimately inhibits the acquisition of an MS/MS event. Here, we present
an advanced peak determination (APD) algorithm that uses an iterative
approach to annotate densely populated <i>m</i>/<i>z</i> regions to increase the number of peptides sampled during
data-dependent LC-MS/MS analyses. The APD algorithm enables nearly
full utilization of the sampling capacity of a quadrupole-Orbitrap-linear
ion trap MS system, which yields up to a 40% increase in unique peptide
identifications from whole cell HeLa lysates (approximately 53 000
in a 90 min LC-MS/MS analysis). The APD algorithm maintains improved
peptide and protein identifications across several modes of proteomic
data acquisition, including varying gradient lengths, different degrees
of prefractionation, peptides derived from multiple proteases, and
phosphoproteomic analyses. Additionally, the use of APD increases
the number of peptides characterized per protein, providing improved
protein quantification. In all, the APD algorithm increases the number
of detectable peptide features, which maximizes utilization of the
high MS/MS capacities and significantly improves sampling depth and
identifications in proteomic experiments