12 research outputs found
Structure and Conservation of <i>Pb</i>SPECT1Δ41.
No full text<p><b>a</b>. Ribbon representation of the four-helix bundle structure of <i>Pb</i>SPECT1Δ41 (4U5A), with individual α-helices in different colors. <b>b</b>. The structure of <i>Pb</i>SPECT1Δ41 viewed down the axis of the four-helix bundle. Coloring of individual α-helices is as in panel a. <b>c</b>. Structure-based sequence alignment of <i>Pb</i>SPECT1Δ41 (Genbank BAD08209.1, PlasmoDB PBANKA_135560) with <i>Plasmodium</i> homologs: <i>P. cynomolgi</i> (XP_004223591.1, PCYB_122110), <i>P. vivax</i> (PVX_083025), <i>P. knowlesi</i> (CAQ41197.1, PKH_121200), <i>P. inui</i> (EUD67722.1), <i>P. vinckei petteri</i> (EUD71736.1), <i>P. chabaudi chabaud</i> (PCHAS_136020), <i>P. yoelii</i> YM (PYYM_1357700), <i>P. falciparum</i> 3D7 (PF3D7_1342500), and <i>P. reichenowi</i> (CDO66209.1). Putative secretion signals were excluded. The secondary structure of <i>Pb</i>SPECT1Δ41 is shown above the sequence. Absolutely conserved residues are in white on a red background, and similar residues are in red; both types are in blue boxes.</p
Cover letter Rankings 1.0
No full texthttp://deepblue.lib.umich.edu/bitstream/2027.42/88574/1/1991_Coverletter_Rankings_1.0_5-13-91.pd
Coherent Oscillations in Chlorosome Elucidated by Two-Dimensional Electronic Spectroscopy
No full textChlorosomes are the most efficient photosynthetic light-harvesting complexes found in nature and consist of many bacteriochlorophyll (BChl) molecules self-assembled into supramolecular aggregates. Here we elucidate the presence and the origin of coherent oscillations in chlorosome at cryogenic temperature using 2D electronic spectroscopy. We observe coherent oscillations of multiple frequencies superimposed on the ultrafast amplitude decay of 2D spectra. Comparison of oscillatory features in the rephasing and nonrephasing 2D spectra suggests that an oscillation of 620 cm<sup>–1</sup> frequency arises from electronic coherence. However, this coherent oscillation can be enhanced by vibronic coupling with intermolecular vibrations of BChl aggregate, and thus it might originate from vibronic coherence rather than pure electronic coherence. Although the 620 cm<sup>–1</sup> oscillation dephases rapidly, the electronic (or vibronic) coherence may still take part in the initial step of energy transfer in chlorosome, which is comparably fast
Proton Transfer of Guanine Radical Cations Studied by Time-Resolved Resonance Raman Spectroscopy Combined with Pulse Radiolysis
No full textThe oxidation of guanine (G) is studied
by using transient absorption
and time-resolved resonance Raman spectroscopies combined with pulse
radiolysis. The transient absorption spectral change demonstrates
that the neutral radical of G (G<sup>•</sup>(−H<sup>+</sup>)), generated by the deprotonation of G radical cation (G<sup>•+</sup>), is rapidly converted to other G radical species.
The formation of this species shows the pH dependence, suggesting
that it is the G radical cation (G<sup>•+</sup>)′ formed
from the protonation at the N7 of G<sup>•</sup>(−H<sup>+</sup>). On one hand, most Raman bands of (G<sup>•+</sup>)′ are up-shifted relative to those of G, indicating the increase
in the bonding order of pyrimidine (Pyr) and imidazole rings. The
(G<sup>•+</sup>)′ exhibits the characteristic CO stretching
mode at ∼1266 cm<sup>–1</sup> corresponding to a C–O
single bond, indicating that the unpaired electron in (G<sup>•+</sup>)′ is localized on the oxygen of the Pyr ring
Conformational Substates of Myoglobin Intermediate Resolved by Picosecond X‑ray Solution Scattering
No full textConformational substates of proteins are generally considered to
play important roles in regulating protein functions, but an understanding
of how they influence the structural dynamics and functions of the
proteins has been elusive. Here, we investigate the structural dynamics
of sperm whale myoglobin associated with the conformational substates
using picosecond X-ray solution scattering. By applying kinetic analysis
considering all of the plausible candidate models, we establish a
kinetic model for the entire cycle of the protein transition in a
wide time range from 100 ps to 10 ms. Four structurally distinct intermediates
are formed during the cycle, and most importantly, the transition
from the first intermediate to the second one (<b>B</b> → <b>C</b>) occurs biphasically. We attribute the biphasic kinetics
to the involvement of two conformational substates of the first intermediate,
which are generated by the interplay between the distal histidine
and the photodissociated CO
Photocycle of Photoactive Yellow Protein in Cell-Mimetic Environments: Molecular Volume Changes and Kinetics
No full textUsing various spectroscopic
techniques such as UV–visible
spectroscopy, circular dichroism spectroscopy, NMR spectroscopy, small-angle
X-ray scattering, transient grating, and transient absorption techniques,
we investigated how cell-mimetic environments made by crowding influence
the photocycle of photoactive yellow protein (PYP) in terms of the
molecular volume change and kinetics. Upon addition of molecular crowding
agents, the ratio of the diffusion coefficient of the blue-shifted
intermediate (pB) to that of the ground species (pG) significantly
changes from 0.92 and approaches 1.0. This result indicates that the
molecular volume change accompanied by the photocycle of PYP in molecularly
crowded environments is much smaller than that which occurs in vitro
and that the pB intermediate under crowded environments favors a compact
conformation due to the excluded volume effect. The kinetics of the
photocycle of PYP in cell-mimetic environments is greatly decelerated
by the dehydration, owing to the interaction between the protein and
small crowding agents, but is barely affected by the excluded volume
effect. The results lead to the inference that the signaling transducer
of PYP may not necessarily utilize the conformational change of PYP
to sense the signaling state
Length and Charge of the Nterminus Regulate the Lifetime of the Signaling State of Photoactive Yellow Protein
No full textPhotoactive yellow protein (PYP) is one of the most extensively
studied photoreceptors. Nevertheless, the role of the N-terminus in
the photocycle and structural transitions is still elusive. Here,
we attached additional amino acids to the N-terminus of PYP and investigated
the effect of the length and charge of additional N-terminal residues
using circular dichroism, two-dimensional nuclear magnetic resonance
(2D-NMR), transient absorption (TA), and transient grating (TG) spectroscopic
techniques. TA experiments showed that, except for negatively charged
residues (5D-PYP), additional N-terminal residues of PYP generally
enable faster dark recovery from the putative signaling state (pB2) to the ground state (pG). TG data showed that although the
degree of structural changes can be controlled by adjusting specific
amino acid residues in the extended N-terminus of N-terminal extended
PYPs (NE-PYPs), the dark recovery times of wt-PYP and NE-PYPs, except
for 5D-PYP, are independent of the structural differences between
pG and pB2 states. These results demonstrate that the recovery
time and the degree of structural change can be regulated by controlling
the length and sequence of N-terminal residues of PYP. The findings
in this study emphasize the need for careful attention to the remaining
amino acid residues when designing recombinant proteins for genetic
engineering purposes
Protein Structural Dynamics of Photoactive Yellow Protein in Solution Revealed by Pump–Probe X-ray Solution Scattering
No full textPhotoreceptor proteins play crucial roles in receiving
light stimuli
that give rise to the responses required for biological function.
However, structural characterization of conformational transition
of the photoreceptors has been elusive in their native aqueous environment,
even for a prototype photoreceptor, photoactive yellow protein (PYP).
We employ pump–probe X-ray solution scattering to probe the
structural changes that occur during the photocycle of PYP in a wide
time range from 3.16 μs to 300 ms. By the analysis of both kinetics
and structures of the intermediates, the structural progression of
the protein in the solution phase is vividly visualized. We identify
four structurally distinct intermediates and their associated five
time constants and reconstructed the molecular shapes of the four
intermediates from time-independent, species-associated difference
scattering curves. The reconstructed structures of the intermediates
show the large conformational changes such as the protrusion of N-terminus,
which is restricted in the crystalline phase due to the crystal contact
and thus could not be clearly observed by X-ray crystallography. The
protrusion of the N-terminus and the protein volume gradually increase
with the progress of the photocycle and becomes maximal in the final
intermediate, which is proposed to be the signaling state. The data
not only reveal that a common kinetic mechanism is applicable to both
the crystalline and the solution phases, but also provide direct evidence
for how the sample environment influences structural dynamics and
the reaction rates of the PYP photocycle
Sterically Controlled Excited-State Intramolecular Proton Transfer Dynamics in Solution
No full textExcited-state intramolecular proton transfer (ESIPT)
is a fundamental
ultrafast photochemical process. Although it has been intensively
studied for the development of novel photonic devices such as organic
light-emitting diodes, the relation between ESIPT reaction and intramolecular
charge transfer (ICT) is still a subject of debate. Furthermore, the
effects of the molecular geometry and of the substituent on ESIPT
and ICT processes are still unclear. To address these issues, we synthesized
a set of four compounds designed to control the electron density distribution
of the proton-donating (PD) group and the steric hindrance between
the PD and the adjacent phenyl groups: three 2-(1-phenyl-1H-imidazo[4,5-f][1,10]phenanthrolin-2-yl)phenol
derivatives, PIPP-Xs (X = H, F, and OMe), and 2-(1-phenyl-1H-imidazo[4,5-f][1,10]phenanthrolin-2-yl)naphthalen-2-ol
(PIPN). We then investigated their ESIPT and ICT dynamics as well
as the related structural changes using femtosecond transient absorption
spectroscopy and theoretical calculations. Although the four compounds
commonly exhibit a dual emission originating from the excited enol
(E*) and keto (K*) tautomers, their emission properties, such as emission
maxima and lifetimes, are systematically modulated by substitution
at the para-position of the PD group. The experimental and time-dependent
density functional theory calculation results showed that the substitution
of an electron-withdrawing group at the para-position of the PD group
and the planarity between the PD and proton-accepting (PA) groups
play important roles in inducing an efficient ESIPT characterized
by increased emission of the K* tautomer. On the other hand, the photoexcitation
for PIPP-Xs induces the formation of cis-K*, which
is the most stable structure, whereas in PIPN the E* tautomer generated
by the photoexcitation is rapidly converted to two species, cis-K* and per-K* with time constants of
per-K* state of PIPN has a charge transfer characteristic, suggesting
intramolecular charge migration induced by the formation of per-K* state. This distinctive dynamics of PIPN is due to
its pretwisted structure between PD and PA groups. The results provided
in this study demonstrate that the molecular geometry plays an important
role in the ESIPT and ICT processes
