scholarly journals Protein Structural Dynamics of Wild-Type and Mutant Homodimeric Hemoglobin Studied by Time-Resolved X-Ray Solution Scattering

2018 ◽  
Vol 19 (11) ◽  
pp. 3633 ◽  
Author(s):  
Cheolhee Yang ◽  
Minseo Choi ◽  
Jong Kim ◽  
Hanui Kim ◽  
Srinivasan Muniyappan ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Conformational Changes ◽  
Structural Transition ◽  
Quaternary Structure ◽  
Heme Binding ◽  
Wild Type ◽  
Time Resolved ◽  
X Ray ◽  
Protein Structural Dynamics ◽  
Cooperative Transition

The quaternary transition between the relaxed (R) and tense (T) states of heme-binding proteins is a textbook example for the allosteric structural transition. Homodimeric hemoglobin (HbI) from Scapharca inaequivalvis is a useful model system for investigating the allosteric behavior because of the relatively simple quaternary structure. To understand the cooperative transition of HbI, wild-type and mutants of HbI have been studied by using time-resolved X-ray solution scattering (TRXSS), which is sensitive to the conformational changes. Herein, we review the structural dynamics of HbI investigated by TRXSS and compare the results of TRXSS with those of other techniques.

scholarly journals Cooperative protein structural dynamics of homodimeric hemoglobin linked to water cluster at subunit interface revealed by time-resolved X-ray solution scattering

2016 ◽  
Vol 3 (2) ◽  
pp. 023610 ◽  
Author(s):  
Jong Goo Kim ◽  
Srinivasan Muniyappan ◽  
Key Young Oang ◽  
Tae Wu Kim ◽  
Cheolhee Yang ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Water Cluster ◽  
Time Resolved ◽  
X Ray ◽  
Subunit Interface ◽  
Protein Structural Dynamics

scholarly journals Protein Structural Dynamics Revealed by Time-Resolved X-ray Solution Scattering

2015 ◽  
Vol 48 (8) ◽  
pp. 2200-2208 ◽  
Author(s):  
Jong Goo Kim ◽  
Tae Wu Kim ◽  
Jeongho Kim ◽  
Hyotcherl Ihee
Keyword(s):  
Structural Dynamics ◽  
Time Resolved ◽  
X Ray ◽  
Protein Structural Dynamics

scholarly journals Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix

2020 ◽  
Author(s):  
James N. Iuliano ◽  
Jinnette Tolentino Collado ◽  
Agnieszka A. Gil ◽  
Pavithran T. Ravindran ◽  
Andras Lukacs ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Conformational Changes ◽  
Interdisciplinary Approach ◽  
Site Directed Mutagenesis ◽  
Side Chain ◽  
Lov Domain ◽  
Time Resolved ◽  
Protein Structural Dynamics ◽  
Dynamics Simulations ◽  
Time Resolved Infrared Spectroscopy

AbstractLight-activated protein domains provide a convenient, modular, and genetically encodable sensor for optogenetics and optobiology. Although these domains have now been deployed in numerous systems, the precise mechanism of photoactivation and the accompanying structural dynamics that modulate output domain activity remain to be fully elucidated. In the C-terminal light, oxygen, voltage (LOV) domain of plant phototropins (LOV2), blue light activation leads to formation of an adduct between a conserved Cys residue and the embedded FMN chromophore, rotation of a conserved Gln (Q513), and unfolding of a helix (Jα-helix) which is coupled to the output partner. In the present work, we focus on the allosteric pathways leading to Jα helix unfolding in Avena sativa LOV2 (AsLOV2) using an interdisciplinary approach involving molecular dynamics simulations extending to 7 μs, time-resolved infrared spectroscopy, solution NMR spectroscopy, and in-cell optogenetic experiments. In the dark state, the side chain of N414 is hydrogen bonded to the backbone N-H of Q513. The simulations predict a lever-like motion of Q513 after Cys adduct formation resulting in loss of the interaction between the side chain of N414 and the backbone C=O of Q513, and formation of a transient hydrogen bond between the Q513 and N414 side chains. The central role of N414 in signal transduction was evaluated by site-directed mutagenesis supporting a direct link between Jα helix unfolding dynamics and the cellular function of the Zdk2-AsLOV2 optogenetic construct. Through this multifaceted approach, we show that Q513 and N414 are critical mediators of protein structural dynamics, linking the ultrafast (sub-ps) excitation of the FMN chromophore to the microsecond conformational changes that result in photoreceptor activation and biological function.

scholarly journals Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering

2010 ◽  
Vol 107 (16) ◽  
pp. 7281-7286 ◽  
Author(s):  
H. S. Cho ◽  
N. Dashdorj ◽  
F. Schotte ◽  
T. Graber ◽  
R. Henning ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Protein Structural Dynamics ◽  
Ray Scattering

scholarly journals Opportunities and challenges for time-resolved studies of protein structural dynamics at X-ray free-electron lasers

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130318 ◽  
Author(s):  
Richard Neutze
Keyword(s):  
Structural Dynamics ◽  
Free Electron ◽  
Free Electron Lasers ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Protein Structural Dynamics ◽  
Structural Biochemistry ◽  
Scientific Questions ◽  
Serial Femtosecond Crystallography

X-ray free-electron lasers (XFELs) are revolutionary X-ray sources. Their time structure, providing X-ray pulses of a few tens of femtoseconds in duration; and their extreme peak brilliance, delivering approximately 10 12 X-ray photons per pulse and facilitating sub-micrometre focusing, distinguish XFEL sources from synchrotron radiation. In this opinion piece, I argue that these properties of XFEL radiation will facilitate new discoveries in life science. I reason that time-resolved serial femtosecond crystallography and time-resolved wide angle X-ray scattering are promising areas of scientific investigation that will be advanced by XFEL capabilities, allowing new scientific questions to be addressed that are not accessible using established methods at storage ring facilities. These questions include visualizing ultrafast protein structural dynamics on the femtosecond to picosecond time-scale, as well as time-resolved diffraction studies of non-cyclic reactions. I argue that these emerging opportunities will stimulate a renaissance of interest in time-resolved structural biochemistry.

The kinetics of conformational changes of α2 -macroglobulin determined by time resolved X-ray solution scattering

FEBS Letters ◽  
1994 ◽  
Vol 337 (2) ◽  
pp. 171-174 ◽  
Author(s):  
Hideo Arakawa ◽  
Takuji Urisaka ◽  
Hirotsugu Tsuruta ◽  
Yoshiyuki Amemiya ◽  
Hiroshi Kihara ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Time Resolved ◽  
X Ray ◽  
Α2 Macroglobulin ◽  
Kinetics Of

scholarly journals Predicting data quality in biological X-ray solution scattering

2018 ◽  
Vol 74 (8) ◽  
pp. 727-738
Author(s):  
Chenzheng Wang ◽  
Yuexia Lin ◽  
Devin Bougie ◽  
Richard E. Gillilan
Keyword(s):  
Conformational Changes ◽  
Sample Path ◽  
Flow Time ◽  
Photon Flux ◽  
Detector Efficiency ◽  
Time Resolved ◽  
Short Sample ◽  
X Ray ◽  
Path Lengths ◽  
Flux Energy

Biological small-angle X-ray solution scattering (BioSAXS) is now widely used to gain information on biomolecules in the solution state. Often, however, it is not obvious in advance whether a particular sample will scatter strongly enough to give useful data to draw conclusions under practically achievable solution conditions. Conformational changes that appear to be large may not always produce scattering curves that are distinguishable from each other at realistic concentrations and exposure times. Emerging technologies such as time-resolved SAXS (TR-SAXS) pose additional challenges owing to small beams and short sample path lengths. Beamline optics vary in brilliance and degree of background scatter, and major upgrades and improvements to sources promise to expand the reach of these methods. Computations are developed to estimate BioSAXS sample intensity at a more detailed level than previous approaches, taking into account flux, energy, sample thickness, window material, instrumental background, detector efficiency, solution conditions and other parameters. The results are validated with calibrated experiments using standard proteins on four different beamlines with various fluxes, energies and configurations. The ability of BioSAXS to statistically distinguish a variety of conformational movements under continuous-flow time-resolved conditions is then computed on a set of matched structure pairs drawn from the Database of Macromolecular Motions (http://molmovdb.org). The feasibility of experiments is ranked according to sample consumption, a quantity that varies by over two orders of magnitude for the set of structures. In addition to photon flux, the calculations suggest that window scattering and choice of wavelength are also important factors given the short sample path lengths common in such setups.

Time-resolved IR spectroscopy reveals mechanistic details of ion transport in the sodium pump Krokinobacter eikastus rhodopsin 2

2019 ◽  
Vol 21 (8) ◽  
pp. 4461-4471 ◽  
Author(s):  
Marvin Asido ◽  
Peter Eberhardt ◽  
Clara Nassrin Kriebel ◽  
Markus Braun ◽  
Clemens Glaubitz ◽  
...  
Keyword(s):  
Ir Spectroscopy ◽  
Comparative Study ◽  
Ion Transport ◽  
Structural Dynamics ◽  
Sodium Pump ◽  
Proton Pumping ◽  
Wild Type ◽  
Time Resolved

We report a comparative study on the structural dynamics of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2 wild type under sodium and proton pumping conditions by means of time-resolved IR spectroscopy.

Picosecond structural dynamics in photoexcited semiconductors probed by time-resolved x-ray diffraction

2004 ◽  
Author(s):  
Kazutaka G. Nakamura ◽  
Hiroaki Kishimura ◽  
Yoichiro Hironaka ◽  
Ken-ichi Kondo
Keyword(s):  
Structural Dynamics ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray
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