Protein Structural Dynamics of Photoactive Yellow Protein in Solution Revealed by Pump–Probe X-ray Solution Scattering

2012 ◽  
Vol 134 (6) ◽  
pp. 3145-3153 ◽  
Author(s):  
Tae Wu Kim ◽  
Jae Hyuk Lee ◽  
Jungkweon Choi ◽  
Kyung Hwan Kim ◽  
Luuk J. van Wilderen ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Photoactive Yellow Protein ◽  
Pump Probe ◽  
X Ray ◽  
Protein Structural Dynamics

scholarly journals Direct Observation of Cooperative Protein Structural Dynamics of Homodimeric Hemoglobin from 100 ps to 10 ms with Pump–Probe X-ray Solution Scattering

2012 ◽  
Vol 134 (16) ◽  
pp. 7001-7008 ◽  
Author(s):  
Kyung Hwan Kim ◽  
Srinivasan Muniyappan ◽  
Key Young Oang ◽  
Jong Goo Kim ◽  
Shunsuke Nozawa ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Direct Observation ◽  
Pump Probe ◽  
X Ray ◽  
Protein Structural Dynamics

scholarly journals X-ray Scattering Studies of Protein Structural Dynamics

2017 ◽  
Vol 117 (12) ◽  
pp. 7615-7672 ◽  
Author(s):  
Steve P. Meisburger ◽  
William C. Thomas ◽  
Maxwell B. Watkins ◽  
Nozomi Ando
Keyword(s):  
Structural Dynamics ◽  
X Ray ◽  
X Ray Scattering ◽  
Protein Structural Dynamics ◽  
Ray Scattering

Temperature-dependent X-ray diffraction as a probe of protein structural dynamics

Nature ◽  
1979 ◽  
Vol 280 (5723) ◽  
pp. 558-563 ◽  
Author(s):  
Hans Frauenfelder ◽  
Gregory A. Petsko ◽  
Demetrius Tsernoglou
Keyword(s):  
Structural Dynamics ◽  
X Ray Diffraction ◽  
Temperature Dependent ◽  
X Ray ◽  
Protein Structural Dynamics

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 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 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 Regulation of Protein Structural Changes by Incorporation of a Small-Molecule Linker

2018 ◽  
Vol 19 (12) ◽  
pp. 3714
Author(s):  
Youngmin Kim ◽  
Cheolhee Yang ◽  
Tae Kim ◽  
Kamatchi Thamilselvan ◽  
Yonggwan Kim ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Small Molecule ◽  
Conformational Changes ◽  
Structural Changes ◽  
Transient Absorption ◽  
Structural Characteristics ◽  
Site Directed Mutagenesis ◽  
Photoactive Yellow Protein ◽  
Fine Control ◽  
Protein Structural Dynamics

Proteins have the potential to serve as nanomachines with well-controlled structural movements, and artificial control of their conformational changes is highly desirable for successful applications exploiting their dynamic structural characteristics. Here, we demonstrate an experimental approach for regulating the degree of conformational change in proteins by incorporating a small-molecule linker into a well-known photosensitive protein, photoactive yellow protein (PYP), which is sensitized by blue light and undergoes a photo-induced N-terminal protrusion coupled with chromophore-isomerization-triggered conformational changes. Specifically, we introduced thiol groups into specific sites of PYP through site-directed mutagenesis and then covalently conjugated a small-molecule linker into these sites, with the expectation that the linker is likely to constrain the structural changes associated with the attached positions. To investigate the structural dynamics of PYP incorporated with the small-molecule linker (SML-PYP), we employed the combination of small-angle X-ray scattering (SAXS), transient absorption (TA) spectroscopy and experiment-restrained rigid-body molecular dynamics (MD) simulation. Our results show that SML-PYP exhibits much reduced structural changes during photo-induced signaling as compared to wild-type PYP. This demonstrates that incorporating an external molecular linker can limit photo-induced structural dynamics of the protein and may be used as a strategy for fine control of protein structural dynamics in nanomachines.

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.

scholarly journals Myelin Basic Protein dynamics from out-of-equilibrium functional state to degraded state in myelin

2019 ◽  
Author(s):  
M. Di Gioacchino ◽  
A. Bianconi ◽  
M. Burghammer ◽  
G. Ciasca ◽  
F. Bruni ◽  
...  
Keyword(s):  
Myelin Basic Protein ◽  
Protein Dynamics ◽  
Functional State ◽  
Structural Dynamics ◽  
Basic Protein ◽  
Physiological State ◽  
X Ray ◽  
Intrinsically Disordered ◽  
Protein Structural Dynamics

ABSTRACTLiving matter is a quasi-stationary out-of-equilibrium system; in this physical condition, structural fluctuations at nano- and meso-scales are needed to understand the physics behind its biological functionality. Myelin has a simple ultrastructure whose fluctuations show correlated disorder in its functional out-of-equilibrium state. However, there is no information on the relationship between this correlated disorder and the dynamics of the intrinsically disordered Myelin Basic Protein (MBP) which is expected to influence the membrane structure and overall functionality. In this work, we have investigated the role of this protein structural dynamics in the myelin ultrastructure fluctuations in and out-of-equilibrium conditions, by using synchrotron Scanning micro X Ray Diffraction and Small Angle X ray Scattering. We have induced the crossover from out-of-equilibrium functional state to in-equilibrium degeneration changing the pH far away from physiological condition. While the observed compression of the cytosolic layer thickness probes the unfolding of the P2 protein and of the cytoplasmic P0 domain (P0cyt), the intrinsic large MBP fluctuations preserve the cytosol structure also in the degraded state. Thus, the transition of myelin ultrastructure from correlated to uncorrelated disordered state, is significantly affected by the unfolding of the P2 and P0 proteins, which in this latter state do not act in synergistic manner with MBP to determine the membrane functionality.STATEMENT OF SIGNIFICANCEA better comprehension of myelin degenerative process and the role of protein dynamics in this biological membrane is a topic issue in today’s scientific community. The myelin ultrastructural fluctuations exhibit correlated disorder in its functional state, that becomes uncorrelated as it degenerates. In this work we elucidate the interplay of protein structural dynamics and myelin ultrastructure in the transition from its functional state to the degraded state. The results highlight that the intrinsically disordered Myelin Basic Protein (MBP) allows to preserve the myelin structure following both the small correlated fluctuations in physiological state and the large disordered fluctuations in degraded conditions, where the myelin functionality is close to being lost and the MBP remains the single active protein.

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