scholarly journals Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls

2017 ◽  
Vol 114 (52) ◽  
pp. 13708-13713 ◽  
Author(s):  
Yingyuan Sun ◽  
Aaron P. Roznowski ◽  
Joshua M. Tokuda ◽  
Thomas Klose ◽  
Alexander Mauney ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Cell Walls ◽  
Structural Changes ◽  
The Other ◽  
Host Bacterium ◽  
Time Resolved ◽  
Viral Attachment ◽  
X Ray ◽  
X Ray Scattering ◽  
Cryo Electron Microscopy

Unlike tailed bacteriophages, which use a preformed tail for transporting their genomes into a host bacterium, the ssDNA bacteriophage ΦX174 is tailless. Using cryo-electron microscopy and time-resolved small-angle X-ray scattering, we show that lipopolysaccharides (LPS) form bilayers that interact with ΦX174 at an icosahedral fivefold vertex and induce single-stranded (ss) DNA genome ejection. The structures of ΦX174 complexed with LPS have been determined for the pre- and post-ssDNA ejection states. The ejection is initiated by the loss of the G protein spike that encounters the LPS, followed by conformational changes of two polypeptide loops on the major capsid F proteins. One of these loops mediates viral attachment, and the other participates in making the fivefold channel at the vertex contacting the LPS.

scholarly journals Photocage-initiated time-resolved solution X-ray scattering investigation of protein dimerization

IUCrJ ◽  
2018 ◽  
Vol 5 (6) ◽  
pp. 667-672 ◽  
Author(s):  
Inokentijs Josts ◽  
Stephan Niebling ◽  
Yunyun Gao ◽  
Matteo Levantino ◽  
Henning Tidow ◽  
...  
Keyword(s):  
Small Molecule ◽  
Conformational Changes ◽  
Structural Changes ◽  
Time Resolved ◽  
Protein Dimerization ◽  
X Ray ◽  
Single Turnover ◽  
X Ray Scattering ◽  
Photoactivatable Proteins ◽  
Ray Scattering

This work demonstrates a new method for investigating time-resolved structural changes in protein conformation and oligomerization via photocage-initiated time-resolved X-ray solution scattering by observing the ATP-driven dimerization of the MsbA nucleotide-binding domain. Photocaged small molecules allow the observation of single-turnover reactions of non-naturally photoactivatable proteins. The kinetics of the reaction can be derived from changes in X-ray scattering associated with ATP-binding and subsequent dimerization. This method can be expanded to any small-molecule-driven protein reaction with conformational changes traceable by X-ray scattering where the small molecule can be photocaged.

Following the structural changes during zinc-induced crystallization of charged membranes using time-resolved solution X-ray scattering

Soft Matter ◽  
2011 ◽  
Vol 7 (4) ◽  
pp. 1512-1523 ◽  
Author(s):  
Moshe Nadler ◽  
Ariel Steiner ◽  
Tom Dvir ◽  
Or Szekely ◽  
Pablo Szekely ◽  
...  
Keyword(s):  
Structural Changes ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Charged Membranes ◽  
Induced Crystallization ◽  
Ray Scattering

scholarly journals Temperature-Jump Solution X-ray Scattering Reveals Distinct Motions in a Dynamic Enzyme

2018 ◽  
Author(s):  
Michael C. Thompson ◽  
Benjamin A. Barad ◽  
Alexander M. Wolff ◽  
Hyun Sun Cho ◽  
Friedrich Schotte ◽  
...  
Keyword(s):  
Protein Dynamics ◽  
Conformational Changes ◽  
Thermal Excitation ◽  
Relaxation Processes ◽  
Spectroscopic Techniques ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Solvent Molecules ◽  
Ray Scattering

AbstractCorrelated motions of proteins and their bound solvent molecules are critical to function, but these features are difficult to resolve using traditional structure determination techniques. Time-resolved methods hold promise for addressing this challenge but have relied on the exploitation of exotic protein photoactivity, and are therefore not generalizable. Temperature-jumps (T-jumps), through thermal excitation of the solvent, have been implemented to study protein dynamics using spectroscopic techniques, but their implementation in X-ray scattering experiments has been limited. Here, we perform T-jump small- and wide-angle X-ray scattering (SAXS/WAXS) measurements on a dynamic enzyme, cyclophilin A (CypA), demonstrating that these experiments are able to capture functional intramolecular protein dynamics. We show that CypA displays rich dynamics following a T-jump, and use the resulting time-resolved signal to assess the kinetics of conformational changes in the enzyme. Two relaxation processes are resolved, which can be characterized by Arrhenius behavior. We also used mutations that have distinct functional effects to disentangle the relationship of the observed relaxation processes. A fast process is related to surface loop motions important for substrate specificity, whereas a slower process is related to motions in the core of the protein that are critical for catalytic turnover. These results demonstrate the power of time-resolved X-ray scattering experiments for characterizing protein and solvent dynamics on the μs-ms timescale. We expect the T-jump methodology presented here will be useful for understanding kinetic correlations between local conformational changes of proteins and their bound solvent molecules, which are poorly explained by the results of traditional, static measurements of molecular structure.

scholarly journals Light-induced structural changes in a full-length cyanobacterial phytochrome probed by time-resolved X-ray scattering

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Derren J. Heyes ◽  
Samantha J. O. Hardman ◽  
Martin N. Pedersen ◽  
Joyce Woodhouse ◽  
Eugenio De La Mora ◽  
...  
Keyword(s):  
Structural Changes ◽  
Full Length ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

scholarly journals Time-resolved crystallography and protein design: signalling photoreceptors and optogenetics

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130568 ◽  
Author(s):  
Keith Moffat
Keyword(s):  
Protein Design ◽  
Structural Changes ◽  
Fast Time ◽  
Free Electron Lasers ◽  
Time Resolved ◽  
X Ray ◽  
Biological Targets ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Exciting Possibility

Time-resolved X-ray crystallography and solution scattering have been successfully conducted on proteins on time-scales down to around 100 ps, set by the duration of the hard X-ray pulses emitted by synchrotron sources. The advent of hard X-ray free-electron lasers (FELs), which emit extremely intense, very brief, coherent X-ray pulses, opens the exciting possibility of time-resolved experiments with femtosecond time resolution on macromolecular structure, in both single crystals and solution. The X-ray pulses emitted by an FEL differ greatly in many properties from those emitted by a synchrotron, in ways that at first glance make time-resolved measurements of X-ray scattering with the required accuracy extremely challenging. This opens up several questions which I consider in this brief overview. Are there likely to be chemically and biologically interesting structural changes to be revealed on the femtosecond time-scale? How shall time-resolved experiments best be designed and conducted to exploit the properties of FELs and overcome challenges that they pose? To date, fast time-resolved reactions have been initiated by a brief laser pulse, which obviously requires that the system under study be light-sensitive. Although this is true for proteins of the visual system and for signalling photoreceptors, it is not naturally the case for most interesting biological systems. To generate more biological targets for time-resolved study, can this limitation be overcome by optogenetic, chemical or other means?

scholarly journals Ca2+-bound calmodulin forms a compact globular structure on binding four trifluoperazine molecules in solution

2000 ◽  
Vol 347 (1) ◽  
pp. 211-215 ◽  
Author(s):  
Norio MATSUSHIMA ◽  
Nobuhiro HAYASHI ◽  
Yuji JINBO ◽  
Yoshinobu IZUMI
Keyword(s):  
Distribution Function ◽  
Conformational Changes ◽  
Small Angle ◽  
Structural Changes ◽  
Radius Of Gyration ◽  
Distance Distribution Function ◽  
Globular Structure ◽  
X Ray ◽  
X Ray Scattering ◽  
Pair Distance Distribution Function

Small-angle X-ray scattering (SAXS), which determines the radius of gyration, Rg, and the pair distance distribution function, was used to investigate the conformational changes of calmodulin (CaM) on binding to an antagonist, trifluoperazine (TFP), with or without Ca2+ in solution. We previously applied this SAXS method to CaM complexed with N-(6-aminohexyl)-5-chloro-1-naphthalenesulphonamide (W-7) [Osawa, Kuwamoto, Izumi, Yap, Ikura, Shibanuma, Yokokura, Hidaka and Matsushima (1999) FEBS Lett. 442, 173-177] and found that the binding of two W-7 TFP molecules to one Ca2+-saturated CaM molecule induces structural changes from a ‘dumb-bell’ shape to a compact globular shape. We report here that the most compact globular shape whose size is consistent with that of the 1:2 Ca2+-saturated CaM-W-7 complex is formed by the binding of four TFP molecules to one Ca2+-saturated CaM molecule. Even in the absence of Ca2+, the conformational changes of CaM occur on TFP binding, giving a slightly smaller Rg than Ca2+-free CaM alone.

scholarly journals On the possibility of the Observation of Intramolecular Reaction Dynamics in Liquids by Time-resolved X-ray Scattering

2002 ◽  
Vol 216 (5) ◽  
Author(s):  
S. Techert ◽  
S. Schmatz
Keyword(s):  
Gas Phase ◽  
Free Electron Laser ◽  
Structural Changes ◽  
Reaction Dynamics ◽  
Structural Studies ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Trans Stilbene

The feasibility of time-resolved structural studies using pulsed X-ray radiation from a 3rd generation synchrotron is discussed and compared with scattering experiments which might be possible with a future free electron laser (X-FEL). As an example, it is shown that the structural changes during the isomerisation process of trans-stilbene into cis-stilbene can be observed using time-resolved X-ray diffraction in the gas-phase as well as in solution.

scholarly journals Photoactivation of Drosophila melanogaster cryptochrome through sequential conformational transitions

2019 ◽  
Vol 5 (7) ◽  
pp. eaaw1531 ◽  
Author(s):  
Oskar Berntsson ◽  
Ryan Rodriguez ◽  
Léocadie Henry ◽  
Matthijs R. Panman ◽  
Ashley J. Hughes ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Conformational Changes ◽  
Structural Changes ◽  
Structural Response ◽  
Biochemical Activity ◽  
Time Resolved ◽  
X Ray ◽  
Molecular Events ◽  
Carboxyl Terminal ◽  
Dynamics Simulations

Cryptochromes are blue-light photoreceptor proteins, which provide input to circadian clocks. The cryptochrome from Drosophila melanogaster (DmCry) modulates the degradation of Timeless and itself. It is unclear how light absorption by the chromophore and the subsequent redox reactions trigger these events. Here, we use nano- to millisecond time-resolved x-ray solution scattering to reveal the light-activated conformational changes in DmCry and the related (6-4) photolyase. DmCry undergoes a series of structural changes, culminating in the release of the carboxyl-terminal tail (CTT). The photolyase has a simpler structural response. We find that the CTT release in DmCry depends on pH. Mutation of a conserved histidine, important for the biochemical activity of DmCry, does not affect transduction of the structural signal to the CTT. Instead, molecular dynamics simulations suggest that it stabilizes the CTT in the resting-state conformation. Our structural photocycle unravels the first molecular events of signal transduction in an animal cryptochrome.

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