'Comet water' ions found in bacterial protein

Jan 10, 2013

Developments arising from new science techniques at Keele University in the UK, the Institut Laue-Langevin (ILL), the flagship centre for neutron science, and the European Synchrotron Radiation Facility (ESRF), have confirmed the presence of hydronium ions in the protein rubredoxin. Rubredoxin is a light weight iron-sulphur protein found in some of the earliest, most basic forms of life, notably bacteria and archaea. These ions, commonly found in comet tails or interstellar space clouds, have been found to be involved in crucial interactions with the protein.

The new results, reported in Angewandte Chemie, combine the use of one of the world's most sophisticated diffractometers with a novel sample preparation process whereby the protein's are replaced with the heavier isotope, deuterium, greatly enhancing the visualisation of hydronium ions.

A new tool for neutron science

Despite their clearly particle-like character, neutrons demonstrate wave like behaviour; when they encounter obstacles whose size is comparable with their wavelength, they scatter in such a way that allows scientists to determine the structure of the material through which the neutrons have passed. Neutrons are particularly good in studying biological materials since they are highly sensitive to lighter atoms such as hydrogen - strongly complementing the capabilities of synchrotron X-rays which are more sensitive to heavier elements.

However in the past neutron scientists have run into difficulties when studying proteins due to excessive levels of background noise in the measured data, drastically limiting the scope of analysis work. This problem can be totally avoided by replacing the hydrogen atoms in the protein by deuterium. In response, a team of scientists at Keele University (Macromolecular Structure Group) in the UK and at the ILL (Life Sciences Group), with the aid of funding from the UK Engineering and Physical Sciences Research Council (EPSRC). have developed a unique Deuteration Laboratory that allows biological macromolecules to be deuterated in a way that optimises the quality of the data collection and of the final results.

This study was carried out through a collaboration involving Keele, the ILL, and the ESRF. Deuterated rubredoxin was produced and the scattering (diffraction) experiments carried out on the ILL's world leading monochromatic neutron beamline D19. Uniquely amongst neutron diffraction instruments, the detector on D19 has a curved 'banana' shape that covers a wide angle around the sample allowing the acquisition of remarkably high-quality data.

Rubredoxin occurs in two forms, or oxidation states, and moves between them by accepting or losing electrons from other molecules in the organism in what are known as redox reactions. These reactions play a critical role in vital biological processes such as respiration, photosynthesis, and nitrogen fixation. An important aspect of this work was therefore to elucidate changes in the protein molecule that could provide an understanding of the way redox mechanisms work – and the role played by hydrogen atoms and water.

The study provided a major advance well beyond anything achieved previously, and has opened up a new and extremely important area of protein science. The team characterised both the reduced and oxidised forms of the protein at near-atomic resolution. Surprisingly, the results showed the presence of numerous hydronium (H3O+) ions within the protein. Whilst H3O+ ions have been identified in chemical systems and in one protein, this is the first time they have been found in a redox protein where they are likely to be deeply implicated in charge transfer.

Furthermore the study demonstrates shifts of hydrogen atoms in relation to hydronium ions following the change between the reduced and oxidised forms of the protein. Dr Maxime Cuypers from Keele University and the Institut Laue-Langevin said: "This work started off as a proof of concept study to understand and exploit the potential of this new combination of techniques. However when we analysed the data it rapidly became obvious that there was a lot more going on than we could have predicted. What we have here is a remarkable set of results that not only demonstrates the unique power of high-resolution monochromatic neutron crystallography and also the use of deuterated proteins to probe protein structures, but also the opening of a totally new area of science that is directly relevant to critical aspects of biological function."

Explore further: A refined approach to proteins at low resolution

More information: onlinelibrary.wiley.com/doi/10… /anie.201207071/full

add to favorites email to friend print save as pdf

Related Stories

Researchers use neutrons to spy on the elusive hydronium ion

Aug 08, 2011

A Los Alamos National Laboratory research team has harnessed neutrons to view for the first time the critical role that an elusive molecule plays in certain biological reactions. The effort could aid in treatment of peptic ...

A new technique for understanding quantum effects in water

Oct 03, 2011

It covers over two thirds of our planet, is essential for life on Earth and its chemical formula is one of the few most people can name, but we still have much to learn about the structure of H2O. Now, scientists ...

Heavy Pyridine Crystallizes Differently

Jan 07, 2009

(PhysOrg.com) -- The nuclei of ordinary hydrogen atoms contain only a single proton. If a neutron is added, the hydrogen becomes deuterium. In principle, molecules that contain deuterium in place of hydrogen ...

Recommended for you

A refined approach to proteins at low resolution

Sep 19, 2014

Membrane proteins and large protein complexes are notoriously difficult to study with X-ray crystallography, not least because they are often very difficult, if not impossible, to crystallize, but also because ...

Base-pairing protects DNA from UV damage

Sep 19, 2014

Ludwig Maximilian University of Munich researchers have discovered a further function of the base-pairing that holds the two strands of the DNA double helix together: it plays a crucial role in protecting ...

User comments : 5

Adjust slider to filter visible comments by rank

Display comments: newest first

kevinrtrs
1 / 5 (7) Jan 10, 2013
a totally new area of protein science that is directly relevant to critical aspects of biological function.

This also means a lot more headaches for evolutionary philosophy because such a complex interaction could not by any stretch of the imagination have arisen through random physical processes.
antialias_physorg
5 / 5 (5) Jan 10, 2013
because such a complex interaction could not by any stretch of the imagination have arisen through random physical processes.

Well, since your imagination stretches about as far as a piece of rock I can imagine that YOUR imagination cannot fathom such a thing.

Then again the 'random process' is a strawman argument - so you have again demonstrated your incompetence (and this time it has taken you only one sentence! You're getting really good at it.)

Evolution isn't random. It's mutation AND selection.

Learn what the world 'evolution' means before using it - that would make you seem a lot smarter.
Torbjorn_Larsson_OM
5 / 5 (4) Jan 11, 2013
Creationists shouldn't comment on science, it is hilarious and makes deconverts from religion, see Dawkins's Converts's Corner.

The elucidation of a phylogenetically shared gene making a protein as a shared trait tests evolution well. It also rejects the creationist idea of random assembly of species, and ultimately their religious text of "from mud to dude and from rib to woman".

And of course it is Evolution 101 that the process is not random, showing once again that creationists couldn't care less about the science but is distraught over ist success.
RealScience
5 / 5 (3) Jan 11, 2013
@Kevin - quit being an inconsiderate hypocrite. It would be inconsiderate for me to go on religious sites and teach science, even though I believe in science, because that's not what the sites' users go there for. It is just as inconsiderate for you to come to a science site and preach your religion.

And you've already had it pointed out several times that natural selection is part of evolution and natural selection is not random. Asking questions and then not listening to the answers is also inconsiderate.

Furthermore you are typing on a computer and using a network that are products of the same scientific process whose results you are dismissing. That's hypocritical.

Does your religion teach you to be an inconsiderate hypocrite? Is that what you think that your god wants?
Mike_Massen
5 / 5 (1) Jan 13, 2013
Kevinrtrs admitted a flawed & bad lack of imagination
This also means a lot more headaches for evolutionary philosophy because such a complex interaction could not by any stretch of the imagination have arisen through random physical processes.
Complex interactions happen all too often, its math(s).

Did you not do permutations & probability in high school ?

Did you get an education in mathematics & have the chance to extend the basic scales with a good teacher ?

I feel sorry for you Kevinrtrs, why are you wasting your time trying to push 'sound bites' of writings from Moses about a claimed deity that is proven to be impotent & cannot communicate *EXCEPT* through a human mind ?

Was Moses a rationale guy ?

Did he use mind altering substances ?

Why wasn't there any law against psychotropics when Moses & his associates wrote the old testament ?

Why couldn't a god make an indestructible bible ?

Why can't a deity stop young children dying from genetic conditions ?

Why Kevin ?