Biochem Blogs

Biochemistry blog, science writing

Highly unusual proteinaceous infectious agents probed by hydrogen/deuterium exchange

Bob Grinshpon

Graduate Student Bob Grinshpon
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Prion proteins are implicated in a perplexing class of infectious diseases called transmissible spongiform encephalopathies (TSEs). Prion proteins are ubiquitous among mammals with roughly 90% sequence identity across species. TSEs include Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy in cattle, AKA mad cow disease.  The disease ontology involves the conversion of the cellular prion protein (PrPc) to a misfolded conformation, (PrPsc), that  accumulates in amyloid-like aggregates and leads to neurodegeneration. The ‘protein only model’ is the currently accepted model that has recently been corroborated with data, and it suggests that the misfolded protein state itself is the only requirement for disease transmission.

The structure of the PrPc has been established (Figure 1), but there has been great difficulty in determining the structure of the rogue PrPsc conformer. Most approaches to probing the structure of ordered aggregates involve the introduction of specific probes, which is not applicable to samples derived from mammalian tissues.  However, hydrogen-deuterium exchange coupled with mass spectrometry analysis is an exception. H/D exchange takes advantage of the rapid exchange of backbone amide hydrogens within unstructured regions compared to the relatively slow exchange of systematically hydrogen bonded structures. In 2011, the Surewicz lab at Case Western Reserve published a Brief Communication in Nature Structural and Molecular Biology (1). The results of this paper offer some of the first spectroscopic insight into disease relevant conformational conversion of prion proteins.

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To Exchange or Not to Exchange?

Michael Goshe

Michael Goshe
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To Exchange or Not to Exchange? That is the question — at least for the graduate students participating in our Proteins Journal Club this semester (my apologies to those members of the Shakespearean Journal Club — although I do like the musical version of Hamlet as performed on Gilligan’s Island).

 

 

 

 

As you may have surmised since this is a biochemistry blog, the topic is hydrogen exchange (HX) in which an amide proton (N-H) of a protein is exchanged for a deuteron (D) where kch is the chemical exchange rate constant and is a function of pH and temperature.

HD exchange reaction

HD exchange reaction

The propensity of an amide proton of an amino acid residue of a protein to deuterium exchange is related to its hydrogen bonding environment. If the amide proton is participating in a strong hydrogen bond with a carbonyl oxygen as occurs in an alpha-helix or beta-sheet, it will be more difficult to exchange with a deuteron than an amide proton that is part of a loop or a region of a protein that has a high degree of flexibility and exposure to solvent (Figure 1). The sites of exchange can be monitored by NMR or mass spectrometry analysis, thus allowing protein folding and structural dynamics to be measured by the accumulation of deuterium.

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The traveling biochemist: Mass Spectrometry in Vancouver

 

Kevin Blackburn

Kevin Blackburn

The 60th American Society for Mass Spectrometry Conference on Mass Spectrometry and Allied Topics was held in Vancouver, British Colombia the week of May 19-May24 at the Vancouver Convention Center.  The meeting is the largest mass spectrometry meeting in the world and covers the full range of MS related topics, from instrument design to every imaginable application of mass spectrometry.

Vancouver

Vancouver

The city was fantastic, other than occasional light showers. As has been the case for the past 15 or so years, applications related to protein analysis, including protein structure and proteomics, comprised well over half of the presentations. The meeting was attended by approximately 6,000 scientists from across the globe, including researchers from industry and academia as well as a large contingent of vendors. Myself and two members of Michael Goshe’s lab, Laura Edwards and Fan Liu, attended the meeting.

Laura Edwards

Laura Edwards

This was Laura’s first ASMS meeting, and she was like a kid at Christmas!  She did, however, actually work on the first day of the meeting as an assistant, skillfully guiding meeting attendees to various meetings and short courses while wearing a neat red ASMS uniform and carrying an “Ask Me” sign!

 

 

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