Biochem Blogs

Biochemistry blog, science writing

To Exchange or Not to Exchange?

Michael Goshe

Michael Goshe
I'm on ScienceSeeker-Microscope

 

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: Enzymes, pathways, proteases, and homeostasis

@biochemprof

Clay Clark – @biochemprofI'm on ScienceSeeker-Microscope

As I’ve written before in this blog, one of the advantages of working in an academic institution is the opportunity of international travel. Science is a world-wide endeavor, and one should take opportunities to visit international colleagues whenever possible. I was invited recently to two international conferences to give seminars on caspases and allostery. The first conference was in Playa Del Carmen – Xcaret, Mexico (Enzymes, Coenzymes and Metabolic Pathways), and the second conference was in Navi Mumbai, India, at ACTREC (Advanced Center for Treatment, Research, and Education in Cancer), part of the TATA Memorial Cancer Center in India.

The enzymes conference in Xcaret was organized by Beatrice Golinelli-Pimpaneau and Elizabeth Komives and focused on enzyme function and regulation, coenzymes, metabolism, and methods for examining enzyme structure and function. There were many good talks on protein conformational changes, protein dynamics, kinases, and morpheeins. (If you are not sure what a morpheein is or how it relates to enzyme allostery, then see the review below by Eileen Jaffee (1)). The schedule of speakers is provided here. The five-day conference was held in the beautiful Occidental Grand Xcaret resort, an all-inclusive environment with great food, drinks, pools, and a private bay for swimming and snorkeling (a couple of pictures are below along with a video of flamingos out for a walk). The weather was ~85 ºF all week, compared to mid-50s in Raleigh, so it was good to be in the Caribbean for a few days. Overall, the environment was terrific, and the seminars were outstanding.

IMG_2366

Playa Del Carmen – Xcaret

Macaws

Macaw at Xcaret Hotel

 

 

 

 

 

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Learning to speak IT

Clay Clark

Clay Clark – @biochemprofI'm on ScienceSeeker-Microscope

 

Recently one of our faculty contacted the IT department to inquire about how OIT (office of information technology) charges for network connections. OIT provides web services for the department, and we’re trying to understand how data and phone services are charged. Our assumption was that the more IP addresses used, the higher the charge. The response to our inquiry is below:

[Name redacted] got in touch with me and mentioned you were interested in how the rate for data network works.  The specific formula for allocating data networking expenses is based on salary expenditures [several accounts mentioned] within a unit. As each unit tends to utilize different methodologies for sharing the expense within the unit, we have generated a spreadsheet for each OUC (2-digit) showing the specifics of how the charge was derived accordingly to the following formula:

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A Happy Glucose Holiday Season

Clay Clark

Clay Clark – @biochemprof I'm on ScienceSeeker-Microscope

 

If you don’t believe in pathways, you might want to listen. Each year in his biochemistry class, Dr. Jim Knopp sings “the glucose song.” This year, he had special visitors from Ladies in Red, an all-female a cappella group associated with the Music Department at NCSU.

To kick off the holiday season, please enjoy The Glucose Song, as sung by Ladies in Red.

To see the lyrics:

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Free energy in the woods

Clay Clark

Clay Clark – @biochemprof I'm on ScienceSeeker-Microscope

The Gibbs Conference on Biothermodynamics recently held its 26th annual meeting in Carbondale, IL. The Gibbs conference began in 1986 with a meeting to discuss the discipline of thermodynamics in biological systems. How does one apply the rigorous techniques utilized in thermodynamic studies to biological systems? How does one move away from the “garbage can thermodynamics,” as described by Gary Ackers, to learn fundamental processes in biology?

As described by Ackers and Bolen (1)

A widespread view of thermodynamics was that:

(1) Thermodynamic approaches were archaic, and, at best, ancillary to the central problems of biochemistry, as reinforced by the commonly-heard slogan ‘thermodynamics can tell us nothing about mechanisms.’

(2) The subject was usually taught poorly or not at all in departments of chemistry and biochemistry.

(3) A long-standing tradition of equating thermodynamics with only a single technique (i.e., calorimetry) had contributed to the narrow and insular perception of the field and its potential.

(4) Thermodynamics had seldom been fused with modem developments of structural analysis and computational chemistry.

The goal was to move away from simply measuring changes in Gibbs free energy to fill in tables found in textbooks and to learn how one can use the techniques to describe cellular reactions – enzymology, protein-protein and protein-ligand interactions, nucleic acid-ligand interactions, biological membranes, to name a few. In doing so, the conference has been spectacularly successful in advancing the field of biothermodynamics.

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The traveling biochemist: Cell death in Barga, Italy

Sarah MacKenzie

Sarah MacKenzie

A few weeks ago I attended my first Gordon Conference on Cell Death in Barga, Italy with my PI, Clay Clark. The conference was located in a beautiful resort nestled in the Tuscan hills off the beaten path between Florence and Pisa. It was a spectacular venue for 170 cell death aficionados to present their most current data and discuss new topics in an informal setting. We arrived in Rome the morning that the conference began, rented a car (we were in line behind Morgan Spurlock) and traversed Italy dodging Italian drivers who have no regard for lanes or speed limits. It is actually a pretty fun experience to drive in Italia! The conference began that evening with two excellent keynote addresses presented by Martin Raff and Richard Youle.

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Using zebrafish to find human cancer drugs

 

Clay Clark

Clay Clark – @biochemprof

My lab in the Department of Molecular & Structural Biochemistry and Dr. Jeff Yoder in the Department of Molecular Biomedical Sciences at NC State University applied for an award from the College of Agriculture and Life Sciences (CALS) at NCSU.

We use zebrafish to screen small molecule drug libraries as a method to characterize potential anti-cancer drugs.

The project was selected as one of three finalists for the Outstanding Faculty Award at the Stewards of the Future: Research for Human Health & Global Sustainability conference.

As a token of encouragement and appreciation, the Board of Directors of the NC Agricultural and Life Sciences Research Foundation offers the first Stewards of the Future Research Awards.  This competition is designed to help showcase the ingenuity and innovation of CALS scientists, and to provide a small award of flexible funding to help support awardees’ research programs.

The other two finalists in the Faculty category are Ignazio Carbone and Jun Tsuji. Each finalist has submitted a two minute video on the project.

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Sh*t graduate students say

Laura Edwards NCSU Biochemistry graduate student

Laura Edwards

 

“Why isn’t this working”? “Should we go get coffee”? “We have some of *this* in our sample.”

Here are a few phrases overheard in the NCSU Biochemistry department.

In the video: Laura Edwards, Annette Bodenheimer, Brian Rogers, Xun Lu.

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