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60 posts · 18,322 views

The NCSU Biochemistry blog is a team effort by the faculty and students of the biochemistry department at NC State University to describe past and current research, science topics of general interest, our opinions of current events in science, and situations that we find humorous at a public university.

Clay Clark
60 posts

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  • October 31, 2014
  • 11:14 AM
  • 134 views

NS1: It’s all about location, location, location

by Clay Clark in Biochem Blogs

  Viruses are minimalists when it comes to genomic data. This light packing of genetic information requires that every protein the virus codes for needs to be as versatile as possible. The flavivirus genus is no exception to this; its genome encodes for three structural proteins (capsid, membrane, and envelope) and seven nonstructural proteins (NS1, […]... Read more »

  • October 10, 2014
  • 10:00 AM
  • 189 views

Ebola Virus VP40 -A protein straight out of “transformers”

by Clay Clark in Biochem Blogs

  Ebola. Just the word is enough to make people panic. Well “Ebola” is actually just a river in the Democratic Republic of the Congo. Of course when they hear the word, most people think about the deadly virus discovered near this river in 1976. To clarify the terminology, “Ebola” is the river; “Ebolavirus” is […]... Read more »

Bornholdt Zachary A., Dafna M. Abelson, Peter Halfmann, Malcolm R. Wood, Yoshihiro Kawaoka, & Erica Ollmann Saphire. (2013) Structural Rearrangement of Ebola Virus VP40 Begets Multiple Functions in the Virus Life Cycle. Cell, 154(4), 763-774. DOI: http://dx.doi.org/10.1016/j.cell.2013.07.015  

Feldmann Heinz. (2011) Ebola haemorrhagic fever. The Lancet, 377(9768), 849-862. DOI: http://dx.doi.org/10.1016/s0140-6736(10)60667-8  

  • October 2, 2014
  • 02:01 PM
  • 120 views

Survivin: You wouldn’t be alive without it

by Clay Clark in Biochem Blogs

  Enzymes perform numerous tasks in order to contribute to the global goal of organism survival. One such enzyme is Survivin. Survivin wears many “hats” within the cell and is a vital part of cellular homeostasis. Here I will introduce you to two of the main processes Survivin regulates. Survivin is a multifunctional protein involved […]... Read more »

  • August 5, 2014
  • 10:00 AM
  • 48 views

Beauty isn’t the only thing skin deep: A story of love, betrayal and MRSA

by Clay Clark in Biochem Blogs

Methicillin-resistant Staphylococcus aureus (MRSA) is a bacteria you have probably read about skimming through the paper while you drink your morning coffee. Who am I kidding? No one reads the paper anymore, so maybe you have seen it on the internet or one of the “non-partisan” T.V. News stations. If not……..this blog may save your […]... Read more »

  • July 9, 2014
  • 10:00 AM
  • 109 views

GluA2 receptor ligand-binding domain: The PacMan that makes things happen

by Clay Clark in Biochem Blogs

This semester’s protein journal club topic was on hydrogen deuterium exchange (HDX). We could discuss any paper that used either mass spectrometry (MS) or nuclear magnetic resonance (NMR) to better understand how an enzyme worked. The paper I discussed focused on how a glutamate receptor’s ligand binding domain (LBD) dynamically interacts with agonists. So let’s […]... Read more »

  • July 1, 2014
  • 10:00 AM
  • 114 views

Response regulators…the new Holy Grail in the world of antibiotics?

by Clay Clark in Biochem Blogs

In this day and age, the human race is plagued with resilient, pathogenic bacteria that can cause serious complications in our lives. These bacteria cause problems because they are resistant to many of our most powerful antibiotics, methicillin and vancomycin for example. Typically, these antibiotics interfere with the biosynthesis of bacterial peptidoglycan—a protective outer-layer of […]... Read more »

  • June 4, 2014
  • 10:00 AM
  • 94 views

The power of persistence: GPCR dynamics revealed by hydrogen-deuterium exchange

by Clay Clark in Biochem Blogs

Have you ever been surprised by a very bright light turning on in a dark room? Think about how you reacted when that happened. You probably covered your eyes or closed them. Your irises contracted to shrink your pupil so less of the painful light made it into your eye. Have you ever thought about […]... Read more »

Zhang Xi, Chien Ellen Y T, Chalmers Michael J, Pascal Bruce D, Gatchalian Jovylyn, Stevens Raymond C, & Griffin Patrick R. (2010) Dynamics of the beta2-adrenergic G-protein coupled receptor revealed by hydrogen-deuterium exchange. Analytical chemistry, 1100-1108. PMID: 20058880  

  • April 15, 2014
  • 10:00 AM
  • 233 views

The perfect marriage of crystallography and mass spectrometry: PI3K

by Clay Clark in Biochem Blogs

  Sorry for the cheesy title, but I’m getting married in a couple of weeks and it is all I can think about (oh, and science of course).  I have to admit that I chose a GREAT paper this time!: “Molecular determinants of PI3Kγ-mediated activation downstream of G-protein–coupled receptors” which was published last year in […]... Read more »

Vadas O., Dbouk H. A., Shymanets A., Perisic O., Burke J. E., Abi Saab W. F., Khalil B. D., Harteneck C., Bresnick A. R., & Nurnberg B. (2013) Molecular determinants of PI3K -mediated activation downstream of G-protein-coupled receptors (GPCRs). Proceedings of the National Academy of Sciences, 110(47), 18862-18867. DOI: 10.1073/pnas.1304801110  

  • April 8, 2014
  • 10:00 AM
  • 170 views

The story of the phospholipase A superfamily

by Clay Clark in Biochem Blogs

  The phospholipase A2 superfamily is a group of enzymes that cleave fatty acid groups from glycerol, in particular acyl groups at the sn-2 position. They contribute to numerous metabolic processes and diseases, including Alzheimer, epilepsy and multiple sclerosis; making this group of proteins very attractive to study. This superfamily includes groups such as secreted, […]... Read more »

  • March 28, 2014
  • 10:00 AM
  • 211 views

Highly unusual proteinaceous infectious agents probed by hydrogen/deuterium exchange

by Clay Clark in Biochem Blogs

  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 […]... Read more »

Smirnovas Vytautas, Baron Gerald S, Offerdahl Danielle K, Raymond Gregory J, Caughey Byron, & Surewicz Witold K. (2011) Structural organization of brain-derived mammalian prions examined by hydrogen-deuterium exchange. Nature Structural , 18(4), 504-506. DOI: 10.1038/nsmb.2035  

  • March 19, 2014
  • 10:00 AM
  • 179 views

Probing the allosteric site of MDM2 during P53 binding using hydrogen/deuterium exchange

by Clay Clark in Biochem Blogs

Exchanging hydrogen for deuterium allows one to explore many facets of protein:protein interactions. Allostery is an important characteristic of some proteins that gives fine tuned control over an active site or substrate binding pocket. MDM2 is an important negative regulator of p53. p53 has a crucial role in many physiological pathways such as DNA repair. When DNA undergoes a […]... Read more »

  • March 14, 2014
  • 10:00 AM
  • 151 views

Why does a glycoprotein need sugar to carry a heart medication?

by Clay Clark in Biochem Blogs

Hydrogen-deuterium exchange (HDX) can tell us a lot about protein structures through its use with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) spectroscopy. Richard Huang of the National Institute of Standards and Technology and Jeffrey Hudgens of the Institute for Bioscience and Biotechnology Research (both from Washington DC suburbs in Maryland) recently used HDX-MS […]... Read more »

  • March 12, 2014
  • 10:00 AM
  • 213 views

Using amide H/D exchange to analyze conformational changes in Pak2 activation

by Clay Clark in Biochem Blogs

  There are a variety of ways that currently exist to analyze the structure of a protein such as X-ray crystallography or NMR. There are also a variety of ways to analyze the conformational changes of the protein. Amide H/D exchange is one such tool. Already having a crystal or NMR structure of a protein […]... Read more »

  • February 28, 2014
  • 09:00 AM
  • 203 views

Studying the moves of a “wrap artist”

by Clay Clark in Biochem Blogs

Let me begin by saying that I think I could have a satisfying career studying the histone proteins simply due to the number of great (/terrible) puns to which they lend themselves. In all fairness, my title was inspired by a 2010 Nature Reviews Cell Biology by Talbert and Henikoff (1); therefore, my sense of […]... Read more »

Talbert Paul B., & Henikoff Steven. (2010) Histone variants — ancient wrap artists of the epigenome. Nature Reviews Molecular Cell Biology, 11(4), 264-275. DOI: 10.1038/nrm2861  

Panchenko T., Sorensen T. C., Woodcock C. L., Kan Z.-y., Wood S., Resch M. G., Luger K., Englander S. W., Hansen J. C., & Black B. E. (2011) Replacement of histone H3 with CENP-A directs global nucleosome array condensation and loosening of nucleosome superhelical termini. Proceedings of the National Academy of Sciences, 108(40), 16588-16593. DOI: 10.1073/pnas.1113621108  

Tachiwana Hiroaki, Kagawa Wataru, Shiga Tatsuya, Osakabe Akihisa, Miya Yuta, Saito Kengo, Hayashi-Takanaka Yoko, Oda Takashi, Sato Mamoru, & Park Sam-Yong. (2011) Crystal structure of the human centromeric nucleosome containing CENP-A. Nature, 476(7359), 232-235. DOI: 10.1038/nature10258  

  • February 20, 2014
  • 02:49 PM
  • 152 views

To Exchange or Not to Exchange?

by Clay Clark in Biochem Blogs

  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 […]... Read more »

Walters B. T., Mayne L., Hinshaw J. R., Sosnick T. R., & Englander S. W. (2013) Folding of a large protein at high structural resolution. Proceedings of the National Academy of Sciences, 110(47), 18898-18903. DOI: 10.1073/pnas.1319482110  

  • January 29, 2014
  • 10:16 AM
  • 249 views

Biobutanol: Re-wiring the cell to produce a potential ethanol replacement

by Clay Clark in Biochem Blogs

  I’ll admit it; I’m guilty of watching my share of doomsday documentaries in the past. Most of them are ridiculous, but it remains interesting to think about the future and our trajectory as a society. What will the world look like in the next hundred years? Will it be a world without disease? Will […]... Read more »

  • January 14, 2014
  • 09:00 AM
  • 253 views

The traveling biochemist: Enzymes, pathways, proteases, and homeostasis

by Clay Clark in Biochem Blogs

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 […]... Read more »

  • January 9, 2014
  • 09:00 AM
  • 336 views

pH 5: The Goldilocks of pH for cellulases

by Clay Clark in Biochem Blogs

With a rapidly increasing need for energy combined with dwindling fossil fuels, new energy sources are being analyzed. The most well known renewable resource is cellulose, which is found in plant cell walls. Cellulose is the most abundant organic polymer … Continue reading →... Read more »

  • January 6, 2014
  • 09:00 AM
  • 252 views

Biohydrogen production by the cyanobacterium Cyanothece

by Clay Clark in Biochem Blogs

Hydrogen is arguably the fuel of the future. As a fuel source, is it considered “zero emission,” and as an energy carrier it combusts to produce heat and water. Pure hydrogen does not however occur naturally and must be produced … Continue reading →... Read more »

Bandyopadhyay Anindita, Stöckel Jana, Min Hongtao, Sherman Louis A., & Pakrasi Himadri B. (2010) High rates of photobiological H2 production by a cyanobacterium under aerobic conditions. Nature Communications, 1(9), 139. DOI: 10.1038/ncomms1139  

Duval S., Danyal K., Shaw S., Lytle A. K., Dean D. R., Hoffman B. M., Antony E., & Seefeldt L. C. (2013) Electron transfer precedes ATP hydrolysis during nitrogenase catalysis. Proceedings of the National Academy of Sciences, 110(41), 16414-16419. DOI: 10.1073/pnas.1311218110  

  • January 3, 2014
  • 09:00 AM
  • 232 views

There was a fire fight

by Clay Clark in Biochem Blogs

Scientists are becoming ever more aware of the need to identify a fuel which will bring us out of the “oil darkness” and into the light of a renewable source of energy. Bio-butanol is not the savior, although it offers … Continue reading →... Read more »

Nielsen Jens Erik, & Borchert Torben V. (2000) Protein engineering of bacterial α-amylases. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, 1543(2), 253-274. DOI: 10.1016/S0167-4838(00)00240-5  

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