Clay Clark

56 posts · 15,635 views

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  • July 9, 2014
  • 10:00 AM
  • 45 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
  • 42 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
  • 40 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
  • 172 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
  • 117 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
  • 147 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
  • 111 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
  • 87 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
  • 163 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
  • 151 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
  • 106 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
  • 201 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
  • 203 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
  • 260 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
  • 203 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
  • 181 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  

  • December 3, 2013
  • 09:00 AM
  • 165 views

Biofuel feasibility

by Clay Clark in Biochem Blogs

Biofuels have recently emerged onto the market after George W. Bush claimed that America is addicted to foreign oil. The security of the biofuels industry is highly reliant on the vested interest of the government and their ability to procure … Continue reading →... Read more »

Park Joshua I., Steen Eric J., Burd Helcio, Evans Sophia S., Redding-Johnson Alyssa M., Batth Tanveer, Benke Peter I., D'haeseleer Patrik, Sun Ning, & Sale Kenneth L. (2012) A Thermophilic Ionic Liquid-Tolerant Cellulase Cocktail for the Production of Cellulosic Biofuels. PLoS ONE, 7(5). DOI: 10.1371/journal.pone.0037010.s004  

Reyes-Ortiz Vimalier, Heins Richard A, Cheng Gang, Kim Edward Y, Vernon Briana C, Elandt Ryan B, Adams Paul D, Sale Kenneth L, Hadi Masood Z, & Simmons Blake A. (2013) Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates. Biotechnology for Biofuels, 6(1), 93. DOI: 10.1186/1754-6834-6-93  

  • November 13, 2013
  • 09:00 AM
  • 224 views

Engineering green algae for enhanced bio-H2 production

by Clay Clark in Biochem Blogs

You can hardly turn on the television or radio these days and not hear a discussion about rising gas prices. When most people set out to buy a new car it’s no doubt that fuel efficiency is one of the … Continue reading →... Read more »

  • October 31, 2013
  • 10:00 AM
  • 227 views

Can algae replace food crops as our biofuel source?

by Clay Clark in Biochem Blogs

What do you think of when you hear the word algae?  I just think of cool looking green stuff that grows in water.  But algae have been getting a lot of press lately for being something much more than that!  … Continue reading →... Read more »

Ito Takuro, Tanaka Miho, Shinkawa Haruka, Nakada Takashi, Ano Yoshitaka, Kurano Norihide, Soga Tomoyoshi, & Tomita Masaru. (2013) Metabolic and morphological changes of an oil accumulating trebouxiophycean alga in nitrogen-deficient conditions. Metabolomics, 9(S1), 178-187. DOI: 10.1007/s11306-012-0463-z  

  • October 29, 2013
  • 10:00 AM
  • 245 views

Grass in the tank

by Clay Clark in Biochem Blogs

Fossil fuels are disappearing. Carbon dioxide released from burning these fuels is accumulating in our atmosphere. Neither half of this planetary carbon problem has an end in sight. The immediate solution to Earth’s carbon problem with respect to transportation can … Continue reading →... Read more »

Gelfand Ilya, Sahajpal Ritvik, Zhang Xuesong, Izaurralde R. César, Gross Katherine L., & Robertson G. Philip. (2013) Sustainable bioenergy production from marginal lands in the US Midwest. Nature, 493(7433), 514-517. DOI: 10.1038/nature11811  

Horn Svein, Vaaje-Kolstad Gustav, Westereng Bjørge, & Eijsink Vincent GH. (2012) Novel enzymes for the degradation of cellulose. Biotechnology for Biofuels, 5(1), 45. DOI: 10.1186/1754-6834-5-45  

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