31 posts · 6,643 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
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- May 30, 2013
- 08:32 AM
- 36 views
RecA: A glimpse into the cosmos
by Clay Clark in Biochem Blogs
Waking up thousands of miles from home was a normal occurrence in the summer months as a child. I was never the first awake, there was always one who was waiting for me. To say my grandfather was an early … Continue reading →... Read more »
Verbenko V. N., Kuznetsova L. V., Krupyan E. P., & Suslov A. V. (2009) Operator-constitutive mutation in the recA gene enhances radiation resistance of Escherichia coli. Russian Journal of Genetics, 45(8), 917-923. DOI: 10.1134/S1022795409080043
Slade Dea, Lindner Ariel B., Paul Gregory, & Radman Miroslav. (2009) Recombination and Replication in DNA Repair of Heavily Irradiated Deinococcus radiodurans. Cell, 136(6), 1044-1055. DOI: 10.1016/j.cell.2009.01.018
Howard-Flanders Paul, West Stephen C., & Stasiak Andrzej. (1984) Role of RecA protein spiral filaments in genetic recombination. Nature, 309(5965), 215-220. DOI: 10.1038/309215a0
- May 15, 2013
- 08:36 AM
- 57 views
Cadmium: toxic to mammals, harmless to a bacterium, helpful to an alga
by Clay Clark in Biochem Blogs
Heavy metal poisoning is a major health concern across the world. Heavy metal ions frequently leak into the environment from industrial waste causing multiple health problems in humans, animals, and other organisms. While there is no universally accepted definition of … Continue reading →... Read more »
Bertin G., & Averbeck D. (2006) Cadmium: cellular effects, modifications of biomolecules, modulation of DNA repair and genotoxic consequences (a review). Biochimie, 88(11), 1549-1559. DOI: 10.1016/j.biochi.2006.10.001
Schwager Stephan, Lumjiaktase Putthapoom, Stöckli Martina, Weisskopf Laure, & Eberl Leo. (2012) The genetic basis of cadmium resistance of . Environmental Microbiology Reports, 4(5), 562-568. DOI: 10.1111/j.1758-2229.2012.00372.x
LEE JENNIFER G., ROBERTS SAMANTHA B., & MOREL FRANÇOIS M. M. (1995) Cadmium: A nutrient for the marine diatom Thalassiosira weissflogii. Limnology and Oceanography, 40(6), 1056-1063. DOI: 10.4319/lo.1995.40.6.1056
- April 25, 2013
- 10:00 AM
- 16 views
Novel industrial applications from salt loving extremophiles
by Clay Clark in Biochem Blogs
This blog will review two recent publications that explore environmentally friendly advances in biotechnology by exploiting halophilic organisms from the family Halobacteriaceae. Halophiles are found in all kingdoms of life. They employ two different survival mechanisms to cope with their typically inhospitable environment. … Continue reading →... Read more »
Karan Ram, Capes Melinda D, DasSarma Priya, & DasSarma Shiladitya. (2013) Cloning, overexpression, purification, and characterization of a polyextremophilic β-galactosidase from the Antarctic haloarchaeon Halorubrum lacusprofundi. BMC Biotechnology, 13(1), 3. DOI: 10.1186/1472-6750-13-3
Zhao Dahe, Cai Lei, Wu Jinhua, Li Ming, Liu Hailong, Han Jing, Zhou Jian, & Xiang Hua. (2013) Improving polyhydroxyalkanoate production by knocking out the genes involved in exopolysaccharide biosynthesis in Haloferax mediterranei. Applied Microbiology and Biotechnology, 97(7), 3027-3036. DOI: 10.1007/s00253-012-4415-3
- April 8, 2013
- 10:00 AM
- 90 views
Rubredoxin the Indestructible
by Clay Clark in Biochem Blogs
Most biochemists have had the “pleasure” of working with proteins that require cool atmospheres and a comfy solvent to keep them temporarily happy (until they randomly decide to aggregate into protein snot). Rubredoxin from the organism Pyrococcus furiosus, on the … Continue reading →... Read more »
Cavagnero Silvia, Zhou Zhi H., Adams Michael W. W., & Chan Sunney I. (1995) Response of Rubredoxin from Pyrococcus furiosus to Environmental Changes: Implications for the Origin of Hyperthermostability. Biochemistry, 34(31), 9865-9873. DOI: 10.1021/bi00031a007
Cavagnero Silvia, Zhou Zhi H., Adams Michael W. W., & Chan Sunney I. (1998) Unfolding Mechanism of Rubredoxin from . Biochemistry, 37(10), 3377-3385. DOI: 10.1021/bi9721804
Borreguero Jose M., He Junhong, Meilleur F., Weiss Kevin L., Brown Craig M., Myles Dean A., Herwig Kenneth W., & Agarwal Pratul K. (2011) Redox-Promoting Protein Motions in Rubredoxin. The Journal of Physical Chemistry B, 115(28), 8925-8936. DOI: 10.1021/jp201346x
- March 26, 2013
- 10:00 AM
- 93 views
The ever important role of thermophiles in biofuel production
by Clay Clark in Biochem Blogs
Well, it’s no secret that there are some major issues with our current dependency on fossil fuels. First of all, they don’t last forever, so at some point we’re going to run out (don’t worry, not any time soon). Second … Continue reading →... Read more »
Rubin Edward M. (2008) Genomics of cellulosic biofuels. Nature, 454(7206), 841-845. DOI: 10.1038/nature07190
Blumer-Schuette Sara E, Kataeva Irina, Westpheling Janet, Adams Michael WW, & Kelly Robert M. (2008) Extremely thermophilic microorganisms for biomass conversion: status and prospects. Current Opinion in Biotechnology, 19(3), 210-217. DOI: 10.1016/j.copbio.2008.04.007
Hamilton-Brehm S. D., Mosher J. J., Vishnivetskaya T., Podar M., Carroll S., Allman S., Phelps T. J., Keller M., & Elkins J. G. (2010) Caldicellulosiruptor obsidiansis sp. nov., an Anaerobic, Extremely Thermophilic, Cellulolytic Bacterium Isolated from Obsidian Pool, Yellowstone National Park. Applied and Environmental Microbiology, 76(4), 1014-1020. DOI: 10.1128/AEM.01903-09
Blumer-Schuette S. E., Giannone R. J., Zurawski J. V., Ozdemir I., Ma Q., Yin Y., Xu Y., Kataeva I., Poole F. L., & Adams M. W. W. (2012) Caldicellulosiruptor Core and Pangenomes Reveal Determinants for Noncellulosomal Thermophilic Deconstruction of Plant Biomass. Journal of Bacteriology, 194(15), 4015-4028. DOI: 10.1128/JB.00266-12
- March 12, 2013
- 10:00 AM
- 66 views
Conan the Bacterium
by Clay Clark in Biochem Blogs
We have all heard of these extremophiles that can thrive in extreme heat, cold, desiccation, acidity, or maybe even extreme radiation. However, the list of extremophiles grows thin as you add multiple life threatening conditions to the fray. Enter: the … Continue reading →... Read more »
Bauermeister Anja, Moeller Ralf, Reitz Günther, Sommer Suzanne, & Rettberg Petra. (2010) Effect of relative humidity on Deinococcus radiodurans' resistance to prolonged desiccation, heat, ionizing, germicidal, and environmentally relevant UV radiation. Microbial ecology. PMID: 21161207
George N. P., Ngo K. V., Chitteni-Pattu S., Norais C. A., Battista J. R., Cox M. M., & Keck J. L. (2012) Structure and Cellular Dynamics of Deinococcus radiodurans Single-stranded DNA (ssDNA)-binding Protein (SSB)-DNA Complexes. Journal of Biological Chemistry, 287(26), 22123-22132. DOI: 10.1074/jbc.M112.367573
- February 27, 2013
- 09:26 AM
- 148 views
I spent the day with Patrick Stewart
by Clay Clark in Biochem Blogs
I spent the day with Patrick Stewart. Not the actor, though both are from England. Patrick Shaw Stewart, to be more specific. He’s one of the founders of Douglas Instruments Ltd. and was here to show us the Oryx, a … Continue reading →... Read more »
Oswald Christine, Smits Sander H. J., Bremer Erhard, & Schmitt Lutz. (2008) Microseeding – A Powerful Tool for Crystallizing Proteins Complexed with Hydrolyzable Substrates. International Journal of Molecular Sciences, 9(7), 1131-1141. DOI: 10.3390/ijms9071131
- February 25, 2013
- 12:45 PM
- 173 views
Chaperonin GroEL- resisting heat shock at any temperature
by Clay Clark in Biochem Blogs
Heat shock is the effect of subjecting a cell to a higher temperature than that of the ideal metabolic temperature of the organism. One of the most typical responses of the cells is transcriptional up-regulation of genes encoding heat shock … Continue reading →... Read more »
Paul S., Singh C., Mishra S., & Chaudhuri T. K. (2007) The 69 kDa Escherichia coli maltodextrin glucosidase does not get encapsulated underneath GroES and folds through trans mechanism during GroEL/GroES-assisted folding. The FASEB Journal, 21(11), 2874-2885. DOI: 10.1096/fj.06-7958com
TRUSCOTT Kaye N., HOJ Peter B., & SCOPES Robert K. (1994) Purification and characterization of chaperonin 60 and chaperonin 10 from the anaerobic thermophile Thermoanaerobacter brockii. European Journal of Biochemistry, 222(2), 277-284. DOI: 10.1111/j.1432-1033.1994.tb18866.x
Yamauchi Seiji, Ueda Yuya, Matsumoto Mika, Inoue Umihiko, & Hayashi Hidenori. (2012) Distinct features of protein folding by the GroEL system from a psychrophilic bacterium, Colwellia psychrerythraea 34H. Extremophiles, 16(6), 871-882. DOI: 10.1007/s00792-012-0483-7
- February 18, 2013
- 08:36 AM
- 158 views
NCSU Biochemistry is going EXTREME!
by Clay Clark in Biochem Blogs
In our Protein Journal Club this semester, we are studying proteins from extremophiles. As their name suggests, extremophiles are organisms that can survive under extreme conditions. These extreme conditions include acidic or basic environments, severe hot or cold environments, lack of … Continue reading →... Read more »
Aghajari Nushin, Haser Richard, Feller Georges, & Gerday Charles. (1998) Crystal structures of the psychrophilic α-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor. Protein Science, 7(6), 1481-1481. DOI: 10.1002/pro.5560070626
Aghajari Nushin, Feller Georges, Gerday Charles, & Haser Richard. (1998) Structures of the psychrophilic Alteromonas haloplanctis α-amylase give insights into cold adaptation at a molecular level. Structure, 6(12), 1503-1516. DOI: 10.1016/S0969-2126(98)00149-X
Feller Georges. (2010) Protein stability and enzyme activity at extreme biological temperatures. Journal of Physics: Condensed Matter, 22(32), 323101. DOI: 10.1088/0953-8984/22/32/323101
Gilis Dimitri. (2006) In Silico Analysis of the Thermodynamic Stability Changes of Psychrophilic and Mesophilic α-Amylases upon Exhaustive Single-Site Mutations. ChemInform, 37(31). DOI: 10.1002/chin.200631215
- December 13, 2012
- 08:09 AM
- 201 views
Order in the cell maintained by a disordered protein?
by Clay Clark in Biochem Blogs
Normally proteins have a globular shape in order to be enzymatically or structurally relevant. Intrinsically disordered proteins (IDPs) broke the protein norms by maintaining their functional roles with little to no overall structure. Most proteins have regions of disorder, such … Continue reading →... Read more »
Kalkhoven Eric. (2004) CBP and p300: HATs for different occasions. Biochemical Pharmacology, 68(6), 1145-1155. DOI: 10.1016/j.bcp.2004.03.045
Vo N, & Goodman R H. (2001) CREB-binding protein and p300 in transcriptional regulation. The Journal of biological chemistry. PMID: 11279224
Avantaggiati M L, Ogryzko V, Gardner K, Giordano A, Levine A S, & Kelly K. (1997) Recruitment of p300/CBP in p53-dependent signal pathways. Cell, 1175-1184. PMID: 9215639
Ferreon Josephine C, Lee Chul Won, Arai Munehito, Martinez-Yamout Maria A, Dyson H Jane, & Wright Peter E. (2009) Cooperative regulation of p53 by modulation of ternary complex formation with CBP/p300 and HDM2. Proceedings of the National Academy of Sciences of the United States of America. PMID: 19357310
- December 6, 2012
- 01:40 PM
- 175 views
Cyclotides: A new ‘wave’ of discovery
by Clay Clark in Biochem Blogs
The cyclotide family is the the largest class of circular proteins with as many as 50,000 predicted members. They are currently only found in the Violaceae, Cucurbitaceae, Rubiaceae and recently (1) Fabaceae family of the plant kingdom (violets, gourds, coffee and legumes, … Continue reading →... Read more »
Poth A. G., Colgrave M. L., Lyons R. E., Daly N. L., & Craik D. J. (2011) From the Cover: Discovery of an unusual biosynthetic origin for circular proteins in legumes. Proceedings of the National Academy of Sciences, 108(25), 10127-10132. DOI: 10.1073/pnas.1103660108
Saska I., Gillon A. D., Hatsugai N., Dietzgen R. G., Hara-Nishimura I., Anderson M. A., & Craik D. J. (2007) An Asparaginyl Endopeptidase Mediates in Vivo Protein Backbone Cyclization. Journal of Biological Chemistry, 282(40), 29721-29728. DOI: 10.1074/jbc.M705185200
- November 13, 2012
- 02:45 PM
- 174 views
The perfect combination: wine, intrinsically disordered proteins and mass spectrometry
by Clay Clark in Biochem Blogs
After spending a great deal of time and energy on cancer research everyday, sometimes I like to go home and down a glass of red wine (or two, depending on the day). Then, I am left to ponder the simpler … Continue reading →... Read more »
GAWEL RICHARD. (1998) Red wine astringency: a review. Australian Journal of Grape and Wine Research, 4(2), 74-95. DOI: 10.1111/j.1755-0238.1998.tb00137.x
Pascal Christine, Poncet-Legrand Céline, Imberty Anne, Gautier Catherine, Sarni-Manchado Pascale, Cheynier Véronique, & Vernhet Aude. (2007) Interactions between a Non Glycosylated Human Proline-Rich Protein and Flavan-3-ols Are Affected by Protein Concentration and Polyphenol/Protein Ratio. Journal of Agricultural and Food Chemistry, 55(12), 4895-4901. DOI: 10.1021/jf0704108
Canon Francis, Ballivian Renaud, Chirot Fabien, Antoine Rodolphe, Sarni-Manchado Pascale, Lemoine Jérôme, & Dugourd Philippe. (2011) Folding of a Salivary Intrinsically Disordered Protein upon Binding to Tannins. Journal of the American Chemical Society, 133(20), 7847-7852. DOI: 10.1021/ja200534f
- November 6, 2012
- 09:32 AM
- 195 views
Retreating to Ocean Isle
by Clay Clark in Biochem Blogs
When you think of Italy you may conjure up images of fine wines, food hearty enough to suppress the most insatiable appetite or natural beauty only a poet could describe, but I think of a birthplace. The birthplace of an … Continue reading →... Read more »
Alon Uri. (2009) How To Choose a Good Scientific Problem. Molecular Cell, 35(6), 726-728. DOI: 10.1016/j.molcel.2009.09.013
Bourne Philip E., & Friedberg Iddo. (2006) Ten Simple Rules for Selecting a Postdoctoral Position. PLoS Computational Biology, 2(11). DOI: 10.1371/journal.pcbi.0020121
Walters Jad, Schipper Joshua L., Swartz Paul, Mattos Carla, & Clark A. Clay. (2012) Allosteric modulation of caspase 3 through mutagenesis. Bioscience Reports, 32(4), 401-411. DOI: 10.1042/BSR20120037
- October 30, 2012
- 01:09 PM
- 223 views
The Bcl-2 family of proteins: A life or death situation
by Clay Clark in Biochem Blogs
If you’ve taken a biochemistry class, you’ve probably heard the structure-function paradigm for proteins: amino acid sequence dictates how the protein will be folded, and the ordered 3D structure of the protein is necessary for function.(1) For example, proper formation … Continue reading →... Read more »
Dunker A.Keith, Lawson J.David, Brown Celeste J, Williams Ryan M, Romero Pedro, Oh Jeong S, Oldfield Christopher J, Campen Andrew M, Ratliff Catherine M, & Hipps Kerry W. (2001) Intrinsically disordered protein. Journal of Molecular Graphics and Modelling, 19(1), 59. DOI: 10.1016/S1093-3263(00)00138-8
Rautureau Gilles J. P., Day Catherine L., & Hinds Mark G. (2010) Intrinsically Disordered Proteins in Bcl-2 Regulated Apoptosis. International Journal of Molecular Sciences, 11(4), 1824. DOI: 10.3390/ijms11041808
Rodi Diane J, Janes Robert W, Sanganee Hitesh J, Holton Robert A, Wallace B.A, & Makowski Lee. (1999) Screening of a library of phage-displayed peptides identifies human Bcl-2 as a taxol-binding protein. Journal of Molecular Biology, 285(1), 203. DOI: 10.1006/jmbi.1998.2303
- October 22, 2012
- 03:47 PM
- 153 views
Free energy in the woods
by Clay Clark in Biochem Blogs
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 … Continue reading →... Read more »
Ackers Gary K., & Bolen D.Wayne. (1997) The Gibbs conference on biothermodynamics: Origins and evolution. Biophysical Chemistry, 64(1-3), 5. DOI: 10.1016/S0301-4622(96)02246-6
Vogt Austin D., & Di Cera Enrico. (2012) Conformational Selection or Induced Fit? A Critical Appraisal of the Kinetic Mechanism. Biochemistry, 51(30), 5902. DOI: 10.1021/bi3006913
Shea Madeline A., Correia John J., & Brenowitz Michael D. (2011) Introduction: Twenty five years of the Gibbs Conference on Biothermodynamics. Biophysical Chemistry, 159(1), 5. DOI: 10.1016/j.bpc.2011.07.002
- October 9, 2012
- 12:54 PM
- 125 views
Lose to gain: a trick that bacteria play to survive from bleach
by Clay Clark in Biochem Blogs
We learned from Biology 101 in college that proteins lose function when they lose their structure. While this is generally true, some proteins, such as heat-shock protein 33 (Hsp33), are actually activated, and thus gain functions, upon losing part of … Continue reading →... Read more »
Ilbert Marianne, Horst Janina, Ahrens Sebastian, Winter Jeannette, Graf Paul C F, Lilie Hauke, & Jakob Ursula. (2007) The redox-switch domain of Hsp33 functions as dual stress sensor. Nature Structural , 14(6), 563. DOI: 10.1038/nsmb1244
Zhao Feng, Ilbert Marianne, Varadan Ranjani, Cremers Claudia M., Hoyos Beatrice, Acin-Perez Rebeca, Vinogradov Valerie, Cowburn David, Jakob Ursula, & Hammerling Ulrich. (2011) Are Zinc-Finger Domains of Protein Kinase C Dynamic Structures That Unfold by Lipid or Redox Activation?. Antioxidants , 14(5), 766. DOI: 10.1089/ars.2010.3773
- September 26, 2012
- 12:42 PM
- 139 views
Retrocyclin – a long lost human protein that could help reduce the spread of HIV
by Clay Clark in Biochem Blogs
The AIDS epidemic has been a pervasive health crisis over the past thirty years. While the rate of death from the disease has declined due to advances in antiviral drugs, reducing the spread of the virus is still an important … Continue reading →... Read more »
Cascales Laura, & Craik David J. (2010) Naturally occurring circular proteins: distribution, biosynthesis and evolution. Organic , 8(22). DOI: 10.1039/c0ob00139b
- September 14, 2012
- 08:16 AM
- 112 views
Understanding a circle: Biological activity and cyclization events associated with biosynthesis of Kalata B1
by Clay Clark in Biochem Blogs
Proteins are the macromolecules that perform the reactions that make life possible. They are comprised of a three-dimensionally folded chain of amino acids connected via peptide bonds. The ends of the amino acid chain are often highly dynamic and can … Continue reading →... Read more »
Huang Y.-H., Colgrave M. L., Daly N. L., Keleshian A., Martinac B., & Craik D. J. (2009) The Biological Activity of the Prototypic Cyclotide Kalata B1 Is Modulated by the Formation of Multimeric Pores. Journal of Biological Chemistry, 284(31), 20707. DOI: 10.1074/jbc.M109.003384
Conlan B. F., Colgrave M. L., Gillon A. D., Guarino R., Craik D. J., & Anderson M. A. (2012) Insights into Processing and Cyclization Events Associated with Biosynthesis of the Cyclic Peptide Kalata B1. Journal of Biological Chemistry, 287(33), 28046. DOI: 10.1074/jbc.M112.347823
- September 7, 2012
- 05:10 PM
- 114 views
Cytobalancing: Coming soon to a cell near you
by Clay Clark in Biochem Blogs
IDPs (intrinsically disordered polypeptides), these naturally occurring regions with no specific structural motifs, can cause quite a bit of trouble. They also help to maintain your life throughout the day, so they should not be considered completely horrible. IDPs are … Continue reading →... Read more »
Zeng Y., He Y., Yang F., Mooney S. M., Getzenberg R. H., Orban J., & Kulkarni P. (2011) The Cancer/Testis Antigen Prostate-associated Gene 4 (PAGE4) Is a Highly Intrinsically Disordered Protein. Journal of Biological Chemistry, 286(16), 13994. DOI: 10.1074/jbc.M110.210765
Metallo Steven J. (2010) Intrinsically disordered proteins are potential drug targets. Current Opinion in Chemical Biology, 14(4), 488. DOI: 10.1016/j.cbpa.2010.06.169
- July 5, 2012
- 05:29 PM
- 289 views
Ferroptosis, another way cells die
by Clay Clark in Biochem Blogs
There are a number of processes that lead to the death of a cell: apoptosis, necrosis, and autophagy are the primary mechanisms – each has a distinct biochemical and morphological fingerprint. In a new paper by Brent Stockwell’s lab at … Continue reading →... Read more »
Dixon Scott J., Lemberg Kathryn M., Lamprecht Michael R., Skouta Rachid, Zaitsev Eleina M., Gleason Caroline E., Patel Darpan N., Bauer Andras J., Cantley Alexandra M., & Yang Wan Seok. (2012) Ferroptosis: An Iron-Dependent Form of Nonapoptotic Cell Death. Cell, 149(5), 1072. DOI: 10.1016/j.cell.2012.03.042
Dolma Sonam, Lessnick Stephen L, Hahn William C, & Stockwell Brent R. (2003) Identification of genotype-selective antitumor agents using synthetic lethal chemical screening in engineered human tumor cells. Cancer Cell, 3(3), 296. DOI: 10.1016/S1535-6108(03)00050-3
Yang Wan Seok, & Stockwell Brent R. (2008) Synthetic Lethal Screening Identifies Compounds Activating Iron-Dependent, Nonapoptotic Cell Death in Oncogenic-RAS-Harboring Cancer Cells. Chemistry , 15(3), 245. DOI: 10.1016/j.chembiol.2008.02.010
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