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Garry Buchko

Garry Buchko

Prototype & Pilot
Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352
509/371-6543

Biography

Dr. Garry W. Buchko is a physical biochemist that first joined PNNL as a postdoctoral fellow with Dr. Michael Kennedy in 1995 and was promoted to senior scientist in 2001. He received his M.Sc. in Chemistry at McMaster University (1986) under the supervision of Drs. Russell Bell and the late Tom Nelson, pioneers in the field of ribonucleic acid synthetic chemistry. This was followed by a doctorate degree in Chemistry at the University of Manitoba (1989) with Dr. Frank Hruska, a pioneer in using NMR spectroscopy to study nucleic acid sugar conformations. His first two postdoctoral experiences were with the radiation biologists Drs. Jean Cadet in Grenoble, France (Laboratoire des Lesions des Acides Nucléique, Centre d'Etudes Nucléaires de Grenoble) and Michael Weinfeld in Edmonton, Alberta (Cross Cancer Institute). His third postdoctoral experience was with the NMR spectroscopist/protein biochemist Dr. Bob Cushley in Burnaby, British Columbia (Institute of Molecular Biology and Biochemistry, Simon Fraser University). Currently, Dr. Buchko is the PNNL component of the Seattle Structural Genomics Center for Infectious Disease (SSGCID, www.ssgcid.org), a consortium of researchers at Seattle BioMed, Emerald BioStructures, and the University of Washington. SSGCID is funded by the National Institute of Allergies and Infectious Diseases (NIAID) and devoted to applying state-of-the-art structural genomics technologies to structurally characterize targeted proteins from NIAID Category A-C pathogens and organisms. In addition to the SSGCID structural biology efforts, Dr. Buchko is also part of a team of PNNL scientists, lead by Dr. Wendy Shaw and funded by National Institute of Dental and Craniofacial Research, studying amelogenin's role in the formation of tooth enamel (biomineralization).

Research Interests

  • Protein structure solution (NMR-based methods or X-ray crystallography).
  • Protein function analysis. A common approach is to determine a structure by XRD and then identify protein-ligand interactions in solution using a suite of NMR experiments (eg: chemical shift perturbation).
  • Biophysical characterization of proteins using a suite of spectroscopies.
  • Protein thermodynamics (isothermal titration calorimetry).
  • Protein dynamics.
  • Intrinsically disordered proteins.
  • Protein-DNA interactions.
  • Infectious diseases.
  • Biomineralization.

Education and Credentials

  • Ph.D., Chemistry, University of Manitoba (1989)
  • M.Sc., Chemistry, McMaster University (1986)
  • B.Sc.(Hons), Biochemistry, University of Manitoba (1983)

Affiliations and Professional Service

  • Canadian Institute of Chemistry

PNNL Publications

2014

  • Reback ML, GW Buchko, BL Kier, B Ginovska-Pangovska, Y Xiong, S Lense, J Hou, JA Roberts, CM Sorensen, S Raugei, TC Squier, and WJ Shaw. 2014. "Enzyme Design From the Bottom Up: An Active Nickel Electrocatalyst with a Structured Peptide Outer Coordination Sphere." Chemistry - A European Journal 20(6):1510-1514.  doi:10.1002/chem.201303976

2013

  • Buchko GW, G Lin, BJ Tarasevich, and WJ Shaw. 2013. "A solution NMR investigation into the impaired self-assembly properties of two murine amelogenins containing the point mutations T21?I or P41?T." Archives of Biochemistry and Biophysics 537(2):217-224.  doi:10.1016/j.abb.2013.07.015
  • Buchko GW, SN Hewitt, WC Van Voorhis, and PJ Myler. 2013. "Solution structure of a putative FKBP-type peptidyl-propyl cis-trans isomerase from Giardia lamblia." Journal of Biomolecular NMR 57(4):369-374.  doi:10.1007/s10858-013-9797-8
  • Lu J, Y Xu, GW Buchko, and WJ Shaw. 2013. "Mineral Association Changes the Secondary Structure and Dynamics of Murine Amelogenin." Journal of Dental Research 92(11):1000-1004.  doi:10.1177/0022034513504929
  • Baugh L, LA Gallagher, R Patrapuvich, MC Clifton, AS Gardberg, TE Edwards, B Armour, DW Begley, SH Dieterich, DM Dranow, J Abendroth, JW Fairman, D Fox III, BL Staker, I Phan, A Gillespie, R Choi, S Nakazawa-Hewitt, MT Nguyen, AJ Napuli, L Barrett, GW Buchko, R Stacy, PJ Myler, LJ Stewart, C Manoil, and WC Van Voorhis. 2013. "Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome." PLoS One 8(1):e53851.  doi:10.1371/journal.pone.0053851
  • Buchko GW, A Jain, ML Reback, and WJ Shaw. 2013. "Structural characterization of the model amphipathic peptide Ac-LKKLLKLLKKLLKL-NH2 in aqueous solution and with 2,2,2-trifluoroethanol and 1,1,1,3,3,3-hexafluoroisopropanol." Canadian Journal of Chemistry 91(6):406-413.  doi:10.1139/cjc-2012-0429
  • Buchko GW, J Abendroth, H Robinson, Y Zhang, SN Hewitt, TE Edwards, WC Van Voorhis, and PJ Myler. 2013. "Crystal structure of a macrophage migration inhibitory factor from Giardia lamblia." Journal of Structural and Functional Genomics 14(2):47-57.  doi:10.1007/s10969-013-9155-9
  • Sagaram US, K El-Mounadi, GW Buchko, HR Berg, J Kaur, R Pandurangi, TJ Smith, and D Shah. 2013. "Structural and functional studies of a phosphatidic acid-binding antifungal plant defensin MtDef4: Identification of an RGFRRR motif governing fungal cell entry." PLoS One 8(12):e82485.  doi:10.1371/journal.pone.0082485
  • Zhang Y, A Gardberg, TE Edwards, B Sankaran, H Robinson, SM Varnum, and GW Buchko. 2013. "Structural Insights into the Functional Role of the Hcn Sub-domain of the Receptor-Binding Domain of the Botulinum Neurotoxin Mosaic Serotype C/D." Biochimie 95(7):1379-1385.  doi:10.1016/j.biochi.2013.03.006

2012

  • Buchko GW, and H Robinson. 2012. "Crystal structure of cce_0566 from Cyanothece 51142, a protein associated with nitrogen fixation in the DUF269 family." FEBS Letters 586(4):350-355.  doi:10.1016/j.febslet.2012.01.037
  • Buchko GW, H Kim, PJ Myler, TC Terwilliger, and CY Kim. 2012. "Chemical shift assignments for Rv0577, a putative glyoxylase associated with virulence from Mycobacterium tuberculosis ." Biomolecular NMR Assignments 6(1):43-46.  doi:10.1007/s12104-011-9322-5
  • Buchko GW, I Phan, L Cron, R Stacy, LJ Stewart, BL Staker, TE Edwards, G Varani, WC Van Voorhis, and PJ Myler. 2012. "Behind Every Good Metabolite there is a Great Enzyme (and perhaps a structure)." Metabolomics 2(6):Article No. e124. 
  • Jain A, GW Buchko, ML Reback, MJ O'Hagan, B Ginovska-Pangovska, JC Linehan, and WJ Shaw. 2012. "Active Hydrogenation Catalyst with a Structured, Peptide-Based Outer-Coordination Sphere." ACS Catalysis 2(10):2114-2118.  doi:10.1021/cs3004177
  • Jin H, Y Zhang, GW Buchko, SM Varnum, H Robinson, TC Squier, and PE Long. 2012. "Structure Determination and Functional Analysis of a Chromate Reductase from Gluconacetobacter hansenii." PLoS One 7(8):Article No. e42432.  doi:10.1371/journal.pone.0042432

2011

  • Buchko GW, I Phan, PJ Myler, TC Terwilliger, and CY Kim. 2011. "Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c." Archives of Biochemistry and Biophysics 506(2):150-156.  doi:10.1016/j.abb.2010.12.001
  • Buchko GW, SN Hewitt, AJ Napuli, WC Van Voorhis, and PJ Myler. 2011. "Solution structure of an arsenate reductase-related protein, YffB, from Brucella melitensis, the etiological agent responsible for brucellosis." Acta Crystallographica. Section F 67(9):1129-1136.  doi:10.1107/S1744309111006336
  • Buchko GW, SN Hewitt, AJ Napuli, WC Van Voorhis, and PJ Myler. 2011. "Solution-state NMR structure and biophysical characterization of zinc-substituted rubredoxin B (Rv3250c) from Mycobacterium tuberculosis." Acta Crystallographica. Section F 67(9):1148-1153.  doi:10.1107/S1744309111008189
  • Buchko GW, TE Edwards, J Abendroth, TL Arakaki, L Law, AJ Napuli, SN Hewitt, WC Van Voorhis, LJ Stewart, BL Staker, and PJ Myler. 2011. "Structure of a Nudix hydrolase (MutT) in the Mg2+ -bound state from Bartonella henselae, the bacterium responsible for cat scratch fever." Acta Crystallographica. Section F 67(9):1078-1083.  doi:10.1107/S1744309111011559
  • Buchko GW. 2011. "Structural genomics - A goldmine of blueprints for structure-based drug design." Metabolomics 1(2):104e.  doi:10.4172/2153-0769.1000104e
  • Zhang Y, GW Buchko, L Qin, H Robinson, and SM Varnum. 2011. "Crystal structure of the receptor binding domain of the botulinum C-D mosaic neurotoxin reveals potential roles of lysines 1118 and 1136 in membrane interactions." Biochemical and Biophysical Research Communications 404(1):407-412.  doi:10.1016/j.bbrc.2010.11.134
  • Stacy R, DW Begley, I Phan, BL Staker, WC Van Voorhis, G Varani, GW Buchko, LJ Stewart, and PJ Myler. 2011. "Structural genomics of infectious disease drug targets: the SSGCID." Acta Crystallographica. Section F 67(9):979-984.  doi:10.1107/S1744309111029204

2010

  • Buchko GW, CY Kim, TC Terwilliger, and PJ Myler. 2010. "Solution Structure of Rv2377c-Founding Member of the MbtH-Like Protein Family." Tuberculosis 90(4):245-251. 
  • Buchko GW, H Robinson, J Abendroth, BL Staker, and PJ Myler. 2010. "Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): Profound asymmetry in the crystal structure of the 'open' state ." Biochemical and Biophysical Research Communications 394(4):1012-1017. 
  • Buchko GW. 2010. "Circular Dichrosim Studies on the Deinococcus Radiodurans Nudix Hydrolase DR_0079: an Atypical Thermal Melt." Protein and Peptide Letters 17(7):831-835. 
  • Tang Z, H Wu, JR Cort, GW Buchko, Y Zhang, Y Shao, IA Aksay, J Liu, and Y Lin. 2010. "Constraint of DNA on Functionalized Graphene Improves Its Biostability and Specificity." Small 6(11):1205-1209.  doi:10.1002/smll.201000024
  • Zhang Y, GW Buchko, L Qin, H Robinson, and SM Varnum. 2010. "Structural analysis of the receptor binding domain of botulinum neurotoxin serotype D." Biochemical and Biophysical Research Communications 401:498-503.  doi:10.1016/j.bbrc.2010.09.063
  • Zhang Y, X Gao, L Qin, GW Buchko, H Robinson, and SM Varnum. 2010. "High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor binding domain of botulinum neurotoxin serotype D." Acta Crystallographica. Section F 66(12):1610-1613.  doi:10.1107/S1744309110039874
  • Buchko GW, BJ Tarasevich, J Roberts, ML Snead, and WJ Shaw. 2010. "A Solution NMR Investigation into the Murine Amelogenin Splice-Variant LRAP (Leucine-Rich Amelogenin Protein)." Biochimica et Biophysica Acta--Proteins and Proteomics 1804(9):1768-1774. 
  • Buchko GW, G Niemann, ES Baker, ME Belov, RD Smith, F Heffron, JN Adkins, and JE McDermott. 2010. "A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins." Molecular Biosystems 6(12):2448-2458.  doi:10.1039/c0mb00097c

2009

  • Buchko GW, H Robinson, and A Addlagatta. 2009. "Structural characterization of the protein cce_0567 from Cyanothece 51142, a metalloprotein associated with nitrogen fixation in the DUF683 family." Biochimica et Biophysica Acta--Proteins and Proteomics 1794(4):627-633. 
  • Buchko GW, SN Hewitt, AJ Napuli, WC Van Voorhis, and PJ Myler. 2009. "Backbone and side chain 1H, 13C, and 15N NMR assignments for the organic hydroperoxide resistance protein (Ohr) from Burkholderia pseudomallei. ." Biomolecular NMR Assignments 3(2):163-166.  doi:10.1007/s12104-009-9165-5
  • Buchko GW. 2009. "Pentapeptide Repeat Proteins and Cyanobacteria." In Handbook on Cyanobacteria: Biochemistry, Biotechnology and Applications, pp. 233-257.  Nova Science Publishers, Hauppauge, NY. 
  • Harvey SD, GW Buchko, RB Lucke, CW Wright, AM Melville, AJ Scott, and BW Wright. 2009. "The Structure and Purity of a Reference Dye Standard used for Quantification of C.I. Solvent Red 164 in Fuels." Dyes and Pigments 82(3):307-315.  doi:10.1016/j.dyepig.2009.01.015
  • Myler PJ, R Stacy, LJ Stewart, BL Staker, WC Van Voorhis, G Varani, and GW Buchko. 2009. "The Seattle Structure Genomics Center for Infectious Disease (SSGCID)." Infectious Disorders Drug Targets 9(5):493-506. 
  • Webb-Robertson BJM, LA McCue, N Beagley, JE McDermott, DS Wunschel, SM Varnum, JZ Hu, NG Isern, GW Buchko, K Mcateer, JG Pounds, SJ Skerret, D Liggitt, and CW Frevert. 2009. "A Bayesian Integration Model of High-Throughput Proteomics and Metabolomics Data for Improved Early Detection of Microbial Infections." In Pacific Symposium on Biocomputing, vol. 14, pp. 451-463.  World Scientific Publishing Co., Singapore, Singapore. 

2008

  • Buchko GW, H Robinson, HB Pakrasi, and MA Kennedy. 2008. "Insights into the structural variation between pentapeptide repeat proteins - Crystal structure of Rfr23 from Cyanothece 51142." Journal of Structural Biology 162(1):184-192. 
  • Buchko GW, O Litvinova, H Robinson, AF Yakunin, and MA Kennedy. 2008. "Functional and structural characterization of DR_0079 from Deinococcus radiodurans, a novel Nudix hydrolase with a preference for cytosine (deoxy) ribonucleoside 5'-di- and triphosphates." Biochemistry 47(25):6571-82. 
  • Buchko GW, JG Bekhazi, JR Cort, NB Valentine, ML Snead, and WJ Shaw. 2008. "1H, 13C, and 15N resonance assignments of murine amelogenin, an enamel biomineralization protein. ." Biomolecular NMR Assignments 2(1):89-91. 
  • Buchko GW, and HJ Sofia. 2008. "Backbone 1H, 13C, and 15N NMR assignments for the Cyanothece 51142 protein cce_0567: a protein associated with nitrogen fixation in the DUF683 family." Biomolecular NMR Assignments 2:25-28. 
  • Buchko GW, BJ Tarasevich, JG Bekhazi, ML Snead, and WJ Shaw. 2008. "A Solution NMR Investigation into the Early Events of Amelogenin Nanosphere Self-Assembly Initiated with Sodium Chloride or Calcium Chloride." Biochemistry 47(50):13215-13222.  doi:10.1021/bi8018288

2007

  • Buchko GW, S Ni, NM Lourette, RC Reeves, and MA Kennedy. 2007. "NMR resonance assignments of the human high mobility group protein HMGA1." Journal of Biomolecular NMR 38(2):185.  doi:10.1007/s10858-006-9116-8

2006

  • Buchko GW, and J Cadet. 2006. "Identification of the a and Anomers of 1-(2-Deoxy-D-Erythro-Pentofuranosyl)-Oxaluric Acid at the Site of Riboflavin-mediated Photooxidation of Guanine in 2'-Deoxyguanosine and Thymidylyl-(3'-5')-2'-Deoxyguanosine." Photochemistry and Photobiology 82(1):191-199. 
  • Buchko GW, CY Kim, TC Terwilliger, and MA Kennedy. 2006. "Solution Structure of the Conserved Hypothetical Protein Rv2302 from Mycobacterium tuberculosis. ." Journal of Bacteriology 188(16):5993-6001.  doi:10.1128/JB.00460-06
  • Buchko GW, H Robinson, S Ni, HB Pakrasi, and MA Kennedy. 2006. "Cloning, expression, crystallization and preliminary crystallographic analysis of a pentapeptide-repeat protein (Rfr23) from bacterium Cyanothece 511421." Acta Crystallographica. Section F 62(12):1251-1254.  doi:10.1107/S174430910604663X
  • Buchko GW, S Ni, H Robinson, EA Welsh, HB Pakrasi, and MA Kennedy. 2006. "Characterization of two potentially universal turn motifs that shape the repeated five-residues fold - Crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142." Protein Science 15(11):2579-2595. 

2005

  • Buchko GW, K McAteer, SS Wallace, and MA Kennedy. 2005. "Solution-state NMR Investigation of DNA Binding Interactions in Escherichia coli Formamidopyrimidine-DNA Glycosylase (Fpg): A Dynamic Description of the DNA/Protein Interface ." DNA Repair 4(3):327-339. 

2004

  • Buchko GW, S Ni, SR Holbrook, and MA Kennedy. 2004. "Solution Structure of Hypothetical Nudix Hydrolase DR0079 from Extremely Radiation-Resistant Deinococcus radiodurans Bacterium." Proteins. Structure, Function, and Bioinformatics 56(1):28-39. 
  • McAteer K, A Aceves Gaona, R Michalczyk, GW Buchko, NG Isern, LA Silks, JH Miller, and MA Kennedy. 2004. "Compensating Bends in a 16 base-pair DNA Oligomer Containing a T3A3 Segment: A NMR Study of Global DNA Curvature." Biopolymers 75(6):497-511. 

2003

  • Buchko GW, S Ni, SR Holbrook, and MA Kennedy. 2003. "H-1, C-13, and N-15 NMR assignments of the hypothetical Nudix protein DR0079 from the extremely radiation-resistant bacterium Deinococcus radiodurans." Journal of Biomolecular NMR 25(2):169-170. 
  • Daughdrill GW, GW Buchko, MV Botuyan, CH Arrowsmith, MS Wold, MA Kennedy, and DF Lowry. 2003. "Chemical shift changes provide evidence for overlapping single-stranded DNA and XPA binding sites on the 70 kDa subunit of human replication protein A." Nucleic Acids Research 31(14):4176-4183. 
  • Holbrook EL, U Schulze-Gahmen, GW Buchko, S Ni, MA Kennedy, and SR Holbrook. 2003. "Purification, crystallization and preliminary X-ray analysis of two Nudix hydrolases from Deinococcus radiodurans." Acta Crystallographica. Section D, Biological Crystallography 59(Pt.4):737-740. 

2002

  • Buchko GW, and M Weinfeld. 2002. "DNA-Targeted 2-Nitroimidazoles: Studies of the Influence of the Phenanthridine-Linked Nitroimidazoles, 2-NLP-3 and 2-NLP-4, on DNA Damage Induced by Ionizing Radiation." Radiation Research 158 (3):302-310. 
  • Buchko GW, SS Wallace, and MA Kennedy. 2002. "Base excision repair: NMR backbone assignments of Escherichia coli formamidopyrimidine-DNA glycosylase." Journal of Biomolecular NMR 22(3):301-302. 

2001

  • Buchko GW, and MA Kennedy. 2001. "Hydroxyapatite Elution Behavior of Human Nucleotide Excision Repair Protein XPA and Fragments of XPA." Protein and Peptide Letters 8 (5)(2001):357-365. 
  • Buchko GW, CS Tung, K Mcateer, NG Isern, LD Spicer, and MA Kennedy. 2001. "DNA-XPA Interactions: A 31P NMR Study of dCCAATAACC Association With the Minimal DNA-Binding Domain (M98-F219) of the Nucleotide Excision Repair Protein XPA." Nucleic Acids Research 29(12):2635-2643. 
  • Buchko GW, NG Isern, LD Spicer, and MA Kennedy. 2001. "Human Nucleotide Excision Repair Protein XPA: NMR Spectroscopic Studies of an XPA Fragment Containing the ERCC1-Binding Region and the Minimal DNA-Binding Domain (M59-F219)." Mutation Research 486(1):1-10. 
  • Lipton AS, GW Buchko, JA Sears, Jr, MA Kennedy, and PD Ellis. 2001. "Zn-67 Solid-State NMR Spectroscopy of the Minimal DNA Binding Domain of Human Nucleotide Excision Repair Protein XPA." Journal of the American Chemical Society 123(5):992-993. 

2000

  • Buchko GW, A Rozek, P Kanda, MA Kennedy, and RJ Cushley. 2000. "Structural Studies of a Baboon (Papio sp.) Plasma Protein Inhibitor of Cholesteryl Ester Transferase." Protein Science 9:1548-1558. 
  • Buchko GW, NJ Hess, and MA Kennedy. 2000. "Cadmium Mutagenicity and Human Nucleotide Excision Repair Protein XPA: CD, EXAFS, and 1H/15N NMR Spectroscopic Studies on the Zinc (II) and Cadmium (II) Associated Minimal DNA-Binding Domain." Carcinogenesis 21(5):1051-1057. 
  • Buchko GW, NJ Hess, and MA Kennedy. 2000. "Human Nucleotide Excision Repair Protein XPA: Summary of EXAFS Studies On the Zn (II), Co (II), and Cd (II) Associated Minimal DNA-Binding Domain." Protein and Peptide Letters 7(1):49-56. 
  • Buchko GW, NJ Hess, V Bandaru, SS Wallace, and MA Kennedy. 2000. "Spectroscopic Studies of Zinc (II) and Cobalt (II) Associated Escherichia Coli Formamidopyrimidine-DNA Glycosylase: Extended X-Ray Absorption Fine Structure Evidence for a Metal-Binding Domain." Biochemistry 39:12441-12449. 

1999

  • Buchko GW, GW Daughdrill, R De Lorimier, S Rao B K, NG Isern, JM Lingbeck, JS Taylor, MS Wold, M Gochin, LD Spicer, DF Lowry, and MA Kennedy. 1999. "Interactions of Human Nucleotide Excision Repair Protein XPA with DNA and RPA70 Delta c327: Chemical Shift Mapping and N-15 NMR Relaxation Studies." Biochemistry 38(46):15116-15128. 
  • Buchko GW, LM Iakoucheva, MA Kennedy, EJ Ackerman, and NJ Hess. 1999. "Extended X-ray Absorption Fine Structure Evidence for a Single Metal Binding Domain in Xenopus Laevis Nucleotide Excision Repair Protein XPA." Biochemical and Biophysical Research Communications 254(1):109-113. 

1998

  • Buchko GW, S Ni, BD Thrall, and MA Kennedy. 1998. "Structural Features of the Minimal DNA Binding Domain (M98-F219) of Human Nucleotide Excision Repair Protein XPA." Nucleic Acids Research 26(11):2779-2788. 

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