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Barry L Stoddard
Department of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States of America

Faculty Member: Chemical Biology > Biocatalysis [ since 7 August 2003 ]
[ Sponsorship ] [ Biography ] [ Evaluations ]
Sponsorship

Barry L Stoddard sponsors free access to F1000 for Institute of Biotechnology Vilnius, Vilnius, Lithuania. Supporting F1000's initiative to make itself available to scientists in all countries, including free access to developing countries (more details).

Biography

Barry Stoddard is a native of the Pacific Northwest, having lived in Northern Idaho and Washington State for all but seven years of his life. After graduating from Sandpoint High School in 1981, he attended Whitman College, graduating with a Bachelor¿s degree in Chemistry (Biology minor) in 1985. After a summer working for the Monsanto Corporation, he entered graduate school at the Massachusetts Institute of Technology, earning his doctoral degree in 1990 in Biophysical Chemistry for research on enzyme mechanism and structure using X-ray crystallography. Following a postdoctoral fellowship at the University of California at Berkeley, Dr. Stoddard joined the faculty at the Fred Hutchinson Cancer Research Center in 1992, teaching and supervising a research laboratory there ever since. Dr. Stoddard was promoted to Full Member status at the FHCRC in 1999, and was appointed associate director of Basic Sciences and director of the graduate program in Molecular and Cellular Biology in 2000. He also holds an affiliate faculty position at the University of Washington College of Medicine in the Department of Biochemistry.

Dr. Stoddard¿s research interests are in the structure, mechanism, and engineering of enzymatic catalysts for basic research and biomedical applications. His lab has conducted wide ranging research on gene-specific endonucleases, nucleotide synthesis and salvage enzymes, blood coagulation factors, and the development of time-resolved crystallographic methods. He has coauthored over 50 research articles and 20 reviews in these fields since 1990. Dr. Stoddard has also served as a consultant on several advisory boards, including those formed for industrial and NASA-sponsored research on microgravity crystallization, and for companies involved in structural biology instrumentation and methodologies.

Dr. Stoddard lives in Bellevue, Washington with his wife Amy, his sons Benjamin and Zachary, and a laborador retriever named Gracie. In his free time he enjoys skiiing and snowboarding, golfing, biking, reading and getting onto the mountains and waters of western Washington.

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Evaluations

A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA.
Martick M, Horan LH, Noller HF, Scott WG
Nature 2008 Aug 14 454(7206):899-902 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Robert Batey / Thorsten Dieckmann / Sabine Müller / Fritz Eckstein / Andres Jaschke / Barry Stoddard / Ian Willis / Eric Westhof
Evaluated 14 Aug 2008

Thioredoxin-mediated reversible dissociation of a stromal multiprotein complex in response to changes in light availability.
Howard TP, Metodiev M, Lloyd JC, Raines CA
Proc Natl Acad Sci U S A 2008 Mar 11 105(10):4056-61 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Lee Sweetlove / Barry Stoddard
Evaluated 3 Jul 2008

A purple acidophilic di-ferric DNA ligase from Ferroplasma.
Ferrer M, Golyshina OV, …, Timmis KN, Golyshin PN
Proc Natl Acad Sci U S A 2008 Jun 24 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard
Evaluated 2 Jul 2008

Enzyme structural plasticity and the emergence of broad-spectrum antibiotic resistance.
Maurice F, Broutin I, …, Collatz E, Dardel F
EMBO Rep 2008 Apr 9(4):344-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 26 Jun 2008

Tyl1a, a TDP-6-deoxy-D-xylo-4-hexulose 3,4-isomerase from Streptomyces fradiae: structure prediction, mutagenesis and solvent isotope incorporation experiments to investigate reaction mechanism.
Tello M, Rejzek M, …, Lawson DM, Field RA
Chembiochem 2008 May 23 9(8):1295-302 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 26 Jun 2008

Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase.
Taouatas N, Drugan MM, Heck AJ, Mohammed S
Nat Methods 2008 May 5(5):405-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 22 May 2008

Kemp elimination catalysts by computational enzyme design.
Röthlisberger D, Khersonsky O, …, Tawfik DS, Baker D
Nature 2008 May 8 453(7192):190-5 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard / Reinhard Sterner / Russ Hille / Andreas Marx / Alfred Wittinghofer / Gabriele Varani
Evaluated 9 Apr 2008

Engineering Protein Allostery: 1.05 A Resolution Structure and Enzymatic Properties of a Na(+)-activated Trypsin.
Page MJ, Carrell CJ, Di Cera E
J Mol Biol 2008 Mar 18 [abstract on PubMed] [related articles] [full text]
Selected by | Barry Stoddard
Evaluated 8 Apr 2008

Structural identification of the pathway of long-range communication in an allosteric enzyme.
Gandhi PS, Chen Z, Mathews FS, Di Cera E
Proc Natl Acad Sci U S A 2008 Feb 12 105(6):1832-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard / Xiayang Qiu
Evaluated 13 Feb 2008

Accurate prediction of enzyme mutant activity based on a multibody statistical potential.
Masso M, Vaisman II
Bioinformatics 2007 Dec 1 23(23):3155-61 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 2 Jan 2008

Crystal structure of the DNA repair enzyme ultraviolet damage endonuclease.
Paspaleva K, Thomassen E, …, Goosen N, Abrahams JP
Structure 2007 Oct 15(10):1316-24 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 2 Jan 2008

Targeting the absence: homozygous DNA deletions as immutable signposts for cancer therapy.
Varshavsky A
Proc Natl Acad Sci U S A 2007 Sep 18 104(38):14935-40 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 15 Oct 2007

The chemistry of protein catalysis.
Holliday GL, Almonacid DE, Mitchell JB, Thornton JM
J Mol Biol 2007 Oct 5 372(5):1261-77 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 11 Oct 2007

Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme.
St Maurice M, Reinhardt L, …, Cleland WW, Rayment I
Science 2007 Aug 24 317(5841):1076-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 11 Sep 2007

Structure and action of the N-oxygenase AurF from Streptomyces thioluteus.
Zocher G, Winkler R, Hertweck C, Schulz GE
J Mol Biol 2007 Oct 12 373(1):65-74 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 11 Sep 2007

Metal-ion-dependent GFP emission in vivo by combining a circularly permutated green fluorescent protein with an engineered metal-ion-binding coiled-coil.
Mizuno T, Murao K, …, Oda M, Tanaka T
J Am Chem Soc 2007 Sep 19 129(37):11378-83 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard / Martin Gruebele
Evaluated 5 Sep 2007

Cleaving mercury-alkyl bonds: a functional model for mercury detoxification by MerB.
Melnick JG, Parkin G
Science 2007 Jul 13 317(5835):225-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 2 Aug 2007

Bacterial DUF199/COG1481 proteins including sporulation regulator WhiA are distant homologs of LAGLIDADG homing endonucleases that retained only DNA binding.
Knizewski L, Ginalski K
Cell Cycle 2007 Jul 6(13):1666-70 [abstract on PubMed] [related articles] [order article]
Selected by | Barry Stoddard
Evaluated 24 Jul 2007

The design and characterization of two proteins with 88% sequence identity but different structure and function.
Alexander PA, He Y, …, Orban J, Bryan PN
Proc Natl Acad Sci U S A 2007 Jul 17 104(29):11963-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard / Nick Grishin / Tobin Sosnick
Evaluated 24 Jul 2007

Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate.
Nandakumar J, Nair PA, Shuman S
Mol Cell 2007 Apr 27 26(2):257-71 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 12 Jun 2007

Ligand binding and allostery can emerge simultaneously.
Liang J, Kim JR, …, Mansell TJ, Ostermeier M
Protein Sci 2007 May 16(5):929-37 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 14 May 2007

A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences.
Smith J, Grizot S, …, Pâques F, Duchateau P
Nucleic Acids Res 2006 34(22):e149 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard
Evaluated 1 May 2007

Three microtubule severing enzymes contribute to the "Pacman-flux" machinery that moves chromosomes.
Zhang D, Rogers GC, Buster DW, Sharp DJ
J Cell Biol 2007 Apr 23 177(2):231-42 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard / Jonathan Scholey
Evaluated 1 May 2007

Site-specific DNA transesterification catalyzed by a restriction enzyme.
Sasnauskas G, Connolly BA, Halford SE, Siksnys V
Proc Natl Acad Sci U S A 2007 Feb 13 104(7):2115-20 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard / Janet Morrow
Evaluated 20 Feb 2007

Investigation of a general base mechanism for ester hydrolysis in C-C hydrolase enzymes of the alpha/beta-hydrolase superfamily: a novel mechanism for the serine catalytic triad.
Li JJ, Bugg TD
Org Biomol Chem 2007 Feb 7 5(3):507-13 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 14 Feb 2007

The c-Myc target gene Rcl (C6orf108) encodes a novel enzyme, deoxynucleoside 5'-monophosphate N-glycosidase.
Ghiorghi YK, Zeller KI, Dang CV, Kaminski PA
J Biol Chem 2007 Mar 16 282(11):8150-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 14 Feb 2007

Structure of dual function iron regulatory protein 1 complexed with ferritin IRE-RNA.
Walden WE, Selezneva AI, …, Theil EC, Volz K
Science 2006 Dec 22 314(5807):1903-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard / Walter Chazin / Russ Hille / Angela Wilks / Daniel Gallie
Evaluated 11 Jan 2007

Structural basis of glmS ribozyme activation by glucosamine-6-phosphate.
Klein DJ, Ferré-D'Amaré AR
Science 2006 Sep 22 313(5794):1752-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Robert Batey / Günter Mayer / David Waugh / Barry Stoddard
Evaluated 30 Nov 2006

Structure of a DNA glycosylase searching for lesions.
Banerjee A, Santos WL, Verdine GL
Science 2006 Feb 24 311(5764):1153-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | James Stivers / Walter Chazin / Barry Stoddard
Evaluated 29 Nov 2006

An antigen produced by splicing of noncontiguous peptides in the reverse order.
Warren EH, Vigneron NJ, …, Riddell SR, Van den Eynde BJ
Science 2006 Sep 8 313(5792):1444-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Laurence Eisenlohr / Peter Jensen / Barry Stoddard
Evaluated 29 Nov 2006

Chimeric thermostable DNA polymerases with reverse transcriptase and attenuated 3'-5' exonuclease activity.
Schönbrunner NJ, Fiss EH, …, Gelfand DH, Myers TW
Biochemistry 2006 Oct 24 45(42):12786-95 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 29 Nov 2006

Exploiting the reversibility of natural product glycosyltransferase-catalyzed reactions.
Zhang C, Griffith BR, …, Li L, Thorson JS
Science 2006 Sep 1 313(5791):1291-4 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard
Evaluated 3 Oct 2006

Crystal structure of alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase: insight into the active site and catalytic mechanism of a novel decarboxylation reaction.
Martynowski D, Eyobo Y, …, Liu A, Zhang H
Biochemistry 2006 Sep 5 45(35):10412-21 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 3 Oct 2006

B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes.
Bielnicki J, Devedjiev Y, …, Joachimiak A, Derewenda ZS
Proteins 2006 Jan 1 62(1):144-51 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 13 Sep 2006

Transcript-assisted transcriptional proofreading.
Zenkin N, Yuzenkova Y, Severinov K
Science 2006 Jul 28 313(5786):518-20 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Brent Iverson / Barry Stoddard / Gabriele Varani
Evaluated 13 Sep 2006

The guanidino-group modifying enzymes: structural basis for their diversity and commonality.
Shirai H, Mokrab Y, Mizuguchi K
Proteins 2006 Sep 1 64(4):1010-23 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 23 Jun 2006

Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease.
Bochtler M, Szczepanowski RH, …, Manakova E, Siksnys V
EMBO J 2006 May 17 25(10):2219-29 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Alfred Pingoud / Barry Stoddard
Evaluated 20 Jun 2006

Multipass membrane protein structure prediction using Rosetta.
Yarov-Yarovoy V, Schonbrun J, Baker D
Proteins 2006 Mar 1 62(4):1010-25 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard
Evaluated 21 Apr 2006

Molecular basis of inhibition of the ribonuclease activity in colicin E5 by its cognate immunity protein.
Luna-Chávez C, Lin YL, Huang RH
J Mol Biol 2006 Apr 28 358(2):571-9 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 21 Apr 2006

Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets.
Arnould S, Chames P, …, Duchateau P, Pâques F
J Mol Biol 2006 Jan 20 355(3):443-58 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 27 Mar 2006

Electron trap for DNA-bound repair enzymes: a strategy for DNA-mediated signaling.
Yavin E, Stemp ED, …, David SS, Barton JK
Proc Natl Acad Sci U S A 2006 Mar 7 103(10):3610-4 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard
Evaluated 8 Mar 2006

Computational design of a single amino acid sequence that can switch between two distinct protein folds.
Ambroggio XI, Kuhlman B
J Am Chem Soc 2006 Feb 1 128(4):1154-61 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 2 Mar 2006

Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III.
Gan J, Tropea JE, …, Waugh DS, Ji X
Cell 2006 Jan 27 124(2):355-66 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 2 Mar 2006

Chaperone holdase activity of human papillomavirus E7 oncoprotein.
Alonso LG, Smal C, …, Salame M, de Prat-Gay G
Biochemistry 2006 Jan 24 45(3):657-67 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 25 Jan 2006

Genomic mining for Aspergillus natural products.
Bok JW, Hoffmeister D, …, Glasner JD, Keller NP
Chem Biol 2006 Jan 13(1):31-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard / David Newman
Evaluated 25 Jan 2006

Direct observation of base-pair stepping by RNA polymerase.
Abbondanzieri EA, Greenleaf WJ, …, Landick R, Block SM
Nature 2005 Nov 24 438(7067):460-5 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Manfred Schliwa / Barry Stoddard
Evaluated 22 Dec 2005

Rev1 employs a novel mechanism of DNA synthesis using a protein template.
Nair DT, Johnson RE, …, Prakash S, Aggarwal AK
Science 2005 Sep 30 309(5744):2219-22 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Fred Dyda / Larry McLaughlin / Martin Egli / Lucio Comai / Barry Stoddard
Evaluated 27 Oct 2005

Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease.
Grazulis S, Manakova E, …, Huber R, Siksnys V
Proc Natl Acad Sci U S A 2005 Nov 1 102(44):15797-802 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard / Alfred Pingoud
Evaluated 27 Oct 2005

A novel peptidoglycan cross-linking enzyme for a beta-lactam-resistant transpeptidation pathway.
Mainardi JL, Fourgeaud M, …, Gutmann L, Arthur M
J Biol Chem 2005 Nov 18 280(46):38146-52 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard
Evaluated 15 Sep 2005

Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing.
Macbeth MR, Schubert HL, …, Hill CP, Bass BL
Science 2005 Sep 2 309(5740):1534-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Wen-hong Li / Barry Stoddard / Kathleen Hall / Susan Wente / Gloria Culver / Song Tan
Evaluated 15 Sep 2005

Expanding the range of substrate acceptance of enzymes: combinatorial active-site saturation test.
Reetz MT, Bocola M, …, Zha D, Vogel A
Angew Chem Int Ed Engl 2005 Jul 4 44(27):4192-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 1 Sep 2005

Cryptic chlorination by a non-haem iron enzyme during cyclopropyl amino acid biosynthesis.
Vaillancourt FH, Yeh E, …, O'Connor SE, Walsh CT
Nature 2005 Aug 25 436(7054):1191-4 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard / Rowena Matthews / Wilhelm Boland / Mark Nelson
Evaluated 1 Sep 2005

Scission of the lactyl ether bond of N-acetylmuramic acid by Escherichia coli "etherase".
Jaeger T, Arsic M, Mayer C
J Biol Chem 2005 Aug 26 280(34):30100-6 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard
Evaluated 29 Jul 2005

Evolution of new nonantibody proteins via iterative somatic hypermutation.
Wang L, Jackson WC, Steinbach PA, Tsien RY
Proc Natl Acad Sci U S A 2004 Nov 30 101(48):16745-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Tullio Pozzan / James Hu / Mark Nelson / Barry Stoddard
Evaluated 29 Jul 2005

Ancient origin of glycosyl hydrolase family 9 cellulase genes.
Davison A, Blaxter M
Mol Biol Evol 2005 May 22(5):1273-84 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard
Evaluated 21 Jun 2005

Interdomain communication in hepatitis C virus polymerase abolished by small molecule inhibitors bound to a novel allosteric site.
Di Marco S, Volpari C, …, Migliaccio G, Carfí A
J Biol Chem 2005 Aug 19 280(33):29765-70 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard / Liang Tong
Evaluated 21 Jun 2005

RecN protein and transcription factor DksA combine to promote faithful recombinational repair of DNA double-strand breaks.
Meddows TR, Savory AP, …, Moore T, Lloyd RG
Mol Microbiol 2005 Jul 57(1):97-110 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 21 Jun 2005

Engineering of vault nanocapsules with enzymatic and fluorescent properties.
Kickhoefer VA, Garcia Y, …, Stewart PL, Rome LH
Proc Natl Acad Sci U S A 2005 Mar 22 102(12):4348-52 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard
Evaluated 20 May 2005

Thioredoxin reductase is irreversibly modified by curcumin: a novel molecular mechanism for its anticancer activity.
Fang J, Lu J, Holmgren A
J Biol Chem 2005 Jul 1 280(26):25284-90 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard
Evaluated 19 May 2005

Highly efficient endogenous human gene correction using designed zinc-finger nucleases.
Urnov FD, Miller JC, …, Gregory PD, Holmes MC
Nature 2005 Jun 2 435(7042):646-51 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard / John Cambier / Makoto Komiyama / Daniel Reines / Charles Coutelle
Evaluated 8 Apr 2005

Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site.
Feder M, Bujnicki JM
BMC Genomics 2005 6(1):21 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Barry Stoddard
Evaluated 24 Mar 2005

The use of carbohydrate microarrays to study carbohydrate-cell interactions and to detect pathogens.
Disney MD, Seeberger PH
Chem Biol 2004 Dec 11(12):1701-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Barry Stoddard
Evaluated 3 Feb 2005