George N Phillips

Summary

Affiliation: University of Wisconsin
Country: USA

Publications

  1. ncbi Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics
    George N Phillips
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    J Struct Funct Genomics 8:73-84. 2007
  2. ncbi The structure at 1.7 A resolution of the protein product of the At2g17340 gene from Arabidopsis thaliana
    Eduard Bitto
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:630-5. 2005
  3. ncbi Structural basis for catalysis by onconase
    J Eugene Lee
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706 1544, USA
    J Mol Biol 375:165-77. 2008
  4. ncbi Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family
    Robert C Tyler
    Center for Eukaryotic Structural Genomics, Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706 1544, USA
    Biochemistry 45:14325-36. 2006
  5. ncbi Structure and mechanism of an ADP-glucose phosphorylase from Arabidopsis thaliana
    Jason G McCoy
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Biochemistry 45:3154-62. 2006
  6. ncbi Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana
    Simon T M Allard
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:647-50. 2005
  7. ncbi X-ray structure of ILL2, an auxin-conjugate amidohydrolase from Arabidopsis thaliana
    Eduard Bitto
    Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, Madison, Wisconsin 53706 1544, USA
    Proteins 74:61-71. 2009
  8. ncbi Structure of human J-type co-chaperone HscB reveals a tetracysteine metal-binding domain
    Eduard Bitto
    Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, Madison, Wisconsin 53706 1544, USA
    J Biol Chem 283:30184-92. 2008
  9. ncbi Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000
    David J Aceti
    Department of Biochemistry, The Center for Eukaryotic Structural Genomics, University of Wisconsin at Madison, Madison, Wisconsin 53706, USA
    Proteins 73:241-53. 2008
  10. ncbi Structure and mechanism of mouse cysteine dioxygenase
    Jason G McCoy
    Center for Eukaryotic Structural Genomics and Department of Biochemistry, University of Wisconsin, Madison, 53706 1544, USA
    Proc Natl Acad Sci U S A 103:3084-9. 2006

Collaborators

Detail Information

Publications90

  1. ncbi Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics
    George N Phillips
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    J Struct Funct Genomics 8:73-84. 2007
    ..Many times proteins qualify in more than one of these categories. Here we review some of the structures that have connections to human health and disease...
  2. ncbi The structure at 1.7 A resolution of the protein product of the At2g17340 gene from Arabidopsis thaliana
    Eduard Bitto
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:630-5. 2005
    ..The structure of At2g17340 represents a new fold in protein conformational space...
  3. ncbi Structural basis for catalysis by onconase
    J Eugene Lee
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706 1544, USA
    J Mol Biol 375:165-77. 2008
    ..No variant, however, was more toxic to human cancer cells than wild-type ONC. Together, these findings provide a cynosure for understanding catalysis of RNA cleavage in a system of high medicinal relevance...
  4. ncbi Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family
    Robert C Tyler
    Center for Eukaryotic Structural Genomics, Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin Madison, 433 Babcock Drive, Madison, Wisconsin 53706 1544, USA
    Biochemistry 45:14325-36. 2006
    ..This work establishes that the domain family COG2388 represents a novel class of acetyltransferase and provides insight into possible mechanistic roles of the conserved Cys76 and His41 residues of this family...
  5. ncbi Structure and mechanism of an ADP-glucose phosphorylase from Arabidopsis thaliana
    Jason G McCoy
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Biochemistry 45:3154-62. 2006
    ..The value of K(eq) in the direction of ADP and glucose-1-P formation is 5.0 at pH 7.0 and 25 degrees C in the absence of a divalent metal ion, and it is 40 in the presence of 1 mM MgCl(2)...
  6. ncbi Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana
    Simon T M Allard
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:647-50. 2005
    ..Protein At3g22680 shows no structural homology to any other known proteins and represents a new fold in protein conformation space...
  7. ncbi X-ray structure of ILL2, an auxin-conjugate amidohydrolase from Arabidopsis thaliana
    Eduard Bitto
    Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, Madison, Wisconsin 53706 1544, USA
    Proteins 74:61-71. 2009
    ..Overall, the structure of ILL2 suggests that this enzyme likely uses a catalytic mechanism that follows the paradigm established for the other enzymes of the M20 peptidase family...
  8. ncbi Structure of human J-type co-chaperone HscB reveals a tetracysteine metal-binding domain
    Eduard Bitto
    Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, Madison, Wisconsin 53706 1544, USA
    J Biol Chem 283:30184-92. 2008
    ..The normal mode analysis of HscB revealed that this L-shaped protein preferentially undergoes a scissors-like motion that correlates well with the conformational changes of human HscB observed in the crystals...
  9. ncbi Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000
    David J Aceti
    Department of Biochemistry, The Center for Eukaryotic Structural Genomics, University of Wisconsin at Madison, Madison, Wisconsin 53706, USA
    Proteins 73:241-53. 2008
    ..Divalent metal cations were not required for activity and had little effect on the reaction...
  10. ncbi Structure and mechanism of mouse cysteine dioxygenase
    Jason G McCoy
    Center for Eukaryotic Structural Genomics and Department of Biochemistry, University of Wisconsin, Madison, 53706 1544, USA
    Proc Natl Acad Sci U S A 103:3084-9. 2006
    ..Details of the predicted active site are used to present and discuss a plausible mechanism of action for the enzyme...
  11. ncbi Comparison of cell-based and cell-free protocols for producing target proteins from the Arabidopsis thaliana genome for structural studies
    Robert C Tyler
    Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Wisconsin 53706, USA
    Proteins 59:633-43. 2005
    ..coli platform when successful yields more protein, as currently needed for crystallization trials for X-ray structure determination...
  12. ncbi Structure of aspartoacylase, the brain enzyme impaired in Canavan disease
    Eduard Bitto
    Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706 1544, USA
    Proc Natl Acad Sci U S A 104:456-61. 2007
    ..The structures also provide a structural framework necessary for understanding the deleterious effects of many missense mutations of human aspartoacylase...
  13. ncbi Structure of an ETHE1-like protein from Arabidopsis thaliana
    Jason G McCoy
    Department of Biochemistry and Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, WI, USA
    Acta Crystallogr D Biol Crystallogr 62:964-70. 2006
    ..In addition, the Arabidopsis ETHE1 protein is used as a model to explain the significance of several mutations in the human enzyme that have been observed in patients with ethylmalonic encephalopathy...
  14. ncbi Discovery of sarcosine dimethylglycine methyltransferase from Galdieria sulphuraria
    Jason G McCoy
    Center for Eukaryotic Structural Genomics and Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    Proteins 74:368-77. 2009
    ..1 degrees C. Modeling of cofactor binding in the active site based on the structure of methoxy mycolic acid synthase 2 revealed a number of conserved interactions within the active site...
  15. ncbi The structure at 2.4 A resolution of the protein from gene locus At3g21360, a putative Fe(II)/2-oxoglutarate-dependent enzyme from Arabidopsis thaliana
    Eduard Bitto
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA
    Acta Crystallograph Sect F Struct Biol Cryst Commun 61:469-72. 2005
    ..The metal-binding site was defined and is similar to the iron(II) binding sites found in other members of the superfamily...
  16. ncbi Structural characterization of CalO2: a putative orsellinic acid P450 oxidase in the calicheamicin biosynthetic pathway
    Jason G McCoy
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706 1544, USA
    Proteins 74:50-60. 2009
    ....
  17. ncbi Membrane association, mechanism of action, and structure of Arabidopsis embryonic factor 1 (FAC1)
    Byung Woo Han
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    J Biol Chem 281:14939-47. 2006
    ....
  18. ncbi Structure and dynamics of UDP-glucose pyrophosphorylase from Arabidopsis thaliana with bound UDP-glucose and UTP
    Jason G McCoy
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    J Mol Biol 366:830-41. 2007
    ..The structures and the observed dynamic changes provide insight into the ordered mechanism of this enzyme and previously described oligomerization effects on catalytic activity...
  19. ncbi Structural analysis of fish versus mammalian hemoglobins: effect of the heme pocket environment on autooxidation and hemin loss
    Roman Aranda
    Department of Biomolecular Chemistry, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Proteins 75:217-30. 2009
    ..Generally rapid rates of lipid oxidation in fish muscle can be partly attributed to the fact that fish Hbs are highly susceptible to oxidative degradation...
  20. ncbi Structural characterization of the mitomycin 7-O-methyltransferase
    Shanteri Singh
    Division of Pharmaceutical Sciences, Wisconsin Center for Natural Product Research, School of Pharmacy, University of Wisconsin Madison, Madison, Wisconsin 53705, USA
    Proteins 79:2181-8. 2011
    ..Given the importance of C7 alkylation to modulate mitomycin redox potential, this study may also present a template toward the future engineering of catalysts to generate uniquely bioactive mitomycins...
  21. ncbi X-ray crystal structures of the conserved hypothetical proteins from Arabidopsis thaliana gene loci At5g11950 and AT2g37210
    Won Bae Jeon
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
    Proteins 65:1051-4. 2006
  22. ncbi The Center for Eukaryotic Structural Genomics
    John L Markley
    Center for Eukaryotic Structural Genomics, Biochemistry Department, University of Wisconsin Madison, Madison, WI 53706, USA
    J Struct Funct Genomics 10:165-79. 2009
    ....
  23. ncbi Structural consequences of effector protein complex formation in a diiron hydroxylase
    Lucas J Bailey
    Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706 1544, USA
    Proc Natl Acad Sci U S A 105:19194-8. 2008
    ..This description provides insight into the functional role of effector protein binding in all carboxylate-bridged diiron hydroxylases...
  24. ncbi Creating protein models from electron-density maps using particle-filtering methods
    Frank DiMaio
    Department of Computer Sciences, University of Wisconsin, Madison, WI 53706, USA
    Bioinformatics 23:2851-8. 2007
    ..Here, we use a sampling method known as particle filtering to produce a set of all-atom protein models. We use the output of ACMI to guide the particle filter's sampling, producing an accurate, physically feasible set of structures...
  25. ncbi The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1
    Christopher M Bianchetti
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Proteins 78:917-31. 2010
    ..However, one of the two human homologs of nitrobindin contains a THAP domain, implying a possible role in apoptosis. Proteins 2010. (c) 2009 Wiley-Liss, Inc...
  26. ncbi Crystal structure of the protein from gene At3g17210 of Arabidopsis thaliana
    Craig A Bingman
    Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
    Proteins 57:218-20. 2004
  27. ncbi Structure and mechanism of the rebeccamycin sugar 4'-O-methyltransferase RebM
    Shanteri Singh
    Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin, Madison, Wisconsin 53705, USA
    J Biol Chem 283:22628-36. 2008
    ....
  28. ncbi X-ray structure of a soluble Rieske-type ferredoxin from Mus musculus
    Elena J Levin
    Department of Biochemistry, University of Wisconsin, Madison, USA
    Acta Crystallogr D Biol Crystallogr 64:933-40. 2008
    ..Based on its high sequence identity, the structure of the human homolog is likely to be modeled well by the mouse Rieske-type ferredoxin structure...
  29. ncbi Small-scale, semi-automated purification of eukaryotic proteins for structure determination
    Ronnie O Frederick
    The University of Wisconsin Center for Eukaryotic Structural Genomics and Department of Biochemistry, University of Wisconsin, Room 141B, 433 Babcock Drive, Madison, WI 53706, USA
    J Struct Funct Genomics 8:153-66. 2007
    ....
  30. ncbi A graphical approach to tracking and reporting target status in structural genomics
    Xiaokang Pan
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706, USA
    J Struct Funct Genomics 8:209-16. 2007
    ..This software package has facilitated inter-group communication, improved the quality and accuracy of information in our LIMS, and increased the efficiency and accuracy of our reports to PepcDB...
  31. ncbi Inhibition of human pancreatic ribonuclease by the human ribonuclease inhibitor protein
    R Jeremy Johnson
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706 1544, USA
    J Mol Biol 368:434-49. 2007
    ..Together, these results provide new insight into an unusual and important protein-protein interaction, and could expedite the development of human ribonucleases as chemotherapeutic agents...
  32. ncbi Structure of pyrimidine 5'-nucleotidase type 1. Insight into mechanism of action and inhibition during lead poisoning
    Eduard Bitto
    Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, Wisconsin 53706 1544, USA
    J Biol Chem 281:20521-9. 2006
    ..35 A) revealed that Pb(II) binds within the active site in a way that compromises function of the cationic cavity, which is required for the recognition and binding of the phosphate group of nucleotides...
  33. ncbi Optimal design of thermally stable proteins
    Ryan M Bannen
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    Bioinformatics 24:2339-43. 2008
    ..The minimization problem is modeled as a shortest path problem in an acyclic graph with nonnegative weights and is solved efficiently using Dijkstra's method...
  34. ncbi Interconversion of functional motions between mesophilic and thermophilic adenylate kinases
    Michael D Daily
    Department of Chemistry, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS Comput Biol 7:e1002103. 2011
    ..This mutational framework can inform the rational design of functionally important flexibility and allostery in other proteins toward engineering novel biochemical pathways...
  35. ncbi Time-dependent atomic coordinates for the dissociation of carbon monoxide from myoglobin
    Roman Aranda
    Department of Biomolecular Chemistry, University of Wisconsin, Madison, USA
    Acta Crystallogr D Biol Crystallogr 62:776-83. 2006
    ....
  36. ncbi Structure and dynamics of gamma-SNAP: insight into flexibility of proteins from the SNAP family
    Eduard Bitto
    Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, Madison, Wisconsin 53706 1544, USA
    Proteins 70:93-104. 2008
    ..We discuss possible consequences related to the flexibility of the SNAP proteins for the mechanism of the 20S complex disassembly during the SNAP receptors recycling...
  37. ncbi Structural characterization of CalO1: a putative orsellinic acid methyltransferase in the calicheamicin-biosynthetic pathway
    Aram Chang
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Acta Crystallogr D Biol Crystallogr 67:197-203. 2011
    ..Consistent with the proposed requirement of an acyl-carrier-protein-bound substrate, this structural study also reveals structural determinants within CalO1 that are anticipated to accommodate an association with an acyl carrier protein...
  38. ncbi Crystal structure of Homo sapiens thialysine Nepsilon-acetyltransferase (HsSSAT2) in complex with acetyl coenzyme A
    Byung Woo Han
    Department of Biochemistry, University of Wisconsin-Madison, 53706-1544, USA
    Proteins 64:288-93. 2006
  39. ncbi The structure at 1.6 Angstroms resolution of the protein product of the At4g34215 gene from Arabidopsis thaliana
    Eduard Bitto
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, USA
    Acta Crystallogr D Biol Crystallogr 61:1655-61. 2005
    ..This residue is positioned in a catalytically competent conformation by nearby residues, including Gln159, Gly160 and Glu161, which are fully conserved in the carbohydrate esterase family 6 enzymes...
  40. ncbi A probabilistic approach to protein backbone tracing in electron density maps
    Frank DiMaio
    Computer Sciences Dept, University of Wisconsin Madison, USA
    Bioinformatics 22:e81-9. 2006
    ..We test ACMI on a set of ten protein density maps (at 2.5 to 4.0 A resolution), and compare our results to alternative approaches. At these resolutions, ACMI offers a more accurate backbone trace than current approaches...
  41. ncbi X-ray structure of Danio rerio secretagogin: A hexa-EF-hand calcium sensor
    Eduard Bitto
    Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, 53706 1544, USA
    Proteins 76:477-83. 2009
    ....
  42. ncbi Application of elastic network models to proteins in the crystalline state
    Demian Riccardi
    Program of Computation and Informatics in Biology and Medicine, University of Wisconsin Madison, Madison, Wisconsin, USA
    Biophys J 96:464-75. 2009
    ..Finally, investigation of the scaling behaviors of the cumulative density of states and the heat capacity indicates that there are still gaps between simplified elastic models and all-atom models for proteins...
  43. ncbi Roles of static and dynamic domains in stability and catalysis of adenylate kinase
    Euiyoung Bae
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 103:2132-7. 2006
    ..Our results highlight specific contributions of dynamics to catalysis in adenylate kinase. Furthermore, the overall strategy and the specific mutagenesis method used in this study can be generally applied...
  44. ncbi Effect of low-complexity regions on protein structure determination
    Ryan M Bannen
    Department of Biochemistry, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53711, USA
    J Struct Funct Genomics 8:217-26. 2007
    ....
  45. ncbi Structure of cellobiose phosphorylase from Clostridium thermocellum in complex with phosphate
    Christopher M Bianchetti
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 67:1345-9. 2011
    ..The 2.4 Å resolution X-ray crystal structure of C. thermocellum CBP reveals the residues involved in coordinating the catalytic phosphate as well as the residues that are likely to be involved in substrate binding and discrimination...
  46. ncbi Complete set of glycosyltransferase structures in the calicheamicin biosynthetic pathway reveals the origin of regiospecificity
    Aram Chang
    Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 108:17649-54. 2011
    ..Multiple glycosyltransferase structures in a single natural product biosynthetic pathway are a valuable resource for understanding regiospecific reactions and substrate selectivities and will help future glycosyltransferase engineering...
  47. ncbi Protein structural variation in computational models and crystallographic data
    Dmitry A Kondrashov
    Department of Biochemistry, University of Wisconsin, Madison, Madison, WI 53706, USA
    Structure 15:169-77. 2007
    ..The comprehensive evaluation demonstrates the costs and benefits of using normal mode potentials of varying complexity...
  48. ncbi Spherical-harmonic decomposition for molecular recognition in electron-density maps
    Frank P DiMaio
    Department of Computer Sciences, University of Wisconsin, 1210 W Dayton St, Madison, WI, USA
    Int J Data Min Bioinform 3:205-27. 2009
    ..We show our new template-matching method improves accuracy and reduces running time, compared to previous approaches. Finally, we extend our method to produce a structural-homology detection algorithm using electron density...
  49. ncbi The structure of flavin-dependent tryptophan 7-halogenase RebH
    Eduard Bitto
    Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
    Proteins 70:289-93. 2008
  50. ncbi The structure at 2.5 A resolution of human basophilic leukemia-expressed protein BLES03
    Eduard Bitto
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:812-7. 2005
    ..It is hypothesized that BLES03 itself may be involved in a biochemical process that requires recognition of nucleic acids...
  51. ncbi Crystal structure of gene locus At3g16990 from Arabidopsis thaliana
    Paul G Blommel
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
    Proteins 57:221-2. 2004
  52. ncbi A phyloproteomic characterization of in vitro autophosphorylation in calcium-dependent protein kinases
    Adrian D Hegeman
    University of Wisconsin Biotechnology Center, Madison, 53706, USA
    Proteomics 6:3649-64. 2006
    ..Homology models were generated for the protein kinase and calmodulin-like domains, each containing two of the five conserved sites, to allow intelligent speculation regarding subsequent lines of investigation...
  53. ncbi Protocols for production of selenomethionine-labeled proteins in 2-L polyethylene terephthalate bottles using auto-induction medium
    Hassan K Sreenath
    Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, 433 Babcock Drive, Madison, WI 53706 1549, USA
    Protein Expr Purif 40:256-67. 2005
    ..These protein preparations have been utilized to solve X-ray crystal structures by multiwavelength anomalous diffraction phasing...
  54. ncbi Structure of T4moC, the Rieske-type ferredoxin component of toluene 4-monooxygenase
    Luke A Moe
    Department of Biochemistry, University of Wisconsin-Madison, USA
    Acta Crystallogr D Biol Crystallogr 62:476-82. 2006
    ..These structural differences are identified as possible contributors to the evolutionary specialization of soluble Rieske-type ferredoxins between the diiron monooxygenases and cis-dihydrodiol-forming dioxygenases...
  55. ncbi Crystal structure of At2g03760, a putative steroid sulfotransferase from Arabidopsis thaliana
    David W Smith
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
    Proteins 57:854-7. 2004
  56. ncbi Comparison of apo- and heme-bound crystal structures of a truncated human heme oxygenase-2
    Christopher M Bianchetti
    Graduate Program in Biophysics, Center for Eukaryotic Structural Genomics, University of Wisconsin, Madison, WI 53706, USA
    J Biol Chem 282:37624-31. 2007
    ..Tyr(154), Lys(199), and Arg(203) orient the heme through direct interactions with the heme propionates. The rearrangements of side chains in heme-bound HO-2 compared with apoHO-2 further elucidate HO-2 heme interactions...
  57. ncbi Expanding the nucleotide and sugar 1-phosphate promiscuity of nucleotidyltransferase RmlA via directed evolution
    Rocco Moretti
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    J Biol Chem 286:13235-43. 2011
    ....
  58. ncbi Bis-methionyl coordination in the crystal structure of the heme-binding domain of the streptococcal cell surface protein Shp
    Roman Aranda
    Department of Biomolecular Chemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    J Mol Biol 374:374-83. 2007
    ..Gel filtration and analytical ultracentrifugation studies indicate that both full-length Shp and Shp(180) are monomeric in dilute aqueous solution...
  59. ncbi Bioinformatic method for protein thermal stabilization by structural entropy optimization
    Euiyoung Bae
    Departments of Biochemistry and Computer Science, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 105:9594-7. 2008
    ..ICE does not require a three-dimensional structure or a large number of homologous sequences, indicating a broad applicability of this method. Our results also highlight the importance of entropy in the stability of protein structures...
  60. ncbi Structure and interactions of the first three RNA recognition motifs of splicing factor prp24
    Euiyoung Bae
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    J Mol Biol 367:1447-58. 2007
    ..Our results suggest that Prp24 binds free U6 RNA primarily with RRMs 1 and 2, which may remodel the U6 secondary structure. The beta-sheet of RRM 3 then influences U4/U6 pairing through interaction with an unidentified ligand...
  61. ncbi Ensemble refinement of protein crystal structures: validation and application
    Elena J Levin
    Department of Biochemistry, University of Wisconsin Madison, Madison, WI 53706, USA
    Structure 15:1040-52. 2007
    ..These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement...
  62. ncbi Crystal structure of Homo sapiens protein LOC79017
    Euiyoung Bae
    Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
    Proteins 70:588-91. 2008
  63. ncbi Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments
    Dmitry A Kondrashov
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Proteins 70:353-62. 2008
    ..8. This suggests that crystal packing selects conformers representative of the solution ensemble, and several different crystal forms give a more complete view of the plasticity of a protein structure...
  64. ncbi Kinetic proofreading by the cavity system of myoglobin: protection from poisoning
    Wilson Radding
    Department of Biochemistry, University of Wisconsin Madison, Madison, Wisconsin, USA
    Bioessays 26:422-33. 2004
    ..The non-equilibrium nature of part 2 should promote the proofreading function of part 1. A simulation using the model demonstrates that the cavity system can in principle proofread, reducing mitochondrial enzyme contamination...
  65. ncbi Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases
    Euiyoung Bae
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    J Biol Chem 279:28202-8. 2004
    ....
  66. ncbi X-ray structure of Arabidopsis At1g77680, 12-oxophytodienoate reductase isoform 1
    Brian G Fox
    University of Wisconsin Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 53706, USA
    Proteins 61:206-8. 2005
  67. ncbi Project management system for structural and functional proteomics: Sesame
    Zsolt Zolnai
    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin Madison, Madison Wisconsin 53706, USA
    J Struct Funct Genomics 4:11-23. 2003
    ..This software is available to parties interested in using it and assisting to guide its further development...
  68. ncbi GRAPE: GRaphical Abstracted Protein Explorer
    Gregory Cipriano
    Department of Computer Sciences, University of Wisconsin Madison Madison, WI 53715, USA
    Nucleic Acids Res 38:W595-601. 2010
    ..Abstracted views provide a fast way to assess both a molecule's shape and its different surface field distributions. GRAPE is freely available at http://grape.uwbacter.org...
  69. ncbi Dynamics of proteins in crystals: comparison of experiment with simple models
    Sibsankar Kundu
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Biophys J 83:723-32. 2002
    ..By incorporating the effect of neighboring molecules in the crystal the correlation is further improved...
  70. ncbi Identifying and engineering ion pairs in adenylate kinases. Insights from molecular dynamics simulations of thermophilic and mesophilic homologues
    Euiyoung Bae
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    J Biol Chem 280:30943-8. 2005
    ..These results provide specific knowledge about stability in adenylate kinases and more generally suggest that molecular dynamics simulations can provide valuable information for identifying and engineering ion pairs...
  71. ncbi Many local motions cooperate to produce the adenylate kinase conformational transition
    Michael D Daily
    Department of Chemistry, University of Wisconsin Madison, 1101 University Avenue, Madison, WI 53706, USA
    J Mol Biol 400:618-31. 2010
    ..Finally, the analytical approach and the insights derived from this work may inform the rational design of flexibility and allostery in proteins...
  72. ncbi Automatic domain decomposition of proteins by a Gaussian Network Model
    Sibsankar Kundu
    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
    Proteins 57:725-33. 2004
    ..Apart from decomposing proteins into structural domains, the algorithm can generally be applied to any large macromolecular system to decompose it into motionally decoupled sub-systems...
  73. ncbi Defining the sequence-recognition profile of DNA-binding molecules
    Christopher L Warren
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 103:867-72. 2006
    ..Solution studies strongly corroborated the sequence preferences identified by the array analysis...
  74. ncbi Crystallization and preliminary X-ray crystallographic analysis of adenosine 5'-monophosphate deaminase (AMPD) from Arabidopsis thaliana in complex with coformycin 5'-phosphate
    Byung Woo Han
    Department of Biochemistry, University of Wisconsin Madison, WI 53706 1544, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:740-2. 2005
    ..325, c = 208.254 A, alpha = beta = 90, gamma = 120 degrees. Diffraction data were collected to 3.34 A resolution from a crystal in complex with coformycin 5'-phosphate and to 4.05 A resolution from a crystal of a mercury derivative...
  75. ncbi Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data
    Dmitry A Kondrashov
    Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
    Biophys J 91:2760-7. 2006
    ..The addition of simple chemical information results in better prediction quality without increasing the size of the coarse-grained model...
  76. ncbi X-ray structure of Arabidopsis At2g06050, 12-oxophytodienoate reductase isoform 3
    Thomas E Malone
    Molecular and Environmental Toxicology Program, University of Wisconsin-Madison, 53706, USA
    Proteins 58:243-5. 2005
  77. ncbi Molecular engineering of myoglobin: influence of residue 68 on the rate and the enantioselectivity of oxidation reactions catalyzed by H64D/V68X myoglobin
    Hui-Jun Yang
    Department of Structural Molecule Science, The Graduate University for Advanced Studies, Okazaki, Myodaiji 444-8585, Japan
    Biochemistry 42:10174-81. 2003
    ..e., H(2)O(2), ABTS, thioanisole) and (2) the polar interactions between tightly hydrogen-bonded water molecules and substrates...
  78. ncbi Watching a protein as it functions with 150-ps time-resolved x-ray crystallography
    Friedrich Schotte
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Science 300:1944-7. 2003
    ....
  79. ncbi SOMoRe: a multi-dimensional search and optimization approach to molecular replacement
    Diane C Jamrog
    Department of Computational and Applied Mathematics, Rice University, Houston, Texas, USA
    Acta Crystallogr D Biol Crystallogr 59:304-14. 2003
    ..Based on these results, this new strategy promises to extend the applicability and robustness of MR...
  80. ncbi Asymmetric sulfoxidation and amine binding by H64D/V68A and H64D/V68S Mb: mechanistic insight into the chiral discrimination step
    Shigeru Kato
    Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan
    J Am Chem Soc 124:8506-7. 2002
    ..The kinetic study of the amine binding shows that the Fe-O bond cleavage in the intermediate may be the chiral discrimination step of the sulfoxidation...
  81. ncbi Bis-methionine ligation to heme iron in the streptococcal cell surface protein Shp facilitates rapid hemin transfer to HtsA of the HtsABC transporter
    Yanchao Ran
    Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana 59718, USA
    J Biol Chem 282:31380-8. 2007
    ....
  82. ncbi Structures of thermophilic and mesophilic adenylate kinases from the genus Methanococcus
    Angela R Criswell
    Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
    J Mol Biol 330:1087-99. 2003
    ..Results of previous mutational studies are interpreted in terms of the crystal structures, and support the importance of hydrophobic interactions in thermostability...
  83. ncbi Understanding protein flexibility through dimensionality reduction
    Miguel L Teodoro
    Department of Biochemistry and Cell Biology and Department of Computer Science, Rice University, 6100 Main Street, MS 140, Houston, TX 77005, USA
    J Comput Biol 10:617-34. 2003
    ....
  84. ncbi Structure of the hypothetical protein At3g17210 from Arabidopsis thaliana
    Betsy L Lytle
    J Biomol NMR 28:397-400. 2004
  85. ncbi High-throughput purification and quality assurance of Arabidopsis thaliana proteins for eukaryotic structural genomics
    Won Bae Jeon
    The Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 433 Bobcock Drive, 53706-1549, USA
    J Struct Funct Genomics 6:143-7. 2005
    ..The protocols have been used successfully to provide high quality proteins that are suitable for structural studies by X-ray crystallography and NMR...
  86. ncbi Probing substates in sperm whale myoglobin using high-pressure crystallography
    Paul Urayama
    Department of Physics, Cornell University, Ithaca, NY 14853, USA
    Structure 10:51-60. 2002
    ..Correlation with low-pH structures suggests observed structural changes are associated with global conformational substates. Methods developed here open up a direct avenue for exploration of the effects of pressure on proteins...
  87. ncbi Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays
    Viktor Stolc
    NASA ARC
    Proc Natl Acad Sci U S A 102:4453-8. 2005
    ..Transcription activities were also detected for many of the intergenic regions and the small RNAs, including tRNA, small nuclear RNA, small nucleolar RNA, and microRNA. Expression of tRNAs correlates with genome-wide amino acid usage...
  88. ncbi Biophysical and kinetic characterization of HemAT, an aerotaxis receptor from Bacillus subtilis
    Wei Zhang
    Department of Biochemistry and Cell Biology, W M Keck Center for Computational Biology, Rice University, Houston, Texas 77005, USA
    Biophys J 88:2801-14. 2005
    ..The unusual ligand-binding properties of HemAT suggest that asymmetry and apparent negative cooperativity play an important role in the signal transduction pathway...
  89. ncbi Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry
    Wei Zhang
    Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
    Structure 11:1097-110. 2003
    ..Tyrosine70 shows distinct conformational changes on one subunit when ligands are removed. Our study suggests that disruption of the symmetry of HemAT plays an important role in initiating the chemotaxis signaling transduction cascade...
  90. ncbi Molecular mechanisms of calcium and magnesium binding to parvalbumin
    M Susan Cates
    Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA
    Biophys J 82:1133-46. 2002
    ....