Thomas Terwilliger

Summary

Affiliation: Los Alamos National Laboratory
Country: USA

Publications

  1. pmc Automatic Fortran to C++ conversion with FABLE
    Ralf W Grosse-Kunstleve
    Lawrence Berkeley National Laboratory, Cyclotron Road, Bldg, 64R0121, Berkeley, CA, 94720 8118, USA
    Source Code Biol Med 7:5. 2012
  2. pmc Crystal structure of AcrB complexed with linezolid at 3.5 Å resolution
    Li Wei Hung
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Struct Funct Genomics 14:71-5. 2013
  3. pmc Finding non-crystallographic symmetry in density maps of macromolecular structures
    Thomas C Terwilliger
    Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USA
    J Struct Funct Genomics 14:91-5. 2013
  4. pmc Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement
    Thomas C Terwilliger
    Bioscience Division and Los Alamos Institutes, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 68:861-70. 2012
  5. pmc Automated ligand fitting by core-fragment fitting and extension into density
    Thomas C Terwilliger
    Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 62:915-22. 2006
  6. pmc Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias
    Thomas C Terwilliger
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 64:515-24. 2008
  7. ncbi request reprint Using prime-and-switch phasing to reduce model bias in molecular replacement
    Thomas C Terwilliger
    Bioscience Division, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 60:2144-9. 2004
  8. ncbi request reprint Structures and technology for biologists
    Thomas C Terwilliger
    Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Nat Struct Mol Biol 11:296-7. 2004
  9. ncbi request reprint SOLVE and RESOLVE: automated structure solution, density modification and model building
    Thomas Terwilliger
    Los Alamos National Laboratory, USA
    J Synchrotron Radiat 11:49-52. 2004
  10. pmc Statistical density modification using local pattern matching
    Thomas C Terwilliger
    Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 59:1688-701. 2003

Research Grants

  1. STRUCTURAL ORGANIZATION AND PROTEOMICS OF TB
    Thomas Terwilliger; Fiscal Year: 2005

Detail Information

Publications67

  1. pmc Automatic Fortran to C++ conversion with FABLE
    Ralf W Grosse-Kunstleve
    Lawrence Berkeley National Laboratory, Cyclotron Road, Bldg, 64R0121, Berkeley, CA, 94720 8118, USA
    Source Code Biol Med 7:5. 2012
    ..abstract:..
  2. pmc Crystal structure of AcrB complexed with linezolid at 3.5 Å resolution
    Li Wei Hung
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Struct Funct Genomics 14:71-5. 2013
    ..5 Å. The structure shows that Linezolid binds to the A385/F386 loops of the symmetric trimer of AcrB. A conformational change of a loop in the bottom of the periplasmic cleft is also observed...
  3. pmc Finding non-crystallographic symmetry in density maps of macromolecular structures
    Thomas C Terwilliger
    Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USA
    J Struct Funct Genomics 14:91-5. 2013
    ..The relationships among correlated regions are then refined to maximize their correlations and are found to accurately represent non-crystallographic symmetry in the map. ..
  4. pmc Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement
    Thomas C Terwilliger
    Bioscience Division and Los Alamos Institutes, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 68:861-70. 2012
    ..The procedure can extend the routine applicability of automated molecular replacement, model building and refinement to search models with over 2 Å r.m.s.d. representing 65-100% of the structure...
  5. pmc Automated ligand fitting by core-fragment fitting and extension into density
    Thomas C Terwilliger
    Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 62:915-22. 2006
    ....
  6. pmc Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias
    Thomas C Terwilliger
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 64:515-24. 2008
    ..The procedure is demonstrated with a molecular-replacement structure and with an experimentally phased structure and a variation on the method is demonstrated by removing model bias from a structure from the Protein Data Bank...
  7. ncbi request reprint Using prime-and-switch phasing to reduce model bias in molecular replacement
    Thomas C Terwilliger
    Bioscience Division, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 60:2144-9. 2004
    ....
  8. ncbi request reprint Structures and technology for biologists
    Thomas C Terwilliger
    Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Nat Struct Mol Biol 11:296-7. 2004
    ..The thousands of new structures likely to be determined and the technologies and infrastructure likely to be developed over the next decade will benefit all biologists...
  9. ncbi request reprint SOLVE and RESOLVE: automated structure solution, density modification and model building
    Thomas Terwilliger
    Los Alamos National Laboratory, USA
    J Synchrotron Radiat 11:49-52. 2004
    ..RESOLVE carries out the identification of NCS, density modification and automated model-building. The procedure is fully automated and can function at resolutions as low as 3 A...
  10. pmc Statistical density modification using local pattern matching
    Thomas C Terwilliger
    Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 59:1688-701. 2003
    ..An iterative phase-improvement process using this approach and other applications of the image-reconstruction method are described and applied to experimental data at resolutions ranging from 2.4 to 2.8 A...
  11. pmc Ligand identification using electron-density map correlations
    Thomas C Terwilliger
    Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 63:101-7. 2007
    ..This approach may be useful in identification of unknown ligands in new macromolecular structures as well as in the identification of which ligands in a mixture have bound to a macromolecule...
  12. pmc Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models
    Thomas C Terwilliger
    Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 63:597-610. 2007
    ....
  13. pmc Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
    Thomas C Terwilliger
    Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 64:61-9. 2008
    ..1 to 3.2 A, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution...
  14. pmc Lessons from structural genomics
    Thomas C Terwilliger
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Annu Rev Biophys 38:371-83. 2009
    ..Finally, rapid deposition of data in public databases has increased the impact and usefulness of the data and international cooperation has advanced the field and improved data sharing...
  15. pmc Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    Thomas C Terwilliger
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 65:582-601. 2009
    ..The wizard is based on tools from the PHENIX package and uses the Bayesian estimates of map quality described here to choose the highest quality solutions after experimental phasing...
  16. pmc Rapid model building of alpha-helices in electron-density maps
    Thomas C Terwilliger
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 66:268-75. 2010
    ..The overall average r.m.s.d. between main-chain atoms in the modeled alpha-helices and the nearest atom with the same name in the refined models of the proteins was 1.3 A...
  17. pmc Rapid model building of beta-sheets in electron-density maps
    Thomas C Terwilliger
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 66:276-84. 2010
    ..8 A in which under 10% were built. The overall average r.m.s.d. of main-chain atoms in the residues built using this method compared with refined models of the structures was 1.5 A...
  18. pmc Rapid chain tracing of polypeptide backbones in electron-density maps
    Thomas C Terwilliger
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 66:285-94. 2010
    ..m.s.d. of 1.61 A for C(alpha) atoms compared with the known refined structures. The method appears to be suitable for rapid evaluation of electron-density map quality...
  19. pmc The success of structural genomics
    Thomas C Terwilliger
    Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545, USA
    J Struct Funct Genomics 12:43-4. 2011
    ..The technologies, the structures, and the biology that were described at the meeting were at the cutting edge of science. Structural genomics has become a success...
  20. ncbi request reprint The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biology
    T C Terwilliger
    Los Alamos National Laboratory, Bioscience Division, Mail Stop M888, Los Alamos, NM 87545, USA
    Tuberculosis (Edinb) 83:223-49. 2003
    ..This review describes the TB Structural Genomics Consortium and some of the proteins for which the Consortium is in the progress of determining three-dimensional structures...
  21. ncbi request reprint Structural genomics in North America
    T C Terwilliger
    Bioscience Division, Los Alamos National Laboratory, New Mexico 87545, USA
    Nat Struct Biol 7:935-9. 2000
    ..Just three years ago, the field was only a concept, independently being discussed by its many inventors. Now it is already a well-organized, increasingly-funded, consortium-based effort to determine protein structures on a large scale...
  22. pmc Statistical density modification with non-crystallographic symmetry
    Thomas C Terwilliger
    Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 58:2082-6. 2002
    ..For crystals with non-crystallographic symmetry (NCS), this allows the use of the expected similarity of electron density at NCS-related points without requiring an implicit assumption that these regions are identical...
  23. pmc Rapid automatic NCS identification using heavy-atom substructures
    Thomas C Terwilliger
    Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 58:2213-5. 2002
    ..Additionally, searches for proper symmetry allow the identification of NCS in cases where only one heavy atom is present per NCS copy...
  24. pmc Map-likelihood phasing
    T C Terwilliger
    Bioscience Division, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 57:1763-75. 2001
    ....
  25. pmc Maximum-likelihood density modification using pattern recognition of structural motifs
    T C Terwilliger
    Bioscience Division, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 57:1755-62. 2001
    ..The method can potentially be used to recognize any common structural motif and incorporate prior knowledge about that motif into density modification...
  26. pmc Maximum-likelihood density modification
    T C Terwilliger
    Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 56:965-72. 2000
    ..d55, 1863-1871]...
  27. pmc Sigma2R, a reciprocal-space measure of the quality of macromolecular electron-density maps
    T C Terwilliger
    Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 55:1174-8. 1999
    ..The formulation is suitable for rapid evaluation of macromolecular crystallographic phases, for phase improvement and for ab initio phasing procedures...
  28. pmc Automated main-chain model building by template matching and iterative fragment extension
    Thomas C Terwilliger
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 59:38-44. 2003
    ..5 A. The algorithm is useful for building a preliminary main-chain model that can serve as a basis for refinement and side-chain addition...
  29. pmc Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methods
    T C Terwilliger
    Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 55:501-5. 1999
    ..The method can be used to evaluate heavy-atom solutions during MAD and MIR structure solutions and to determine the handedness of the structure if anomalous data have been measured...
  30. pmc Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. density
    T C Terwilliger
    Structural Biology Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 55:1872-7. 1999
    ..This statistic can be calculated in real space or in reciprocal space and has potential uses in evaluation of heavy-atom solutions in the MIR and MAD methods as well as for evaluation of trial phase sets in ab initio phasing procedures...
  31. pmc Automated MAD and MIR structure solution
    T C Terwilliger
    Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 55:849-61. 1999
    ..The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations...
  32. pmc Class-directed structure determination: foundation for a protein structure initiative
    T C Terwilliger
    Structural Biology Group, Los Alamos National Laboratory, New Mexico 87545, USA
    Protein Sci 7:1851-6. 1998
    ..Such a shift in approach would be the foundation for a broad protein structure initiative targeting classes of proteins important for biotechnology and for a fundamental understanding of protein function...
  33. pmc Automated side-chain model building and sequence assignment by template matching
    Thomas C Terwilliger
    Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 59:45-9. 2003
    ..The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer...
  34. pmc Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement
    Thomas C Terwilliger
    Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 59:1174-82. 2003
    ..m.s.d. of main-chain atoms from the refined structure of 0.20 to 0.62 A. The algorithm is useful for building preliminary models of macromolecules suitable for an experienced crystallographer to extend, correct and fully refine...
  35. ncbi request reprint Automated structure solution, density modification and model building
    Thomas C Terwilliger
    Bioscience Division, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Acta Crystallogr D Biol Crystallogr 58:1937-40. 2002
    ..The entire process can be carried out in a fully automatic fashion in many cases...
  36. ncbi request reprint Engineering soluble proteins for structural genomics
    Jean Denis Pédelacq
    Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Nat Biotechnol 20:927-32. 2002
    ..Analysis of the structure provides insight into the substrate specificity of the enzyme and the improved solubility of the variant...
  37. ncbi request reprint Engineering and characterization of a superfolder green fluorescent protein
    Jean Denis Pédelacq
    Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Nat Biotechnol 24:79-88. 2006
    ..X-ray crystallographic structural analyses helped explain the enhanced folding of superfolder GFP relative to folding reporter GFP...
  38. ncbi request reprint SOLVE and RESOLVE: automated structure solution and density modification
    Thomas C Terwilliger
    Los Alamos National Laboratory, Los Alamos, New Mexico 87545
    Methods Enzymol 374:22-37. 2003
    ....
  39. pmc Automated, high-throughput platform for protein solubility screening using a split-GFP system
    Pawel Listwan
    Bioscience Division, MS M888, Los Alamos National Laboratory, Bikini Atoll Rd, SM30, Los Alamos, NM 87545, USA
    J Struct Funct Genomics 10:47-55. 2009
    ..The optimized liquid-handling protocol can be used for rapid determination of the optimal, compact domains from single ORFS, collections of ORFS, or cDNA libraries...
  40. ncbi request reprint Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein
    Stephanie Cabantous
    Bioscience Division, MS M888, Los Alamos National Laboratory, PO Box 1663, Los Alamos, New Mexico 87545, USA
    Nat Biotechnol 23:102-7. 2005
    ..The split GFP system is simple and does not change fusion protein solubility...
  41. ncbi request reprint Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosis
    Beom Seop Rho
    Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    J Mol Biol 361:850-63. 2006
    ..The M. tuberculosis Tpx is dimeric both in solution and in the crystal structure. Amino acid residues from both monomers delineate the active site pocket...
  42. pmc The optimization of in vitro high-throughput chemical lysis of Escherichia coli. Application to ACP domain of the polyketide synthase ppsC from Mycobacterium tuberculosis
    Pawel Listwan
    Bioscience Division, MS M888, Los Alamos National Laboratory, Bikini Atoll Rd, SM30, Los Alamos, NM 87545, USA
    J Struct Funct Genomics 11:41-9. 2010
    ....
  43. ncbi request reprint Recent advances in GFP folding reporter and split-GFP solubility reporter technologies. Application to improving the folding and solubility of recalcitrant proteins from Mycobacterium tuberculosis
    Stephanie Cabantous
    Bioscience Division, Los Alamos National Laboratory, MS M888, Los Alamos, NM 87545, USA
    J Struct Funct Genomics 6:113-9. 2005
    ..2005) Nat. Biotechnol. 23, 102-107]. Together, the GFP folding reporter and split-GFP technologies offer a comprehensive system for manipulating and improving protein folding and solubility...
  44. pmc Analysis of nucleoside-binding proteins by ligand-specific elution from dye resin: application to Mycobacterium tuberculosis aldehyde dehydrogenases
    Chang Yub Kim
    Advanced Measurement Science Group B 9, Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
    J Struct Funct Genomics 10:291-301. 2009
    ..5 and RMSD = 1.5 A), Rv0223c appears to belong to the ALDH-2 class. An altered oligomerization domain in the Rv0223c structure seems to keep this protein as monomer whereas native human ALDH-2 is a multimer...
  45. pmc Structural and functional features of an NDP kinase from the hyperthermophile crenarchaeon Pyrobaculum aerophilum
    Jean Denis Pédelacq
    Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Protein Sci 14:2562-73. 2005
    ..A structural analysis of the evolved NDP kinase in conjunction with mutagenesis experiments suggests that the substrate specificity of the P. aerophilum NDP kinase is related to the presence of these two inserts...
  46. ncbi request reprint Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis
    Jean Denis Pédelacq
    Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Proteins 62:563-9. 2006
    ..The shape and size of the putative binding pocket is markedly different from that of members of the PNPOx family, which may indicate some significant changes in the FMN binding mode of this protein relative to members of the family...
  47. pmc New molecular reporters for rapid protein folding assays
    Stephanie Cabantous
    Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS ONE 3:e2387. 2008
    ....
  48. ncbi request reprint The TB structural genomics consortium: providing a structural foundation for drug discovery
    Celia W Goulding
    Bioscience Division, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Curr Drug Targets Infect Disord 2:121-41. 2002
    ..The Consortium has determined structures of 28 proteins from TB to date. These protein structures are already providing a basis for drug discovery efforts...
  49. pmc Domain orientation in the inactive response regulator Mycobacterium tuberculosis MtrA provides a barrier to activation
    Natalia Friedland
    Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Biochemistry 46:6733-43. 2007
    ..The domain orientation exhibited by MtrA also provides a rationale for the variation in linker length that is observed within the OmpR/PhoB family of response regulators...
  50. ncbi request reprint The structure and computational analysis of Mycobacterium tuberculosis protein CitE suggest a novel enzymatic function
    Celia W Goulding
    Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095 1570, USA
    J Mol Biol 365:275-83. 2007
    ..We propose a novel enzymatic function for M. tuberculosis CitE in fatty acid biosynthesis that is analogous to bacterial citrate lyase but producing acetyl-CoA rather than a protein-bound CoA derivative...
  51. ncbi request reprint The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis
    Barnali N Chaudhuri
    UCLA Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Structure 11:753-64. 2003
    ..The apparent conservation of certain detailed structural characteristics suggests that KPHMT is distantly related by divergent evolution to enzymes in unrelated pathways, including isocitrate lyase and phosphoenolpyruvate mutase...
  52. ncbi request reprint Functional linkages can reveal protein complexes for structure determination
    Sul Min Kim
    Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
    Structure 15:1079-89. 2007
    ..We offer a database of inferred linkages corresponding to likely protein complexes for some 629,952 pairs of proteins in 154 prokaryotes and archaea...
  53. ncbi request reprint RIKEN aids international structural genomics efforts
    Shigeyuki Yokoyama
    Nature 445:21. 2007
  54. ncbi request reprint Mycobacterium tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathway
    Katherine A Kantardjieff
    Department of Chemistry and Biochemistry and W M Keck Foundation Center for Molecular Structure, California State University Fullerton, Fullerton, CA 92834, USA
    Acta Crystallogr D Biol Crystallogr 60:895-902. 2004
    ..The 1.7 A native structure determined by the consortium facilities is reported and implications for in silico screening of ligands for structure-guided drug design are discussed...
  55. ncbi request reprint Automatic solution of heavy-atom substructures
    Charles M Weeks
    Hauptman Woodward Medical Research Institute, 73 High Street, Buffalo, New York 14203, USA
    Methods Enzymol 374:37-83. 2003
  56. ncbi request reprint Recent developments in the PHENIX software for automated crystallographic structure determination
    Paul D Adams
    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    J Synchrotron Radiat 11:53-5. 2004
    ..Here, the features of PHENIXare reviewed and the recent advances in infrastructure and algorithms are briefly described...
  57. ncbi request reprint PHENIX: building new software for automated crystallographic structure determination
    Paul D Adams
    Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 4 230, Berkeley, CA 94720, USA
    Acta Crystallogr D Biol Crystallogr 58:1948-54. 2002
    ..This new software will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer...
  58. ncbi request reprint Structure of pyrR (Rv1379) from Mycobacterium tuberculosis: a persistence gene and protein drug target
    Katherine A Kantardjieff
    Department of Chemistry and Biochemistry and W M Keck Foundation Center for Molecular Structure, California State University Fullerton, Fullerton, CA 92834, USA
    Acta Crystallogr D Biol Crystallogr 61:355-64. 2005
    ..In silico screening of pyrimidine-nucleoside analogs has revealed a number of potential lead compounds that, if bound to Mtb pyrR, could facilitate transcriptional attenuation, particularly cyclopentenyl nucleosides...
  59. pmc Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination
    J Rajan Prabu
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:731-4. 2006
    ..A detailed analysis of plasticity in the RuvA molecules has led to insights into the invariant and variable regions, thus providing a framework for understanding regional flexibility in various aspects of RuvA function...
  60. pmc Independent tyrosyl contributions to the CD of Ff gene 5 protein and the distinctive effects of Y41H and Y41F mutants on protein-protein cooperative interactions
    Tung Chung Mou
    Department of Molecular and Cell Biology, The University of Texas at Dallas, Richardson, Texas 75083 0688, USA
    Protein Sci 11:601-13. 2002
    ..Thus, protein-protein and g5p-ssDNA interactions appeared to be mutually influenced by ionic strength, indicative of correlated changes in the ssDNA binding and cooperativity loops of the protein or of indirect structural constraints...
  61. doi request reprint From no expression to high-level soluble expression in Escherichia coli by screening a library of the target proteins with randomized N-termini
    Kyoung Hoon Kim
    Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Korea
    Methods Mol Biol 426:187-95. 2008
    ..coli. This chapter describes the results of a test of this approach with a bacterial protein (the HI0952 gene product) that is not well expressed in E. coli...
  62. doi request reprint Automated structure solution with the PHENIX suite
    Peter H Zwart
    Lawrence Berkeley National Laboratory, Berkeley, CA, USA
    Methods Mol Biol 426:419-35. 2008
    ..The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI...
  63. ncbi request reprint An automated high-throughput screening method for the identification of high-yield, soluble protein variants using cell-free expression and systematic truncation
    Evan H Bursey
    Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS4R0230, Berkeley, CA 94720, USA
    J Struct Funct Genomics 7:139-47. 2006
    ..We have applied this method to 32 problematic targets from the TB Structural Genomics Consortium. Experimental results of these studies are reported...
  64. ncbi request reprint Is one solution good enough?
    Nicholas Furnham
    Nat Struct Mol Biol 13:184-5; discussion 185. 2006
  65. pmc Solution structure of the conserved hypothetical protein Rv2302 from Mycobacterium tuberculosis
    Garry W Buchko
    Fundamental Sciences, Biological Sciences Division, Battelle, Pacific Northwest National Laboratory, P O Box 999, Mail Stop K8 98, Richland, WA 99352, USA
    J Bacteriol 188:5993-6001. 2006
    ..Dali searches using the structure closest to the average structure do not identify any high similarities to any other known protein structure, suggesting that the structure of Rv2302 may represent a novel protein fold...
  66. pmc Protein production and purification
    Susanne Gräslund
    Karolinska Institutet, Scheeles vag 2, 171 77 Stockholm, Sweden
    Nat Methods 5:135-46. 2008
    ..This review presents methods that could be applied at the outset of any project, a prioritized list of alternate strategies and a list of pitfalls that trip many new investigators...
  67. ncbi request reprint Binding and reversible denaturation of double-stranded DNA by Ff gene 5 protein
    Tung Chung Mou
    Department of Molecular and Cell Biology, Mail Stop FO31, University of Texas at Dallas, P O Box 830688, Richardson, TX 75083 0688, USA
    Biopolymers 70:637-48. 2003
    ..d(T)] is melted in the presence of the wild-type, Y26F, or Y34F proteins, the poly[d(A)] and poly[d(T)] strands are separately sequestered such that renaturation of the duplex is facilitated in 2 mM Na(+)...

Research Grants2

  1. STRUCTURAL ORGANIZATION AND PROTEOMICS OF TB
    Thomas Terwilliger; Fiscal Year: 2005
    ..The structural and functional information obtained in this project is to be placed in the public domain by timely deposition in publicly available databases. ..