Research Topics
| Thomas TerwilligerSummaryAffiliation: Los Alamos National Laboratory Country: USA Publications
Research Grants
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Detail Information
Publications
Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinementThomas 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...- The success of structural genomicsThomas 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... 
The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biologyT 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...- Statistical density modification using local pattern matchingThomas 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... - SOLVE and RESOLVE: automated structure solution, density modification and model buildingThomas 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... - Structures and technology for biologistsThomas 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... - Using prime-and-switch phasing to reduce model bias in molecular replacementThomas 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.... - Lessons from structural genomicsThomas 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... - Automated ligand fitting by core-fragment fitting and extension into densityThomas C Terwilliger
Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
Acta Crystallogr D Biol Crystallogr 62:915-22. 2006.... - Ligand identification using electron-density map correlationsThomas 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... - Interpretation of ensembles created by multiple iterative rebuilding of macromolecular modelsThomas C Terwilliger
Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
Acta Crystallogr D Biol Crystallogr 63:597-610. 2007.... - Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizardThomas 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... - Iterative-build OMIT maps: map improvement by iterative model building and refinement without model biasThomas 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... - Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizardThomas 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... - Rapid model building of alpha-helices in electron-density mapsThomas 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... - Rapid model building of beta-sheets in electron-density mapsThomas 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... - Rapid chain tracing of polypeptide backbones in electron-density mapsThomas 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... - Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinementThomas 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... - Automated side-chain model building and sequence assignment by template matchingThomas 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... - Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methodsT 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... - Sigma2R, a reciprocal-space measure of the quality of macromolecular electron-density mapsT 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... - Automated structure solution, density modification and model buildingThomas 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... - Maximum-likelihood density modificationT 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]... - Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. densityT 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... - Map-likelihood phasingT 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.... - Maximum-likelihood density modification using pattern recognition of structural motifsT 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... - Structural genomics in North AmericaT 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... - Automated MAD and MIR structure solutionT 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... - Statistical density modification with non-crystallographic symmetryThomas 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... - Class-directed structure determination: foundation for a protein structure initiativeT 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... - Automated main-chain model building by template matching and iterative fragment extensionThomas 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... - Rapid automatic NCS identification using heavy-atom substructuresThomas 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... - Engineering soluble proteins for structural genomicsJean 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... - Engineering and characterization of a superfolder green fluorescent proteinJean 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... - SOLVE and RESOLVE: automated structure solution and density modificationThomas C Terwilliger
Los Alamos National Laboratory, Los Alamos, New Mexico 87545
Methods Enzymol 374:22-37. 2003.... - Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosisBeom 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... - Protein tagging and detection with engineered self-assembling fragments of green fluorescent proteinStephanie 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... - Automated, high-throughput platform for protein solubility screening using a split-GFP systemPawel 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... - Analysis of nucleoside-binding proteins by ligand-specific elution from dye resin: application to Mycobacterium tuberculosis aldehyde dehydrogenasesChang 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... - Structural and functional features of an NDP kinase from the hyperthermophile crenarchaeon Pyrobaculum aerophilumJean 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... - Recent advances in GFP folding reporter and split-GFP solubility reporter technologies. Application to improving the folding and solubility of recalcitrant proteins from Mycobacterium tuberculosisStephanie 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... - Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosisJean 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... - The optimization of in vitro high-throughput chemical lysis of Escherichia coli. Application to ACP domain of the polyketide synthase ppsC from Mycobacterium tuberculosisPawel 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.... - New molecular reporters for rapid protein folding assaysStephanie Cabantous
Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
PLoS ONE 3:e2387. 2008.... - Domain orientation in the inactive response regulator Mycobacterium tuberculosis MtrA provides a barrier to activationNatalia 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... - The TB structural genomics consortium: providing a structural foundation for drug discoveryCelia 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... - Recent developments in the PHENIX software for automated crystallographic structure determinationPaul 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... 
Automated structure solution with the PHENIX suitePeter 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...- Solution structure of the conserved hypothetical protein Rv2302 from Mycobacterium tuberculosisGarry 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... - Functional linkages can reveal protein complexes for structure determinationSul 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... - From no expression to high-level soluble expression in Escherichia coli by screening a library of the target proteins with randomized N-terminiKyoung 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... - The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosisBarnali 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... - Automatic solution of heavy-atom substructuresCharles M Weeks
Hauptman-Woodward Medical Research Institute, 73 High Street, Buffalo, New York 14203, USA
Methods Enzymol 374:37-83. 2003 - Mycobacterium tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathwayKatherine 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... - PHENIX: building new software for automated crystallographic structure determinationPaul 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... - Structure of pyrR (Rv1379) from Mycobacterium tuberculosis: a persistence gene and protein drug targetKatherine 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... - Is one solution good enough?Nicholas Furnham
Nat Struct Mol Biol 13:184-5; discussion 185. 2006 - Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombinationJ 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... - The structure and computational analysis of Mycobacterium tuberculosis protein CitE suggest a novel enzymatic functionCelia 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... - Independent tyrosyl contributions to the CD of Ff gene 5 protein and the distinctive effects of Y41H and Y41F mutants on protein-protein cooperative interactionsTung-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... - RIKEN aids international structural genomics effortsShigeyuki Yokoyama
Nature 445:21. 2007 - An automated high-throughput screening method for the identification of high-yield, soluble protein variants using cell-free expression and systematic truncationEvan 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... - Binding and reversible denaturation of double-stranded DNA by Ff gene 5 proteinTung-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(+)... - Protein production and purificationSusanne 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...
Research Grants
- STRUCTURAL ORGANIZATION AND PROTEOMICS OF TBThomas 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. ..