Rapid model building of α-helices in electron-density maps

A method for rapid model building of α-helices at moderate resolution is presented.

[1]  P. Lynne Howell,et al.  Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength , 1998, Nature Structural Biology.

[2]  Kevin Cowtan,et al.  The Buccaneer software for automated model building. 1. Tracing protein chains. , 2006, Acta crystallographica. Section D, Biological crystallography.

[3]  Axel T Brunger,et al.  Considerations for the refinement of low-resolution crystal structures. , 2006, Acta crystallographica. Section D, Biological crystallography.

[4]  Dong Yang,et al.  Structure of the Methanococcus jannaschii Mevalonate Kinase, a Member of the GHMP Kinase Superfamily* , 2002, The Journal of Biological Chemistry.

[5]  William I. Weis,et al.  Three-Dimensional Structure of the Armadillo Repeat Region of β-Catenin , 1997, Cell.

[6]  Jude W. Shavlik,et al.  Creating protein models from electron-density maps using particle-filtering methods , 2007, Bioinform..

[7]  Reinhard Jahn,et al.  Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution , 1998, Nature.

[8]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[9]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[10]  Sung-Hou Kim,et al.  Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): A novel fold with a conserved sequence motif , 2004, Proteins.

[11]  James C Sacchettini,et al.  Crystal Structures of Mycolic Acid Cyclopropane Synthases fromMycobacterium tuberculosis * , 2002, The Journal of Biological Chemistry.

[12]  J C Sacchettini,et al.  Crystal structure of quinolinic acid phosphoribosyltransferase from Mmycobacterium tuberculosis: a potential TB drug target. , 1998, Structure.

[13]  Z Otwinowski,et al.  Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site. , 2000, Structure.

[14]  M. James,et al.  Structure and refinement of penicillopepsin at 1.8 A resolution. , 1983, Journal of molecular biology.

[15]  D E McRee,et al.  XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density. , 1999, Journal of structural biology.

[16]  G N Murshudov,et al.  Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis. , 2001, Journal of molecular biology.

[17]  Thomas C. Terwilliger,et al.  Electronic Reprint Biological Crystallography Automated Main-chain Model Building by Template Matching and Iterative Fragment Extension , 2022 .

[18]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination , 2022 .

[19]  O. Dideberg,et al.  Crystal Structure of UDP-N-acetylmuramoyl-l-alanyl-d-glutamate:meso-Diaminopimelate Ligase from Escherichia Coli * , 2001, The Journal of Biological Chemistry.

[20]  Thomas J Oldfield.  Automated tracing of electron-density maps of proteins. , 2003, Acta crystallographica. Section D, Biological crystallography.

[21]  Axel T. Brünger,et al.  Crystal structure of the hCASK PDZ domain reveals the structural basis of class II PDZ domain target recognition , 1998, Nature Structural Biology.

[22]  Sung-Hou Kim,et al.  Crystal structure of a stress inducible protein from Mycoplasma pneumoniae at 2.85 Å resolution , 2003, Journal of Structural and Functional Genomics.

[23]  A T Brünger,et al.  Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases , 1996, Science.

[24]  D. Levitt,et al.  A new software routine that automates the fitting of protein X-ray crystallographic electron-density maps. , 2001, Acta crystallographica. Section D, Biological crystallography.

[25]  G. Sheldrick,et al.  Degradation pathway of the phosphonate ciliatine: crystal structure of 2-aminoethylphosphonate transaminase. , 2002, Biochemistry.

[26]  Anastassis Perrakis,et al.  Automated protein model building combined with iterative structure refinement , 1999, Nature Structural Biology.

[27]  A. Brünger,et al.  Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP , 1998, Nature Structural Biology.

[28]  Thomas R Ioerger,et al.  TEXTAL system: artificial intelligence techniques for automated protein model building. , 2003, Methods in enzymology.

[29]  Henry H Nguyen,et al.  Crystal structure of NusA from Thermotoga maritima and functional implication of the N-terminal domain. , 2003, Biochemistry.

[30]  A. Brunger,et al.  NSF N-terminal domain crystal structure: models of NSF function. , 1999, Molecular cell.

[31]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[32]  T C Terwilliger,et al.  Dialysis against a Solution Containing 50 Mm Na 2 so 4 and 1 Mm Edta, with the Ph Adjusted to 8.2, Using 1 N H 2 so 4 , 1999 .

[33]  G J Kleywegt,et al.  Template convolution to enhance or detect structural features in macromolecular electron-density maps. , 1997, Acta crystallographica. Section D, Biological crystallography.

[34]  Sung-Hou Kim,et al.  Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[35]  V S Lamzin,et al.  Ribonuclease from Streptomyces aureofaciens at atomic resolution. , 1996, Acta crystallographica. Section D, Biological crystallography.

[36]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[37]  Randy J. Read,et al.  Dauter Iterative model building , structure refinement and density modification with the PHENIX AutoBuild wizard , 2007 .

[38]  J. Deisenhofer,et al.  Synapsin I is structurally similar to ATP‐utilizing enzymes , 1998, The EMBO journal.

[39]  L. Regan,et al.  Dramatic structural and thermodynamic consequences of repacking a protein's hydrophobic core. , 2000, Structure.

[40]  A. Brunger,et al.  Structural characterization of the intramolecular interaction between the SH3 and guanylate kinase domains of PSD-95. , 2001, Molecular cell.

[41]  M. Baker,et al.  Identification of secondary structure elements in intermediate-resolution density maps. , 2007, Structure.

[42]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[43]  P. Adams,et al.  Conformational variability in the refined structure of the chaperonin GroEL at 2.8 Å resolution , 1995, Nature Structural Biology.

[44]  A. Brunger,et al.  Structural Basis of Rab Effector Specificity Crystal Structure of the Small G Protein Rab3A Complexed with the Effector Domain of Rabphilin-3A , 1999, Cell.

[45]  P. De Camilli,et al.  Epsin 1 Undergoes Nucleocytosolic Shuttling and Its Eps15 Interactor Nh2-Terminal Homology (Enth) Domain, Structurally Similar to Armadillo and Heat Repeats, Interacts with the Transcription Factor Promyelocytic Leukemia Zn2+ Finger Protein (Plzf) , 2000, The Journal of cell biology.

[46]  Sujata Sharma,et al.  Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis , 2000, Nature Structural Biology.

[47]  Crystal Structure of Lyme Disease Variable Surface Antigen VlsE of Borrelia burgdorferi * , 2002, The Journal of Biological Chemistry.

[48]  A. Fairlamb,et al.  The High Resolution Crystal Structure of RecombinantCrithidia fasciculata Tryparedoxin-I* , 1999, The Journal of Biological Chemistry.

[49]  T A Jones,et al.  Electron-density map interpretation. , 1997, Methods in enzymology.

[50]  K. Diederichs,et al.  Refined crystal structure and mutagenesis of human granulocyte‐macrophage colony‐stimulating factor , 1996, Proteins.

[51]  Sung-Hou Kim,et al.  Crystal structure of TM1457 from Thermotoga maritima. , 2005, Journal of structural biology.

[52]  A. Brunger,et al.  Crystal Structure of the Cytosolic C2a-C2b Domains of Synaptotagmin III , 1999, The Journal of cell biology.

[53]  J. Krahn,et al.  Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli , 1998, Protein science : a publication of the Protein Society.

[54]  Mark A Depristo,et al.  Crystallographic refinement by knowledge-based exploration of complex energy landscapes. , 2005, Structure.

[55]  Thomas Oldfield.  Pattern-recognition methods to identify secondary structure within X-ray crystallographic electron-density maps. , 2002, Acta crystallographica. Section D, Biological crystallography.

[56]  Poul Nissen,et al.  Phosphoryl Transfer and Calcium Ion Occlusion in the Calcium Pump , 2004, Science.

[57]  I. Rayment,et al.  Three-dimensional structure of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica. , 2002, Biochemistry.

[58]  A. Krainer,et al.  Crystal structure of human p32, a doughnut-shaped acidic mitochondrial matrix protein. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[59]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[60]  N. Pace,et al.  High-resolution structure of RNase P protein from Thermotoga maritima , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[61]  J. Tanner,et al.  Flavin reductase P: structure of a dimeric enzyme that reduces flavin. , 1996, Biochemistry.

[62]  Sung-Hou Kim,et al.  Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima , 2003, Protein science : a publication of the Protein Society.

[63]  T C Terwilliger,et al.  Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[64]  T C Terwilliger,et al.  Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 A resolution. , 1998, Structure.