Rapid chain tracing of polypeptide backbones in electron-density maps

Terwilliger, Thomas C.

doi:10.1107/s0907444910000272

Title: Rapid chain tracing of polypeptide backbones in electron-density maps

Journal Article · Fri Feb 12 00:00:00 EST 2010 · Acta Crystallographica. Section D: Biological Crystallography

DOI:https://doi.org/10.1107/s0907444910000272· OSTI ID:1625667

Terwilliger, Thomas C. ^[1]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

A method for the rapid tracing of polypeptide backbones has been developed. The method creates an approximate chain tracing that is useful for visual evaluation of whether a structure has been solved and for use in scoring the quality of electron-density maps. The essence of the method is to (i) sample candidate C^α positions at spacings of approximately 0.6 Å along ridgelines of high electron density, (ii) list all possible nonapeptides that satisfy simple geometric and density criteria using these candidate C^α positions, (iii) score the nonapeptides and choose the highest scoring ones, and (iv) find the longest chains that can be made by connecting nonamers. An indexing and storage scheme that allows a single calculation of most distances and density values is used to speed up the process. The method was applied to 42 density-modified electron-density maps at resolutions from 1.5 to 3.8 Å. A total of 21 428 residues in these maps were traced in 24 CPU min with an overall r.m.s.d. of 1.61 Å for C^α atoms compared with the known refined structures. The method appears to be suitable for rapid evaluation of electron-density map quality.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1625667

Journal Information:: Acta Crystallographica. Section D: Biological Crystallography, Vol. 66, Issue 3; ISSN 0907-4449

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 5 works

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References (52)

Haloalkane Dehalogenases: Structure of a Rhodococcus Enzyme ^† ^, ^‡ Newman, Janet; Peat, Thomas S.; Richard, Ruth Biochemistry, Vol. 38, Issue 49 https://doi.org/10.1021/bi9913855	journal	December 1999
Automated protein model building combined with iterative structure refinement Perrakis, Anastassis; Morris, Richard; Lamzin, Victor S. Nature Structural Biology, Vol. 6, Issue 5, p. 458-463 https://doi.org/10.1038/8263	journal	May 1999
Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution Sutton, R. Bryan; Fasshauer, Dirk; Jahn, Reinhard Nature, Vol. 395, Issue 6700 https://doi.org/10.1038/26412	journal	September 1998
The High Resolution Crystal Structure of Recombinant Crithidia fasciculata Tryparedoxin-I Alphey, Magnus S.; Leonard, Gordon A.; Gourley, David G. Journal of Biological Chemistry, Vol. 274, Issue 36 https://doi.org/10.1074/jbc.274.36.25613	journal	September 1999
Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima Shin, Dong Hae; Roberts, Anne; Jancarik, Jaru Protein Science, Vol. 12, Issue 7 https://doi.org/10.1110/ps.0302703	journal	July 2003
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S090744490705024X	journal	December 2007
The protein data bank: A computer-based archival file for macromolecular structures Bernstein, Frances C.; Koetzle, Thomas F.; Williams, Graheme J. B. Archives of Biochemistry and Biophysics, Vol. 185, Issue 2 https://doi.org/10.1016/0003-9861(78)90204-7	journal	January 1978
Conformational variability in the refined structure of the chaperonin GroEL at 2.8 Å resolution Braig, Kerstin; Adams, Paul D.; Brünger, Axel T. Nature Structural & Molecular Biology, Vol. 2, Issue 12 https://doi.org/10.1038/nsb1295-1083	journal	December 1995
Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein. Skinner, M. M.; Zhang, H.; Leschnitzer, D. H. Proceedings of the National Academy of Sciences, Vol. 91, Issue 6 https://doi.org/10.1073/pnas.91.6.2071	journal	March 1994
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Terwilliger, Thomas C.; Adams, Paul D.; Read, Randy Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.49142	text	January 2009
Crystal structure of a stress inducible protein from Mycoplasma pneumoniae at 2.85 Å resolution Choi, In-Geol; Shin, Dong Hae; Brandsen, Jeroen Journal of Structural and Functional Genomics, Vol. 4, Issue 1, p. 31-34 https://doi.org/10.1023/A:1024625122089	journal	January 2003
Synapsin I is structurally similar to ATP-utilizing enzymes Esser, L. The EMBO Journal, Vol. 17, Issue 4 https://doi.org/10.1093/emboj/17.4.977	journal	February 1998
PHENIX : building new software for automated crystallographic structure determination Adams, Paul D.; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 11 https://doi.org/10.1107/S0907444902016657	journal	October 2002
Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus Shin, D. H.; Yokota, H.; Kim, R. Proceedings of the National Academy of Sciences, Vol. 99, Issue 12 https://doi.org/10.1073/pnas.132241399	journal	June 2002
Improved methods for building protein models in electron density maps and the location of errors in these models Jones, T. A.; Zou, J. Y.; Cowan, S. W. Acta Crystallographica Section A Foundations of Crystallography, Vol. 47, Issue 2, p. 110-119 https://doi.org/10.1107/S0108767390010224	journal	March 1991
NSF N-Terminal Domain Crystal Structure Yu, Richard C.; Jahn, Reinhard; Brunger, Axel T. Molecular Cell, Vol. 4, Issue 1 https://doi.org/10.1016/S1097-2765(00)80191-4	journal	July 1999
Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli Muchmore, Christine R. A.; Krahn, Joseph M.; Smith, Janet L. Protein Science, Vol. 7, Issue 1 https://doi.org/10.1002/pro.5560070104	journal	January 1998
Automated main-chain model building by template matching and iterative fragment extension Terwilliger, Thomas C. Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 1 https://doi.org/10.1107/S0907444902018036	journal	December 2002
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard Terwilliger, Thomas C.; Adams, Paul D.; Read, Randy J. Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 6 https://doi.org/10.1107/S0907444909012098	journal	May 2009
Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength Turner, Mary A.; Yuan, Chong-Sheng; Borchardt, Ronald T. Nature Structural Biology, Vol. 5, Issue 5 https://doi.org/10.1038/nsb0598-369	journal	May 1998
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) Hyman, Joel; Chen, Hong; Di Fiore, Pier Paolo Journal of Cell Biology, Vol. 149, Issue 3 https://doi.org/10.1083/jcb.149.3.537	journal	May 2000
Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP Yu, Richard C.; Hanson, Phyllis I.; Jahn, Reinhard Nature Structural Biology, Vol. 5, Issue 10 https://doi.org/10.1038/2368	journal	October 1998
Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis Ducros, Valérie M. -A; Lewis, Richard J.; Verma, Chandra S. Journal of Molecular Biology, Vol. 306, Issue 4 https://doi.org/10.1006/jmbi.2001.4443	journal	March 2001
Crystal structure of human p32, a doughnut-shaped acidic mitochondrial matrix protein Jiang, J.; Zhang, Y.; Krainer, A. R. Proceedings of the National Academy of Sciences, Vol. 96, Issue 7 https://doi.org/10.1073/pnas.96.7.3572	journal	March 1999
Crystallographic Refinement by Knowledge-Based Exploration of Complex Energy Landscapes DePristo, Mark A.; de Bakker, Paul I. W.; Johnson, Russell J. K. Structure, Vol. 13, Issue 9 https://doi.org/10.1016/j.str.2005.06.008	journal	September 2005
High-resolution structure of RNase P protein from Thermotoga maritima Kazantsev, A. V.; Krivenko, A. A.; Harrington, D. J. Proceedings of the National Academy of Sciences, Vol. 100, Issue 13 https://doi.org/10.1073/pnas.0932597100	journal	June 2003
Degradation Pathway of the Phosphonate Ciliatine: Crystal Structure of 2-Aminoethylphosphonate Transaminase ^† ^, ^‡ Chen, Celia C. H.; Zhang, H.; Kim, A. D. Biochemistry, Vol. 41, Issue 44 https://doi.org/10.1021/bi026231v	journal	November 2002
The protein data bank: A computer-based archival file for macromolecular structures Bernstein, Frances C.; Koetzle, Thomas F.; Williams, Graheme J. B. Journal of Molecular Biology, Vol. 112, Issue 3 https://doi.org/10.1016/S0022-2836(77)80200-3	journal	May 1977
Crystal structure of quinolinic acid phosphoribosyltransferase from Mycobacterium tuberculosis: a potential TB drug target Sharma, Vivek; Grubmeyer, Charles; Sacchettini, James C. Structure, Vol. 6, Issue 12 https://doi.org/10.1016/S0969-2126(98)00156-7	journal	December 1998
Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement Terwilliger, Thomas C. Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 7 https://doi.org/10.1107/S0907444903009922	journal	June 2003
Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): A novel fold with a conserved sequence motif Chen, Shengfeng; Jancrick, Jaru; Yokota, Hisao Proteins: Structure, Function, and Bioinformatics, Vol. 55, Issue 4 https://doi.org/10.1002/prot.10593	journal	April 2004
Three-dimensional pattern recognition: An approach to automated interpretation of electron density maps of proteins Greer, Jonathan Journal of Molecular Biology, Vol. 82, Issue 3 https://doi.org/10.1016/0022-2836(74)90591-9	journal	January 1974
Flavin Reductase P: Structure of a Dimeric Enzyme That Reduces Flavin ^† ^, ^‡ Tanner, John J.; Lei, Benfang; Tu, Shiao-Chun Biochemistry, Vol. 35, Issue 42 https://doi.org/10.1021/bi961400v	journal	January 1996
The Buccaneer software for automated model building. 1. Tracing protein chains Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 9 https://doi.org/10.1107/S0907444906022116	journal	August 2006
Fitting molecular fragments into electron density Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S0907444907033938	journal	December 2007
Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP Yu, Richard C.; Hanson, Phyllis I.; Jahn, Reinhard Nature Structural Biology, Vol. 5, Issue 9 https://doi.org/10.1038/1843	journal	September 1998
Three-Dimensional Structure of the l -Threonine- O -3-phosphate Decarboxylase (CobD) Enzyme from Salmonella enterica ^† ^, ^‡ Cheong, Cheom-Gil; Bauer, Cary B.; Brushaber, Kevin R. Biochemistry, Vol. 41, Issue 15 https://doi.org/10.1021/bi012111w	journal	April 2002
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Fast procedure for reconstruction of full-atom protein models from reduced representations Rotkiewicz, Piotr; Skolnick, Jeffrey Journal of Computational Chemistry, Vol. 29, Issue 9 https://doi.org/10.1002/jcc.20906	journal	January 2008
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. International Union of Crystallography (IUCr) https://doi.org/10.17863/cam.52329	journalarticle	January 2008
XtalView/Xfit—A Versatile Program for Manipulating Atomic Coordinates and Electron Density McRee, Duncan E. Journal of Structural Biology, Vol. 125, Issue 2-3 https://doi.org/10.1006/jsbi.1999.4094	journal	April 1999
Crystal structure of TM1457 from Thermotoga maritima Shin, Dong Hae; Lou, Yun; Jancarik, Jaru Journal of Structural Biology, Vol. 152, Issue 2 https://doi.org/10.1016/j.jsb.2005.08.008	journal	November 2005
Crystal structure of the hCASK PDZ domain reveals the structural basis of class II PDZ domain target recognition Daniels, Danette L.; Cohen, Alexandra R.; Anderson, James M. Nature Structural Biology, Vol. 5, Issue 4 https://doi.org/10.1038/nsb0498-317	journal	March 1998
Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases Burling, F. T.; Weis, W. I.; Flaherty, K. M. Science, Vol. 271, Issue 5245 https://doi.org/10.1126/science.271.5245.72	journal	January 1996
TEXTAL System: Artificial Intelligence Techniques for Automated Protein Model Building Ioerger, Thomas R.; Sacchettini, James C. Methods in Enzymology https://doi.org/10.1016/S0076-6879(03)74012-9	book	January 2003
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 Langer, Gerrit; Cohen, Serge X.; Lamzin, Victor S. Nature Protocols, Vol. 3, Issue 7 https://doi.org/10.1038/nprot.2008.91	journal	June 2008
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
Crystal Structure of NusA from Thermotoga Maritima and Functional Implication of the N-Terminal Domain Shin, Dong Hae; Nguyen, Henry Huy; Jancarik, Jaru Biochemistry, Vol. 42, Issue 46 https://doi.org/10.1021/bi035118h	journal	October 2003
Crystal Structure of the Cytosolic C2a-C2b Domains of Synaptotagmin III: Implications for Ca Sutton, R. Bryan; Ernst, James A.; Brunger, Axel T. The Journal of Cell Biology, Vol. 147, Issue 3 https://doi.org/10.1083/jcb.147.3.589	journal	November 1999
Identification of Secondary Structure Elements in Intermediate-Resolution Density Maps Baker, Matthew L.; Ju, Tao; Chiu, Wah Structure, Vol. 15, Issue 1 https://doi.org/10.1016/j.str.2006.11.008	journal	January 2007
Creating protein models from electron-density maps using particle-filtering methods DiMaio, F.; Kondrashov, D. A.; Bitto, E. Bioinformatics, Vol. 23, Issue 21 https://doi.org/10.1093/bioinformatics/btm480	journal	October 2007
Structure and refinement of penicillopepsin at 1.8 Å resolution James, Michael N. G.; Sielecki, Anita R. Journal of Molecular Biology, Vol. 163, Issue 2 https://doi.org/10.1016/0022-2836(83)90008-6	journal	January 1983

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