Rapid chain tracing of polypeptide backbones in electron-density maps

doi:10.1107/S0907444910000272

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

Abstract

A method for rapid chain tracing of polypeptide backbones at moderate resolution is presented. 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{sup 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{sup 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{sup α} atoms compared with the known refined structures. The method appears to be suitable formore »« less

Authors:

Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov ^[1]

Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

Publication Date:: Mon Mar 01 00:00:00 EST 2010

OSTI Identifier:: 22347930

Resource Type:: Journal Article

Journal Name:: Acta Crystallographica. Section D: Biological Crystallography

Additional Journal Information:: Journal Volume: 66; Journal Issue: Pt 3; Other Information: PMCID: PMC2827349; PMID: 20179340; PUBLISHER-ID: dz5184; OAI: oai:pubmedcentral.nih.gov:2827349; Copyright (c) Terwilliger 2010; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0907-4449

Country of Publication:: Denmark

Language:: English

Subject:: 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ATOMS; CHAINS; DENSITY; DISTANCE; ELECTRON DENSITY; ELECTRONS; FASTENING; RESOLUTION; VELOCITY

Citation Formats


                    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov. Rapid chain tracing of polypeptide backbones in electron-density maps.  Denmark: N. p., 2010. 
        Web.  doi:10.1107/S0907444910000272.

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                    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov. Rapid chain tracing of polypeptide backbones in electron-density maps.  Denmark.  https://doi.org/10.1107/S0907444910000272

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                    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov. 2010.  
        "Rapid chain tracing of polypeptide backbones in electron-density maps".  Denmark.  https://doi.org/10.1107/S0907444910000272.

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@article{osti_22347930,

  title        = {Rapid chain tracing of polypeptide backbones in electron-density maps},

  author       = {Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov},

  abstractNote = {A method for rapid chain tracing of polypeptide backbones at moderate resolution is presented. 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{sup 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{sup 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{sup α} atoms compared with the known refined structures. The method appears to be suitable for rapid evaluation of electron-density map quality.},

  doi          = {10.1107/S0907444910000272},

  url          = {https://www.osti.gov/biblio/22347930},
  journal      = {Acta Crystallographica. Section D: Biological Crystallography},

  issn         = {0907-4449},

  number       = Pt 3,

  volume       = 66,

  place        = {Denmark},

  year         = {Mon Mar 01 00:00:00 EST 2010},

  month        = {Mon Mar 01 00:00:00 EST 2010}

}

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Rapid chain tracing of polypeptide backbones in electron-density maps

Journal Article Terwilliger, Thomas - Acta Crystallographica. Section D: Biological Crystallography

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 mademore »« less
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A method for the identification of α-helices in electron-density maps at low resolution followed by interpretation at moderate to high resolution is presented. Rapid identification is achieved at low resolution, where α-helices appear as tubes of density. The positioning and direction of the α-helices is obtained at moderate to high resolution, where the positions of side chains can be seen. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 Å. An average of 63% of the α-helical residues in these proteins were built and an average of 76% of themore »« less
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Title: Rapid chain tracing of polypeptide backbones in electron-density maps

Abstract

Citation Formats

Refined crystal structure and mutagenesis of human granulocyte-macrophage colony-stimulating factor journal, November 1996

Fast procedure for reconstruction of full-atom protein models from reduced representations journal, January 2008

Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli journal, January 1998

Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): A novel fold with a conserved sequence motif journal, April 2004

Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis journal, March 2001

XtalView/Xfit—A Versatile Program for Manipulating Atomic Coordinates and Electron Density journal, April 1999

Three-dimensional pattern recognition: An approach to automated interpretation of electron density maps of proteins journal, January 1974

Structure and refinement of penicillopepsin at 1.8 Å resolution journal, January 1983

Crystal structure of TM1457 from Thermotoga maritima journal, November 2005

Crystallographic Refinement by Knowledge-Based Exploration of Complex Energy Landscapes journal, September 2005

Identification of Secondary Structure Elements in Intermediate-Resolution Density Maps journal, January 2007

Three-Dimensional Structure of the Armadillo Repeat Region of β-Catenin journal, September 1997

Structural Basis of Rab Effector Specificity journal, February 1999

Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site journal, May 2000

Dramatic Structural and Thermodynamic Consequences of Repacking a Protein's Hydrophobic Core journal, December 2000

Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 å resolution journal, September 1998

Structural Characterization of the Intramolecular Interaction between the SH3 and Guanylate Kinase Domains of PSD-95 journal, December 2001

Three-Dimensional Structure of the l -Threonine- O -3-phosphate Decarboxylase (CobD) Enzyme from Salmonella enterica † , ‡ journal, April 2002

Degradation Pathway of the Phosphonate Ciliatine: Crystal Structure of 2-Aminoethylphosphonate Transaminase † , ‡ journal, November 2002

Crystal Structure of NusA from Thermotoga Maritima and Functional Implication of the N-Terminal Domain journal, October 2003

Flavin Reductase P: Structure of a Dimeric Enzyme That Reduces Flavin † , ‡ journal, January 1996

Haloalkane Dehalogenases: Structure of a Rhodococcus Enzyme † , ‡ journal, December 1999

Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP journal, September 1998

Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution journal, September 1998

Automated protein model building combined with iterative structure refinement journal, May 1999

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Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus journal, June 2002

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The High Resolution Crystal Structure of Recombinant Crithidia fasciculata Tryparedoxin-I journal, September 1999

Crystal Structure of UDP- N -acetylmuramoyl-l-alanyl-d-glutamate: meso -Diaminopimelate Ligase from Escherichia Coli journal, December 2000

Structure of the Methanococcus jannaschii Mevalonate Kinase, a Member of the GHMP Kinase Superfamily journal, December 2001

Crystal Structures of Mycolic Acid Cyclopropane Synthases from Mycobacterium tuberculosis journal, March 2002

Crystal Structure of Lyme Disease Variable Surface Antigen VlsE of Borrelia burgdorferi journal, June 2002

Crystal Structure of the Cytosolic C2a-C2b Domains of Synaptotagmin III: Implications for Ca journal, November 1999

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) journal, May 2000

Creating protein models from electron-density maps using particle-filtering methods journal, October 2007

Synapsin I is structurally similar to ATP-utilizing enzymes journal, February 1998

A new software routine that automates the fitting of protein X-ray crystallographic electron-density maps journal, June 2001

Automated tracing of electron-density maps of proteins journal, February 2003

Building of RNA and DNA double helices into electron density journal, May 2008

Rapid model building of β-sheets in electron-density maps journal, February 2010

Rapid model building of α-helices in electron-density maps journal, February 2010

Ribonuclease from Streptomyces aureofaciens at Atomic Resolution journal, March 1996

Modified Phased Translation Functions and their Application to Molecular-Fragment Location journal, September 1998

Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima journal, July 2003

Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases journal, January 1996

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. text, January 2009

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. journalarticle, January 2008

The protein data bank: A computer-based archival file for macromolecular structures journal, January 1978

Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP journal, October 1998

The Protein Data Bank journal, January 2000

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps journal, October 2018

Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps journal, March 2020

Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps journal, March 2020

Refined crystal structure and mutagenesis of human granulocyte-macrophage colony-stimulating factor
journal, November 1996

Fast procedure for reconstruction of full-atom protein models from reduced representations
journal, January 2008

Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli
journal, January 1998

Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): A novel fold with a conserved sequence motif
journal, April 2004

Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis
journal, March 2001

XtalView/Xfit—A Versatile Program for Manipulating Atomic Coordinates and Electron Density
journal, April 1999

Three-dimensional pattern recognition: An approach to automated interpretation of electron density maps of proteins
journal, January 1974

Structure and refinement of penicillopepsin at 1.8 Å resolution
journal, January 1983

Crystal structure of TM1457 from Thermotoga maritima
journal, November 2005

Crystallographic Refinement by Knowledge-Based Exploration of Complex Energy Landscapes
journal, September 2005

Identification of Secondary Structure Elements in Intermediate-Resolution Density Maps
journal, January 2007

Three-Dimensional Structure of the Armadillo Repeat Region of β-Catenin
journal, September 1997

Structural Basis of Rab Effector Specificity
journal, February 1999

Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site
journal, May 2000

Dramatic Structural and Thermodynamic Consequences of Repacking a Protein's Hydrophobic Core
journal, December 2000

Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 å resolution
journal, September 1998

Structural Characterization of the Intramolecular Interaction between the SH3 and Guanylate Kinase Domains of PSD-95
journal, December 2001

Three-Dimensional Structure of the l -Threonine- O -3-phosphate Decarboxylase (CobD) Enzyme from Salmonella enterica ^† ^, ^‡
journal, April 2002

Degradation Pathway of the Phosphonate Ciliatine: Crystal Structure of 2-Aminoethylphosphonate Transaminase ^† ^, ^‡
journal, November 2002

Crystal Structure of NusA from Thermotoga Maritima and Functional Implication of the N-Terminal Domain
journal, October 2003

Flavin Reductase P: Structure of a Dimeric Enzyme That Reduces Flavin ^† ^, ^‡
journal, January 1996

Haloalkane Dehalogenases: Structure of a Rhodococcus Enzyme ^† ^, ^‡
journal, December 1999

Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP
journal, September 1998

Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution
journal, September 1998

Automated protein model building combined with iterative structure refinement
journal, May 1999

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7
journal, June 2008

Crystal structure of the hCASK PDZ domain reveals the structural basis of class II PDZ domain target recognition
journal, March 1998

Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength
journal, May 1998

Conformational variability in the refined structure of the chaperonin GroEL at 2.8 Å resolution
journal, December 1995

High-resolution structure of RNase P protein from Thermotoga maritima
journal, June 2003

Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus
journal, June 2002

Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein.
journal, March 1994

Crystal structure of human p32, a doughnut-shaped acidic mitochondrial matrix protein
journal, March 1999

The High Resolution Crystal Structure of Recombinant Crithidia fasciculata Tryparedoxin-I
journal, September 1999

Crystal Structure of UDP- N -acetylmuramoyl-l-alanyl-d-glutamate: meso -Diaminopimelate Ligase from Escherichia Coli
journal, December 2000

Structure of the Methanococcus jannaschii Mevalonate Kinase, a Member of the GHMP Kinase Superfamily
journal, December 2001

Crystal Structures of Mycolic Acid Cyclopropane Synthases from Mycobacterium tuberculosis
journal, March 2002

Crystal Structure of Lyme Disease Variable Surface Antigen VlsE of Borrelia burgdorferi
journal, June 2002

Crystal Structure of the Cytosolic C2a-C2b Domains of Synaptotagmin III: Implications for Ca
journal, November 1999

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)
journal, May 2000

Creating protein models from electron-density maps using particle-filtering methods
journal, October 2007

Synapsin I is structurally similar to ATP-utilizing enzymes
journal, February 1998

A new software routine that automates the fitting of protein X-ray crystallographic electron-density maps
journal, June 2001

Automated tracing of electron-density maps of proteins
journal, February 2003

Building of RNA and DNA double helices into electron density
journal, May 2008

Rapid model building of β-sheets in electron-density maps
journal, February 2010

Rapid model building of α-helices in electron-density maps
journal, February 2010

Ribonuclease from Streptomyces aureofaciens at Atomic Resolution
journal, March 1996

Modified Phased Translation Functions and their Application to Molecular-Fragment Location
journal, September 1998

Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima
journal, July 2003

Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases
journal, January 1996

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.
text, January 2009

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.
journalarticle, January 2008

The protein data bank: A computer-based archival file for macromolecular structures
journal, January 1978

Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP
journal, October 1998

The Protein Data Bank
journal, January 2000

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps
journal, October 2018

Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps
journal, March 2020

Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps
journal, March 2020