Fast and accurate conversion of atomic models into electron density maps

O.S. Sorzano Carlos; Vargas Javier; Otón Joaquín; Abrishami Vahid; M. de la Rosa-Trevín José; del Riego Sandra; Fernández-Alderete Alejandro; Martínez-Rey Carlos; Marabini Roberto; M. Carazo José; O.S. Sorzano Carlos; Vargas Javier; Otón Joaquín; Abrishami Vahid; M. de la Rosa-Trevín José; del Riego Sandra; Fernández-Alderete Alejandro; Martínez-Rey Carlos; Marabini Roberto; M. Carazo José

doi:10.3934/biophy.2015.1.8

AIMS Biophysics

2015, Volume 2, Issue 1: 8-20. doi: 10.3934/biophy.2015.1.8

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Research article Special Issues

Fast and accurate conversion of atomic models into electron density maps

1.
National Center of Biotechnology (CSIC), c/Darwin, 3, Campus Univ. Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain;
2.
Bioengineering Lab., Escuela Politécnica Superior, Univ. San Pablo CEU, Campus Urb. Montepríncipe s/n, 28668, Boadilla del Monte, Madrid, Spain;
3.
Escuela Politécnica Superior, Univ. Autónoma de Madrid, Campus Univ. Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain

Received: 01 February 2015 Accepted: 11 March 2015 Published: 17 March 2015

New image processing methodologies and algorithms have greatly contributed to the signi cant progress in three-dimensional electron microscopy (3DEM) of biological complexes we have seen over the last decades. Naturally, the availability of accurate procedures for the objective testing of new algorithms is a crucial requirement for the further advancement of the eld. A good and accepted testing work ow involves the generation of realistic 3DEM-like maps of biological macromolecules from which some measure of ground truth can be derived, ideally because their 3D atomic structure is already known. In this work we propose a very accurate generation of maps using atomic form factors for electron scattering. We thoroughly review current approaches in the eld, quantitatively demonstrating the bene ts of the new methodology. Additionally, we study a concrete example of the use of this approach for hypothesis testing in 3D Electron Microscopy.
- Atom models,
- Electron scattering,
- Filter design,
- Image formation,
- 3D signals,
- Electron microscopy
Citation: O.S. Sorzano Carlos, Vargas Javier, Otón Joaquín, Abrishami Vahid, M. de la Rosa-Trevín José, del Riego Sandra, Fernández-Alderete Alejandro, Martínez-Rey Carlos, Marabini Roberto, M. Carazo José. Fast and accurate conversion of atomic models into electron density maps[J]. AIMS Biophysics, 2015, 2(1): 8-20. doi: 10.3934/biophy.2015.1.8

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Abstract

New image processing methodologies and algorithms have greatly contributed to the signi cant progress in three-dimensional electron microscopy (3DEM) of biological complexes we have seen over the last decades. Naturally, the availability of accurate procedures for the objective testing of new algorithms is a crucial requirement for the further advancement of the eld. A good and accepted testing work ow involves the generation of realistic 3DEM-like maps of biological macromolecules from which some measure of ground truth can be derived, ideally because their 3D atomic structure is already known. In this work we propose a very accurate generation of maps using atomic form factors for electron scattering. We thoroughly review current approaches in the eld, quantitatively demonstrating the bene ts of the new methodology. Additionally, we study a concrete example of the use of this approach for hypothesis testing in 3D Electron Microscopy.

References

[1]	H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, P. Bourne (2000) The protein data bank.Nucleic Acids Research 28: 235-242.
[2]	J. R. Bilbao-Castro, C. O. S. Sorzano, I. García, J. J. Fernández (2004) Phan3D: design of biological phantoms in 3D electron microscopy.Bioinformatics 20: 3286-3288.
[3]	K. Braig, Z. Otwinowski, R. Hegde, D. C. Boisvert, A. Joachimiak, A. L. Horwich, P. B. Sigler (1994) The crystal structure of the bacterial chaperonin GroEL at 2.8á.Nature 371: 578-586.
[4]	C. T. Chantler (2000) Detailed tabulation of atomic form factors, photoelectric absorption and scattering cross section, and mass attenuation coe cients in the vicinity of absorption edges in the soft x-rays (z=30-36, z=60-89, e=0.1kev-10kev), addressing convergence issues of earlier work.J. Phys. Chem. Ref. Data 29: 597-1048.
[5]	M. S. Chapman, A. Trzynka, B. K. Chapman (2013) Atomic modeling of cryo-electron microscopy reconstructions - joint re nement of model and imaging parameters..J. Structural Biology 182: 10-21.
[6]	Collaborative (1994) Collaborative computational project no. 4, The CCP4 Suite: Programs for Protein Crystallography.Acta Crystallo- graphica D50: 760-763.
[7]	H. A. David, H. N. Nagaraja (2003) Order statistics.John Wiley and Sons .
[8]	W. R. Dillon, M. Goldstein (1984) Multivariate analysis: Methods and applications.John Wiley, New York, USA .
[9]	J. Frank (2006) Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State.Oxford Univ. Press, New York, USA .
[10]	J. Frank, M. Radermacher, P. Penczek, J. Zhu, Y. Li, M. Ladjadj, A. Leith (1996) SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related elds..J. Structural Biology 116: 190-199.
[11]	P. Ge, Z. H. Zhou (2011) Hydrogen-bonding networks and rna bases revealed by cryo electron microscopy suggest a triggering mechanism for calcium switches..Proc. Natl. Acad. Sci. USA 108: 9637-9642.
[12]	G. Harauz, M. van Heel (1986) Exact lters for general geometry three dimensional reconstruction.Optik 73: 146-156.
[13]	R. Henderson, A. Sali, M. L. Baker, B. Carragher, B. Devkota, K. H. Downing, E. H. Egelman, Z. Feng, J. Frank, N. Grigorieff, W. Jiang, S. J. Ludtke, O. Medalia, P. A. Penczek, P. B. Rosenthal, M. G. Rossmann, M. F. Schmid, G. F. Schr?üder, A. C. Steven, D. L. Stokes, J. D. Westbrook, W. Wriggers, H. Yang, J. Young, H. M. Berman, W. Chiu, G. J. Kleywegt, C. L. Lawson (2012) Outcome of the rst electron microscopy validation task force meeting..Structure 20: 205-214.
[14]	B. Heymann, D. Belnap (2007) Bsoft: Image processing and molecular modeling for electron microscopy.J. Structural Biology 157: 3-18.
[15]	S. Jonic, C. O. S. Sorzano, N. Boisset (2008) Comparison of single-particle analysis and electron tomography approaches: an overview.J. Microscopy 232: 562-579.
[16]	D. C. Joy (1995) Monte Carlo Modeling for Electron Microscopy and Microanalysis.Oxford Univ. Press, London, England .
[17]	E. Kirkland (1998) Advanced computing in electron microscopy.Plenum press, New York, USA .
[18]	C. L. Lawson, M. L. Baker, C. Best, C. Bi, M. Dougherty, P. Feng, G. van Ginkel, B. Devkota, I. Lagerstedt, S. J. Ludtke, R. H. Newman, T. J. Old eld, I. Rees, G. Sahni, R. Sala, S. Velankar, J. Warren, J. D. Westbrook, K. Henrick, G. J. Kleywegt, H. M. Berman, W. Chiu (2011) Emdatabank.org: uni ed data resource for cryoem..Nucleic Acids Res 39: D456-D464.
[19]	R. M. Lewitt (1992) Alternatives to voxels for image representation in iterative reconstruction algorithms.Physics in Medicine & Biology 37: 705-716.
[20]	H. Lilliefors (1967) On the kolmogorov-smirnov test for normality with mean and variance unknown.J. American Statistical Association 62: 399-402.
[21]	S. J. Ludtke, P. R. Baldwin, W. Chiu (1999) EMAN: Semiautomated software for high-resolution single-particle reconstructions.J. Structural Biology 128: 82-97.
[22]	A. Oppenheim, R. Schafer, J. Buck (1999) Discrete-time signal processing, 2nd edition.Prentice-Hall .
[23]	L. M. Peng (2005) Electron atomic scattering factors, debye-waller factors and the optical potential for high-energy electron diffraction.J. Electron Microscopy 54: 199-207.
[24]	L. M. Peng, G. Ren, S. L. Dudarev, M. J. Whelan (1996) Robust parameterization of elastic and absorptive electron atomic scattering factors.Acta Crystallographica A52: 257-276.
[25]	P. W. Rose, B. Beran, C. Bi, W. F. Bluhm, D. Dimitropoulos, D. S. Goodsell, A. Prlic, M. Quesada, G. B. Quinn, J. D. Westbrook, J. Young, B. Yukich, C. Zardecki, H. M. Berman, P. E. Bourne (2011) The rcsb protein data bank: redesigned web site and web services..Nucleic Acids Res 39: D392-D401.
[26]	H. Rullgård, L.-G. Ofverstedt, S. Masich, B. Daneholt, O. Oktem (2011) Simulation of transmission electron microscope images of biological specimens..J Microsc 243: 234-256.
[27]	S. H. W. Scheres (2012) A Bayesian view on cryo-EM structure determination..J. Molecular Biology 415: 406-418.
[28]	G. H. Smith, R. E. Burge (1962) The analytical representation of atomic scattering amplitudes for electrons.Acta Crystallographica 15: 182-186.
[29]	C. O. S. Sorzano, S. Jonic, M. Cottevieille, E. Larquet, N. Boisset, S. Marco (2007) 3D electron microscopy of biological nanomachines: principles and applications.European Biophysics Journal 36: 995-1013.
[30]	C. O. S. Sorzano, R. Marabini, J. Velázquez-Muriel, J. R. Bilbao-Castro, S. H. W. Scheres, J. M. Carazo, A. Pascual-Montano (2004) XMIPP: A new generation of an open-source image processing package for electron microscopy.J. Structural Biology 148: 194-204.
[31]	C. O. S. Sorzano, R. Marabini, N. Boisset, E. Rietzel, R. Schröder, G. T. Herman, J. M. Carazo (2001) The effect of overabundant projection directions on 3D reconstruction algorithms.J. Structural Biology 133: 108-118.
[32]	J. C. H. Spence (1993) On the accurate measurement of structure-factor amplitudes and phases by electron diffraction.Acta Crystallographica A49: 231-260.
[33]	P. A. Stadelmann (1987) EMS - a software package for electron diffraction analysis and HREM image simulation in materials science.Ultramicroscopy 21: 131-146.
[34]	S. M. Stagg, J. Pulokas, D. Fellmann, A. Cheng, J. D. Quispe, S. P. Mallick, R. M. Avila, B. Carragher, C. S. Potter (2006) Automated cryoem data acquisition and analysis of 284,742 particles of groel.Nature 439: 234-238.
[35]	F. Tama, O. Miyashita, C. L. Brooks (2004) Flexible multi-scale tting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis..J Mol Biol 337: 985-999.
[36]	F. Tama, O. Miyashita, C. L. Brooks III (2004) Normal mode based exible tting of high-resolution structure into low-resolution experimental data from cryo-EM.J. Structural Biology 147: 315-326.
[37]	E. Tjioe, K. Lasker, B. Webb, H. J. Wolfson, A. Sali (2011) Multi t: a web server for tting multiple protein structures into their electron microscopy density map..Nucleic Acids Res 39: W167-W170.
[38]	M. Topf, K. Lasker, B. Webb, H. Wolfson, W. Chiu, A. Sali (2008) Protein structure tting and re nement guided by cryo-em density..Structure 16: 295-307.
[39]	L. G. Trabuco, E. Villa, K. Mitra, J. Frank, K. Schulten (2008) Flexible tting of atomic structures into electron microscopy maps using molecular dynamics..Structure 16: 673-683.
[40]	M. Unser, A. Aldroubi, M. Eden (1993) B-Spline signal processing: Part I - theory.IEEE Trans. Signal Processing 41: 821-832.
[41]	M. Unser, A. Aldroubi, M. Eden (1993) B-Spline signal processing: Part II-E cient design and applications.IEEE Trans. Signal Processing 41: 834-848.
[42]	M. van Heel, G. Harauz, E. V. Orlova, R. Schmidt, M. Schatz (1996) A new generation of the IMAGIC image processing system.J. Structural Biology 116: 17-24.
[43]	M. Vulović, R. B. G. Ravelli, L. J. van Vliet, A. J. Koster, I. Lazić, U. Lücken, H. Rullgård, O. Öktem, B. Rieger (2013) Image formation modeling in cryo-electron microscopy..J Struct Biol 183: 19-32.
[44]	A. J. C. Wilson (ed.) (1995) International tables for crystallography, 500.Kluwer Academics Publisher .
[45]	W. Wriggers (2010) Using situs for the integration of multi-resolution structures..Biophys Rev 2: 21-27.
[46]	W. Wriggers, R. A. Milligan, J. A. McCammon (1999) Situs: A package for docking crystal structures into low-resolution maps from electron microscopy.J. Structural Biology 125: 185-195.
[47]	X. Zhang, L. Jin, Q. Fang, W. H. Hui, Z. H. Zhou (2010) 3.3 a cryo-em structure of a nonenveloped virus reveals a priming mechanism for cell entry..Cell 141: 472-482.

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