Flexible fitting in 3D-EM with incomplete data on superfamily variability.

We present a substantial improvement of S-flexfit, our recently proposed method for flexible fitting in three dimensional electron microscopy (3D-EM) at a resolution range of 8-12A, together with a comparison of the method capabilities with Normal Mode Analysis (NMA), application examples and a user's guide. S-flexfit uses the evolutionary information contained in protein domain databases like CATH, by means of the structural alignment of the elements of a protein superfamily. The added development is based on a recent extension of the Singular Value Decomposition (SVD) algorithm specifically designed for situations with missing data: Incremental Singular Value Decomposition (ISVD). ISVD can manage gaps and allows considering more aminoacids in the structural alignment of a superfamily, extending the range of application and producing better models for the fitting step of our methodology. Our previous SVD-based flexible fitting approach can only take into account positions with no gaps in the alignment, being appropriate when the superfamily members are relatively similar and there are few gaps. However, with new data coming from structural proteomics works, the later situation is becoming less likely, making ISVD the technique of choice for further works. We present the results of using ISVD in the process of flexible fitting with both simulated and experimental 3D-EM maps (GroEL and Poliovirus 135S cell entry intermediate).

[1]  Adrian A Canutescu,et al.  Cyclic coordinate descent: A robotics algorithm for protein loop closure , 2003, Protein science : a publication of the Protein Society.

[2]  Matthew Brand,et al.  Incremental Singular Value Decomposition of Uncertain Data with Missing Values , 2002, ECCV.

[3]  Y. Kawata,et al.  Functional communications between the apical and equatorial domains of GroEL through the intermediate domain. , 1999, Biochemistry.

[4]  Alberto Santamaría-Pang,et al.  Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies. , 2006, Structure.

[5]  Neil A. Ranson,et al.  Location of a folding protein and shape changes in GroEL–GroES complexes imaged by cryo-electron microscopy , 1994, Nature.

[6]  Gideon Schreiber,et al.  Folding and binding: an extended family business , 2005 .

[7]  M. Baker,et al.  Bridging the information gap: computational tools for intermediate resolution structure interpretation. , 2001, Journal of molecular biology.

[8]  M. Baker,et al.  Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. , 2005, Journal of structural biology.

[9]  Helen R Saibil,et al.  The Chaperonin ATPase Cycle: Mechanism of Allosteric Switching and Movements of Substrate-Binding Domains in GroEL , 1996, Cell.

[10]  M. Baker,et al.  Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. , 2006, Journal of molecular biology.

[11]  E. Arnold,et al.  Structure of poliovirus type 2 Lansing complexed with antiviral agent SCH48973: comparison of the structural and biological properties of three poliovirus serotypes. , 1997, Structure.

[12]  Nikolaus Grigorieff,et al.  Low-resolution structure refinement in electron microscopy. , 2003, Journal of structural biology.

[13]  M G Rossmann,et al.  Interaction of the poliovirus receptor with poliovirus. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[15]  M. Rossmann,et al.  Fitting atomic models into electron-microscopy maps. , 2000, Acta crystallographica. Section D, Biological crystallography.

[16]  Osvaldo Olmea,et al.  MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison , 2002, Protein science : a publication of the Protein Society.

[17]  David Baker,et al.  Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[18]  K. Wilson,et al.  Efficient anisotropic refinement of macromolecular structures using FFT. , 1999, Acta crystallographica. Section D, Biological crystallography.

[19]  J. Weissman,et al.  Mechanism of GroEL action: Productive release of polypeptide from a sequestered position under groes , 1995, Cell.

[20]  Alasdair C. Steven,et al.  Molecular Tectonic Model of Virus Structural Transitions: the Putative Cell Entry States of Poliovirus , 2000, Journal of Virology.

[21]  Zbyszek Otwinowski,et al.  The crystal structure of the bacterial chaperonln GroEL at 2.8 Å , 1994, Nature.

[22]  Andrej Sali,et al.  Combining electron microscopy and comparative protein structure modeling. , 2005, Current opinion in structural biology.

[23]  P B Sigler,et al.  GroEL/GroES: structure and function of a two-stroke folding machine. , 1998, Journal of structural biology.

[24]  J. Carazo,et al.  Electron microscopy study of GroEL chaperonin: different views of the aggregate appear as a function of cell growth temperature. , 1991, Journal of structural biology.

[25]  Frances M. G. Pearl,et al.  The CATH domain structure database. , 2005, Methods of biochemical analysis.

[26]  F. Hartl.  Molecular chaperones in cellular protein folding , 1996, Nature.

[27]  D. Filman,et al.  Structural studies of poliovirus mutants that overcome receptor defects , 1997, Nature Structural Biology.

[28]  F. Tama,et al.  Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. , 2004, Journal of molecular biology.

[29]  A. Horwich,et al.  The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex , 1997, Nature.

[30]  S Birmanns,et al.  Using situs for flexible and rigid-body fitting of multiresolution single-molecule data. , 2001, Journal of structural biology.

[31]  W. Chiu,et al.  Seeing GroEL at 6 A resolution by single particle electron cryomicroscopy. , 2004, Structure.

[32]  William H. Press,et al.  Numerical recipes in C , 2002 .

[33]  B. Lindqvist,et al.  Distinct cellular receptor interactions in poliovirus and rhinoviruses , 2000, The EMBO journal.

[34]  J. Sambrook,et al.  Protein folding in the cell , 1992, Nature.

[35]  A. Horwich,et al.  GroEL‐Mediated protein folding , 1997, Protein science : a publication of the Protein Society.

[36]  M. S. Chapman,et al.  Fitting of high-resolution structures into electron microscopy reconstruction images. , 2005, Structure.

[37]  Karsten Suhre,et al.  ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement , 2004, Nucleic Acids Res..

[38]  Russ B. Altman,et al.  Missing value estimation methods for DNA microarrays , 2001, Bioinform..

[39]  Alasdair C. Steven,et al.  The Structure of the Poliovirus 135S Cell Entry Intermediate at 10-Angstrom Resolution Reveals the Location of an Externalized Polypeptide That Binds to Membranes , 2005, Journal of Virology.

[40]  B L Trus,et al.  Three-dimensional structure of poliovirus receptor bound to poliovirus. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[41]  N. Volkmann,et al.  Quantitative fitting of atomic models into observed densities derived by electron microscopy. , 1999, Journal of structural biology.

[42]  C. Georgopoulos,et al.  The universally conserved GroE (Hsp60) chaperonins. , 1991, Annual review of microbiology.

[43]  Mark Gerstein,et al.  Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic , 2002, Proteins.

[44]  Pablo Chacón,et al.  Fast rotational matching of rigid bodies by fast Fourier transform acceleration of five degrees of freedom. , 2003, Acta crystallographica. Section D, Biological crystallography.

[45]  Sjors H W Scheres,et al.  SPI-EM: towards a tool for predicting CATH superfamilies in 3D-EM maps. , 2005, Journal of molecular biology.

[46]  F. Hartl,et al.  Mitochondrial heat-shock protein hsp60 is essential for assembly of proteins imported into yeast mitochondria , 1989, Nature.

[47]  Roger W. Hendrix,et al.  Homologous plant and bacterial proteins chaperone oligomeric protein assembly , 1988, Nature.

[48]  H. Saibil.  What can electron microscopy tell us about chaperoned protein folding? , 1996, Folding & design.

[49]  A. Horwich,et al.  Structure and function in GroEL-mediated protein folding. , 1998, Annual review of biochemistry.

[50]  P. Chacón,et al.  Multi-resolution contour-based fitting of macromolecular structures. , 2002, Journal of molecular biology.