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 8–12 Å, together with a comparison of the method capabilities with Normal Mode Analysis (NMA), application examples and a use...

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Bibliographic Details
Published in:Journal of structural biology 2007-05, Vol.158 (2), p.165-181
Main Authors: Velazquez-Muriel, Javier A., Carazo, José-Marı´a
Format: Article
Language:English
Subjects:
Algorithms
Chaperonin 60 - ultrastructure
Flexible fitting
Imaging, Three-Dimensional - methods
ISVD
Mathematical Computing
Microscopy, Electron
Proteins - ultrastructure
Software
Three dimensional electron microscopy
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Summary: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 8–12 Å, 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).
ISSN:1047-8477
1095-8657
DOI:10.1016/j.jsb.2006.10.014