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Institut de Biologie StructuraleGrenoble / France

Contact person(s) related to this article / FARIAS ESTROZI Leandro

Development of MR Techniques

AMoRe: a suite of programs to solve a crystal structure by molecular replacement (MR)

The idea of molecular replacement (MR) is to build a tentative crystal structure using known molecular models, similar to the actual molecules that constitute the crystal, in order to start model building or refinement. The problem is to determine the positions of the models within the crystal cell, which is ultimately done by comparing observed and calculated structure factors, for selected positions of the independent molecules within the cell.

AMoRe (Navaza, 2001) is a suite of script-driven programs for molecular replacement with the following main characteristics:

many putative solutions are explored by means of fast algorithms;
correlation coefficients are used as the main criteria of selection;
the information coming from already positioned models is automatically incorporated into the procedure;
there is a high degree of automation.
The program is freely available upon request to the authors.

Contacts:
- Jorge Navaza : jorge.navaza@ibs.fr
- Stefano Trapani : stefano.trapani@ibs.fr

References
Navaza, J. (2001) Implementation of molecular replacement in AMoRe. Acta Cryst. D57, 1367- 1372

Using ensembles of structures as MR search probes

It is widely recognized that the outcome of a MR search depends to a large extent on the structural similarity between the search model and the unknown structure. Indeed, the structure of a close homologue, generally with more than 30% sequence similarity, is normally required.

Owing to the vast quantity of data now existing in the Protein Data Bank, it often occurs, for a particular crystallographic problem, that several deposited structures may be available as models, with different sequence similarity or in different conformations. Instead of considering just one experimental structure (the supposedly "closest" to the unknown crystal structure), it has been proposed that in these cases a more effective MR model may be obtained by taking into account the structural and sequence information coming from all the known homologues. Following this line, the use of hybrid models, built on the basis of alignments of homologous sequences, has given positive results in some difficult MR cases. The result of this approach, however, are extremely sensible to the quality of the sequence alignment (Schwarzenbacher et al., 2004).

As an alternative to the "hybrid" model, we propose the use of ensembles of superposed homologous structures, where the regions of structural variability/flexibility are implicitly weighted, with respect to the conserved regions, by the model itself. This kind of model has strict analogies with NMR solved structures, whose use in MR has already been object of study by other researchers (Chen, 2001). For the construction of the ensembles, we propose the superposition of the models based on the electron density correlation rather than the rmsd between equivalent atoms.

Contacts:
- Jorge Navaza : jorge.navaza@ibs.fr
- Stefano Trapani : stefano.trapani@ibs.fr


Ensemble of 15 structures used as MR probe


MR solution

References

Chen, Y. W. (2001) Solution solution: using NMR models for molecular replacement. Acta Cryst. D57, 1457-1461.

Schwarzenbacher, R., Godzik, A., Grzechnik, S. K. & Jaroszewski, L. (2004) The importance of alignment accuracy for molecular replacement. Acta Cryst. D60, 1229-1236.

Rotational search

Rotational search is a common computational task in object analysis and comparison. For example, in molecular replacement, the orientations of the molecules in a crystal are obtained by superposing the crystal Patterson function onto a rotated version of a model Patterson function. In the case of 3D EM reconstruction procedures, the orientation of the particles in the sample can be obtained by superposing the 2D projections of rotated versions of a 3D model onto the particle images.

Fast 3D rotational search. Applications in MR.

Rotational search procedures are commonly based on expansions in series of spherical harmonic (SH) and Wigner D-functions. In this way one can exploit the symmetry properties of these functions with respect to the 3D-rotation group.

The rotational search routines implemented in our programs exploit the Fourier representation of SHs and D-functions for all angular variables. In this way, the rotational search can be sped up by means of 3D Fast Fourier Transform (FFT) algorithms. Also, the Fourier representation avoids singularity issues arising from SH and D recursive calculations.

We have written and implemented 3D FFT rotation search algorithms into the AMoRe molecular replacement software (Trapani & Navaza, 2006). The resulting code performs faster and produces results with at least the same accuracy as the original code. The new code aims at permitting accurate and more rapid computations at high angular resolution of the rotation function of large particles such as viral particles.

Contacts:
- Jorge Navaza : jorge.navaza@ibs.fr
- Stefano Trapani : stefano.trapani@ibs.fr

References

Trapani, S. & Navaza, J. (2006) Calculation of spherical harmonics and Wigner d functions by FFT. Applications to fast rotational matching in molecular replacement and implementation into AMoRe. Acta Cryst. A62, 262-269.