Automated search-model discovery and preparation for structure solution by molecular replacement.

A novel automation pipeline for macromolecular structure solution by molecular replacement is described. There is a special emphasis on the discovery and preparation of a large number of search models, all of which can be passed to the core molecular-replacement programs. For routine molecular-replacement problems, the pipeline automates what a crystallographer might do and its value is simply one of convenience. For more difficult cases, the pipeline aims to discover the particular template structure and model edits required to produce a viable search model and may succeed in finding an efficacious combination that would be missed otherwise. The pipeline is described in detail and a number of examples are given. The examples are chosen to illustrate successes in real crystallography problems and also particular features of the pipeline. It is concluded that exploring a range of search models automatically can be valuable in many cases.

[1]  Bernhard Rupp,et al.  Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein–nucleic acid complex crystals , 2003, Protein science : a publication of the Protein Society.

[2]  A. Vagin,et al.  MOLREP: an Automated Program for Molecular Replacement , 1997 .

[3]  J. Thornton,et al.  PQS: a protein quaternary structure file server. , 1998, Trends in biochemical sciences.

[4]  Sameer Velankar,et al.  E-MSD: the European Bioinformatics Institute Macromolecular Structure Database , 2003, Nucleic Acids Res..

[5]  Anna Tramontano,et al.  Evaluating the usefulness of protein structure models for molecular replacement , 2005, ECCB/JBI.

[6]  Tim J. P. Hubbard,et al.  SCOP database in 2002: refinements accommodate structural genomics , 2002, Nucleic Acids Res..

[7]  Rodrigo Lopez,et al.  Multiple sequence alignment with the Clustal series of programs , 2003, Nucleic Acids Res..

[8]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[9]  Geoffrey J. Barton,et al.  The Jalview Java alignment editor , 2004, Bioinform..

[10]  A. Lesk,et al.  How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. , 1980, Journal of molecular biology.

[11]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[12]  I. Bahar,et al.  Gaussian Dynamics of Folded Proteins , 1997 .

[13]  Tirion,et al.  Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. , 1996, Physical review letters.

[14]  Stephen K Burley,et al.  X-ray structure of a Rex-family repressor/NADH complex insights into the mechanism of redox sensing. , 2005, Structure.

[15]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[16]  K. Katoh,et al.  MAFFT version 5: improvement in accuracy of multiple sequence alignment , 2005, Nucleic acids research.

[17]  Lior Cohen,et al.  X-ray structure and mutagenesis of the scorpion depressant toxin LqhIT2 reveals key determinants crucial for activity and anti-insect selectivity. , 2007, Journal of molecular biology.