Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies.
A method for flexible fitting of molecular models into three-dimensional electron microscopy (3D-EM) reconstructions at a resolution range of 8-12 A is proposed. The approach uses the evolutionarily related structural variability existing among the protein domains of a given superfamily, according to structural databases such as CATH. A structural alignment of domains belonging to the superfamily, followed by a principal components analysis, is performed, and the first three principal components of the decomposition are explored. Using rigid body transformations for the secondary structure elements (SSEs) plus the cyclic coordinate descent algorithm to close the loops, stereochemically correct models are built for the structure to fit. All of the models are fitted into the 3D-EM map, and the best one is selected based on crosscorrelation measures. This work applies the method to both simulated and experimental data and shows that the flexible fitting was able to produce better results than rigid body fitting.
Velazquez-Muriel
Javier-Angel
JA
Biocomputing Unit, National Center for Biotechnology-CSIC, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain.
Valle
Mikel
M
Santamaría-Pang
Alberto
A
Kakadiaris
Ioannis A
IA
Carazo
José-María
JM
D000595:Amino Acid Sequence; D003198:Computer Simulation; D030562:Databases, Protein; D019143:Evolution, Molecular; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008854:Microscopy, Electron / Q000379:methods*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D012996:Solutions / Q000737:chemistry
D012996:Solutions