TY - JOUR
T1 - Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images
AU - Velázquez-Muriel, Javier
AU - Lasker, Keren
AU - Russel, Daniel
AU - Phillips, Jeremy
AU - Webb, Benjamin M.
AU - Schneidman-Duhovny, Dina
AU - Sali, Andrej
PY - 2012/11/13
Y1 - 2012/11/13
N2 - To obtain a structural model of a macromolecular assembly by single-particle EM, a large number of particle images need to be collected, aligned, clustered, averaged, and finally assembled via reconstruction into a 3D density map. This process is limited by the number and quality of the particle images, the accuracy of the initial model, and the compositional and conformational heterogeneity. Here, we describe a structure determination method that avoids the reconstruction procedure. The atomic structures of the individual complex components are assembled by optimizing a match against 2D EM class-average images, an excluded volume criterion, geometric complementarity, and optional restraints from proteomics and chemical cross-linking experiments. The optimization relies on a simulated annealing Monte Carlo search and a divide-and-conquer message-passing algorithm. Using simulated and experimentally determined EM class averages for 12 and 4 protein assemblies, respectively, we showthat a few class averages can indeed result in accurate models for complexes of as many as five subunits. Thus, integrative structural biology can now benefit from the relative ease with which the EM class averages are determined.
AB - To obtain a structural model of a macromolecular assembly by single-particle EM, a large number of particle images need to be collected, aligned, clustered, averaged, and finally assembled via reconstruction into a 3D density map. This process is limited by the number and quality of the particle images, the accuracy of the initial model, and the compositional and conformational heterogeneity. Here, we describe a structure determination method that avoids the reconstruction procedure. The atomic structures of the individual complex components are assembled by optimizing a match against 2D EM class-average images, an excluded volume criterion, geometric complementarity, and optional restraints from proteomics and chemical cross-linking experiments. The optimization relies on a simulated annealing Monte Carlo search and a divide-and-conquer message-passing algorithm. Using simulated and experimentally determined EM class averages for 12 and 4 protein assemblies, respectively, we showthat a few class averages can indeed result in accurate models for complexes of as many as five subunits. Thus, integrative structural biology can now benefit from the relative ease with which the EM class averages are determined.
KW - Computational biology
KW - Integrative modeling
KW - Structural determination
UR - http://www.scopus.com/inward/record.url?scp=84869223926&partnerID=8YFLogxK
U2 - https://doi.org/10.1073/pnas.1216549109
DO - https://doi.org/10.1073/pnas.1216549109
M3 - مقالة
C2 - 23112201
SN - 0027-8424
VL - 109
SP - 18821
EP - 18826
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 46
ER -