Determining the architectures of macromolecular assemblies.
To understand the workings of a living cell, we need to know the architectures of its macromolecular assemblies. Here we show how proteomic data can be used to determine such structures. The process involves the collection of sufficient and diverse high-quality data, translation of these data into spatial restraints, and an optimization that uses the restraints to generate an ensemble of structures consistent with the data. Analysis of the ensemble produces a detailed architectural map of the assembly. We developed our approach on a challenging model system, the nuclear pore complex (NPC). The NPC acts as a dynamic barrier, controlling access to and from the nucleus, and in yeast is a 50 MDa assembly of 456 proteins. The resulting structure, presented in an accompanying paper, reveals the configuration of the proteins in the NPC, providing insights into its evolution and architectural principles. The present approach should be applicable to many other macromolecular assemblies.
Department of Bioengineering and Therapeutic Sciences, and California Institute for Quantitative Biosciences, Byers Hall, Suite 503B, 1700 4th Street, University of California at San Francisco, San Francisco, California 94158-2330, USA.
Frank
F
Alber
Svetlana
S
Dokudovskaya
Liesbeth M
LM
Veenhoff
Wenzhu
W
Zhang
Julia
J
Kipper
Damien
D
Devos
Adisetyantari
A
Suprapto
Orit
O
Karni-Schmidt
Rosemary
R
Williams
Brian T
BT
Chait
Michael P
MP
Rout
Andrej
A
Sali
D002470:Cell Survival; D019295:Computational Biology; D046911:Macromolecular Substances / Q000032:analysis / Q000737:chemistry / Q000378:metabolism; D016253:Microscopy, Immunoelectron; D008954:Models, Biological; D022022:Nuclear Pore / Q000737:chemistry* / Q000378:metabolism* / Q000648:ultrastructure; D028861:Nuclear Pore Complex Proteins / Q000032:analysis / Q000737:chemistry* / Q000378:metabolism* / Q000648:ultrastructure; D011485:Protein Binding; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000166:cytology* / Q000378:metabolism / Q000648:ultrastructure*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D012680:Sensitivity and Specificity; D035501:Uncertainty
D046911:Macromolecular Substances; C097894:NUP84 protein, S cerevisiae; D028861:Nuclear Pore Complex Proteins; D029701:Saccharomyces cerevisiae Proteins