In the Nov. 29, 2007 edition of the journal Nature, a collaboration of scientists from the University of California at San Francisco and The Rockefeller University in New York have revealed the three-dimensional structure of the nuclear pore complex (NPC), the “gatekeeper” of the nucleus of a cell. The study, carried out over several years, determined the structure by adopting a puzzle-solving approach that integrated experimental and computations techniques.
The NPC is a dynamic assembly of proteins that forms passages in the envelope surrounding the nucleus. The NPC controls the access of materials in and out of the nucleus, which contains genetic material. In the fungus yeast, in which the study was carried out, the NPC comprises of 30 different types of proteins that form a structure with at least 456 protein molecules, many of which (called phenylalanine-glycine repeat nucleoporins) allow molecules like DNA and proteins to be shuffled through the NPC.
Professor of Biology Dominic Poccia, who studies nuclear membranes, explained, “I think two of the least well understood and most beautiful structures in the eukaryotic cell are the centrioles of the centrosomes and the pores of the nuclear envelope, although both are clearly important and their malfunction brings cells to a halt. Oddly enough, the former has a 9-fold rotational symmetry, the latter, 8-fold. The nuclear pores are clearly essential to the transport of mRNAs to the cytoplasm where genetic information becomes functional protein machinery. Without this, the genome is just a phone book or blueprint.”
To determine the architecture of the NPC, scientists first generated data through several experiments, each of which provided a small clue to the relative position and interactions of different protein molecules. While each experiment provided little information about the structure of the NPC, a single three-dimensional structure was determined by combining all the data through computational means. Scientists then corroborated this structure directly by comparing it to experimentally determined data not included in these calculations.
From the determined structure, the scientists could start making several inferences about the major features of the NPC. An important finding was that parts of the complex that connected it to the inner and outer membranes of the nucleus showed protein arrangement patterns that have been uniquely
observed for some proteins involved in transport of molecules between locations inside a cell, suggesting that these structures are evolutionarily related. Moreover, in addition to the 8-fold symmetry of the complex, the authors observed an additional level of structural repetition in the NPC that appeared to have arisen from gene duplication. Based on their NPC structure, the scientists hypothesized that such duplication events led to the evolution of the complex we now see from a simpler progenitor NPC.
While the study demonstrates the immense potential of integrated experimental and computational approaches in elucidating the structures of other macromolecular complexes, it does have some limitations. In particular, while the study used relatively low resolution data, more elaborate description of the evolutionary origin, transport mechanism and assembly pathway of the NPC require higher resolution information. In addition, the model is a static picture, and scientists wish to have a dynamic understanding of the NPC.
Poccia also stressed that “although solving the structure of the very complex pores at this level is important, it is only a first step to figuring out not only its mechanical properties, but its transport selectivity.” He added, “And let’s not forget that it is a bidirectional gate, permitting certain cytoplasmic molecules to gain access to the nuclear interior including the chromosomes.”
Amherst College Professor of Biology Patrick Williamson, summarized the findings of the study, “These folks have really done two things,” he said. “One is to figure out how to take the kind of low resolution data that are generally used to describe such structures and use them all at once to generate a structure that has a higher resolution than is available from any one data set by itself. The other is to provide a framework that describes how the nuclear pore proteins interact with each other.
“It is wonderful to see over the years structures that we could only visualize as though through frosted glass appearing with increasing clarity,” added Poccia. “This is a major step forward.”
(A movie showing the three-dimensional structure of the NPC can be viewed for free at http://www.nature.com/nature/journal/v450/n7170/suppinfo/nature06405.html)