Determining the architectures of macromolecular assemblies

@article{Alber2007DeterminingTA,
  title={Determining the architectures of macromolecular assemblies},
  author={Frank Alber and Svetlana Dokudovskaya and Liesbeth M. Veenhoff and Wenzhu Zhang and Julia Kipper and Damien P. Devos and Adisetyantari Suprapto and Orit Karni-Schmidt and Rosemary Williams and Brian T. Chait and Michael P. Rout and Andrej Sali},
  journal={Nature},
  year={2007},
  volume={450},
  pages={683-694}
}
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… 

Integrating diverse data for structure determination of macromolecular assemblies.

An approach to integrate structural information gathered at multiple levels of the biological hierarchy--from atoms to cells--into a common framework is proposed, illustrated by determining the configuration of the 456 proteins in the nuclear pore complex from baker's yeast.

Modeling of proteins and their assemblies with the Integrative Modeling Platform.

A protocol for this integration is described, whereby the information is converted to a set of spatial restraints and a variety of optimization procedures can be used to generate models of the assembly structures that satisfy the restraints as well as possible.

Modeling of proteins and their assemblies with the integrative modeling platform.

A protocol for this integration is described, whereby the information is converted to a set of spatial restraints and a variety of optimization procedures can be used to generate models that satisfy the restraints as much as possible.

Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints

This work proposes a computational approach, defined by its three main components: a hierarchical representation of the assembly, a scoring function consisting of spatial restraints derived from experimental data, and an optimization method that generates structures consistent with the data.

Assessing the Reconstruction of Macromolecular Assemblies : the Example of the Nuclear Pore Complex

The reconstruction of large protein assemblies is a major challenge due to their plasticity and due to the flexibility of the proteins involved. An emerging trend to cope with these uncertainties

Modeling Macromolecular Complexes: A Journey Across Scales

This chapter presents concepts and tools aiming at improving the understanding of the link between the static structures of macromolecular complexes and their biophysical/biological properties and novel insights into real biological problems gained thanks to these modeling tools.

The molecular architecture of the nuclear pore complex

The molecular architecture of the yeast NPC is determined, revealing that half of the NPC is made up of a core scaffold, which is structurally analogous to vesicle-coating complexes.

Assessing the Reconstruction of Macro-molecular Assemblies: the Example of the Nuclear Pore Complex

The reconstruction of large protein assemblies is a major challenge due to their plasticity and due to the flexibility of the proteins involved. An emerging trend to cope with these uncertainties

Computational Structural Biology of Macromolecular Interactions

Current developments in low-resolution experimental structure determination methods, such as cryo-electron microscopy and small-angle x-ray scattering, set the stage for integrative modeling protocols that can combine several sources of data, bridge different resolutions and different types of information, and offer an holistic view of the biological molecular machines.

The Structure of the Nuclear Pore Complex (An Update).

The powerful combination of bottom-up and top-down approaches toward determining the structure of the NPC offers a paradigm for uncovering the architectures of other complex biological machines to near-atomic resolution.
...

References

SHOWING 1-10 OF 51 REFERENCES

The molecular architecture of the nuclear pore complex

The molecular architecture of the yeast NPC is determined, revealing that half of the NPC is made up of a core scaffold, which is structurally analogous to vesicle-coating complexes.

Simple fold composition and modular architecture of the nuclear pore complex

The small number of predicted fold types in the NPC and their internal symmetries suggest that the bulk of the NPC structure has evolved through extensive motif and gene duplication from a simple precursor set of only a few proteins.

The Yeast Nuclear Pore Complex: Composition, Architecture, and Transport Mechanism

A map of the molecular architecture of the yeast NPC is presented and evidence for a Brownian affinity gating mechanism for nucleocytoplasmic transport is provided.

Architecture of the Xenopus nuclear pore complex revealed by three- dimensional cryo-electron microscopy

Three dimensional structures for both membrane-associated and detergent- extracted Xenopus NPCs, imaged in frozen buffers by cryo-electron microscopy, suggest a minimal domain model for the spoke-ring complex which may account for the observed plasticity of this assembly.

Nuclear Pore Complex Structure and Dynamics Revealed by Cryoelectron Tomography

The central plug/transporter of nuclear pore complexes was variable in volume and could occupy different positions along the nucleocytoplasmic axis, which supports the notion that it essentially represents cargo in transit.

Modular self‐assembly of a Y‐shaped multiprotein complex from seven nucleoporins

The reconstitution of seven proteins into a heptameric 0.5 MDa nuclear pore subcomplex is reported, which document that the Nup84p–Nup133p complex self‐assembles in a modular concept from distinct smaller nucleoporin construction sets.

Snapshots of nuclear pore complexes in action captured by cryo-electron tomography

Cryo-electron tomography is used to study the structure of nuclear pore complexes in their functional environment, that is, in intact nuclei of Dictyostelium discoideum and a new image-processing strategy compensating for deviations of the asymmetric units from a perfect eight-fold symmetry enabled the structure to be refined and to identify new features.
...