Cell biology: Brief encounters bolster contacts

@article{Blundell2006CellBB,
  title={Cell biology: Brief encounters bolster contacts},
  author={Tom L. Blundell and Juan Fern{\'a}ndez-Recio},
  journal={Nature},
  year={2006},
  volume={444},
  pages={279-280}
}
Molecules often work together in complexes to carry out their functions in the cell. But how do they get together in such a dynamic environment? A structural study follows proteins as they meet their partners.Close encountersProtein–protein interactions are involved in a large number of biological processes, and though X-ray crystallography and nuclear magnetic resonance spectroscopy can be used to examine two (or more) proteins in a complex, it is difficult to establish how the two proteins… Expand
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References

SHOWING 1-10 OF 14 REFERENCES
Visualization of transient encounter complexes in protein–protein association
TLDR
Using paramagnetic relaxation enhancement, this work directly demonstrates the existence and visualize the distribution of an ensemble of transient, non-specific encounter complexes under equilibrium conditions for a relatively weak protein–protein complex between the amino-terminal domain of enzyme I and the phosphocarrier protein HPr. Expand
Close encounters of the transient kind: protein interactions in the photosynthetic redox chain investigated by NMR spectroscopy.
TLDR
The structural information, in combination with kinetic and theoretical analyses of protein complexes, provides new insight into the nature of transient protein interactions. Expand
Anchor residues in protein-protein interactions.
TLDR
It is shown that the mechanism for molecular recognition requires one of the interacting proteins to anchor a specific side chain in a structurally constrained binding groove of the other protein, providing a steric constraint that helps to stabilize a native-like bound intermediate. Expand
Is one solution good enough?
TLDR
The ever-increasing computational processing power available, combined with the pre-existing and emerging automated methods for structure determination, principally driven by the structural genomics initiatives, means the production of collections of models is now a realistic and relatively effortless procedure. Expand
Rapid, electrostatically assisted association of proteins
TLDR
The rapid association of barnase and its intracellular inhibitor barstar has been analysed from the effects of mutagenesis and electrostatic screening and its principles may be used for protein design. Expand
Detecting transient intermediates in macromolecular binding by paramagnetic NMR
TLDR
It is shown that intermolecular paramagnetic relaxation enhancement (PRE) provides a means of directly detecting the presence of, and investigating the nature of, low population transient intermediates under equilibrium conditions. Expand
Functional organization of the yeast proteome by systematic analysis of protein complexes
TLDR
The analysis provides an outline of the eukaryotic proteome as a network of protein complexes at a level of organization beyond binary interactions, which contains fundamental biological information and offers the context for a more reasoned and informed approach to drug discovery. Expand
Identification of protein-protein interaction sites from docking energy landscapes.
TLDR
Protein docking simulations and analysis of the interaction energy landscapes are applied to identify protein-protein interaction sites to guide the design of mutations on the surfaces of proteins, provide geometrical details of a possible interaction, and help to annotate protein surfaces in structural proteomics. Expand
Protein docking along smooth association pathways
  • C. Camacho, S. Vajda
  • Chemistry, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 2001
TLDR
The method accounts for the dominant driving forces at the different length scales of the protein binding process, allowing for an efficient selection of a downhill path on the evolving receptor-ligand-free energy landscape. Expand
The Electron Transfer Complex between Cytochrome c552 and the CuA Domain of the Thermus thermophilus ba3 Oxidase
TLDR
The chemical shift analysis performed for both redox states provided a topological description of the contact surface on each partner molecule, suggesting that alterations of the electron distribution in the porphyrin ring due to formation of the protein-protein complex are apparently sensed even beyond the heme propionate groups. Expand
...
1
2
...