Macromolecular Modeling Blog ™

Congratulations, the SGC (Structural Genomics Consortium) just released the 1000th high resolution protein structure!

The 1000th structure – PDB ID 2xml – belongs to JmjD2C, a protein involved in epigenetic signalling. JmjD2C is known to play a key a role in the maintenance of self renewal in stem cells as well as roles in cancer.

I'm the 1000'th structure solved by the SGC. PDB id 2XML

B.t.w. the news release by the welcome trust received intense coverage by science news websites and blogs (mostly reposting, e.g. Genetic Engineering and BioTech News,The Medical News, Biology News Net,Red Orbit,Science Daily & PhysOrg.com)

There are several forms of peptide-protein interactions, one of which are globular PPIs mediated by a dominant linear peptide at the interface. To what extent could peptides extracted from a globular protein monomer be used to inhibit the interaction to its partner? In this work, we have investigated the possibility of deriving peptides from the interface of globular proteins to design inhibitors that would compete with their native interaction.
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We present Rosetta FlexPepDock, a novel tool for refining coarse peptide–protein models that allows significant changes in both peptide backbone and side chains. We obtain high resolution models, often of sub-angstrom backbone quality, over an extensive and general benchmark of 89 peptide–protein interactions.

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How can peptides overcome the entropic cost involved in switching from an unstructured, flexible peptide to a rigid, well-defined bound structure? What are the strategies used by peptides in? order to bind their protein receptor? How is this different than protein-protein interactions? In this work we performed A structure-based analysis of peptide-protein interactions to try and answer these questions.

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Peptide-protein interactions are a key component of the cellular protein-protein interaction network. These interactions, in which one partner is a globular protein (or domain) and the other is a flexible linear peptide are very prevalent, and play a role in major cellular processes, predominantly in signaling and regulatory networks. Due to their abundance and cardinal role in regulatory interactions, flexible peptides are in many cases implicated in human disease and cancer. Consequently, peptide-protein interactions are gaining much interest of late. The Furman group have recently published a series of papers on the subject of peptide-protein interactions (disclaimer – these were partly authored by yours truly). In this post I will introduce the subject and the motivation to investigate these interactions and in later posts of this ‘mini-series’ I will get into more details on this on-going research.
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