Sep
28
2010
5

Deriving Inhibitory Peptides from Globular Protein–Protein Interactions

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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Sep
27
2010
2

Sub-angstrom modeling of complexes between flexible peptides and globular proteins

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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Sep
25
2010
4

The Structural Basis of Peptide-Protein Binding Strategies

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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Sep
24
2010
5

Introducing Peptide-Protein Interactions

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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Oct
28
2009
0

Dynamic interactions of proteins in complex networks: a more structured view.

Amelie Stein, Roland A Pache, Pau Bernadó, Miquel Pons, Patrick Aloy (FEBS Journal, 2009)

This recent mini-review by Stein et al. focuses on the mechanisms that enable dynamic, transient, short lived interactions in cellular networks. Of special interest are the always popular “motif recognition domain”-“short flexible peptide” interactions. However, post translational modifications and regulation by disorder are also discussed. We concise the review further to some basic/interesting/anecdotal/”pondering worthy” points.

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Dec
11
2008
0

Structural and Thermodynamic Approach to Peptide Immunogenicity

Carlos J. Camacho et al. study the relationship between peptide stabilities and their immunogenicity. They present a model system of several peptides corresponding to portions of murine HRS which are capable of inducing anti-protein antibodies of varying affinity and temporal persistence. On this system they show by molecular dynamics simulations, that sequences of the most immunogenic peptides correspond to highly ordered structural motifs in the parent protein. Competitive ELISAs provide direct evidence that these peptides share structural determinants with native protein. More interestingly they address the question of how can these less stable peptides induce the same immunogenic response. By Nir London

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