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Understanding protein recognition using structural features
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Marin-Lopez, Manuel A., Planas-Iglesias, Joan, Bonet, Jaume, Poglayen, Daniel, Garcia-Garcia, Javier, Fernandez-Fuentes, Narcis and Oliva, Baldo (2015) Understanding protein recognition using structural features. In: 29th Annual Symposium of the Protein Society, Barcelona, Spain, 22 -25 Jul 2015. Published in: Protein Science, 24 p. 245. ISSN 0961-8368.
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Abstract
Protein-Protein interactions (PPIs) play a crucial role in virtually all cell processes. Thus, understanding the molecular mechanism of protein recognition is a critical challenge in molecular biology. Previous works in this field show that not only the binding region but also the rest of the protein is involved in the interac- tion, suggesting a funnel-like recognition model as responsible of facilitating the interacting process. Fur- ther more, we have previously shown that three-dimensional local structural features (groups of protein loops) define characteristic patterns (interaction signatures) that can be used to predict whether two pro- teins will interact or not. A notable trait of this prediction system is that interaction signatures can be denoted as favouring or disfavouring depending on their role on the promotion of the molecular binding. Here, we use such features in order to determine differences between the binding interface and the rest of the protein surface in known PPIs. Particularly, we study computationally three different groups of protein-protein interfaces: i) native interfaces (the actual binding patches of the interacting pairs), ii) par- tial interfaces (the docking between a binding patch and a non-interacting patch), and iii) back-to-back interfaces (the docking between non-interacting patches for both of the interacting proteins). Our results show that the interaction signatures in partial interfaces are much less favoured than the ones observed in native and back-to-back interfaces. We hypothesise that this phenomenon is related to the dynamics of the molecular association process. Back-to-back interfaces preserve the exposure of the real interacting patches (thus, allowing the formation of a native interface), while in a partial interface one interacting patch is sequestered and becomes unavailable to form a native interaction.
Item Type: | Conference Item (Paper) | ||||
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Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School | ||||
Journal or Publication Title: | Protein Science | ||||
Publisher: | John Wiley & Sons Ltd. | ||||
ISSN: | 0961-8368 | ||||
Official Date: | 2015 | ||||
Dates: |
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Volume: | 24 | ||||
Page Range: | p. 245 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Conference Paper Type: | Paper | ||||
Title of Event: | 29th Annual Symposium of the Protein Society | ||||
Type of Event: | Conference | ||||
Location of Event: | Barcelona, Spain | ||||
Date(s) of Event: | 22 -25 Jul 2015 |
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