Publications by authors named "Luis Angel Rodriguez-Lumbreras"

The endothelial protein C receptor (EPCR) is a fundamental component of the vascular system in mammals due to its contribution in maintaining blood in a non-prothrombotic state, which is crucial for overall life development. It accomplishes this by enhancing the conversion of protein C (PC) into the anticoagulant activated protein C (APC), with this property being dependent on a known EPCR conformation that enables direct interaction with PC/APC. In this study, we report a previously unidentified conformation of EPCR whereby Tyr154, critical for PC/APC binding, shows a striking non-canonical configuration.

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Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to tackle these challenges. The latest resources on protein complexes and interfaces were exploited to derive a benchmark dataset consisting of 1677 homodimer protein crystal structures, including a balanced mix of physiological and non-physiological complexes.

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Proteins and nucleic acids are essential biological macromolecules for cell life. Indeed, interactions between proteins and DNA regulate many biological processes such as protein synthesis, signal transduction, DNA storage, or DNA replication and repair. Despite their importance, less than 4% of total structures deposited in the Protein Data Bank (PDB) correspond to protein-DNA complexes, and very few computational methods are available to model their structure.

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Article Synopsis
  • - The study focuses on understanding how proteins interact at the molecular level, which is important for unraveling their functions, especially since experimental data on protein-protein complexes is limited.
  • - Computational methods like pyDock have been developed to fill this gap, using various energy factors to assess how well proteins can dock together, and have proven effective in community tests like CAPRI and CASP.
  • - The text explains how to use pyDock for modeling protein structures and explores its applications in predicting binding modes, using experimental restraints, estimating binding affinity, and modeling protein assemblies.
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