12 research outputs found
Protein-protein modelling using cryo-EM restraints
The recent improvements in cryo-electron microscopy (cryo-EM) in the past few
years are now allowing to observe molecular complexes at atomic resolution. As
a consequence, numerous structures derived from cryo-EM are now available in
the Protein Data Bank. However, if for some complexes atomic resolution is
reached, this is not true for all. This is also the case in cryo-electron
tomography where the achievable resolution is still limited. Furthermore the
resolution in a cryo-EM map is not a constant, with often outer regions being
of lower resolution, possibly linked to conformational variability. Although
those low to medium resolution EM maps (or regions thereof) cannot directly
provide atomic structure of large molecular complexes, they provide valuable
information to model the individual components and their assembly into them.
Most approaches for this kind of modelling are performing rigid fitting of the
individual components into the EM density map. While this would appear an
obvious option, they ignore key aspects of molecular recognition, the
energetics and flexibility of the interfaces. Moreover, these often restricts
the modelling to a unique source of data, the EM density map. In this chapter,
we describe a protocol where an EM map is used as restraint in HADDOCK to guide
the modelling process.Comment: 28 pages including 7 figure
Molecular Modeling of the Interaction Between Stem Cell Peptide and Immune Receptor in Plants
© Springer Science+Business Media, LLC, part of Springer Nature 2020. Molecular docking enables comprehensive exploration of interactions between chemical moieties and proteins. Modeling and docking approaches are useful to determine the three-dimensional (3D) structure of experimentally uncrystallized proteins and subsequently their interactions with various inhibitors and activators or peptides. Here, we describe a protocol for carrying out molecular modeling and docking of stem cell peptide CLV3p on plant innate immune receptor FLS2