![]() ![]() Gan HH, Gunsalus KC (2013) Tertiary structure-based analysis of microRNA-target interactions. Whitford PC, Ahmed A, Yu Y, Hennelly SP, Tama F, Spahn CM, Onuchic JN, Sanbonmatsu KY (2011) Excited states of ribosome translocation revealed through integrative molecular modeling. Tuszynska I, Matelska D, Magnus M, Chojnowski G, Kasprzak JM, Kozlowski LP, Dunin-Horkawicz S, Bujnicki JM (2014) Computational modeling of protein-RNA complex structures. Ke A, Doudna JA (2004) Crystallization of RNA and RNA-protein complexes. Hoskins AA, Moore MJ (2012) The spliceosome: a flexible, reversible macromolecular machine. Pichon C, Felden B (2007) Proteins that interact with bacterial small RNA regulators. Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Biochim Biophys Acta 190(2):381–390ĭemeshkina N, Jenner L, Yusupova G, Yusupov M (2010) Interactions of the ribosome with mRNA and tRNA. Moller W, Amons R, Groene JC, Garrett RA, Terhorst CP (1969) Protein-ribonucleic acid interactions in ribosomes. #Dock it solves protein how toThis study is meant to help the user of docking software understand how to grapple with a typical realistic problem in RNA–protein docking, understand what to expect in the way of difficulties, and recognize the current limitations. We show that by introducing experimental information, the structure of the bound complex is rendered far more likely to be within reach. In this study, we show ways to approach this problem by computational docking methods, either with a fully automated NPDock server or with a workflow of methods for generation of many alternative structures followed by selection of the most likely solution. This has inspired a growing interest in finding ways to predict these RNA–protein complexes. X-ray crystallography has added a few solved RNA–protein complexes to the repertoire however, it remains challenging to capture these complexes and often only the unbound structures are available. In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs.ĭrug design and discovery GPCRs Molecular modeling Protein–protein docking Transmembrane proteins Water-soluble proteins.A significant part of biology involves the formation of RNA–protein complexes. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. ![]()
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