ABSTRACT
Protein-protein recognition is a key element of life at the molecular level. Our understanding of the principles of protein recognition is still limited. However, a significant amount of information on the subject has been already accumulated and analyzed. The structure of protein-protein complexes is generally more difficult to determine than the structure of individual proteins. However, the number of experimentally determined complexes is statistically significant. The
Overview .................................................................................................................. 21 Introduction ..............................................................................................................22 Databases .................................................................................................................23 Parallels between Protein Recognition and Protein Folding ....................................25 Complementarity, Recognition Motifs, and Hot Spots ............................................27 Large-Scale Recognition Factors .............................................................................29 Intermolecular Energy Landscape ...........................................................................34 Implications for Docking .........................................................................................36 Acknowledgments .................................................................................................... 37 References ................................................................................................................ 38
databases of protein-protein complexes are important for systematic studies of protein interactions and the design of new predictive tools. A number of such databases have been compiled and widely utilized in the research community. The underlying physical principles of protein folding and binding are the same, which translates into the similarity of the recognition factors in folding and docking. The concepts of steric and physicochemical complementarity are the basis for many modeling techniques applicable to both problems. Structural recognition factors relate to energy landscape characteristics that help understand the formation of complexes and create better modeling tools. The multiscale approach to modeling protein interactions reflects the nature of protein recognition, which involves the larger structural factors facilitating complex formation and the smaller local factors responsible for the final lock of the molecules within the complex.
