Protein interfaces analysis

Valdar, W.S., Thornton, J.M. Protein-protein interfaces Analysis of amino acid conservation in homodimers. Proteins 2001, 42(1), 108-24. 

Detailed analysis of the lambda repressor led to the important concept that transcription regulatory proteins have several functional domains. For example, lambda repressor binds to DNA with high affinity. Repressor monomers form dimers, dimers interact with each other, and repressor interacts with RNA polymerase. The protein-DNA interface and the three protein-protein interfaces all involve separate and distinct domains of the repressor molecule. As will be noted below (see Figure 39—17), this is a characteristic shared by most (perhaps all) molecules that regulate transcription. 

O. D. Sanni, M. S. Wagner, D. G. Briggs, D. G. Castner and J. C. Vickerman, Classification of adsorbed protein static ToF SIMS spectra by principal component analysis and neural networks, Surface and Interface Analysis, 33, 715 728 (2002). 

Bourgeas R, Basse M-J, Morelli X et al (2010) Atomic analysis of protein-protein interfaces with known inhibitors the 2P2I database. PloS One5 e9598... 

In the most comprehensive structural analysis to date, Lo Conte et al.11 studied 75 protein-protein complexes comprising 24 protease-inhibitor, 19 antibody-antigen, and 32 other complexes (including 9 further enzyme-inhibitor and 11 signal transduction complexes). The authors found that protein-protein interfaces typically have a size of 1600 400 A2 with a few complexes exhibiting very large (2000—4660 A2) or very small (less than 1000 A2) interfaces. With respect to their chemical nature, the interfaces were found to... 

Schreiber G, Fersht AR (1995) Energetics of protein-protein interactions analysis of the barnase-barstar interface by single mutations and double mutant cycles, J Mol Biol, 248 -178 1X9... 

However, a number of biological findings could not be explained by the CPCA analysis. The authors attribute this to the fact that the ephrin-Eph kinase interactions are best described by an induced fit mechanism. The necessary computational assumption of keeping the protein structure rigid did not reflect the flexibility of the protein interfaces and their structural adaptability. The homology models, on the other hand, provided a rigid protein structure that is biased by the template protein EphB2. 

Sundberg EJ, Andersen PS, Schlievert PM, Kaijalainen K, Mariuzza RA Structural, energetic, and functional analysis of a protein-protein interface at distinct stages of affinity maturation. Structure 2003 11 1151-1161. 

Tsai CJ et al (1997) Studies of protein-protein interfaces a statistical analysis of the hydrophobic effect. Protein Sci 6(l) 53-64... 

Bordner AJ, Abagyan R (2005) Statistical analysis and prediction of protein-protein interfaces. Proteins 60 353-366... 

Jochim AL, Arora PS (2010) Systematic analysis of helical protein interfaces reveals targets for synthetic inhibitors. ACS Chem Biol 5 919-923... 

Fig. 5 Layout of an integrated microchip for full protein process analysis. The system consists of a cell lysis unit (i), a unit for the solid phase extraction of the entire proteome or a subpopulation of the proteome (2), 2D electrophoresis unit to sort the protein mixture into discrete components (5), solid-phase proteolytic reactors (4), and an on-line interface to MS, either ESI or MALDI...

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