@article {2015|1657, title = {Changes in protein structure at the interface accompanying complex formation.}, journal = {Iucrj}, volume = {2}, number = {Pt 6}, year = {2015}, month = {nov}, pages = {643{\textendash}652}, publisher = {Department of Biochemistry, Bose Institute , P-1/12 CIT Scheme VIIM, Kolkata 700 054, India.}, abstract = {Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another molecule need to be characterized for a proper understanding of molecular recognition as well as for the successful implementation of docking algorithms. Here, unbound (U) and bound (B) forms of protein structures from the Protein-Protein Interaction Affinity Database are compared in order to enumerate the changes that occur at the interface atoms/residues in terms of the solvent-accessible surface area (ASA), secondary structure, temperature factors (B factors) and disorder-to-order transitions. It is found that the interface atoms optimize contacts with the atoms in the partner protein, which leads to an increase in their ASA in the bound interface in the majority (69\%) of the proteins when compared with the unbound interface, and this is independent of the root-mean-square deviation between the U and B forms. Changes in secondary structure during the transition indicate a likely extension of helices and strands at the expense of turns and coils. A reduction in flexibility during complex formation is reflected in the decrease in B factors of the interface residues on going from the U form to the B form. There is, however, no distinction in flexibility between the interface and the surface in the monomeric structure, thereby highlighting the potential problem of using B factors for the prediction of binding sites in the unbound form for docking another protein. 16\% of the proteins have missing (disordered) residues in the U form which are observed (ordered) in the B form, mostly with an irregular conformation; the data set also shows differences in the composition of interface and non-interface residues in the disordered polypeptide segments as well as differences in their surface burial.}, doi = {10.1107/S2052252515015250}, author = {Chakravarty, Devlina and Janin, Jo{\"e}l and Charles H. Robert and Chakrabarti, Pinak} } @article {2013|1976, title = {Reassessing buried surface areas in protein-protein complexes.}, journal = {Protein Sci.}, volume = {22}, year = {2013}, month = {aug}, pages = {1453{\textendash}57}, abstract = {

The buried surface area (BSA), which measures the size of the interface in a protein-protein complex may differ from the accessible surface area (ASA) lost upon association (which we call DSA), if conformation changes take place. To evaluate the DSA, we measure the ASA of the interface atoms in the bound and unbound states of the components of 144 protein-protein complexes taken from the Protein-Protein Interaction Affinity Database of Kastritis et al. (2011). We observe differences exceeding 20\%, and a systematic bias in the distribution. On average, the ASA calculated in the bound state of the components is 3.3\% greater than in their unbound state, and the BSA, 7\% greater than the DSA. The bias is observed even in complexes where the conformation changes are small. An examination of the bound and unbound structures points to a possible origin: local movements optimize contacts with the other component at the cost of internal contacts, and presumably also the binding free energy.

}, keywords = {binding free energy, conformation changes, protein-protein interaction, solvent accessible surface}, doi = {10.1002/pro.2330}, author = {Chakravarty, Devlina and Guharoy, Mainak and Robert, Charles H. and Chakrabarti, Pinak and Janin, Jo{\"e}l} }