By Joel Janin and Shoshana J. Wodak (Eds.)
Protein modules have interaction in a mess of interactions with each other and with different mobile elements, significantly with DNA. those interactions are a imperative point of protein functionality of serious relevance within the post-genomic period. This quantity describes a panel of methods for reading protein modules and their interactions, starting from bioinformatics to actual chemistry, to biochemistry, with an emphasis at the structure-function dating in protein-protein complexes fascinated about mobile tactics together with sign transduction. Key gains* entire assessment of alternative features of macromolecule interactions* Computational and bioinformatics facets of examining protein modules and their interactions* Emphasis on structure-function dating in protein-protein complexes interested by mobile tactics
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Additional info for Protein Modules and Protein-Protein Interaction
1998) play a central role. , face (B %1200 A 1999). There is a growing scienti®c interest in low-af®nity protein± protein recognition not only in cell adhesion, but also in signal transduction and a variety of regulatory processes. Thus, we expect to see more examples in coming years of protein±protein complexes with interfaces Ê 2 , poor atomic packing, few direct H-bonds, between 1100 and 1200 A and no signi®cant conformational change in the component proteins. Alternatively, a complex may have a standard size interface and a low af®nity if it displays conformational changes.
11, which shows the energetics of a protein antigen, hen lysozyme, binding to the Fab fragment of the HyHel5 monoclonal antibody and of an inhibitor, barstar, binding to an enzyme, barnase. The two complexes have interfaces of a similar (standard) size, and their formation involves small conformational changes. Both interfaces are about 50% nonpolar and contain 11±13 hydrogen bonds, but barnase±barstar has more charged groups making these bonds. This may be one reason that the ®rst complex is more stable, its Kd being %10À13 M and that of HyHel5±lysozyme %10À10 M.
Energetics of an antigen±antibody complex and an enzyme±inhibitor complex. , 1993) ]. Their dissociation enthalpy DH and free enthalpy DG are calculated as the sum of ®ve terms: the energy of van der Waals (vdw ) and electrostatic (elec ) interactions between the two molecules; the hydration enthalpy or free enthalpy of nonpolar and of polar groups at the interface; and a gas-phase entropy change (ÀTDS gas). The vdw and elec terms are obtained by energy minimization in gas phase with the dielectric constant adjusted to e 3.