http://192.168.1.40:8080/xmlui/handle/123456789/1123 2026-05-31T14:24:22Z http://192.168.1.40:8080/xmlui/handle/123456789/2306 A Dissection of Specific and Non-specific Protein-Protein Interfaces Bahadur, R. P.; Chakrabarti, Pinakpani; Rodier, F.; Janin, J. We compare the geometric and physical-chemical properties of interfaces involved in specific and non-specific protein-protein interactions in crystal structures reported in the Protein Data Bank. Specific interactions are illustrated by 70 protein-protein complexes and by subunit contacts in 122 homodimeric proteins; non-specific interactions are illustrated by 188 pairs of monomeric proteins making crystal-packing contacts selected to bury more than 800 A(2) of protein surface. A majority of these pairs have 2-fold symmetry and form "crystal dimers" that cannot be distinguished, from real dimers on the basis of the interface size or symmetry The chemical and amino acid compositions of the large crystal-packing interfaces resemble the protein solvent-accessible surface. These interfaces are less hydrophobic than in homodimers and contain much fewer fully buried atoms. We develop a residue propensity score and a hydrophobic interaction score to assess preferences seen in the chemical and amino acid compositions of the different types of interfaces, and we derive indexes to evaluate the atomic packing, which we find to be less compact at nonspecific than at specific interfaces. We test the capacity of these parameters to identify homodimeric proteins in crystal structures, and show that a simple combination of the non-polar interface area and the fraction of buried interface atoms assigns the quaternary structure of 88% of the homodimers and 77% of the monomers in our data set correctly. These success rates increase to 93-95% when the residue propensity score of the interfaces is taken into consideration. DOI: 10.1016/j.jmb.2003.12.073 2004-02-27T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2303 Disulfide bonds, their stereospecific environment and conservation in protein structures Bhattacharya, R.; Pal, D.; Chakrabarti, Pinakpani We studied the specificity of the non-bonded interaction in the environment of 572 disulfide bonds in 247 polypeptide chains selected from the Protein Data Bank. The preferred geometry of interaction of peptide oxygen atoms is along the back of the two covalent bonds at the sulfur atom of half cystine. With aromatic residues the geometries that direct one of the sulfur lone pair of electrons into the aromatic pi-system are avoided; an orientation in which the sulfide plane is normal or inclined to the aromatic plane and on top of its edge is normally preferred. The importance of the S...aromatic interaction is manifested in the high degree of its conservation across members in homologous protein families. These interactions, while providing extra overall stability to the native fold and reducing the accessibility of the disulfide bond and thereby preventing exchange reactions, also set the orientation of the conserved aromatic rings for further interactions and binding to another molecule. The conformational features and the mode of interactions of disulfide bridges should be useful for molecular design and protein engineering experiments. DOI: 10.1093/protein/gzh093 2004-11-01T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2215 310-Helix adjoining α-helix and β-strand: Sequence and structural features and their conservation Pal, L.; Dasgupta, B.; Chakrabarti, Pinakpani Does the amino acid use at the terminal positions of an α-helix become altered depending on the context-more specifically, when there is an adjoining 310-helix, and can a single helical cylinder encompass the resultant composite helix? An analysis of 138 and 107 cases of 3 10-α and α-310 composite helices, respectively, found in known protein structures indicate that the secondary structural element occurring first imposes its characteristics on the sequence of the structural element coming next. Thus, when preceded by a 3 10-helix, the preference of praline to occur at the N1 position of an α-helix is shifted to the N2 position, a typical characteristic of the C-terminal capping of the 310-helix. When an α- or a 3 10-helix leads into a helix of the other type, there is a bend at the junction, especially for the 310-α composite, with the two junction residues facing inward and buried within the structure. Thus a single helical cylinder may not properly represent a composite helix, the bend providing a means for the tertiary structure to assume a globular shape, very much akin to what a proline-induced kink does to an α-helix. The tertiary structural context in which β-310 and 310-β composites occurs can be different, causing the angle between the secondary structural elements in the two cases to be different. Composites of 3 10-helices and β-strands are much more conserved among members in families of homologous structures than those between two types of helices; in many of the former instances, the 310-helix constitutes the loops in β-hairpin or β-β-corner motifs. The overall fold of the chain may be more conserved than the actual identify of the secondary structure elements in a composite. DOI: 10.1002/bip.20266 2005-06-15T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2214 Hydration of protein-protein interfaces Rodier, F.; Bahadur, R. P.; Chakrabarti, Pinakpani; Janin, J. We present an analysis of the water molecules immobilized at the protein-protein interfaces of 115 homodimeric proteins and 46 protein-protein complexes, and compare them with 173 large crystal packing interfaces representing nonspecific interactions. With an average of 15 waters per 1000 angstrom(2) of interface area, the crystal packing interfaces are more hydrated than the specific interfaces of homodimers and complexes, which have 10-11 waters per 1000 angstrom(2), reflecting the more hydrophilic composition of crystal packing interfaces. Very different patterns of hydration are observed: Water molecules may form a ring around interfaces that remain "dry," or they may permeate "wet" interfaces. A majority of the specific interfaces are dry and most of the crystal packing interfaces are wet, but counterexamples exist in both categories. Water molecules at interfaces form hydrogen bonds with protein groups, with a preference for the main-chain carbonyl and the charged side-chains of Glu, Asp, and Arg. These interactions are essentially the same in specific and nonspecific interfaces, and very similar to those observed elsewhere on the protein surface. Water-mediated polar interactions are as abundant at the interfaces as direct protein-protein hydrogen bonds, and they may contribute to the stability of the assembly. DOI: 10.1002/prot.20478 2005-07-01T00:00:00Z