http://192.168.1.40:8080/xmlui/handle/123456789/1475 Sun, 31 May 2026 15:24:09 GMT 2026-05-31T15:24:09Z http://192.168.1.40:8080/xmlui/handle/123456789/2340 ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces Saha, R. P.; Bahadur, R. P.; Pal, A.; Mandal, S.; Chakrabarti, Pinak Molecular recognition is all pervasive in biology. Protein molecules are involved in enzyme regulation, immune response, signal transduction, oligomer assembly, etc. Delineation of physical and chemical features of the interface formed by protein-protein association would allow us to better understand protein interaction networks on one hand, and to design molecules that can engage a given interface and thereby control protein function on the other hand. Results: ProFace is a suite of programs that uses a file, containing atomic coordinates of a multichain molecule, as input and analyzes the interface between any two or more subunits. The interface residues are shown segregated into spatial patches (if such a clustering is possible based on an input threshold distance) and/or core and rim regions. A number of physicochemical parameters defining the interface is tabulated. Among the different output files, one contains the list of interacting residues across the interface. Results can be used to infer if a particular interface belongs to a homodimeric molecule. Conclusion: A web-server, ProFace (available at http://www.boseinst.ernet.in/resources/bioinfo/stag.html) has been developed for dissecting protein-protein interfaces and deriving various physicochemical parameters. DOI: 10.1186/1472-6807-6-11 Wed, 07 Jun 2006 00:00:00 GMT http://192.168.1.40:8080/xmlui/handle/123456789/2340 2006-06-07T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2338 Domain analysis of a groundnut calcium-dependent protein kinase - Nuclear localization sequence in the junction domain is coupled with nonconsensus calcium binding domains Raichaudhuri, A.; Bhattacharyya, R.; Chaudhuri, S.; Chakrabarti, Pinak; DasGupta, M. The signature of calcium-dependent protein kinases (CDPKs) is a C-terminal calmodulin-like domain (CaMLD) with four consensus calcium-binding sites. A junction domain (JD) joins the kinase with CaMLD and interacts with them through its autoinhibitory and CaMLD binding subdomains, respectively. We noted several CDPKs additionally have a bipartite nuclear localization signal (NLS) sequence as a subdomain in their JD, and this feature is obligatorily coupled with the absence of consensus calcium-binding sites in their respective CaMLDs. These predicted features are substantiated by undertaking investigations on a CDPK (gi: 67479988) isolated from cultured groundnut ( Arachis hypogea) cells. This kinase can bind 3.1 mol of Ca2+ under saturating conditions with a considerably high K-d of 392 mu M as compared with its canonical counterparts. CD spectroscopic analysis, however, indicates the intramolecular structural changes accompanied with calcium binding to be similar to canonical CDPKs. Attesting to the presence of NLS in the JD, the endogenous kinase is localized in the nucleus of osmotically stressed Arachis cells, and in vitro binding assays indicate the NLS in the JD to interact with nuclear transport factors of the importin family. Homology modeling also indicates the feasibility of interaction of importins with the NLS present in the JD of such CDPKs in their activated form. The possible significance of obligatory coupling between the presence of NLS in the junction domain and atypical calcium binding properties of these CDPKs is discussed in the light of the known mechanisms of activation of these kinases. DOI: 10.1074/jbc.M511001200 Fri, 14 Apr 2006 00:00:00 GMT http://192.168.1.40:8080/xmlui/handle/123456789/2338 2006-04-14T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2311 3(10)-Helix Adjoining a -Helix and b -Strand: Sequence and Structural Features and Their Conservation Pal, L; Dasgupta, B; Chakrabarti, Pinak Does the amino acid use at the terminal positions of an a-helix become altered depending on the context-more specifically. when there is an adjoining 3(10)-helix, and can a single helical cylinder encompass the resultant composite helix? An analysis of 138 and 107 cases of 3(10)-alpha and alpha-3(10) 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 proline to occur at the N1 position of all alpha-helix is shifted to the N2 position, a typical characteristic of the C-terminal capping of the 3(10)-helix. When an alpha- or a 3(10)-helix leads into a helix of the other type, there is a bend at the junction, especiaily for the 3(10)-alpha 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 alpha-helix. The tertiary structural context in which beta-3(10) and 3(10)-beta 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 beta-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 3(10)-helix constitutes the loops in beta-hairpin or beta-beta-corner motifs. The overall fold of the chain may be more conserved than the actual identify of the secondary, structure elements in a composite. Biopolymers, Vol. 78, 147–162 (2005) Wed, 15 Jun 2005 00:00:00 GMT http://192.168.1.40:8080/xmlui/handle/123456789/2311 2005-06-15T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2309 Conservation and relative importance of residues across protein-protein interfaces Guharoy, M.; Chakrabarti, Pinak A core region surrounded by a rim characterizes biological interfaces. We ascertain the importance of the core by showing the sequence entropies of the residues comprising the core to be smaller than those in the rim. Such a distinction is not seen in the 2-fold-related, non physiological interfaces formed in crystal lattices of monomeric proteins, thereby providing a procedure for characterizing the oligomeric state from crystal structures of protein molecules. This method is better than those that rely on the comparison of the sequence entropies in the interface and the rest of the protein surface, especially in cases where the surface harbors additional binding sites. To a good approximation there is a correlation between the accessible surface area lost because of complexation and Delta Delta G values obtained through alanine-scanning mutagenesis (26-38 cal per angstrom 2 of the surface buried) for residues located in the core, a relationship that is not discernable for rim residues. If, however, a residue participates in hydrogen bonding across the interface, the extent of stabilization is 52 cal/mol per 1 angstrom 2 of the nonpolar surface area buried by the residue. As opposed to an amino acid classification used earlier, an environment-based grouping of residues yields a better discrimination in the sequence entropy between the core and the rim. DOI: 10.1073/pnas.0505425102 Tue, 25 Oct 2005 00:00:00 GMT http://192.168.1.40:8080/xmlui/handle/123456789/2309 2005-10-25T00:00:00Z