http://192.168.1.40:8080/xmlui/handle/123456789/1118 Sun, 31 May 2026 12:08:55 GMT 2026-05-31T12:08:55Z http://192.168.1.40:80/xmlui/bitstream/id/621c1be5-05a7-4740-8d15-a04453fc559f/gautambasu.jpg http://192.168.1.40:8080/xmlui/handle/123456789/1118 http://192.168.1.40:8080/xmlui/handle/123456789/2462 Metal binding to cowpea chlorotic mottle virus using terbium(III) fluorescence (M-T-2003-04) Basu,Gautam; Allen, M.; Willits, D.; Young, M.; Douglas, T. Metals are thought to play a role in the structure of many viruses. The crystal structure of the T=3 icosahedral cowpea chlorotic mottle virus (CCMV) suggests the presence of 180 unique metal-binding sites in the assembled protein cage. Each of these sites is thought to involve the coordination of the metal by five amino acids contributed from two adjacent coat protein subunits. We have used fluorescence resonance energy transfer (FRET), from tryptophan residues proximal to the putative metal-binding sites, to probe Tb(III) binding to the virus. Binding of Tb(III) was investigated on the wild-type virus and a mutant where the RNA binding ability of the virus was removed. Tb(III) binding was observed both in the wild-type virus (K-d=19 muM) and the mutant (K-d=17 muM), as monitored by the increase in Tb(III) fluorescence (545 nm) and concomitant decrease in tryptophan fluorescence (342 nm). Competitive binding experiments showed Ca(II) to have about 100-fold less affinity for the binding sites (K-d=1.97 mM). This is the first direct evidence of metal binding to the putative metal-binding sites, originally suggested from the crystal structure of CCMV. DOI: 10.1007/s00775-003-0470-7 Mon, 01 Sep 2003 00:00:00 GMT http://192.168.1.40:8080/xmlui/handle/123456789/2462 2003-09-01T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2437 Electrostatic potential of nucleotide-free protein is sufficient for discrimination between adenine and guanine-specific binding sites Basu, Gautam; Sivanesan, D.; Kawabata, T.; Go, N. Despite sharing many common features, adenine-binding and guanine-binding sites in proteins often show a clear preference for the cognate over the non-cognate ligand. We have analyzed electrostatic potential (ESP) patterns at adenine and guanine-binding sites of a large number of non-redundant proteins where each binding site was first annotated as adenine/guanine-specific or non-specific from a survey of primary literature. We show that more than 90% of ESP variance at the binding sites is accounted for by only two principal component ESP vectors, each aligned to molecular dipoles of adenine and guanine. Projected on these principal component vectors, the adenine/guanine-specific and nonspecific binding sites, including adenine-containing dinucleotides, show non-overlapping distributions. Adenine or guanine specificities of the binding sites also show high correlation with the corresponding electrostatic replacement (cognate by non-cognate ligand) energies. High correlation coefficients (0.94 for 35 adenine-binding sites and 1.0 for 20 guanine-binding sites) were obtained when adenine/guanine specificities were predicted using the replacement energies. Our results demonstrate that ligand-free protein ESP is an excellent indicator for discrimination between adenine and guanine-specific binding sites and that ESP of ligand-free protein can be used as a tool to annotate known and putative purine-binding sites in proteins as adenine or guanine-specific. DOI: 10.1016/j.jmb.2004.07.047 Fri, 17 Sep 2004 00:00:00 GMT http://192.168.1.40:8080/xmlui/handle/123456789/2437 2004-09-17T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2416 Expanded turn conformations: Characterization and sequence-structure correspondence in alpha-turns with implications in helix folding Dasgupta, B.; Pal, L.; Basu, Gautam; Chakrabarti, Pinak Like the beta-turns, which are characterized by a limiting distance between residues two positions apart (i, i+3), a distance criterion (involving residues at positions i and i+4) is used here to identify a-turns from a database of known protein structures. At least 15 classes of alpha-turns have been enumerated based on the location in the phi,psi space of the three central residues (i+1 to i+3)-one of the major being the class AAA, where the residues occupy the conventional helical backbone torsion angles. However, moving towards the C-terminal end of the turn, there is a shift in the phi, psi angles towards more negative phi, such that the electrostatic repulsion between two consecutive carbonyl oxygen atoms is reduced. Except for the last position (i+4), there is not much similarity in residue composition at different positions of hydrogen and non-hydrogen bonded AAA turns. The presence or absence of Pro at i+1 position of alpha- and beta-turns has a bearing on whether the turn is hydrogen-bonded or without a hydrogen bond. In the tertiary structure, alpha-turns are more likely to be found in beta-hairpin loops. The residue composition at the beginning of the hydrogen bonded AAA alpha-turn has similarity with type I beta-turn and N-terminal positions of helices, but the last position matches with the C-terminal capping position of helices, suggesting that the existence of a "helix cap signal" at i+4 position prevents alpha-turns from growing into helices. Our results also provide new insights into alpha-helix nucleation and folding. DOI: 10.1002/prot.20064 Sat, 01 May 2004 00:00:00 GMT http://192.168.1.40:8080/xmlui/handle/123456789/2416 2004-05-01T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/2355 Paramagnetic viral nanoparticles as potential high-relaxivity magnetic resonance contrast agents Allen, M; Bulte, J. W. M.; Liepold, L.; Basu, Gautam; Zywicke, H. A.; Frank, J. A.; Young, M.; Douglas, T. In order to compensate for the inherent high threshold of detectability of MR contrast agents, there has been an active interest in the development of paramagnetic nanoparticles incorporating high payloads of Gd3+ with high molecular relaxivities. Toward this end, the protein cage of Cowpea chlorotic mottle virus (CCMV), having 180 metal binding sites, is being explored. In vivo CCMV binds Ca2+ at specific metal binding sites; however, Gd3+ can also bind at these sites. Using fluorescence resonance energy transfer we have characterized the binding affinity of Gd3+ to the metal binding sites by competition experiments with Tb3+. The measured dissociation constant (K-d) for Gd3+ bound to the virus is 31 mu M. The T-1 and T-2 relaxivities of solvent water protons in the presence of Gd3+-bound CCMV were 202 and 376 mM(-1) s(-1), respectively, at 61 MHz Larmor frequency. The unusually high relaxivity values of the Gd3+-CCMV are largely a result of the nanoparticle virus size and the large number of Gd3+ ions bound to the virus. These preliminary results should encourage further investigations into the use of viral protein cages as a new platform for MR contrast agents. DOI: 10.1002/mrm.20614 Sat, 01 Oct 2005 00:00:00 GMT http://192.168.1.40:8080/xmlui/handle/123456789/2355 2005-10-01T00:00:00Z