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S S Rajan

Publications and source records attributed to S S Rajan.

At least 19 recordsLinked to original sources
PubMed2006

The study of helical distortions due to environmental changes: choice of parameters.

Parameters like interhelical angles, helical parameters, levels of distortions, etc., have been analysed to test their sensitivity to environmental changes using a method developed in this laboratory. This analysis was done on protein structures solved under different environmental conditions like temperature and pH, and ligand binding. The study reveals that the helical parameters are not sensitive enough to study the effect of environmental changes on protein helices. On the other hand the helical distortions as well as changes in the interhelical angles are more sensitive to these changes. The study also provides with additional information like the origin of distortions in a helix when a ligand binds to a protein, bending in helical axis, identification and extent of domain movements, etc.

Algorithms↗
PubMed2006

Effect of DNA structural flexibility on promoter strength--molecular dynamics studies of E. coli promoter sequences.

To study possible correlations between promoter activity and the structural flexibility of the DNA helix, we have carried out unrestrained molecular dynamics simulations of the -10 consensus region sequence and five variants forming the -10 region of various Escherichia coli promoter sequences. Analyses of the trajectories obtained from the simulations show that the consensus sequence has a pattern of two structurally flexible nucleotide steps sandwiched between two stiff steps. In the other sequences, this pattern varies in consonance with the change in the sequence. The variations in the patterns show correlation with the promoter strength.

Base Sequence↗
PubMed2005

Structure of d(TGCGCG).d(CGCGCA) in two crystal forms: effect of sequence and crystal packing in Z-DNA.

The sequence d(TGCGCG).d(CGCGCA) crystallized in two crystal forms, orthorhombic and hexagonal, in the presence of cobalt hexammine chloride, a known inducer of the left-handed Z-form of DNA. The crystal structures have been solved and refined at 1.71 A resolution in space group P2(1)2(1)2(1) and 2.0 A resolution in space group P6(5). The orthorhombic structure contains one Z-DNA hexamer duplex, while the hexagonal structure contains two hexamer duplexes in the structure. Of the latter, one is situated on a crystallographic sixfold screw axis, leading to disorder. This paper reports the effects of sequence and crystal packing on the structure of Z-type DNA. The structures lend additional support to the authors' earlier conclusion that a stretch of four C.G base pairs is sufficient to nucleate and define the regular model of the left-handed helix based on the structure of d(CGCGCG)2.

Base Pairing↗
PubMed2005

The isomeric compounds nimbolide and isonimbolide.

Nimbolide [systematic name: (4alpha,5alpha,6alpha,7alpha,15beta,17alpha)-7,15:21,23-diepoxy-6-hydroxy-4,8-dimethyl-1-oxo-18,24-dinor-11,12-secochola-2,13,20,22-tetraene-4,11-dicarboxylic acid gamma-lactone methyl ester], C27H30O7, was isolated from the leaves of Azadirachta indica, and its isomer, isonimbolide [systematic name: (4alpha,5alpha,6alpha,7alpha,15alpha)-7,15:21,23-diepoxy-6-hydroxy-4,8-dimethyl-1-oxo-18,24-dinor-11,12-secochola-2,16,20,22-tetraene-4,11-dicarboxylic acid gamma-lactone methyl ester], was prepared from a novel rearrangement reaction of nimbolide, using boron trifluoride etherate and tetrabutylammonium bromide. The reaction conditions are probably responsible for the ether cleavage, double-bond rearrangement and reformation of the ether linkage. As a result, there are conformational changes in two cyclopentane rings and the side-chain -CH2COOMe group. In isonimbolide, an R(4)(4)(24) hydrogen-bond motif is observed.

Azadirachta↗
PubMed2004

Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA)*d(TGCGCG) in two crystal forms.

We report here the crystal structure of the DNA hexamer duplex d(CGCGCA)*d(TGCGCG) at 1.71 A resolution. The crystals, in orthorhombic space group, were grown in the presence of cobalt hexammine, a known inducer of the left-handed Z form of DNA. The interaction of this ion with the DNA helix results in a change of the adenine base from the common amino tautomeric form to the imino tautomer. Consequently the A:T base pair is disrupted from the normal Watson-Crick base pairing to a 'wobble' like base pairing. This change is accommodated easily within the helix, and the helical parameters are those expected for Z-DNA. When the cobalt hexammine concentration is decreased slightly in the crystallization conditions, the duplex crystallizes in a different, hexagonal space group, with two hexamer duplexes in the asymmetric unit. One of these is situated on a crystallographic 6-fold screw axis, leading to disorder. The tautomeric shift is not observed in this space group. We show that the change in inter-helix interactions that lead to the two different space groups probably arise from the small decrease in ion concentration, and consequently disordered positions for the ion.

Base Pairing↗
PubMed2003

A new clerodane diterpene with antifeedant activity from Teucrium tomentosum.

A new diterpene, viz. 3beta-acetoxy-4alpha,18:15,16-diepoxy-6beta,12-dihydroxyneocleroda-13(16),14-dien-19,20-olide, C(22)H(28)O(8), exhibiting antifeedant activity against Spodoptera litura was isolated from the aerial parts of Teucrium tomentosum and its structure is reported. One of the two fused rings has a distorted-chair conformation and the other has a chair conformation. The molecules in the crystal are stabilized via O--H...O and C--H...O hydrogen bonds.

Animals↗
PubMed2003

Samaderin B and C from Samadera indica.

Samaderin B, or (1R,2S,5R,5aR,7aS,11S,11aS,11bR,14S)-1,7,7a,11,11a,11b-hexahydro-1,11-dihydroxy-8,11a,14-trimethyl-2H-5a,2,5-(methanoxymetheno)naphth[1,2-d]oxepine-4,6,10(5H)-trione, C(19)H(22)O(7), and samaderin C, or (1R,2S,5R,5aR,7aS,10S,11S,11aS,11bR,14S)-7,7a,10,11,11a,11b-hexahydro-1,10,11-trihydroxy-8,11a,14-trimethyl-2H-5a,2,5-(methanoxymetheno)naphth[1,2-d]oxepine-4,6(1H,5H)-dione, C(19)H(24)O(7), were isolated from the seed kernels of Samadera indica and were shown to exhibit antifeedant activity against Spodoptera litura third-instar larvae. The replacement of the carbonyl group in samaderin B by a hydroxy group in samaderin C causes conformational changes at the substitution site, but the overall conformation is not affected; however, the compounds pack differently in the crystal lattice.

Crystallography, X-Ray↗
PubMed2003

Antifeedant neo-clerodanes from Teucrium tomentosum Heyne. (Labiatae).

From the acetone extract of Teucrium tomentosum, a new antifeedant neo-clerodane diterpenoid teuctosin (1) was isolated along with teuflin (2), teucrin-H(2) (3), 6beta-hydroxyteuscordin (4), 6beta-acetylteuscordin (5) and montanin-D (6). The structure of the new compound was elucidated comprehensively using 1D and 2D NMR methods and confirmed by X-ray crystallography. All the compounds showed effective antifeedancy against Plutella xylostella and Spodoptera litura at 10 mug/cm(2) of leaf area.

Animals↗
PubMed2002

8-(2-bromo-3-methoxy-3-methylbutyl)-7-methoxycoumarin.

The title compound, C(16)H(19)BrO(4), is a derivative of osthol, isolated from the seeds of Imperatoria Osthruthium. The structure was solved in space group P-1, with two molecules in the asymmetric unit, and was refined to a final R factor of 0.064. The two molecules in the asymmetric unit differ in the orientation of their brominated substituent group. The benzopyran ring displays aromatic character. The packing of the molecules in the lattice is mainly due to C-H...O hydrogen bonds.

Anti-Inflammatory Agents↗
PubMed2002

Azadirachtol, a tetranortriterpenoid from neem kernels.

The title compound, dimethyl (-)-(2aR,3R,4R,4aS,5R,7aS,8R,10S,10aR)-3,8,10-trihydroxy-4-[(2R,6R)-2-hydroxy-11-methyl-5,7,10-trioxatetracyclo[6.3.1.0(2,6)0(9,11)]dodec-3-en-9-yl]-4-methylperhydroisobenzofurano[5,4,3a-cd]isobenzofuran-5,10a-diacetate, C(28)H(36)O(13), which exhibits higher antifeedant activity than azadirachtin-A, a known potent antifeedant, was isolated from neem kernels. The asymmetric unit of the structure contains two independent molecules, which differ in the conformations of their functional groups and also in the conformations of some of the rings. The relative orientation between the decalin and furanyl moieties is similar to that observed in the majority of azadirachtin structures, but is different from that in azadirachtin-A. The two symmetry-independent molecules are linked into dimeric units by intermolecular O-H.O hydrogen bonds.

Azadirachta↗
PubMed2002

2',3'-Dehydrosalannol.

The title compound, methyl (2aS,3R,5R,5aS,6S,6aS,8R,9aS,10aR,10bR,10cS)-8-(3-furyl)-2a,4,5,5a,6,6a,8,9,9a,10a,10b,10c-dodecahydro-3-hydroxy-2a,5a,6a,7-tetramethyl-5-(3-methylbut-2-enoyloxy)-2H,3H-cyclopenta[4',5']furo[2',3':6,5]benzo[cd]isobenzofuran-6-acetate, C(32)H(42)O(8), was isolated from uncrushed green leaves of Azadirachta indica A. Juss (neem) and has been found to possess antifeedant activity against Spodptera litura. The conformations of the functional groups are similar to those of 3-desacetylsalannin, which was isolated from neem kernels. The molecules are linked into chains by intermolecular O-H.O hydrogen bonds.

Journal Article↗
PubMed2002

Insect antifeedant activity of tetranortriterpenoids from the Rutales. A perusal of structural relations.

Structure-related insect antifeedant relationship of 56 limonoids (both natural and modified) from the plants belonging to the order Rutales was attempted considering substitution patterns, oxidation states, and hydrophobicity, as well as distant geometry derived through conformational analysis on molecular modeling. Orientation of the furan and hydroxylation at specific carbon sites have been shown to influence the antifeedancy against the fall armyworm, Spodoptera litura.

Animals↗
PubMed2002

Structure of d(TGCGCA)2 at 293 K: comparison of the effects of sequence and temperature.

The crystal structure of a hexameric DNA fragment with the sequence d(TGCGCA)(2) has been solved and refined at 293 K at a resolution of 1.64 A. The molecule adopts a left-handed Z-type helical conformation which is common in alternating pyrimidine-purine sequences. The presence of A.T base pairs at the two terminals does not perturb the structure to any great degree. However, several sequence-specific microstructural changes are noticeable. The structure of the identical sequence determined at 120 K involving somewhat different crystallization conditions has been reported previously [Harper et al. (1998), Acta Cryst. D54, 1273-1284]. A comparison of the present structure with that at low temperature and with that of d(CGCGCG)(2) shows that the effect of the change in sequence is greater than the combined effect of changes in temperature and environment.

Base Pairing↗
PubMed2000

Photooxidation of cedrelone, a tetranortriterpenoid from Toona ciliata.

Cedrelone, a tetranortriterpenoid on photolysis by UV light yields a true photooxidation product 3 [14 beta,15beta,22beta,23beta-diepoxy-6-hydroxy-1,5, 20(22)-meliatriene-2,7,21-trione] whose structure is well established by NMR studies and confirmed by X-ray crystallography, along with product 4 [14 beta,15beta-epoxy-6,23-dihydroxy-1,5,20(22)-meliatriene-2,7, 21-trione]. Addition of rose bengal increases the rate of photooxidation whereas DABCO decreases rate of photolysis proving the involvement of singlet oxygen in the photooxygenation. Both the photoproducts exhibited antifeedant activity.

Crystallography, X-Ray↗
PubMed1998

Analysis of the conformational stability of the active domain of recombinant mouse TIMP-1 by intrinsic fluorescence.

Intrinsic fluorescence was used to examine the stability of an active, N-terminal domain of mouse tissue inhibitor of metalloproteinase (TIMP-1) fused with an N-terminal polyhistidine tag. Emission and quenching studies suggested that the single tryptophan is on the protein surface partially exposed to solvent. The TIMP-1 recombinant unfolded reversibly in the presence of guanidinium chloride with the transition midpoint at 2.35M; extrapolation gave a stabilization free energy of 5.1 kcal mol-1 at 25 degrees C. Analysis of the temperature dependence of the fluorescence intensity gave a melting transition with midpoint at 51 degrees C and an enthalpy and heat capacity change on unfolding of 32 kcal mol-1 and 0.45 kcal K-1 mol-1, respectively, values comparable to other single domain proteins. Comparison with literature data indicated that the stability of mouse recombinant TIMP-1 more closely resembled that of human metalloproteinase inhibitor TIMP-2 than TIMP-1 despite closer homology to the human TIMP-1 protein.

Acrylamide↗
PubMed1998

A novel multi-segment surface coil for neuro-functional magnetic resonance imaging.

The construction of two novel mult-segment (MS) resonators are described. The signal-to-noise ratio (SNR) and B1 homogeneity of the coils are compared with that of a surface coil and a standard quadrature head coil. The images obtained with the MS designs revealed a surface coil-like fall-off in signal with depth. The SNR offered by MS coils was found to be better than the head coil at depths less than approximately 6 cm. Bilateral motor cortex activation on normal subjects performing finger tapping tasks is demonstrated.

Equipment Design↗
PubMed1998

Presence of an N-terminal polyhistidine tag facilitates stable expression of an otherwise unstable N-terminal domain of mouse tissue inhibitor of metalloproteinase-1 in Escherichia coli.

The active N-terminal domain of the mouse tissue inhibitor of metalloproteinases-1 is a 14.1-kDa polypeptide with three disulfide bonds. When expressed using a T7 system in Escherichia coli, this truncated protein, in contrast to the WT protein, was found only in trace amounts in the cell. However, when the coding sequence was placed downstream of a 60-bp sequence that encoded an in-frame histidine-rich "tag," the fusion product (NF.TIMP*His) was expressed in considerably increased abundance. WT.TIMP-1 was expressed in abundance with or without the tag. The mRNAs encoding the various forms of TIMP were present in similar amounts in all four cases. NF.TIMP*His, renatured and purified on a nickel affinity column, was found to be about 10-fold less effective than native human TIMP-2 at inhibiting cleavage of collagen type I by human fibroblast collagenase. A thrombin cleavage site in the tag was susceptible to cleavage by low levels of a contaminating proteinase.

Animals↗