Biomedical subjects

Girjesh Govil

Publications and source records attributed to Girjesh Govil.

7 recordsLinked to original sources

PubMed2006

Mechanism of action of L-arginine on the vitality of spermatozoa is primarily through increased biosynthesis of nitric oxide.

The ability of sperm to fertilize the egg is primarily dependent on sperm motility and membrane integrity. Nitric oxide (NO) plays a decisive role in regulating multiple functions within the male reproductive system. The aim of the present study is to determine the mechanism by which L-arginine confers a protective action on spermatozoa obtained from the goat epididymis. NO is synthesized from L-arginine by the enzyme nitric oxide-synthase (NOS) present in spermatozoa. A possible participation of NO and NOS in arginine action has been suggested.

Animals↗

PubMed2005

Structure of daunomycin complexed to d-TGATCA by two-dimensional nuclear magnetic resonance spectroscopy.

The anthracycline antibiotic daunomycin, having four fused rings and an amino sugar, is being used in the treatment of acute leukemia. Binding to DNA is generally believed to be essential for its activity. We have studied the interaction of daunomycin with DNA hexamer sequence d-(TGATCA)2 by titrating up to two drug molecules per duplex using nuclear magnetic resonance spectroscopy. The solution structure of 2:1 drug to DNA complex based on two dimensional nuclear Overhauser enhancement (NOE) spectroscopy and molecular dynamics calculations has been studied. The change in conformation of drug molecule on binding to DNA, deoxyribose conformation and glycosidic bond rotation has been obtained. The absence of sequential NOE connectivities at d-T1pG2 and d-C5pA6 sites shows that the drug chromophore intercalates between these two base pairs. This is substantiated by intermolecular NOEs observed between nucleotide base protons and aromatic ring protons of drug molecule. A set of 17 intermolecular NOE interactions allowed the structure to be derived by restrained molecular dynamics simulations, which have been compared with that obtained by X-ray analysis. Several specific interactions between the drug and DNA protons are found to stabilize the formation of drug-DNA complex.

Antibiotics, Antineoplastic↗

PubMed2005

Restrained molecular dynamics studies on complex of adriamycin with DNA hexamer sequence d-CGATCG.

Adriamycin is an anthracycline anticancer drug used widely for solid tumors in spite of its adverse side effects. The solution structure of 2:1 adriamycin-d-(CGATCG)(2) complex has been studied by restrained molecular dynamics simulations. The restraint data set consists of several intramolecular and intermolecular nuclear Overhauser enhancement cross-peaks obtained from two-dimensional nuclear magnetic resonance spectroscopy data. The drug is found to intercalate between CG and GC base pairs at two d-CpG sites. The drug-DNA complex is stabilized via specific hydrogen bonding and van der Waal's interactions involving 4OCH(3), O5, 6OH, and NH(3)(+) moiety of daunosamine sugar, and rings A protons. The O-glycosidic bond C7-O7-C1'-C2' lies in the range 138 degrees -160 degrees during the course of simulations. The O6-H6...O5 hydrogen bond is stable while O11-H11...O12 hydrogen bond is not favored. The intercalating base pairs are buckled and minor groove is wider in the complex. The phosphate on one strand at intercalation site C1pG2 is in B(I) conformation and the phosphates directly lying on opposite strand is in B(II) conformation. The phosphorus on adjacent site G2pA3 is in B(II) conformation and hence a distinct pattern of B(I) and B(II) conformations is induced and stabilized. The role of various functional groups by which the molecular action is mediated has been discussed and correlated to the available biochemical evidence.

Doxorubicin↗

PubMed2004

Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spectroscopy and restrained molecular dynamics.

The 5' d-TpG 3' element is a part of DNA sequences involved in regulation of gene expression and is also a site for intercalation of several anticancer drugs. Solution conformation of DNA duplex d-TGATCA containing this element has been investigated by two-dimensional NMR spectroscopy. Using a total of 12 torsional angles and 121 distance constraints, structural refinement has been carried out by restrained molecular dynamics (rMDs) in vacuum up to 100 ps. The structure is characterized by a large positive roll at TpG/CpA base pair step and large negative propeller twist for AT and TA base pairs. The backbone torsional angle, gamma(O5'-C5'-C4'-C3'), of T1 residue adopts a trans-conformation which is corroborated by short intra nucleotide T1H6-T1H5' (3.7A) distance in nuclear overhauser effect spectroscopy (NOESY) spectra while the backbone torsional angle, beta(P-O5'-C5'-C4'), exists in trans as well as gauche state for T1 and C5 residues. There is evidence of significant flexibility of the sugar-phosphate backbone with rapid inter-conversion between two different conformers at TpG/CpA base pair step. The base sequence dependent variations and local structural heterogeneity have important implications in specific recognition of DNA by ligands.

Base Sequence↗

PubMed2004

Substance P: structure, function, and therapeutics.

Extensive efforts since 1931, on the structural determination of the mammalian tachykinin SP by NMR, CD and IR have turned out to be inconclusive. Studies are now being concentrated on the structural properties and characteristics of various NK receptors (NK(1), NK(2) and NK(3)) with the help of genetics, cloning, receptor engineering, mutagenesis and modeling. This knowledge is now being fruitfully used in the development of non-peptide NK(1) receptor antagonists that essentially block the pharmacological effects of SP. It is now being realized that the simultaneous blockade of two or more receptors gives promising results in emesis, depression and pulmonary obstructive diseases. In addition to the synthetic compounds, the discovery of antagonists from natural origin has added a great value to this field. In this review we have made an attempt to present the structural characteristics of SP, its analogs and antagonists, the structural characteristics of the NK receptor, and structure activity relationships that have helped to improve the therapeutic utilities of SP antagonists.

Amino Acid Sequence↗

PubMed2003

Structure of DNA hexamer sequence d-CGATCG by two-dimensional nuclear magnetic resonance spectroscopy and restrained molecular dynamics.

Solution conformation of self-complementary DNA duplex d-CGATCG, containing 5' d-CpG 3' site for intercalation of anticancer drug, daunomycin and adriamycin, has been investigated by nuclear magnetic resonance (NMR) spectroscopy. Complete resonance assignments of all the protons (except some H5'/H5" protons) have been obtained following standard procedures based on double quantum filtered correlation spectroscopy (dQF COSY) and two-dimensional nuclear Overhauser effect (NOE) spectra. Analysis of sums of coupling constants in one-dimensional NMR spectra, cross peak patterns in dQF COSY spectra and inter proton distances shows that the DNA sequence assumes a conformation close to the B-DNA family. The deoxyribose sugar conformation is in dynamic equilibrium with predominantly S-type conformer and a minor N-type conformer with N<-->S equilibrium varying with temperature. At 325 K, the mole fraction of the N-conformer increases for some of the residues by approximately 9%. Using a total of 10 spin-spin coupling constants and 112 NOE intensities, structural refinement has been carried out using Restrained Molecular Dynamics (rMD) with different starting structures, potential functions and rMD protocols. It is observed that pseudorotation phase angle of deoxyribose sugar for A3 and T4 residues is approximately 180 degrees and approximately 120 degrees, respectively while all other residues are close to C2'endo-conformation. A large propeller twist (approximately -18 degrees) and smallest twist angle (approximately 31 degrees) at A3pT4 step, in the middle of the sequence, a wider (12 A) and shallower (3.0 A) major groove with glycosidic bond rotation as high anti at both the ends of hexanucleotide are observed. The structure shows base-sequence dependent variations and hence strong local structural heterogeneity, which may have implications in ligand binding.

Antibiotics, Antineoplastic↗

PubMed2002

NMR structure of a parallel-stranded DNA duplex at atomic resolution.

DNA dodecamers have been designed with two cytosines on each end and intervening A and T stretches, such that the oligomers have fully complementary A:T base pairs when aligned in the parallel orientation. Spectroscopic (UV, CD and IR), NMR and molecular dynamics studies have shown that oligomers having the sequences d(CCATAATTTACC) and d(CCTATTAAATCC) form a parallel-stranded duplex when dissolved at 1:1 stoichiometry in aqueous solution. This is due to the C:C+ clamps on either end and extensive mismatches in the antiparallel orientation. The structure is stable at neutral and acidic pH. At higher temperatures, the duplex melts into single strands in a highly cooperative fashion. All adenine, cytosine and thymine nucleotides adopt the anti conformation with respect to the glycosidic bond. The A:T base pairs form reverse Watson-Crick base pairs. The duplex shows base stacking and NOEs between the base protons T(H6)/A(H8) and the sugar protons (H1'/H2'/H2") of the preceding nucleotide, as has been observed in antiparallel duplexes. However, no NOEs are observed between base protons H2/H6/H8 of sequential nucleotides, though such NOEs are observed between T(CH3) and A(H8). A three-dimensional structure of the parallel-stranded duplex at atomic resolution has been obtained using molecular dynamics simulations under NMR constraints. The simulated structures have torsional angles very similar to those found in B-DNA duplexes, but the base stacking and helicoid parameters are significantly different.

Base Pairing↗