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Kaushik Ghosh

Publications and source records attributed to Kaushik Ghosh.

15 recordsLinked to original sources
PubMed2005

Spectroscopic and biochemical characterization of heme binding to yeast Dap1p and mouse PGRMC1p.

Yeast damage-associated response protein (Dap1p) and mouse progesterone receptor membrane component-1 protein (mPGRMC1p) belong to a highly conserved class of putative membrane-associated progesterone binding proteins (MAPR), with Dap1p and inner zone antigen (IZA), the rat homologue of mPGRMC1p, recently being reported to bind heme. While primary structure analysis reveals similarities to the cytochrome b(5) motif, neither of the two axial histidines responsible for ligation to the heme is present in any of the MAPR proteins. In this paper, EPR, MCD, CD, UV-vis, and general biochemical methods have been used to characterize the nature of heme binding in both Dap1p and a His-tagged, membrane anchor-truncated mPGRMC1p. As isolated, Dap1p is a tetramer which can be converted to a dimer upon addition of 150 mM salt. The heme is noncovalently attached, with a maximal, in vitro, heme loading of approximately 30%, for both proteins. CD and fluorescence spectroscopies indicate a well-ordered structure, suggesting the low level of heme loading is probably not due to improperly folded protein. EPR confirmed a five-coordinate, high-spin, ferric resting state for both proteins, indicating one axial amino acid ligand, in contrast to the six-coordinate, low-spin, ferric state of cytochrome b(5). The MCD spectrum confirmed this conclusion for Dap1p and indicated the axial ligand is most likely a tyrosine and not a histidine, or a cysteine; however, an aspartic acid residue could not be conclusively ruled out. Potential axial ligands, which are conserved in all MAPRs, were mutated (Y78F, D118A, and Y138F) and purified to homogeneity. The Y78F and D118A mutants were found to bind heme; however, Y138F did not. This result is consistent with the MCD data and indicates that Tyr138 is most likely the axial ligand to the heme in Dap1p.

Amino Acid Sequence↗
PubMed2005

Reductive nitrosylation and proton-assisted bridge splitting of a (mu-oxo)dimanganese(III) complex derived from a polypyridine ligand with one carboxamide group.

Aerobic oxidation of the Mn(II) complex [Mn(Papy3)(H2O)](ClO4) (1, PaPy3- is the anion of the designed ligand N,N-bis(2-pyridylmethyl)amine-N-ethyl-2-pyridine-2-carboxamide) in acetonitrile affords the (mu-oxo)dimanganese(III) complex [(Mn(PaPy3))2(mu-O)](ClO4)2 (3) in high yield. The unsupported single oxo bridge between the two high-spin Mn(III) centers in 3 is readily cleaved upon addition of proton sources such as phenol, acetic acid, and benzoic acid, and complexes of the type [Mn(PaPy3)(L)](ClO4) (5, L = PhO-; 6, L = AcO-; 7, L = BzO-) are formed. The basicity of the bridge is evident by the fact that simple addition of methanol to a solution of 3 in acetonitrile affords the methoxide complex [Mn(PaPy3)(OMe)](ClO4) (4). The structures of 3-5 and 7 have been determined. Passage of NO through a solution of 3 in acetonitrile produces the [Mn-NO]6 nitrosyl [Mn(PaPy3)(NO)](ClO4) (2) via reductive nitrosylation. Complexes 4-7 also afford the [Mn-NO]6 nitrosyl 2 upon reaction with NO. In the latter case, the anionic O-based ligands (such as MeO- and PhO-) act as built-in bases and promote reductive nitrosylation of the Mn(III) complexes.

Crystallography, X-Ray↗
PubMed2005

Preferential synapsis of loxP sites drives ordered strand exchange in Cre-loxP site-specific recombination.

The bacteriophage P1 Cre recombinase catalyzes site-specific recombination between 34-base-pair loxP sequences in a variety of topological contexts. This reaction is widely used to manipulate DNA molecules in applications ranging from benchtop cloning to genome modifications in transgenic animals. Despite the simple, highly symmetric nature of the Cre-loxP system, there is strong evidence that the reaction is asymmetric; the 'bottom' strands in the recombining loxP sites are preferentially exchanged before the 'top' strands. Here, we address the mechanistic basis for ordered strand exchange in the Cre-loxP recombination pathway. Using suicide substrates containing 5'-bridging phosphorothioate linkages at both cleavage sites, fluorescence resonance energy transfer between synapsed loxP sites and a Cre mutant that can cleave the bridging phosphorothioate linkage but not a normal phosphodiester linkage, we showed that preferential formation of a specific synaptic complex between loxP sites imposes ordered strand exchange during recombination and that synapsis stimulates cleavage of loxP sites.

Base Sequence↗
PubMed2005

Linkage disequilibrium mapping of quantitative-trait Loci by selective genotyping.

The principles of linkage disequilibrium mapping of dichotomous diseases can be well applied to the mapping of quantitative-trait loci through the method of selective genotyping. In 1999, M. Slatkin considered a truncation selection (TS) approach. We propose in this report an extended TS approach and an extreme-rank-selection (ERS) approach. The properties of these selection approaches are studied analytically. By using a simulation study, we demonstrate that both the extended TS approach and the ERS approach provide remarkable improvements over Slatkin's original TS approach.

Genotype↗
PubMed2005

Transition metal carbene chemistry. 4. Nucleophilic attachment of DABCO to fischer carbene complexes in MeCN.

Rate constants for the attachment of DABCO (1,4-diazabicyclo[2.2.2]octane) to Fischer carbene complexes of the type (CO)(5)Cr=C(XR)C(6)H(4)Z (X = O and S) in dry MeCN at 25 degrees C are reported. Hammett rho values are 2.18 +/- 0.13 and 0.89 +/- 0.07 for DABCO reactions with (CO)(5)Cr=C(OMe)C(6)H(4)Z (10-Cr-Z) and (CO)(5)Cr=C(SMe)C(6)H(4)Z (11-Cr-Z), respectively. The rho values for the reaction of 10-Cr-Z and 11-Cr-Z with CH(CN)(2)(-) in 50% MeCN-50% H(2)O (v/v) are comparable to the present reactions. The reaction of DABCO with 10-Cr-Z is more closely related to the reaction of (n-Bu)(3)P with (CO)(5)W=C(OMe)C(6)H(5)-Z (23) which also provided a rho value 2.22. The much higher rho values and hence much higher reactivity of methoxy carbene complexes over the corresponding thiomethyl derivatives fit a pattern observed previously for alkoxide ion, OH(-), amine, and thiolate ion nucleophiles, and a rational explanation comes from the consideration of the substituent effects not only on the transition state but also on the reactant. A major difference between 10-Cr-Z and 11-Cr-Z is that the pi-donor effect of the methoxy group is much stronger than that of thiomethyl group. This leads to a substantial contribution of the zwitterionic form to the structure of 10-Cr-Z with much more localized positive charge on the methoxy group than the negative charge on the (CO)(5)Cr moiety. This leads to overall destabilization by an electron-withdrawing phenyl substituents resulting an increase in reactivity. The ethoxycarbene complexes are somewhat less reactive than their methoxy counterparts due to the somewhat more ground state stabilization through its stronger pi donor effect and partly due to steric crowding exerted by the slightly larger ethoxy group in the transition state. Higher k(1)(W)/k(1)(Cr) ratios for (thiomethyl)carbene complexes than methoxy or ethoxycarbene complexes are related to the intrinsic rate constant which is higher for ((thiomethyl)carbene)tungsten complexes than the corresponding Cr ones resulting in an enhanced ratio.

Journal Article↗
PubMed2004

Peptide trapping of the Holliday junction intermediate in Cre-loxP site-specific recombination.

Cre recombinase is a prototypical member of the tyrosine recombinase family of site-specific recombinases. Members of this family of enzymes catalyze recombination between specific DNA sequences by cleaving and exchanging one pair of strands between the two substrate sites to form a 4-way Holliday junction (HJ) intermediate and then resolve the HJ intermediate to recombinant products by a second round of strand exchanges. Recently, hexapeptide inhibitors have been described that are capable of blocking the second strand exchange step in the tyrosine recombinase recombination pathway, leading to an accumulation of the HJ intermediate. These peptides are active in the lambda-integrase, Cre recombinase, and Flp recombinase systems and are potentially important tools for both in vitro mechanistic studies and as in vivo probes of cellular function. Here we present biochemical and crystallographic data that support a model where the peptide inhibitor binds in the center of the recombinase-bound DNA junction and interacts with solvent-exposed bases near the junction branch point. Peptide binding induces large conformational changes in the DNA strands of the HJ intermediate, which affect the active site geometries in the recombinase subunits.

Anisotropy↗
PubMed2004

Reactions of NO with Mn(II) and Mn(III) centers coordinated to carboxamido nitrogen: synthesis of a manganese nitrosyl with photolabile NO.

The Mn(II) and Mn(III) complexes of the pentadentate ligand N,N-bis(2-pyridylmethyl)amine-N-ethyl-2-pyridine-2-carboxamide (PaPy3H; H is the dissociable carboxamide H), namely, [Mn(PaPy3)(H2O)]ClO4 (1) and [Mn(PaPy3)(Cl)]ClO4 (2), with bound carboxamido nitrogen have been isolated and characterized. The high-spin Mn(II) center in 1 is very sensitive to dioxygen, and this complex is rapidly converted into 2 upon reaction with Cl- in air. The bound carboxamido nitrogen in 1 is responsible for this sensitivity toward oxidation since the analogous Schiff base complex [Mn(SBPy3)Cl]ClO4 (4) is very resistant to oxidation. Reaction of NO with 1 affords the diamagnetic [Mn-NO]6 nitrosyl [Mn(PaPy3)(NO)]ClO4 (5). Complexes with no bound carboxamido nitrogen such as 4 and [Mn(PaPy3H)(Cl)2] (3) do not react with NO. No reaction with NO is observed with the Mn(III) complexes 2 and [Mn(PaPy3)(MeCN)]2+ either. Collectively these reactions indicate that NO reacts only with the Mn(II) center ligated to at least one carboxamido nitrogen. Both the carbonyl and N-O stretching frequencies (nu(CO) and nu(NO)) of the present and related complexes strongly suggest a [low-spin Mn(II)-NO*] formulation for 5. The alternative description [low-spin Mn(I)-NO+] is not supported by the spectroscopic and redox behavior of 5. Complex 5 is the first example of a [Mn-NO]6 nitrosyl that exhibits photolability of NO upon illumination with low-intensity tungsten lamps in solvents such as MeCN and H2O. The rapid NO loss from 5 leads to the formation of the corresponding solvato species [Mn(PaPy3)(MeCN)]2+ under aerobic conditions. Oxidation of 5 with (NH4)2[Ce(NO3)6] in MeCN affords the highly reactive paramagnetic (S = 1/2) [MnNO]5 nitrosyl [Mn(PaPy3)(NO)](NO3)2 (6) in high yield. Spectroscopic and magnetic studies confirm a [low-spin Mn(II)-NO+] formulation for 6. The N-O stretching frequencies (nu(NO)) of 5, 6, and analogous nitrosyls reported by other groups collectively suggest that nu(NO) is a better indicator of the oxidation state of NO (NO+, NO*, or NO-) in non-heme iron and other transition-metal complexes with bound NO.

Ligands↗
PubMed2004

pH-dependent autocleavage of lambda repressor occurs in the operator-bound form: characterization of lambda repressor autocleavage.

The first-order rate constants for the RecA-independent, spontaneous, pH-dependent autocleavage of the lambda cI repressor was measured in the present study at pH 10.6 at 27, 37 and 42 degrees C respectively. Autocleavage of the repressor occurs also at pH 9 and 8, although at progressively slower rates. We demonstrate that the spontaneous autocleavage occurs also in the operator-bound state, at a rate either higher than or equal to the rate in solution, depending on the pH value. Owing to the near equality of the rate constant in both operator-free and operator-bound repressors, it can be inferred that the cleavage site has a similar structure and dynamics with respect to the catalytic site in both forms at neutral pH. Covalent modification using PMSF, brought about by a large molar excess of the reagent, inhibits autocleavage of the lambda repressor. The difficulty in obtaining this covalent modification is rationalized using our recent lambda repressor models. Bimolecular type II trans -cleavage was observed previously for mutant LexA repressors lacking a crucial catalytic serine or lysine residue [Kim and Little (1993) Cell (Cambridge, Mass.) 73, 1165-1173], but it could still be cleaved by an 85-202 'enzyme' fragment possessing an improved or hypercleavable character lacking its own cleavage site. Such a type II trans -cleavage was not observed with the covalently modified intact lambda repressor used as substrate and the purified wild-type lambda repressor 112-236 fragment used as the 'enzyme'. All these results show that for the wild-type lambda repressor, the catalytic site is close to the cleavage site in both operator-free and -bound states. In the lytic pathway, the repressor is mainly cleaved via RecA-mediated cleavage, which occurs much faster than the spontaneous autocleavage; the possible biological significance of this slow, spontaneous, but constant, autocleavage is related to the lysogenic state, when RecA-mediated cleavage is absent.

Catalytic Domain↗
PubMed2004

An intramedullary tumor presenting with hyperhidrosis.

A case of a cervical intramedullary tumor is reported whose presentation was with disabling hyperhidrosis. The symptom resolved after surgical debulking of the tumor. Hyperhidrosis as a presenting manifestation of an intramedullary tumor has not been reported earlier.

Astrocytoma↗
PubMed2003

A high-resolution NMR study of long-lived water molecules in both oxidation states of a minimal cytochrome c.

The interaction of water with oxidized and reduced cytochrome c from the Gram-positive bacterium Bacillus pasteurii (a 71-amino acid long monoheme cytochrome) is investigated through CLEANEX experiments and (15)N-edited ePHOGSY and Tr-ROESY experiments. It appears that a water molecule gives rise to dipolar cross-relaxation with the amide protons of Gly74 and Ile75, with a residence time longer than 0.4 ns, to account for a negative NOE. Such water molecule is present in both the oxidized and reduced species and in the X-ray structure. It appears to have a structural role. Other possible roles are discussed by comparison with the water molecules present in other c-type cytochromes. The amide proton of Cys35 is found to exchange rapidly with the solvent in the oxidized but not in the reduced protein, at variance with H/D exchange experiments, which probe a different time scale. The present data confirm that electron-transfer proteins evolved to minimize reorganization energy upon change of the oxidation state, even though the consequent variation of charge of the metal ion may induce some changes in the structure and/or dynamics of the protein.

Bacillus↗
PubMed2003

A comparative three-dimensional model of the carboxy-terminal domain of the lambda repressor and its use to build intact repressor tetramer models bound to adjacent operator sites.

A model for residues 93-236 of the lambda repressor (1gfx) was predicted, based on the UmuD(') crystal structure, as part of four intact repressor molecules bound to two adjacent operator sites. The structure of region 136-230 in 1gfx was found to be nearly identical to the independently determined crystal structure of the 132-236 fragment, 1f39, released later by the PDB. Later, two more tetrameric models of the lambda repressor tetramer bound to two adjacent operator sites were constructed by us; in one of these, 1j5g, the N-domain and C-domain coordinates and hence monomer-monomer and dimer-dimer interactions are almost the same as in 1gfx, but the structure of the linker region is partly based on the linker region of the LexA dimer in 1jhe; in the other, 1lwq, the crystalline tetramer for region 140-236 has been coopted from the crystal structure deposited in 1kca, the operator DNA and N-domain coordinates of which are same as those in 1gfx and 1j5g, but the linker region is partly based on the LexA dimer structures 1jhe and 1jhh. Monomer-monomer interactions at the same operator site are stabilized by exposed hydrophobic side chains in beta-strands while cooperative interactions are mostly confined to beta(6) and some adjacent residues in both 1gfx and 1j5g. Mutational data, existence of a twofold axis relating two C-domains within a dimer, and minimization of DNA distortion between adjacent operator sites allow us to roughly position the C-domain with respect to the N-domain for both 1gfx and 1j5g. The study correlates these models with functional, biochemical, biophysical, and immunological data on the repressor in the literature. The oligomerization mode observed in the crystal structure of 132-236 may not exist in the intact repressor bound to the operator since it is shown to contradict several published biochemical data on the intact repressor.

Amino Acid Sequence↗
PubMed2002

The unfolding of oxidized c-type cytochromes: the instructive case of Bacillus pasteurii.

The reversible unfolding of oxidized Bacillus pasteurii cytochrome c(553) by guanidinium chloride under equilibrium conditions has been monitored by NMR and optical spectroscopy. The results obtained indicate that unfolding takes place through a mechanism involving the detachment from heme iron coordination of the sulfur of the Met71 axial ligand and yielding either a high spin (HS) or a low spin (LS(1)) species, depending on the pH value. In the LS(1) form the Met71 is replaced by another protein ligand, possibly Lys. The ligand exchange reaction does not reach completion until the protein backbone reaches a largely unfolded state, as monitored through 1H-15N NMR experiments, thus demonstrating that there is a significant correlation between formation of the Fe-S bond and native structure stability. 1H/2H exchange data, however, show that helix alpha(3), the C-terminal region of helix alpha(4), and helix alpha(5) maintain low exchangeability of the amide protons in the LS(1) form. This finding most likely implies that these regions maintain some ordered non-covalent structure, in which the amide moieties are involved in H-bonds. Finally, a folding mechanism is proposed and discussed in terms of analogies and differences with the larger mitochondrial cytochrome c proteins. It is concluded that the thermodynamic stability of the region around the metal cofactor is determined by the chemical nature of the residues around the axial methionine residue.

Bacillus↗
PubMed2002

Cre-loxP biochemistry.

Cre recombinase is now widely used to carry out complex manipulations of DNA molecules both in vitro and in vivo. For in vitro experiments, there is a clear need for highly pure preparations of Cre and of Cre mutants that serve as controls or supply an altered activity or specificity. In vivo experiments utilizing Cre variants also often require in vitro characterization and some applications involve transfection of purified enzyme to achieve transient activity in the cell. This review outlines a detailed protocol for purification of native Cre and describes straightforward assays that can be used to test for recombination activity in vitro. The design of experiments to trap the intermediates of Cre-loxP site-specific recombination for biophysical studies is also presented. The methods described should be useful to any investigator with a need for purified Cre recombinase and should be broadly applicable to related site-specific recombination systems.

DNA↗
PubMedDate not supplied

A new method of predicting US and state-level cancer mortality counts for the current calendar year.

Every January for more than 40 years, the American Cancer Society (ACS) has estimated the total number of cancer deaths that are expected to occur in the United States and individual states in the upcoming year. In a collaborative effort to improve the accuracy of the predictions, investigators from the National Cancer Institute and the ACS have developed and tested a new prediction method. The new method was used to create the mortality predictions for the first time in Cancer Statistics, 2004 and Cancer Facts & Figures 2004. The authors present a conceptual overview of the previous ACS method and the new state-space method (SSM), and they review the results of rigorous testing to determine which method provides more accurate predictions of the observed number of cancer deaths from the years 1997 to 1999. The accuracy of the methods was compared using squared deviations (the square of the predicted minus observed values) for each of the cancer sites for which predictions are published as well as for all cancer sites combined. At the national level, the squared deviations were not consistently lower for every cancer site for either method, but the average squared deviations (averaged across cancer sites, years, and sex) was substantially lower for the SSM than for the ACS method. During the period 1997 to 1999, the ACS estimates of deaths were usually greater than the observed numbers for all cancer sites combined and for several major individual cancer sites, probably because the ACS method was less sensitive to recent changes in cancer mortality rates (and associated counts) that occurred for several major cancer sites in the early and mid 1990s. The improved accuracy of the new method was particularly evident for prostate cancer, for which mortality rates changed dramatically in the late 1980s and early 1990s. At the state level, the accuracy of the two methods was comparable. Based on these results, the ACS has elected to use the new method for the annual prediction of the number of cancer deaths at the national and state levels.

Cause of Death↗