The Experts below are selected from a list of 43455 Experts worldwide ranked by ideXlab platform
Gregory L Verdine - One of the best experts on this subject based on the ideXlab platform.
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the trajectory of intrahelical lesion recognition and extrusion by the human 8 oxoguanine DNA glycosylase
Nature Communications, 2020Co-Authors: Uddhav K Shigdel, Martin Karplus, Victor Ovchinnikov, Seungjoo Lee, Jenny A Shih, Kwangho Nam, Gregory L VerdineAbstract:Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack. The structures reveal that hOGG1 engages the DNA using different protein-DNA contacts from those observed in the previously determined lesion recognition complex and other hOGG1-DNA complexes. By applying molecular dynamics simulations, we have determined the pathways taken by the lesion and normal bases when extruded from the DNA Helix and their associated free energy profiles. These results reveal how the human oxoG DNA glycosylase hOGG1 locates the lesions inside the DNA Helix and facilitates their extrusion for repair.
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structural and biochemical analysis of DNA Helix invasion by the bacterial 8 oxoguanine DNA glycosylase mutm
Journal of Biological Chemistry, 2013Co-Authors: Roujia Sung, Michael Zhang, Y Qi, Gregory L VerdineAbstract:MutM is a bacterial DNA glycosylase that serves as the first line of defense against the highly mutagenic 8-oxoguanine (oxoG) lesion, catalyzing glycosidic bond cleavage of oxoG to initiate base excision DNA repair. Previous work has shown that MutM actively interrogates DNA for the presence of an intrahelical oxoG lesion. This interrogation process involves significant buckling and bending of the DNA to promote extrusion of oxoG from the duplex. Structural snapshots have revealed several different highly conserved residues that are prominently inserted into the duplex in the vicinity of the target oxoG before and after base extrusion has occurred. However, the roles of these Helix-invading residues during the lesion recognition and base extrusion process remain unclear. In this study, we set out to probe the function of residues Phe114 and Met77 in oxoG recognition and repair. Here we report a detailed biochemical and structural characterization of MutM variants containing either a F114A or M77A mutation, both of which showed significant decreases in the efficiency of oxoG repair. These data reveal that Met77 plays an important role in stabilizing the lesion-extruded conformation of the DNA. Phe114, on the other hand, appears to destabilize the intrahelical state of the oxoG lesion, primarily by buckling the target base pair. We report the observation of a completely unexpected interaction state, in which the target base pair is ruptured but remains fully intrahelical; this structure vividly illustrates the disruptive influence of MutM on the target base pair.
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structural origins of DNA target selection and nucleobase extrusion by a DNA cytosine methyltransferase
Journal of Biological Chemistry, 2012Co-Authors: Andriy Didovyk, Gregory L VerdineAbstract:Abstract Epigenetic methylation of cytosine residues in DNA is an essential element of genome maintenance and function in organisms ranging from bacteria to humans. DNA 5-cytosine methyltransferase enzymes (DCMTases) catalyze cytosine methylation via reaction intermediates in which the DNA is drastically remodeled, with the target cytosine residue extruded from the DNA Helix and plunged into the active site pocket of the enzyme. We have determined a crystal structure of M.HaeIII DCMTase in complex with its DNA substrate at a previously unobserved state, prior to extrusion of the target cytosine and frame-shifting of the DNA recognition sequence. The structure reveals that M.HaeIII selects the target cytosine and destabilizes its base-pairing through a precise, focused and coordinated assault on the duplex DNA, which isolates the target cytosine from its nearest neighbors and thereby facilitates its extrusion from DNA.
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structure of a DNA glycosylase searching for lesions
Science, 2006Co-Authors: Anirban Banerjee, Webster L Santos, Gregory L VerdineAbstract:DNA glycosylases must interrogate millions of base pairs of undamaged DNA in order to locate and then excise one damaged nucleobase. The nature of this search process remains poorly understood. Here we report the use of disulfide cross-linking (DXL) technology to obtain structures of a bacterial DNA glycosylase, MutM, interrogating undamaged DNA. These structures, solved to 2.0 angstrom resolution, reveal the nature of the search process: The protein inserts a probe residue into the helical stack and severely buckles the target base pair, which remains intrahelical. MutM therefore actively interrogates the intact DNA Helix while searching for damage.
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the crystal structure of haelll methyltransferase covalently complexed to DNA an extrahelical cytosine and rearranged base pairing
Cell, 1995Co-Authors: Karin M Reinisch, Gregory L Verdine, Lin Chen, William N LipscombAbstract:Abstract Many organisms expand the information content of their genome through enzymatic methylation of cytosine residues. Here we report the 2.8 A crystal structure of a bacterial DNA (cytosine-5)-methyltransferase (DCMtase), M. Haelll, bound covalently to DNA. In this complex, the substrate cytosine is extruded from the DNA Helix and inserted into the active site of the enzyme, as has been observed for another DCMtase, M. Hhal. The DNA Is bound In a cleft between the two domains of the protein and is distorted from the characteristic B-form conformation at Its recognition sequence. A comparison of structures shows a variation In the mode of DNA recognition: M. Haelli differs from M. Hhal in that the remaining bases in its recognition sequence undergo an extensive rearrangement in their pairing. In this process, the bases are unstacked, and a gap 8 A long opens in the DNA.
Ahmed Kamal - One of the best experts on this subject based on the ideXlab platform.
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synthesis DNA binding ability and evaluation of antitumour activity of triazolo 1 2 4 benzothiadiazine linked pyrrolo 2 1 c 1 4 benzodiazepine conjugates
Bioorganic & Medicinal Chemistry, 2008Co-Authors: Ahmed Kamal, Naseer M A Khan, Srinivasa K Reddy, Aarti Juvekar, Subrata Sen, Y V V Srikanth, Nisha Kurian, Surekha ZingdeAbstract:A series of triazolobenzothiadiazine-pyrrolobenzodiazepine conjugates linked through different alkane spacers have been prepared. These compounds have exhibited significant cytotoxicity against most of the cell lines examined. Compound 5a displays GI(50) values from 1.83 to 2.38 microM against seven human tumour cell lines, and is identified as a promising lead compound from this series. Their DNA thermal denaturation studies have also been carried out, and one of the compounds 5c elevates the DNA Helix melting temperature of the CT-DNA by 2.6 degrees C after incubation for 36 h.
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1 2 4 benzothiadiazine linked pyrrolo 2 1 c 1 4 benzodiazepine conjugates synthesis DNA binding affinity and cytotoxicity
Bioorganic & Medicinal Chemistry Letters, 2007Co-Authors: Ahmed Kamal, Naseer M A Khan, Srinivasa K Reddy, Kaleem S Ahmed, Shiva M Kumar, Aarti Juvekar, Subrata Sen, Surekha ZingdeAbstract:Abstract Benzothiadiazine–pyrrolobenzodiazepine conjugates linked through different alkane spacers have been prepared. These new classes of hybrid molecules exhibit cytotoxicity against many cancer cell lines. Their DNA thermal denaturation studies have been carried out and one of the compounds ( 4b ) elevates the DNA Helix melting temperature of the CT-DNA by 6.7 °C after incubation for 36 h.
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synthesis and DNA binding ability of pyrrolo 2 1 c 1 4 benzodiazepine azepane conjugates
Bioorganic & Medicinal Chemistry Letters, 2006Co-Authors: Ahmed Kamal, Rajasekhar D Reddy, P Murali Mohan S ReddyAbstract:Abstract A series of pyrrolobenzodiazepine–azepane conjugates linked through different alkane spacers have been prepared and their DNA thermal denaturation studies have been carried out. One of the compound (4b), elevates the DNA Helix melting temperature of the CT-DNA by 2.0 °C after incubation for 36 h at 37 °C.
Surekha Zingde - One of the best experts on this subject based on the ideXlab platform.
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synthesis DNA binding ability and evaluation of antitumour activity of triazolo 1 2 4 benzothiadiazine linked pyrrolo 2 1 c 1 4 benzodiazepine conjugates
Bioorganic & Medicinal Chemistry, 2008Co-Authors: Ahmed Kamal, Naseer M A Khan, Srinivasa K Reddy, Aarti Juvekar, Subrata Sen, Y V V Srikanth, Nisha Kurian, Surekha ZingdeAbstract:A series of triazolobenzothiadiazine-pyrrolobenzodiazepine conjugates linked through different alkane spacers have been prepared. These compounds have exhibited significant cytotoxicity against most of the cell lines examined. Compound 5a displays GI(50) values from 1.83 to 2.38 microM against seven human tumour cell lines, and is identified as a promising lead compound from this series. Their DNA thermal denaturation studies have also been carried out, and one of the compounds 5c elevates the DNA Helix melting temperature of the CT-DNA by 2.6 degrees C after incubation for 36 h.
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1 2 4 benzothiadiazine linked pyrrolo 2 1 c 1 4 benzodiazepine conjugates synthesis DNA binding affinity and cytotoxicity
Bioorganic & Medicinal Chemistry Letters, 2007Co-Authors: Ahmed Kamal, Naseer M A Khan, Srinivasa K Reddy, Kaleem S Ahmed, Shiva M Kumar, Aarti Juvekar, Subrata Sen, Surekha ZingdeAbstract:Abstract Benzothiadiazine–pyrrolobenzodiazepine conjugates linked through different alkane spacers have been prepared. These new classes of hybrid molecules exhibit cytotoxicity against many cancer cell lines. Their DNA thermal denaturation studies have been carried out and one of the compounds ( 4b ) elevates the DNA Helix melting temperature of the CT-DNA by 6.7 °C after incubation for 36 h.
Martin Karplus - One of the best experts on this subject based on the ideXlab platform.
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the trajectory of intrahelical lesion recognition and extrusion by the human 8 oxoguanine DNA glycosylase
Nature Communications, 2020Co-Authors: Uddhav K Shigdel, Martin Karplus, Victor Ovchinnikov, Seungjoo Lee, Jenny A Shih, Kwangho Nam, Gregory L VerdineAbstract:Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack. The structures reveal that hOGG1 engages the DNA using different protein-DNA contacts from those observed in the previously determined lesion recognition complex and other hOGG1-DNA complexes. By applying molecular dynamics simulations, we have determined the pathways taken by the lesion and normal bases when extruded from the DNA Helix and their associated free energy profiles. These results reveal how the human oxoG DNA glycosylase hOGG1 locates the lesions inside the DNA Helix and facilitates their extrusion for repair.
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structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA
Nature, 2005Co-Authors: Anirban Banerjee, Wei Yang, Martin KarplusAbstract:How DNA repair proteins distinguish between the rare sites of damage and the vast expanse of normal DNA is poorly understood. Recognizing the mutagenic lesion 8-oxoguanine (oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G). Here we report the use of a covalent trapping strategy to capture a human oxoG repair protein, 8-oxoguanine DNA glycosylase I (hOGG1), in the act of interrogating normal DNA. The X-ray structure of the trapped complex features a target G nucleobase extruded from the DNA Helix but denied insertion into the lesion recognition pocket of the enzyme. Free energy difference calculations show that both attractive and repulsive interactions have an important role in the preferential binding of oxoG compared with G to the active site. The structure reveals a remarkably effective gate-keeping strategy for lesion discrimination and suggests a mechanism for oxoG insertion into the hOGG1 active site. Oxidative DNA damage is thought to be involved in tumorigenesis, and specifically the enzyme ‘hOGG1’ that identifies 8-oxoguanine (differing in just two atoms from normal guanine) has been linked to lung and possibly kidney cancer. A structural study in which hOGG1 (8-oxoguanine DNA glycosylase I) was trapped in the act of testing normal DNA for defects shows how it performs the essential gate-keeping role. Surprisingly, the guanine residue is not inserted into the lesion-recognition pocket, but is located at an alternative extrahelical site. This helps explain how DNA repair proteins can locate lesions embedded in a vast excess of normal DNA and can remove nucleosides from the DNA Helix without damaging normal bases.
Elmar G. Weinhold - One of the best experts on this subject based on the ideXlab platform.
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2 aminopurine flipped into the active site of the adenine specific DNA methyltransferase m taqi crystal structures and time resolved fluorescence
Journal of the American Chemical Society, 2007Co-Authors: Thomas Lenz, Robert K Neely, David T F Dryden, Eleanor Y M Bonnist, Goran Pljevaljcic, Axel J Scheidig, Anita C Jones, Elmar G. WeinholdAbstract:We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA Helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short (∼50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by π-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the propo...
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structure of the n6 adenine DNA methyltransferase m taqi in complex with DNA and a cofactor analog
Nature Structural & Molecular Biology, 2001Co-Authors: Karsten Goedecke, Axel J Scheidig, Elmar G. Weinhold, Marc Pignot, Roger S GoodyAbstract:The 2.0 A crystal structure of the N6-adenine DNA methyltransferase M•TaqI in complex with specific DNA and a nonreactive cofactor analog reveals a previously unrecognized stabilization of the extrahelical target base. To catalyze the transfer of the methyl group from the cofactor S-adenosyl-l-methionine to the 6-amino group of adenine within the double-stranded DNA sequence 5′-TCGA-3′, the target nucleoside is rotated out of the DNA Helix. Stabilization of the extrahelical conformation is achieved by DNA compression perpendicular to the DNA Helix axis at the target base pair position and relocation of the partner base thymine in an interstrand π-stacked position, where it would sterically overlap with an innerhelical target adenine. The extrahelical target adenine is specifically recognized in the active site, and the 6-amino group of adenine donates two hydrogen bonds to Asn 105 and Pro 106, which both belong to the conserved catalytic motif IV of N6-adenine DNA methyltransferases. These hydrogen bonds appear to increase the partial negative charge of the N6 atom of adenine and activate it for direct nucleophilic attack on the methyl group of the cofactor.