Thirumananseri Kumarevel - Academia.edu (original) (raw)

Papers by Thirumananseri Kumarevel

Research paper thumbnail of Divalent metal ion coordination distance comparison for different metal ions observed in the complex structures

<b>Copyright information:</b>Taken from "Characterization of the metal ion bindi... more <b>Copyright information:</b>Taken from "Characterization of the metal ion binding site in the anti-terminator protein, HutP, of "Nucleic Acids Research 2005;33(17):5494-5502.Published online 28 Sep 2005PMCID:PMC1236978.© The Author 2005. Published by Oxford University Press. All rights reserved A schematic hexa-coordination of the metal ions, drawn and numbered as in . The metal ion binding sites observed in the asymmetric unit were averaged individually and are depicted in the figures.

Research paper thumbnail of Analysis of the abilities of various metal ions to mediate the HutPâ RNA interactions

<b>Copyright information:</b>Taken from "Characterization of the metal ion bindi... more <b>Copyright information:</b>Taken from "Characterization of the metal ion binding site in the anti-terminator protein, HutP, of "Nucleic Acids Research 2005;33(17):5494-5502.Published online 28 Sep 2005PMCID:PMC1236978.© The Author 2005. Published by Oxford University Press. All rights reserved Fifteen divalent and two monovalent cations were analyzed by a gel-shift assay, as described in . The amounts of complexed and free RNA were used to calculate the percentage of metal ion interactions involved in making the ternary complex. The percentages from three independent experiments were averaged (standard errors, ±5), are plotted against the metal ions.

Research paper thumbnail of Histidine utilizing () operon of Schematic representation of the operon, showing the arrangement of the , terminator/anti-terminator (+459 to +571 nt), and structural genes

<b>Copyright information:</b>Taken from "Characterization of the metal ion bindi... more <b>Copyright information:</b>Taken from "Characterization of the metal ion binding site in the anti-terminator protein, HutP, of "Nucleic Acids Research 2005;33(17):5494-5502.Published online 28 Sep 2005PMCID:PMC1236978.© The Author 2005. Published by Oxford University Press. All rights reserved

Research paper thumbnail of Forecasting the spread of COVID-19 using LSTM network

BMC Bioinformatics, 2021

Background The novel coronavirus (COVID-19) is caused by severe acute respiratory syndrome corona... more Background The novel coronavirus (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2, and within a few months, it has become a global pandemic. This forced many affected countries to take stringent measures such as complete lockdown, shutting down businesses and trade, as well as travel restrictions, which has had a tremendous economic impact. Therefore, having knowledge and foresight about how a country might be able to contain the spread of COVID-19 will be of paramount importance to the government, policy makers, business partners and entrepreneurs. To help social and administrative decision making, a model that will be able to forecast when a country might be able to contain the spread of COVID-19 is needed. Results The results obtained using our long short-term memory (LSTM) network-based model are promising as we validate our prediction model using New Zealand’s data since they have been able to contain the spread of COVID-19 and bring the daily new cases t...

Research paper thumbnail of Crystal structure of nucleosome complex with human testis-specific histone variants, Th2a

Research paper thumbnail of Crystal structure of Aquifex aeolicus gene product Aq1627: a putative phosphoglucosamine mutase reveals a unique C-terminal end-to-end disulfide linkage

Mol. BioSyst., 2017

The crystal structure of Aq1627 protein from Aquifex aeolicus, a hyperthermophilic bacterium has ... more The crystal structure of Aq1627 protein from Aquifex aeolicus, a hyperthermophilic bacterium has been solved, which reveals a unique end-to-end disulfide linkage.

Research paper thumbnail of Crystallization and preliminary X-ray diffraction studies of the metal-ion-mediated ternary complex of the HutP protein with -histidine and its cognate RNA

Bba Proteins Proteomics, 2004

Research paper thumbnail of Purification, crystallization and preliminary X-ray crystallographic analysis of ST1022, a putative member of the Lrp/AsnC family of transcriptional regulators isolated from<i>Sulfolobus tokodaii</i>strain 7

Acta crystallographica, Nov 1, 2007

The Lrp/AsnC family of transcriptional regulators, also known as feast/famine transcriptional reg... more The Lrp/AsnC family of transcriptional regulators, also known as feast/famine transcriptional regulators, are widely distributed among bacteria and archaea. This family of proteins are likely to be involved in cellular metabolism, with exogenous amino acids functioning as effectors. Here, the crystallization and preliminary X-ray diffraction analysis of ST1022, a member of the Lrp/AsnC family of proteins, is reported with and without exogenous glutamine as the effector molecule. The crystals of native ST1022 and of the putative complex belong to the tetragonal space group I422, with unit-cell parameters a = b = 103.771, c = 73.297 Å and a = b = 103.846, c = 73.992 Å , respectively. Preliminary X-ray diffraction data analysis and molecular-replacement solution revealed the presence of one monomer per asymmetric unit.

Research paper thumbnail of Crystal Structure of Thr134 to Ala of ST1022-Glutamine Complex from Sulfolobus tokodaii 7

Research paper thumbnail of Crystal structure of pterin-4-alpha-carbinolamine dehydratase (pterin carbinolamine dehydratase) from Geobacillus kaustophilus HTA426

Research paper thumbnail of RNA polymerase-Gfh1 complex (Crystal type 1)

Research paper thumbnail of Crystal structure of a hypothetical protein (Aq_1549) from Aquifex aeolicus VF5

Research paper thumbnail of Allosteric activation of HutP protein, that regulates transcription of hut operon in Bacillus subtilis, mediated by various analogs of histidine

Huff is an RNA-binding protein which regulates the expression of the histidine utilization (hut) ... more Huff is an RNA-binding protein which regulates the expression of the histidine utilization (hut) operon in Bacillus subtilk by binding to cis-acting regulatory sequences on the hut mRNA in the presence of Lhistidine. In the case of HutP-RNA interactions, Lhistidhe plays an allosteric activation role i.e. only the activated HutP specifically recognize the hut mRNA. In the present study, we analyzed various analogs of Lhistidine to evaluate the important functional groups of Ghistidine that is responsible for the activation of HutP. Our analysis clearly suggests that imidazole group of a L-histidine plays a vital role for the activation. Our analysis also revealed efficient analogs of L-histidine for the activation, for example, Lhistidine p-naphthylamide and L-Histidine benzyl ester.

Research paper thumbnail of 転写制御タンパク質ＨｕｔＰの立体構造とアンチターミネーション機構

Research paper thumbnail of Revelation of Anti-Termination Mechanism - Through Structural and Functional Analyses of HutP

Regulating gene expression directly at the mRNA level represents a novel approach in the control ... more Regulating gene expression directly at the mRNA level represents a novel approach in the control of cellular processes in all organisms. In this respect, RNA-binding proteins, while in the presence of their cognate ligands, play a key role by targeting the mRNA to regulate its expression through attenuation or anti-termination mechanisms. Although many proteins are known to use these mechanisms in the regulation of gene expression, no structural insights have been revealed, to date, to explain how these proteins trigger the conformation for the recognition of RNA. This review describes the HutP mediated anti-termination mechanism by combining the in vivo, in vitro and X-ray analyses of the activated conformation of HutP, initiated by the coordination of L-histidine and Mg 2+ ions, based on our previous and recently solved crystal structures (uncomplexed HutP, HutP-Mg 2+ , HutP-L-histidine, HutP-Mg 2+-L-histidine, HutP-Mg 2+-Lhistidine-RNA (21-mer and 55-mer)). In this anti-termination process, HutP initiates destabilization at the 5'-end of its mRNA by binding to the first UAG-rich region and then accesses the second UAG-rich region, located downstream of the stable G-C-rich segment of the terminator stem. By this mode of action, HutP appears to disrupt the G-C rich terminator stem loop, and allow the RNA polymerase to pass through the destabilized terminator, thus it prevents premature termination of transcription in the RNA segment preceding the regions encoding for the genes responsible for histidine degradation.

Research paper thumbnail of The MarR Family of Transcriptional Regulators - A Structural Perspective

Research paper thumbnail of Barium and Protein–RNA Interactions

Research paper thumbnail of Crystal structure of the manganese transport regulatory protein from Escherichia coli

Proteins: Structure, Function, and Bioinformatics, 2009

Crystal structure of the manganese transport regulatory protein from Escherichia coli Tomoyuki Ta... more Crystal structure of the manganese transport regulatory protein from Escherichia coli Tomoyuki Tanaka, Akeo Shinkai, Yoshitaka Bessho, Thirumananseri Kumarevel,* and Shigeyuki Yokoyama* 1 Advanced Photon Technology Division, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan 2 Photon Science Research Division, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan 3 Systems and Structural Biology Research Team, Systems and Structural Biology Center, RIKEN Yokohama Institute, Yokohama 230-0045, Japan 4 Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan

Research paper thumbnail of Crystal structure of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8

Proteins: Structure, Function, and Bioinformatics, 2009

Crystal structure of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8 Thirumananseri Kum... more Crystal structure of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8 Thirumananseri Kumarevel,* Tomoyuki Tanaka, Akeo Shinkai, and Shigeyuki Yokoyama 1 RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo, Japan 2 Systems and Structural Biology Center, Yokohama Institute, RIKEN, Tsurumi, Yokohama, Japan 3 Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan

Research paper thumbnail of Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector l -glutamine: implications of effector binding in molecular association and DNA binding

Nucleic Acids Research, 2008

Genome analyses have revealed that members of the Lrp/AsnC family of transcriptional regulators a... more Genome analyses have revealed that members of the Lrp/AsnC family of transcriptional regulators are widely distributed among prokaryotes, including both bacteria and archaea. These regulatory proteins are involved in cellular metabolism in both global and specific manners, depending on the availability of the exogenous amino acid effectors. Here we report the first crystal structure of glutamine receptor protein (Grp) from Sulfolobus tokodaii strain 7, in the ligand-free and glutamine-bound (Grp-Gln) forms. Although the overall structures of both molecules are similar, a significant conformational change was observed at the ligand [L-glutamine (Gln)] binding site in the effector domain, which may be essential for further stabilization of the octameric structure, and in turn for facilitating DNA binding. In addition, we predicted promoter for the grp gene, and these analyses suggested the importance of cooperative binding to the protein. To gain insights into the ligand-induced conformational changes, we mutated all of the ligand-binding residues in Grp, and revealed the importance of Gln binding by biochemical and structural analyses. Further structural analyses showed that Y77 is crucial for ligand binding, and that the residues T132 and T134, which are highly conserved among the Lrp family of proteins, fluctuates between the active and inactive conformations, thus affecting protein oligomerization for DNA binding.

Research paper thumbnail of Divalent metal ion coordination distance comparison for different metal ions observed in the complex structures

<b>Copyright information:</b>Taken from "Characterization of the metal ion bindi... more <b>Copyright information:</b>Taken from "Characterization of the metal ion binding site in the anti-terminator protein, HutP, of "Nucleic Acids Research 2005;33(17):5494-5502.Published online 28 Sep 2005PMCID:PMC1236978.© The Author 2005. Published by Oxford University Press. All rights reserved A schematic hexa-coordination of the metal ions, drawn and numbered as in . The metal ion binding sites observed in the asymmetric unit were averaged individually and are depicted in the figures.

Research paper thumbnail of Analysis of the abilities of various metal ions to mediate the HutPâ RNA interactions

<b>Copyright information:</b>Taken from "Characterization of the metal ion bindi... more <b>Copyright information:</b>Taken from "Characterization of the metal ion binding site in the anti-terminator protein, HutP, of "Nucleic Acids Research 2005;33(17):5494-5502.Published online 28 Sep 2005PMCID:PMC1236978.© The Author 2005. Published by Oxford University Press. All rights reserved Fifteen divalent and two monovalent cations were analyzed by a gel-shift assay, as described in . The amounts of complexed and free RNA were used to calculate the percentage of metal ion interactions involved in making the ternary complex. The percentages from three independent experiments were averaged (standard errors, ±5), are plotted against the metal ions.

Research paper thumbnail of Histidine utilizing () operon of Schematic representation of the operon, showing the arrangement of the , terminator/anti-terminator (+459 to +571 nt), and structural genes

<b>Copyright information:</b>Taken from "Characterization of the metal ion bindi... more <b>Copyright information:</b>Taken from "Characterization of the metal ion binding site in the anti-terminator protein, HutP, of "Nucleic Acids Research 2005;33(17):5494-5502.Published online 28 Sep 2005PMCID:PMC1236978.© The Author 2005. Published by Oxford University Press. All rights reserved

Research paper thumbnail of Forecasting the spread of COVID-19 using LSTM network

BMC Bioinformatics, 2021

Background The novel coronavirus (COVID-19) is caused by severe acute respiratory syndrome corona... more Background The novel coronavirus (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2, and within a few months, it has become a global pandemic. This forced many affected countries to take stringent measures such as complete lockdown, shutting down businesses and trade, as well as travel restrictions, which has had a tremendous economic impact. Therefore, having knowledge and foresight about how a country might be able to contain the spread of COVID-19 will be of paramount importance to the government, policy makers, business partners and entrepreneurs. To help social and administrative decision making, a model that will be able to forecast when a country might be able to contain the spread of COVID-19 is needed. Results The results obtained using our long short-term memory (LSTM) network-based model are promising as we validate our prediction model using New Zealand’s data since they have been able to contain the spread of COVID-19 and bring the daily new cases t...

Research paper thumbnail of Crystal structure of nucleosome complex with human testis-specific histone variants, Th2a

Research paper thumbnail of Crystal structure of Aquifex aeolicus gene product Aq1627: a putative phosphoglucosamine mutase reveals a unique C-terminal end-to-end disulfide linkage

Mol. BioSyst., 2017

The crystal structure of Aq1627 protein from Aquifex aeolicus, a hyperthermophilic bacterium has ... more The crystal structure of Aq1627 protein from Aquifex aeolicus, a hyperthermophilic bacterium has been solved, which reveals a unique end-to-end disulfide linkage.

Research paper thumbnail of Crystallization and preliminary X-ray diffraction studies of the metal-ion-mediated ternary complex of the HutP protein with -histidine and its cognate RNA

Bba Proteins Proteomics, 2004

Research paper thumbnail of Purification, crystallization and preliminary X-ray crystallographic analysis of ST1022, a putative member of the Lrp/AsnC family of transcriptional regulators isolated from<i>Sulfolobus tokodaii</i>strain 7

Acta crystallographica, Nov 1, 2007

The Lrp/AsnC family of transcriptional regulators, also known as feast/famine transcriptional reg... more The Lrp/AsnC family of transcriptional regulators, also known as feast/famine transcriptional regulators, are widely distributed among bacteria and archaea. This family of proteins are likely to be involved in cellular metabolism, with exogenous amino acids functioning as effectors. Here, the crystallization and preliminary X-ray diffraction analysis of ST1022, a member of the Lrp/AsnC family of proteins, is reported with and without exogenous glutamine as the effector molecule. The crystals of native ST1022 and of the putative complex belong to the tetragonal space group I422, with unit-cell parameters a = b = 103.771, c = 73.297 Å and a = b = 103.846, c = 73.992 Å , respectively. Preliminary X-ray diffraction data analysis and molecular-replacement solution revealed the presence of one monomer per asymmetric unit.

Research paper thumbnail of Crystal Structure of Thr134 to Ala of ST1022-Glutamine Complex from Sulfolobus tokodaii 7

Research paper thumbnail of Crystal structure of pterin-4-alpha-carbinolamine dehydratase (pterin carbinolamine dehydratase) from Geobacillus kaustophilus HTA426

Research paper thumbnail of RNA polymerase-Gfh1 complex (Crystal type 1)

Research paper thumbnail of Crystal structure of a hypothetical protein (Aq_1549) from Aquifex aeolicus VF5

Research paper thumbnail of Allosteric activation of HutP protein, that regulates transcription of hut operon in Bacillus subtilis, mediated by various analogs of histidine

Huff is an RNA-binding protein which regulates the expression of the histidine utilization (hut) ... more Huff is an RNA-binding protein which regulates the expression of the histidine utilization (hut) operon in Bacillus subtilk by binding to cis-acting regulatory sequences on the hut mRNA in the presence of Lhistidine. In the case of HutP-RNA interactions, Lhistidhe plays an allosteric activation role i.e. only the activated HutP specifically recognize the hut mRNA. In the present study, we analyzed various analogs of Lhistidine to evaluate the important functional groups of Ghistidine that is responsible for the activation of HutP. Our analysis clearly suggests that imidazole group of a L-histidine plays a vital role for the activation. Our analysis also revealed efficient analogs of L-histidine for the activation, for example, Lhistidine p-naphthylamide and L-Histidine benzyl ester.

Research paper thumbnail of 転写制御タンパク質ＨｕｔＰの立体構造とアンチターミネーション機構

Research paper thumbnail of Revelation of Anti-Termination Mechanism - Through Structural and Functional Analyses of HutP

Regulating gene expression directly at the mRNA level represents a novel approach in the control ... more Regulating gene expression directly at the mRNA level represents a novel approach in the control of cellular processes in all organisms. In this respect, RNA-binding proteins, while in the presence of their cognate ligands, play a key role by targeting the mRNA to regulate its expression through attenuation or anti-termination mechanisms. Although many proteins are known to use these mechanisms in the regulation of gene expression, no structural insights have been revealed, to date, to explain how these proteins trigger the conformation for the recognition of RNA. This review describes the HutP mediated anti-termination mechanism by combining the in vivo, in vitro and X-ray analyses of the activated conformation of HutP, initiated by the coordination of L-histidine and Mg 2+ ions, based on our previous and recently solved crystal structures (uncomplexed HutP, HutP-Mg 2+ , HutP-L-histidine, HutP-Mg 2+-L-histidine, HutP-Mg 2+-Lhistidine-RNA (21-mer and 55-mer)). In this anti-termination process, HutP initiates destabilization at the 5'-end of its mRNA by binding to the first UAG-rich region and then accesses the second UAG-rich region, located downstream of the stable G-C-rich segment of the terminator stem. By this mode of action, HutP appears to disrupt the G-C rich terminator stem loop, and allow the RNA polymerase to pass through the destabilized terminator, thus it prevents premature termination of transcription in the RNA segment preceding the regions encoding for the genes responsible for histidine degradation.

Research paper thumbnail of The MarR Family of Transcriptional Regulators - A Structural Perspective

Research paper thumbnail of Barium and Protein–RNA Interactions

Research paper thumbnail of Crystal structure of the manganese transport regulatory protein from Escherichia coli

Proteins: Structure, Function, and Bioinformatics, 2009

Crystal structure of the manganese transport regulatory protein from Escherichia coli Tomoyuki Ta... more Crystal structure of the manganese transport regulatory protein from Escherichia coli Tomoyuki Tanaka, Akeo Shinkai, Yoshitaka Bessho, Thirumananseri Kumarevel,* and Shigeyuki Yokoyama* 1 Advanced Photon Technology Division, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan 2 Photon Science Research Division, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan 3 Systems and Structural Biology Research Team, Systems and Structural Biology Center, RIKEN Yokohama Institute, Yokohama 230-0045, Japan 4 Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan

Research paper thumbnail of Crystal structure of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8

Proteins: Structure, Function, and Bioinformatics, 2009

Crystal structure of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8 Thirumananseri Kum... more Crystal structure of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8 Thirumananseri Kumarevel,* Tomoyuki Tanaka, Akeo Shinkai, and Shigeyuki Yokoyama 1 RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo, Japan 2 Systems and Structural Biology Center, Yokohama Institute, RIKEN, Tsurumi, Yokohama, Japan 3 Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan

Research paper thumbnail of Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector l -glutamine: implications of effector binding in molecular association and DNA binding

Nucleic Acids Research, 2008

Genome analyses have revealed that members of the Lrp/AsnC family of transcriptional regulators a... more Genome analyses have revealed that members of the Lrp/AsnC family of transcriptional regulators are widely distributed among prokaryotes, including both bacteria and archaea. These regulatory proteins are involved in cellular metabolism in both global and specific manners, depending on the availability of the exogenous amino acid effectors. Here we report the first crystal structure of glutamine receptor protein (Grp) from Sulfolobus tokodaii strain 7, in the ligand-free and glutamine-bound (Grp-Gln) forms. Although the overall structures of both molecules are similar, a significant conformational change was observed at the ligand [L-glutamine (Gln)] binding site in the effector domain, which may be essential for further stabilization of the octameric structure, and in turn for facilitating DNA binding. In addition, we predicted promoter for the grp gene, and these analyses suggested the importance of cooperative binding to the protein. To gain insights into the ligand-induced conformational changes, we mutated all of the ligand-binding residues in Grp, and revealed the importance of Gln binding by biochemical and structural analyses. Further structural analyses showed that Y77 is crucial for ligand binding, and that the residues T132 and T134, which are highly conserved among the Lrp family of proteins, fluctuates between the active and inactive conformations, thus affecting protein oligomerization for DNA binding.