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Papers by Shankar Raj Devkota

Chemokines, the key regulators of leukocyte trafficking, are attractive targets for anti-inflamma... more Chemokines, the key regulators of leukocyte trafficking, are attractive targets for anti-inflammatory therapy. Evasins are anti-inflammatory, chemokine-binding proteins found in tick saliva, with important therapeutic potential. However, therapeutic application of evasins will require manipulation of their chemokine target selectivity. Here we describe a new family of evasins, class A3 evasins, that is unique to the tick genus Amblyomma and distinguished from “classical” class A1 evasins by an additional disulfide-bonded pair of cysteine residues near the chemokine recognition interface. The class A3 evasin EVA-AAM1001 (EVA-A) bound to CC chemokines and inhibited their receptor activation. However, unlike class A1 evasins, EVA-A did not utilise N- and C-terminal regions to differentiate chemokine targets. Instead, structures of EVA-A bound to four chemokines revealed a deep hydrophobic pocket, unique to class A3 evasins, that interacts with the residue immediately following the CC m...

<p>(a) The ribbon model showing the interaction between σ^W<sub&gt... more <p>(a) The ribbon model showing the interaction between σ^W₄ and RsiW. (b) The model of -35 element recognition by σ^W₄, generated by the superimposition with the structure of <i>E</i>.<i>coli</i> σ^E₄/-35 element (PDB ID: <b>2H27</b>). (a, b) σ^W₄ ribbon models are drawn in the same orientation. α1’ in RsiW interacts directly with the recognition helix for the -35 element binding. The N-terminal helical bundle (α1’-α3’) of RsiW sterically restricts the DNA recognition of SigW. (c) The ribbon model showing the interaction between σ^W₂ and RsiW. (d) The model of the -10 element recognition by σ^W₂, generated by the superimposition with the structure of <i>T</i>. <i>acuaticus</i> σ2/single strand -10 element (PDB ID: <b>3UGO</b>). (c, d) The σ^W₂ surface for the recognition of the -10 element is blocked by σ^W₄ binding in the SigW/RsiW complex, rather than being blocked directly by RsiW.</p

The Scientific World Journal, 2021

Spondias pinnata (L.f.) Kurz. (family: Anacardiaceae) is a wild deciduous tree indigenous to sout... more Spondias pinnata (L.f.) Kurz. (family: Anacardiaceae) is a wild deciduous tree indigenous to southeast Asian countries. Different parts of this plant are used traditionally for the treatment and cure of various disorders and illnesses. S. pinnata leaves are used to prevent and treat diabetes in traditional Balinese medicine. However, scientific study on the antihyperglycemic effect of its leaves has not been reported yet. Therefore, this study aims to perform phytochemical screening and investigate the hypoglycemic potential of S. pinnata leaves extract. Preliminary phytochemical screening of the hydroethanolic extract was performed following the standard tests. In vivo hypoglycemic activity of the leaves extract was evaluated using normal and glucose-loaded rats. The results displayed the presence of phytochemical constituents such as saponins, phenolic compounds, flavonoids, and terpenoids. S. pinnata (500 mg/kg) and metformin (100 mg/kg) exhibited a significant (p < 0.05) decr...

Proceedings of the National Academy of Sciences

As natural chemokine inhibitors, evasin proteins produced in tick saliva are potential therapeuti... more As natural chemokine inhibitors, evasin proteins produced in tick saliva are potential therapeutic agents for numerous inflammatory diseases. Engineering evasins to block the desired chemokines and avoid off-target side effects requires structural understanding of their target selectivity. Structures of the class A evasin EVA-P974 bound to human CC chemokine ligands 7 and 17 (CCL7 and CCL17) and to a CCL8-CCL7 chimera reveal that the specificity of class A evasins for chemokines of the CC subfamily is defined by conserved, rigid backbone–backbone interactions, whereas the preference for a subset of CC chemokines is controlled by side-chain interactions at four hotspots in flexible structural elements. Hotspot mutations alter target preference, enabling inhibition of selected chemokines. The structure of an engineered EVA-P974 bound to CCL2 reveals an underlying molecular mechanism of EVA-P974 target preference. These results provide a structure-based framework for engineering evasin...

Kathmandu Univ Med J (KUMJ), 2003

Introduction: Noise pollution in urban cities is a serious problem and steadily increasing over t... more Introduction: Noise pollution in urban cities is a serious problem and steadily increasing over the years. This has direct and indirect affect to the people that can lead to the health hazard. Objectives: To find out environmental noise induced health effect on people residing in an urban community and to predict the risk of the environmental noise induced hearing loss Material and methods: One hundred fifty questionnaires were filled up for the environmental noise pollution survey. For the case control study, 36 exposed and 25 non-exposed residents of Kupondole were included. Based on the place of residence (main road and 20 min. walking distance from the main road), subjects were divided into exposed and non-exposed group concerning environmental noise. Demographic data and information about health problems was obtained by a structured interview. Audiometric test was performed using manual audiometer. Odds ratios (OR) and their 95% confidence intervals (95% CI) for noise induced hearing loss were estimated using logistic regression. Adjustment for occupational noise was done Results: The major health effect induced by the environmental noise was observed as lack of concentration followed by irritation, fatigue and headache. The crude OR and 95% CI for the exposed subjects was 4.2 (1.4, 12). After adjustment for occupational noise, the OR (95% CI) was 4.0 (1.2, 13). Conclusion: This study shows that exposure to noise causes wide range of health effects. For the exposed subjects there was an increased risk of noise induced hearing loss. The risk was significantly increased also after adjusting for occupational noise.

PLOS ONE

Sigma factors are key proteins that mediate the recruitment of RNA polymerase to the promoter reg... more Sigma factors are key proteins that mediate the recruitment of RNA polymerase to the promoter regions of genes, for the initiation of bacterial transcription. Multiple sigma factors in a bacterium selectively recognize their cognate promoter sequences, thereby inducing the expression of their own regulons. In this paper, we report the crystal structure of the σ4 domain of Bacillus subtilis SigW bound to the-35 promoter element. Purine-specific hydrogen bonds of the-35 promoter element with the recognition helix α9 of the σ4 domain occurs at three nucleotides of the consensus sequence (G-35 , A-34 , and G'-31 in G-35 A-34 A-33 A-32 C-31 C-30 T-29). The hydrogen bonds of the backbone with the α7 and α8 of the σ4 domain occurs at G'-30. These results elucidate the structural basis of the selective recognition of the promoter by SigW. In addition, comparison of SigW structures complexed with the-35 promoter element or with anti-sigma RsiW reveals that DNA recognition and anti-sigma factor binding of SigW are mutually exclusive.

PloS one, 2017

Bacillus subtilis SigW is localized to the cell membrane and is inactivated by the tight interact... more Bacillus subtilis SigW is localized to the cell membrane and is inactivated by the tight interaction with anti-sigma RsiW under normal growth conditions. Whereas SigW is discharged from RsiW binding and thus initiates the transcription of its regulon under diverse stress conditions such as antibiotics and alkaline shock. The release and activation of SigW in response to extracytoplasmic signals is induced by the regulated intramembrane proteolysis of RsiW. As a ZAS (Zinc-containing anti-sigma) family protein, RsiW has a CHCC zinc binding motif, which implies that its anti-sigma activity may be regulated by the state of zinc coordination in addition to the proteolytic cleavage of RsiW. To understand the regulation mode of SigW activity by RsiW, we determined the crystal structures of SigW in complex with the cytoplasmic domain of RsiW, and compared the conformation of the CHCC motif in the reduced/zinc binding and the oxidized states. The structures revealed that RsiW inhibits the pr...

Changes in the U.S. peanut program have resulted in drastically decreased planted acres and force... more Changes in the U.S. peanut program have resulted in drastically decreased planted acres and forced many peanut producers in the Southwest to consider alternative crops. This study examined the economic risk associated with producing peanuts and common alternatives to peanuts. Seedless watermelon is an alternative for risk preferring farmers whereas, irrigated peanut is the best choice for risk averse farmers.

Chemokines, the key regulators of leukocyte trafficking, are attractive targets for anti-inflamma... more Chemokines, the key regulators of leukocyte trafficking, are attractive targets for anti-inflammatory therapy. Evasins are anti-inflammatory, chemokine-binding proteins found in tick saliva, with important therapeutic potential. However, therapeutic application of evasins will require manipulation of their chemokine target selectivity. Here we describe a new family of evasins, class A3 evasins, that is unique to the tick genus Amblyomma and distinguished from “classical” class A1 evasins by an additional disulfide-bonded pair of cysteine residues near the chemokine recognition interface. The class A3 evasin EVA-AAM1001 (EVA-A) bound to CC chemokines and inhibited their receptor activation. However, unlike class A1 evasins, EVA-A did not utilise N- and C-terminal regions to differentiate chemokine targets. Instead, structures of EVA-A bound to four chemokines revealed a deep hydrophobic pocket, unique to class A3 evasins, that interacts with the residue immediately following the CC m...

<p>(a) The ribbon model showing the interaction between σ^W<sub&gt... more <p>(a) The ribbon model showing the interaction between σ^W₄ and RsiW. (b) The model of -35 element recognition by σ^W₄, generated by the superimposition with the structure of <i>E</i>.<i>coli</i> σ^E₄/-35 element (PDB ID: <b>2H27</b>). (a, b) σ^W₄ ribbon models are drawn in the same orientation. α1’ in RsiW interacts directly with the recognition helix for the -35 element binding. The N-terminal helical bundle (α1’-α3’) of RsiW sterically restricts the DNA recognition of SigW. (c) The ribbon model showing the interaction between σ^W₂ and RsiW. (d) The model of the -10 element recognition by σ^W₂, generated by the superimposition with the structure of <i>T</i>. <i>acuaticus</i> σ2/single strand -10 element (PDB ID: <b>3UGO</b>). (c, d) The σ^W₂ surface for the recognition of the -10 element is blocked by σ^W₄ binding in the SigW/RsiW complex, rather than being blocked directly by RsiW.</p

The Scientific World Journal, 2021

Spondias pinnata (L.f.) Kurz. (family: Anacardiaceae) is a wild deciduous tree indigenous to sout... more Spondias pinnata (L.f.) Kurz. (family: Anacardiaceae) is a wild deciduous tree indigenous to southeast Asian countries. Different parts of this plant are used traditionally for the treatment and cure of various disorders and illnesses. S. pinnata leaves are used to prevent and treat diabetes in traditional Balinese medicine. However, scientific study on the antihyperglycemic effect of its leaves has not been reported yet. Therefore, this study aims to perform phytochemical screening and investigate the hypoglycemic potential of S. pinnata leaves extract. Preliminary phytochemical screening of the hydroethanolic extract was performed following the standard tests. In vivo hypoglycemic activity of the leaves extract was evaluated using normal and glucose-loaded rats. The results displayed the presence of phytochemical constituents such as saponins, phenolic compounds, flavonoids, and terpenoids. S. pinnata (500 mg/kg) and metformin (100 mg/kg) exhibited a significant (p < 0.05) decr...

Proceedings of the National Academy of Sciences

As natural chemokine inhibitors, evasin proteins produced in tick saliva are potential therapeuti... more As natural chemokine inhibitors, evasin proteins produced in tick saliva are potential therapeutic agents for numerous inflammatory diseases. Engineering evasins to block the desired chemokines and avoid off-target side effects requires structural understanding of their target selectivity. Structures of the class A evasin EVA-P974 bound to human CC chemokine ligands 7 and 17 (CCL7 and CCL17) and to a CCL8-CCL7 chimera reveal that the specificity of class A evasins for chemokines of the CC subfamily is defined by conserved, rigid backbone–backbone interactions, whereas the preference for a subset of CC chemokines is controlled by side-chain interactions at four hotspots in flexible structural elements. Hotspot mutations alter target preference, enabling inhibition of selected chemokines. The structure of an engineered EVA-P974 bound to CCL2 reveals an underlying molecular mechanism of EVA-P974 target preference. These results provide a structure-based framework for engineering evasin...

Kathmandu Univ Med J (KUMJ), 2003

Introduction: Noise pollution in urban cities is a serious problem and steadily increasing over t... more Introduction: Noise pollution in urban cities is a serious problem and steadily increasing over the years. This has direct and indirect affect to the people that can lead to the health hazard. Objectives: To find out environmental noise induced health effect on people residing in an urban community and to predict the risk of the environmental noise induced hearing loss Material and methods: One hundred fifty questionnaires were filled up for the environmental noise pollution survey. For the case control study, 36 exposed and 25 non-exposed residents of Kupondole were included. Based on the place of residence (main road and 20 min. walking distance from the main road), subjects were divided into exposed and non-exposed group concerning environmental noise. Demographic data and information about health problems was obtained by a structured interview. Audiometric test was performed using manual audiometer. Odds ratios (OR) and their 95% confidence intervals (95% CI) for noise induced hearing loss were estimated using logistic regression. Adjustment for occupational noise was done Results: The major health effect induced by the environmental noise was observed as lack of concentration followed by irritation, fatigue and headache. The crude OR and 95% CI for the exposed subjects was 4.2 (1.4, 12). After adjustment for occupational noise, the OR (95% CI) was 4.0 (1.2, 13). Conclusion: This study shows that exposure to noise causes wide range of health effects. For the exposed subjects there was an increased risk of noise induced hearing loss. The risk was significantly increased also after adjusting for occupational noise.

PLOS ONE

Sigma factors are key proteins that mediate the recruitment of RNA polymerase to the promoter reg... more Sigma factors are key proteins that mediate the recruitment of RNA polymerase to the promoter regions of genes, for the initiation of bacterial transcription. Multiple sigma factors in a bacterium selectively recognize their cognate promoter sequences, thereby inducing the expression of their own regulons. In this paper, we report the crystal structure of the σ4 domain of Bacillus subtilis SigW bound to the-35 promoter element. Purine-specific hydrogen bonds of the-35 promoter element with the recognition helix α9 of the σ4 domain occurs at three nucleotides of the consensus sequence (G-35 , A-34 , and G'-31 in G-35 A-34 A-33 A-32 C-31 C-30 T-29). The hydrogen bonds of the backbone with the α7 and α8 of the σ4 domain occurs at G'-30. These results elucidate the structural basis of the selective recognition of the promoter by SigW. In addition, comparison of SigW structures complexed with the-35 promoter element or with anti-sigma RsiW reveals that DNA recognition and anti-sigma factor binding of SigW are mutually exclusive.

PloS one, 2017

Bacillus subtilis SigW is localized to the cell membrane and is inactivated by the tight interact... more Bacillus subtilis SigW is localized to the cell membrane and is inactivated by the tight interaction with anti-sigma RsiW under normal growth conditions. Whereas SigW is discharged from RsiW binding and thus initiates the transcription of its regulon under diverse stress conditions such as antibiotics and alkaline shock. The release and activation of SigW in response to extracytoplasmic signals is induced by the regulated intramembrane proteolysis of RsiW. As a ZAS (Zinc-containing anti-sigma) family protein, RsiW has a CHCC zinc binding motif, which implies that its anti-sigma activity may be regulated by the state of zinc coordination in addition to the proteolytic cleavage of RsiW. To understand the regulation mode of SigW activity by RsiW, we determined the crystal structures of SigW in complex with the cytoplasmic domain of RsiW, and compared the conformation of the CHCC motif in the reduced/zinc binding and the oxidized states. The structures revealed that RsiW inhibits the pr...

Changes in the U.S. peanut program have resulted in drastically decreased planted acres and force... more Changes in the U.S. peanut program have resulted in drastically decreased planted acres and forced many peanut producers in the Southwest to consider alternative crops. This study examined the economic risk associated with producing peanuts and common alternatives to peanuts. Seedless watermelon is an alternative for risk preferring farmers whereas, irrigated peanut is the best choice for risk averse farmers.