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  1. AU="Sujay Ray"
  2. AU="Raziel J Davison"
  3. AU="O'Connor, Andrew"
  4. AU="Mendoza, Luis Alfonso"
  5. AU="Shadyro, Oleg I"
  6. AU="Duce, James A"
  7. AU="Jiménez‐Yuste, Victor"
  8. AU=Jang Jinah
  9. AU="Ullman, Natalie L"
  10. AU="Ding, Xiao-Qiang"
  11. AU="Goyal, Madhav"
  12. AU="Schwarz, E Bimla"
  13. AU="Yamamoto, Naoyuki"
  14. AU="Mansi, Ruaa Abdullah"
  15. AU="Feng, Ruifang"
  16. AU="Rzaigui, Mohamed"
  17. AU="Kuznetsova, Iren"
  18. AU="Töreki, Josefin"
  19. AU="Simon Hatcher" AU="Simon Hatcher"
  20. AU="Gui, Wenwu"
  21. AU="Komdeur, Annemarijn"
  22. AU="Stange, E. F."
  23. AU="McKenzie, Jodi A"
  24. AU="Chung, Mei"
  25. AU="Cezmi A Akdis"
  26. AU="Schlechter, Chelsey R"
  27. AU=Hedayati Manouchehr Ahmadi AU=Hedayati Manouchehr Ahmadi
  28. AU="Gould, Sven B"
  29. AU="Ko, Kyung Dae"
  30. AU="Elaheh Mahmoodi-Khaledi"
  31. AU=Jenkins Kathy J
  32. AU="Joseph Burgess"
  33. AU="Barbosa da Costa, Alana Vitor"
  34. AU="François Lebargy"
  35. AU=Serag Eman AU=Serag Eman
  36. AU="Yang, Guichun"
  37. AU="Amory, Jonathan R"
  38. AU="Reformat, Marek"

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Treffer 1 - 10 von insgesamt 12

Suchoptionen

  1. Artikel ; Online: Editorial

    Seong Ho Kim / Sujay Ray / Isaac T. S. Li

    Frontiers in Molecular Biosciences, Vol

    Surveying Life One Molecule at a Time: Single Molecule Methods Dig Deeper Into Contemporary Biology

    2022  Band 9

    Schlagwörter single molecule FRET (smFRET) ; DNA nanoarchitecture ; DNA helicase ; single-molecule techniques ; molecular tension probe ; DNA secondary structures ; Biology (General) ; QH301-705.5
    Sprache Englisch
    Erscheinungsdatum 2022-07-01T00:00:00Z
    Verlag Frontiers Media S.A.
    Dokumenttyp Artikel ; Online
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  2. Artikel ; Online: Structural Stability, Transitions, and Interactions within SoxYZCD-Thiosulphate from Sulfurimonas denitrificans

    Sujay Ray / Arundhati Banerjee

    Journal of Biophysics, Vol

    An In Silico Molecular Outlook for Maintaining Environmental Sulphur Cycle

    2016  Band 2016

    Abstract: Thiosulphate oxidation (an essential mechanism) serves to maintain the global sulphur cycle. Earlier experimental and computational studies dealt with environmental thiosulphate oxidation but none dealt with thiosulphate oxidation from deep ocean belts. ... ...

    Abstract Thiosulphate oxidation (an essential mechanism) serves to maintain the global sulphur cycle. Earlier experimental and computational studies dealt with environmental thiosulphate oxidation but none dealt with thiosulphate oxidation from deep ocean belts. Wet-laboratory experimental research shows that epsilon-proteobacteria Sulfurimonas denitrificans possess sox (sulphur-oxidizing) operon and perform thiosulphate oxidation efficiently underneath the oceans. From this specific sox operon, SoxCD complex recycles the thiosulphate-bound SoxY from SoxYZ complex to balance the environmental sulphur cycle. So, four chief proteins were variedly modeled and relevant simulated interactive structures were obtained. The final simulated tetraprotein complex (SoxYZCD) from docked SoxYZ and SoxCD complexes was disclosed to be a highly interactive one with predominant ionic residues. Free energy of folding, solvent accessibility, and conformational shifts (coil-like conformation to helices and sheets) were observed in SoxYZ complex after interacting with SoxCD. The stability of the complex (SoxYZCD) after simulation was also observed through the electrostatic surface potential values. These evaluations were rationalized via biostatistics. This aids SoxCD for recycling SoxY along with thiosulphate, which remains interconnected by four H-bonds with SoxY. Therefore, this novel exploration is endowed with the detailed molecular viewpoint for maintaining the sulphur cycle (globally) including the ocean belts.
    Schlagwörter Biology (General) ; QH301-705.5
    Thema/Rubrik (Code) 500
    Sprache Englisch
    Erscheinungsdatum 2016-01-01T00:00:00Z
    Verlag Hindawi Publishing Corporation
    Dokumenttyp Artikel ; Online
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  3. Artikel ; Online: Corrigendum to “Structural Stability, Transitions, and Interactions within SoxYZCD-Thiosulphate from Sulfurimonas denitrificans

    Sujay Ray / Arundhati Banerjee

    Journal of Biophysics, Vol

    An In Silico Molecular Outlook for Maintaining Environmental Sulphur Cycle”

    2016  Band 2016

    Schlagwörter Biology (General) ; QH301-705.5
    Sprache Englisch
    Erscheinungsdatum 2016-01-01T00:00:00Z
    Verlag Hindawi Publishing Corporation
    Dokumenttyp Artikel ; Online
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  4. Artikel ; Online: Structural Exploration and Conformational Transitions in MDM2 upon DHFR Interaction from Homo sapiens

    Arundhati Banerjee / Sujay Ray

    Scientifica, Vol

    A Computational Outlook for Malignancy via Epigenetic Disruption

    2016  Band 2016

    Abstract: Structural basis for exploration into MDM2 and MDM2-DHFR interaction plays a vital role in analyzing the obstruction in folate metabolism, nonsynthesis of purines, and further epigenetic regulation in Homo sapiens. Therefore, it leads to suppression of ... ...

    Abstract Structural basis for exploration into MDM2 and MDM2-DHFR interaction plays a vital role in analyzing the obstruction in folate metabolism, nonsynthesis of purines, and further epigenetic regulation in Homo sapiens. Therefore, it leads to suppression of normal cellular behavior and malignancy. This has been earlier documented via yeast two-hybrid assays. So, with a novel outlook, this study explores the molecular level demonstration of the best satisfactory MDM2 model selection after performing manifold modeling techniques. Z-scores and other stereochemical features were estimated for comparison. Further, protein-protein docking was executed with MDM2 and the experimentally validated X-ray crystallographic DHFR. Residual disclosure from the best suited simulated protein complex disclosed 18 side chain and 3 ionic interactions to strongly accommodate MDM2 protein into the pocket-like zone in DHFR due to the positive environment by charged residues. Lysine residues from MDM2 played a predominant role. Moreover, evaluation from varied energy calculations, folding rate, and net area for solvent accessibility implied the active participation of MDM2 with DHFR. Fascinatingly, conformational transitions from coils to helices and β-sheets after interaction with DHFR affirm the conformational strength and firmer interaction of human MDM2-DHFR. Therefore, this probe instigates near-future clinical research and interactive computational investigations with mutations.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2016-01-01T00:00:00Z
    Verlag Hindawi Limited
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel: Structural insight, mutation and interactions in human Beta-catenin and SOX17 protein: A molecular-level outlook for organogenesis

    Banerjee, Arundhati / Sujay Ray

    Gene. 2017 Apr. 30, v. 610

    2017  

    Abstract: Essential human proteins; SOX17-HMG domain and beta-catenin uphold a major responsibility for vertebrate gastrulation and embryonic development. Earlier experimental assays document their interaction and states that upon M76A and G103R mutation, their ... ...

    Abstract Essential human proteins; SOX17-HMG domain and beta-catenin uphold a major responsibility for vertebrate gastrulation and embryonic development. Earlier experimental assays document their interaction and states that upon M76A and G103R mutation, their interaction varied. Till date, there was no computational analysis for either of proteins as well as their respective residues for the interaction. The present study extracted and analyzed the experimentally validated 3D models of SOX17-HMG domain and beta-catenin. After analysis of the evolutionarily conserved residues and the sequence-level alteration, the mutated SOX17-HMG protein was re-modeled, demonstrated and energy minimized. Molecular dynamics simulation was performed upon the docked complex of beta-catenin with wild-type and mutant-type protein, individually. Comparable analysis for interaction studies revealed reduction of predominant ionic interactions from 16 (wild-type) to 5 (mutant-type). Glu residues from wild-type protein played a pivotal role forming 50% of the ionic interactions alone. Fascinatingly, statistically significant deductions for several stability calculations deduced the mutant-type protein/complex to form unsteady interaction with beta-catenin. Again, helix-to-coil transition in mutant-type protein supported its weaker conformation. This probe depicts the paramount molecular-level detailed scrutiny for the essential human proteins and disclosure of the mutational analysis, which might tend to hinder the signal transduction. It instigates the future development for the pharmaceutical research.
    Schlagwörter beta catenin ; energy ; gastrulation ; humans ; models ; molecular dynamics ; mutation ; mutational analysis ; organogenesis ; signal transduction
    Sprache Englisch
    Erscheinungsverlauf 2017-0430
    Umfang p. 118-126.
    Erscheinungsort Elsevier B.V.
    Dokumenttyp Artikel
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2017.01.026
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  6. Artikel: Mutations and interactions in human ERα and bZIP proteins: An in silico approach for cell signaling in breast oncology

    Banerjee, Arundhati / Sujay Ray

    Gene. 2017 Apr. 30, v. 610

    2017  

    Abstract: Metastasis of breast cancer serves the most aggravating cause for transience in breast cancer patients. Accumulating evidences suggest that signal transduction in human breast cancers commences in estrogen-reliant pattern via signaling of the estrogen- ... ...

    Abstract Metastasis of breast cancer serves the most aggravating cause for transience in breast cancer patients. Accumulating evidences suggest that signal transduction in human breast cancers commences in estrogen-reliant pattern via signaling of the estrogen-receptor α-subunit (ERα) and XBP-1 (bZIP-domain) proteins. Furthermore, earlier investigations from SAGE and GST pull-down assay, also state that a point mutation in ERα leads to a risky factor by resulting into hyper-responsiveness towards estrogen and increased proliferation of breast cancer cells. So, a molecular-level exploration into the signaling mechanism is a prime requisite for future clinical and therapeutic progress.Present study explores primarily the residual participation of the two essential proteins from humans to boost the signaling mechanism in malignant breast tumors. So, 3D structures of the respective monomer proteins were demonstrated and mutated protein was homology modeled after the satisfaction of the stereo-chemical features. The functionality was observed to be conserved after mutation. Abrupt increment in protein-protein interactions was studied for the individual optimized and Molecular Dynamics simulated protein complexes. Revelation from supportive statistical significances for several energy calculations, solvent accessibility areas, electrostatic surface potentials and interaction studies led to confer that after mutation, the complex and the individual protein were the most stable and the best interactive one. For metastasis in breast cancer cells, polar charged residues hold a significant contribution.Therefore, this investigation provides a cogent framework for the interactive studies associated with breast cancer and an exposure towards the lethal impact on mutation.
    Schlagwörter basic-leucine zipper transcription factors ; breast neoplasms ; breasts ; energy ; humans ; metastasis ; molecular dynamics ; neoplasm cells ; patients ; point mutation ; protein-protein interactions ; signal transduction ; solvents
    Sprache Englisch
    Erscheinungsverlauf 2017-0430
    Umfang p. 90-102.
    Erscheinungsort Elsevier B.V.
    Dokumenttyp Artikel
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2017.01.012
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  7. Artikel: Structural insight with mutational impact on tyrosinase and PKC-β interaction from Homo sapiens: Molecular modeling and docking studies for melanogenesis, albinism and increased risk for melanoma

    Banerjee, Arundhati / Sujay Ray

    Gene. 2016 Oct. 30, v. 592, no. 1

    2016  

    Abstract: Human tyrosinase, is an important protein for biosynthetic pathway of melanin. It was studied to be phosphorylated and activated by protein kinase-C, β-subunit (PKC-β) through earlier experimentations with in vivo evidences. Documentation documents that ... ...

    Abstract Human tyrosinase, is an important protein for biosynthetic pathway of melanin. It was studied to be phosphorylated and activated by protein kinase-C, β-subunit (PKC-β) through earlier experimentations with in vivo evidences. Documentation documents that mutation in two essentially vital serine residues in C-terminal end of tyrosinase leads to albinism. Due to the deficiency of protective shield like enzyme; melanin, albinos are at an increased peril for melanoma and other skin cancers. So, computational and residue-level insight including a mutational exploration with evolutionary importance into this mechanism lies obligatory for future pathological and therapeutic developments. Therefore, functional tertiary models of the relevant proteins were analyzed after satisfying their stereo-chemical features. Evolutionarily paramount residues for the activation of tyrosinase were perceived via multiple sequence alignment phenomena. Mutant-type tyrosinase protein (S98A and S102A) was thereby modeled, maintaining the wild-type proteins' functionality. Furthermore, this present comparative study discloses the variation in the stable residual participation (for mutant-type and wild-type tyrosinase-PKCβ complex). Mainly, an increased number of polar negatively charged residues from the wild-type tyrosinase participated with PKC-β, predominantly. Fascinatingly supported by evaluation of statistical significances, mutation even led to a destabilizing impact in tyrosinase accompanied by conformational switches with a helix-to-coil transition in the mutated protein. Even the allosteric sites in the protein got poorly hampered upon mutation leading to weaker tendency for binding partners to interact.
    Schlagwörter albino ; biochemical pathways ; Homo sapiens ; humans ; melanin ; melanogenesis ; melanoma ; molecular models ; mutation ; protein kinase C ; proteins ; risk ; sequence alignment ; serine ; skin neoplasms
    Sprache Englisch
    Erscheinungsverlauf 2016-1030
    Umfang p. 99-109.
    Erscheinungsort Elsevier B.V.
    Dokumenttyp Artikel
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2016.07.046
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  8. Artikel: Molecular modeling, mutational analysis and conformational switching in IL27: An in silico structural insight towards AIDS research

    Banerjee, Arundhati / Sujay Ray

    Gene. 2016 Jan. 15, v. 576, no. 1

    2016  

    Abstract: The advancement in proteomics and bioinformatics provokes to discern the molecular-level probe for HIV inhibitor; human interleukin-27 (IL27). Documentation documents that tyrosine residues in IL27 play a pivotal role for interacting with HIV, causing ... ...

    Abstract The advancement in proteomics and bioinformatics provokes to discern the molecular-level probe for HIV inhibitor; human interleukin-27 (IL27). Documentation documents that tyrosine residues in IL27 play a pivotal role for interacting with HIV, causing apoptosis of the HIV+ cells. Primarily, 3D structure of human wild-type (WT) IL27 was built through manifold molecular modeling techniques after the satisfaction of stereo-chemical properties. Its essential tyrosine residues were identified. Two mutant models for IL27 were prepared following the similar protocol by first substituting the tyrosine residues with glycine (MT_G) and then with alanine (MT_A) in the WT protein. Molecular dynamics (MD) simulation was performed to obtain a stable conformation. Conformational alterations in WT, MT_G and MT_A (before and after MD simulation) disclosed that MT_A was the steadiest one with the best secondary structure conformation supported by statistical significances. Though huge RMSD variations were observed on superimposing the MT structures on WT individually, the MTs were examined to share similar SCOP/CATH fold with TM-score=0.8, indicating that they retained their functionality even after mutation. Electrostatic surface potential again unveiled MT_A to be the most stable one. MT_A was thereby revealed to be the potent peptide inhibitor for HIV. This probe presents a pathway to investigate and compare the bio-molecular interaction of WT IL27 and MT_A IL27 (strongest model) with HIV in the future. This is the first report regarding the structural biology of IL27 accompanied by alteration at its genetic level and delving into the unknown residue-level and functional biochemistry for bringing about an annihilation towards AIDS.
    Schlagwörter alanine ; apoptosis ; bioinformatics ; glycine (amino acid) ; Human immunodeficiency virus ; humans ; molecular dynamics ; molecular models ; mutants ; mutation ; proteomics ; tyrosine
    Sprache Englisch
    Erscheinungsverlauf 2016-0115
    Umfang p. 72-78.
    Erscheinungsort Elsevier B.V.
    Dokumenttyp Artikel
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2015.09.075
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  9. Artikel ; Online: Exploring the role of SoxA and SoxX in sulphur oxidation in Allochromatium vinosum through Protein - protein docking

    Sujay Ray / Angshuman Bagchi

    Pure and Applied Biology, Vol 2, Iss 2, Pp 53-

    An in silico approach

    2013  Band 56

    Abstract: Thiosulphate (S2O32-) is a stable and environmentally abundant sulphur compound of intermediate oxidation state and fulfils an important role in the natural sulphur cycle. There are main two types of thiosulfate-oxidizing Sox enzyme system type one group ...

    Abstract Thiosulphate (S2O32-) is a stable and environmentally abundant sulphur compound of intermediate oxidation state and fulfils an important role in the natural sulphur cycle. There are main two types of thiosulfate-oxidizing Sox enzyme system type one group 1 forms sulfur globules as intermediates Allochromatium vinosum (A.vino or A.vinosum)), group 2 which does not form sulphur globules as intermediate form for example Paracoccus pantotrophus . Sox genes in A. vinosum, are separated into three gene clusters. Cluster one comprises Alvin_2108 to Alvin_2112.The second gene cluster extends between Alvin_2165 and Alvin_2167 .The third gene cluster includes Alvin_2168 to Alvin_2182.Where SoxX, SoxA, are encoded by Alvin_2168 to Alvin_2169. In the present work, homology modeling has been used to build the three dimensional structures of SoxA, and SoxX. With the help of protein -protein docking and Protein Interaction Calculator (PIC) sever the amino acid residues of these proteins involved in the interactions have been identified. The interactions between the SoxA, and SoxX proteins are mediated mainly through hydrogen bonding, hydrophobic interaction, electrostatic interaction. Possible mechanisms of interaction between the SoxA, and SoxX have identified in spite the absence of SoxK.
    Schlagwörter Homology modeling ; Protein-protein interactions ; Docking simulations _ Environmental sulphur balance ; Sox operon ; Sulfur oxidation ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2013-06-01T00:00:00Z
    Verlag International Society of Pure and Applied Biology (ISPAB)
    Dokumenttyp Artikel ; Online
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  10. Artikel ; Online: A combination of circulating microRNA-375-3p and chemokines CCL11, CXCL12, and G-CSF differentiate Crohn’s disease and intestinal tuberculosis

    Susree Roy / Suchandrima Ghosh / Mallica Banerjee / Sayantan Laha / Dipanjan Bhattacharjee / Rajib Sarkar / Sujay Ray / Arko Banerjee / Ranajoy Ghosh / Aniket Halder / Alakendu Ghosh / Raghunath Chatterjee / Simanti Datta / Gopal Krishna Dhali / Soma Banerjee

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Band 10

    Abstract: Abstract Differentiation of Crohn’s disease (CD) from intestinal tuberculosis (ITB) is a big challenge to gastroenterologists because of their indistinguishable features and insensitive diagnostic tools. A non-invasive biomarker is urgently required to ... ...

    Abstract Abstract Differentiation of Crohn’s disease (CD) from intestinal tuberculosis (ITB) is a big challenge to gastroenterologists because of their indistinguishable features and insensitive diagnostic tools. A non-invasive biomarker is urgently required to distinguish ITB/CD patients particularly in India, a TB endemic region, where CD frequency is increasing rapidly due to urbanization. Among the three differentially expressed miRNAs obtained from small RNA transcriptomic profiling of ileocaecal/terminal ileal tissue of ITB/CD patients (n = 3), only two down-regulated miRNAs, miR-31-5p, and miR-215-5p showed comparable data in qRT-PCR. Out of which, only miR-215-5p was detectable in the patient’s plasma, but there was no significant difference in expression between ITB/CD. On the other hand, miR-375-3p, the pulmonary TB specific marker was found in higher amount in the plasma of ITB patients than CD while reverse expression was observed in the ileocaecal/terminal ileal tissues of the same patients. Next, using Bioplex pro-human cytokine 48-plex screening panel, only three chemokines, Eotaxin-1/CCL11, SDF-1α/CXCL12, and G-CSF have noted significantly different levels in the serum of ITB/CD patients. ROC analysis has revealed that compared to a single molecule, a combination of miR-375-3p + Eotaxin-1/CCL11 + SDF-1α /CXCL12 + G-CSF showed a better AUC of 0.83, 95% CI (0.69–0.96) with 100% specificity and positive predictive value while sensitivity, negative predictive value, and accuracy were 56%, 69%, and 78% respectively in distinguishing ITB from CD. This study suggests that a combination of plasma markers shows better potential in differentiating ITB from CD than a single marker and this panel of markers may be used for clinical management of ITB/CD patients.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 610
    Sprache Englisch
    Erscheinungsdatum 2021-12-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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