RESEARCH ARTICLES
RESEARCH ARTICLES
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2025
2025
63. Sahoo BR, Deng X, Wong E.....Bardwell JCA.
Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein.
Nature Communications, 2025
In Press
Link
62. Sahoo BR, Bardwell JCA.
Protein and RNA chaperones.
Molecular Aspects of Medicine, 2025
https://doi.org/10.1016/j.mam.2025.101384
61. Sahoo BR, Watanabe-Nakayama T, Suladze S, Anantharamaiah GM, Reif B, Ramamoorthy A.
Bifunctional nanodisc platforms for studies on self-assembly and amyloid fibrillation.
Chemical Communications, 2025
https://doi.org/10.1039/D5CC00972C
2024
2024
60. Huettemann P, Mahadevan P, Lempart J, Tse E, Dehury B, Edwards BFP., Southworth DR, Sahoo BR , Jakob U.
Amyloid accelerator polyphosphate fits as the mystery density in α-synuclein fibrils.
PLOS Biology, 2024
https://doi.org/10.1371/journal.pbio.3002650
59. Sahoo BR, Kocman V, Clark N, et al. Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation.
Nucleic Acids Research, 2024
https://doi.org/10.1093/nar/gkae229
58. Sahoo BR, Subramanian V, Bardwell JCA. Backbone 1H, 13C, and 15N chemical shift assignments for human SERF2.
Biomolecular NMR Assignments (2024) 18:51–57
https://doi.org/10.1007/s12104-024-10167-5
57. Arenas JL, Lesma J, Ha-Duong T, et al. Composition and Conformation of Hetero- versus Homo-Fluorinated Triazolamers Influence their Activity on Islet Amyloid Polypeptide Aggregation.
Chem.Eur.J.2024,30,e202303887
https://doi.org/10.1002/chem.202303887
2023
2023
56. Sahoo BR and Ramamoorthy A. Direct interaction between the transmembrane helices stabilize cytochrome P450 2B4 and cytochrome b5 redox complex.
Biophysical Chemistry, 2023
doi: 10.1016/j.bpc.2023.107092
55. Sahoo BR and Bardwell JCA. SERF, a family of tiny highly conserved, highly charged proteins with enigmatic functions.
The FEBS Journal, 2023
doi: 10.1016/j.jmb.2021.166993
54. Vajhadin F, Mazloum-Ardakani, Sahoo BR, et al. Hierarchal polyaniline-folic acid nanostructures act as a platform for electrochemical detection of tumor cells.
Analytical Biochemistry, 2023
https://doi.org/10.1016/j.ab.2022.11491
2022
2022
53. Sahoo BR, Souders II CL, Nakayama WT, et al. Conformational Tuning of Amylin by Charged Styrene-maleic-acid Copolymers.
J Mol Biol 434 (2), 2022, 167385
doi: 10.1016/j.jmb.2021.166993
52. Chakravorty A, McCalpin SD, Sahoo BR, et al. Free Gangliosides Can Alter Amyloid-β Aggregation.
J. Phys. Chem. Lett. 2022, 13, 40, 9303-9308
https://doi.org/10.1021/acs.jpclett.2c02362
2021
2021
51. Maharana J, Maharana D, Bej A, et al. Structural Elucidation of Inter-CARD Interfaces involved in NOD2 Tandem CARD Association and RIP2 Recognition.
J Phys. Chem. B 2021, doi: https://doi.org/10.1021/acs.jpcb.1c06176
50. Sahoo BR, Panda P, Liang W, et al. Degradation of Alzheimer's amyloid-β by a catalytically inactive insulin-degrading enzyme.
J Mol Biol 2021, doi: 10.1016/j.jmb.2021.166993
49. Khemtemourian L, Antoniciello F, Sahoo BR, et al. Investigation of the effects of two major secretory granules components, insulin and zinc, on human-IAPP amyloid aggregation and membrane damage.
Chemistry and Physics of Lipids 2021, 237, 105083
48. Nguyen PH, Ramamoorthy A, Sahoo BR, et al. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.
Chem. Rev. 2021, 121, 4, 2545–2647
2020
2020
48. Sciacca MF, Lolicato F, Tempra C, et al., Lipid-Chaperone Hypothesis: A Common Molecular Mechanism of Membrane Disruption by Intrinsically Disordered Proteins.
ACS Chem. Neurosci. 2020, 11, 24, 4336–4350
47. Sahoo BR. Structure of fish Toll-like receptors (TLR) and NOD-like receptors (NLR).
Int. J. Biol. Macromol. 2020
46. Ravula T, Sahoo BR, Dai X, Ramamoorthy A. Natural-abundance 17O NMR spectroscopy of magnetically aligned lipid nanodiscs.
Chem Comm 2020
45. Watanabe-Nakayama T, Sahoo BR, Ramamoorthy A, Ono K. High-Speed Atomic Force Microscopy Reveals the Structural Dynamics of the Amyloid-β and Amylin Aggregation Pathways.
Int. J. Mol. Sci. 2020, 21, 12, 4287
44. Cox SJ, Lam B, Prasad A, Marietta HA, Stander NV, Joel JG Sahoo BR, et al. High-Throughput Screening at the Membrane Interface Reveals Inhibitors of Amyloid-β.
Biochemistry 2020, 59, 24, 2249–2258
43. Sahoo BR, Cox SJ, Ramamoorthy A. High-resolution probing of early events in amyloid-β aggregation related to Alzheimer's disease.
Chem Comm 2020, 56: 4627-4639.
42. Bharadwaj P, Solomon T, Sahoo BR, Ignasiak K, et al. Amylin and beta-amyloid proteins interact to form amorphous heterocomplexes with enhanced toxicity in neuronal cells.
Sci Rep 2020, 10(1):10356
41. Sahoo BR, Bekier II ME, Liu Z, et al. Structural interaction of apolipoprotein A-I mimetic peptide with amyloid-β generates toxic hetero-oligomers.
J Mol Biol 2020, 432: 1020-1034.
2019
2019
40. Lin Y, Sahoo BR, Ozawa D, Kinoshita M, et al. Diverse structural conversion and aggregation pathways of Alzheimerʼs amyloid-β (1–40).
ACS Nano 2019, 13: 8766-8783.
39. Sahoo BR, Genjo T, Moharana KC, Ramamoorthy A: Self-assembly of polymer-encased lipid nanodiscs and membrane protein reconstitution.
J Phys Chem B 2019, 123: 4562-4570.
38. Sahoo BR, Genjo T, Nakayama-Watanabe T, Stoddard AK, Ando T, Yasuhara K, Fierke CA, Ramamoorthy A:
A cationic polymethacrylate-copolymer acts as an agonist for beta-amyloid and antagonist for amylin fibrillation.
Chem Science 2019, 10:3976-3986.
37. Sahoo BR, Genjo T, Bekier M, Cox SJ, Stoddard AK, Ivanova M, Yasuhara K, Fierke CA, Wang Y, Ramamoorthy A: Alzheimer's amyloid-beta intermediates generated using polymer-nanodiscs.
Chem Commun (Camb) 2018, 54:12883-12886.
2018
2018
36. Sahoo BR, Genjo T, Cox SJ, Stoddard AK, Anantharamaiah GM, Fierke C, Ramamoorthy A: Nanodisc-Forming Scaffold Protein Promoted Retardation of Amyloid-Beta Aggregation.
J Mol Biol 2018, 430:4230-4244.
35. Barnaba C, Sahoo BR, Ravula T, Medina-Meza IG, Im SC, Anantharamaiah GM, Waskell L, Ramamoorthy A: Cytochrome-P450-Induced Ordering of Microsomal Membranes Modulates Affinity for Drugs.
Angew Chem Int Ed Engl 2018, 57:3391-3395.
34. Maruyama K, Takayama Y, Sugisawa E, Yamanoi Y, Yokawa T, Kondo T, Ishibashi KI, Sahoo BR, Takemura N, Mori Y, et al.: The ATP Transporter VNUT Mediates Induction of Dectin-1-Triggered Candida Nociception.
iScience 2018, 6:306-318.
33. Lee YH, Lin Y, Cox SJ, Kinoshita M, Sahoo BR, Ivanova M, Ramamoorthy A: Zinc boosts EGCG's hIAPP amyloid Inhibition both in solution and membrane.
Biochim Biophys Acta Proteins Proteom 2018.
32. Yasuhara K, Arakida J, Ravula T, Ramadugu SK, Sahoo BR, Kikuchi J, Ramamoorthy A: Spontaneous Lipid Nanodisc Formation by Amphiphilic Polymethacrylate Copolymers.
J. Am. Chem. Soc. 2017, 139: 18657-18663.
2017
2017
31. Maruyama K, Takayama Y, Kondo T, Ishibashi KI, Sahoo BR, Kanemaru H, Kumagai Y, Martino MM, Tanaka H, Ohno N, et al.: Nociceptors Boost the Resolution of Fungal Osteoinflammation via the TRP Channel-CGRP-Jdp2 Axis.
Cell Rep 2017, 19:2730-2742.
30. Sahoo BR, Maruyama K, Edula JR, Tougan T, Lin Y, Lee YH, Horii T, Fujiwara T: Mechanistic and structural basis of bioengineered bovine Cathelicidin-5 with optimized therapeutic activity.
Sci Rep 2017, 7:44781.
29. Sahoo BR, Fujiwara T: Conformational states of HAMP domains interacting with sensory rhodopsin membrane systems: an integrated all-atom and coarse-grained molecular dynamics simulation approach.
Mol Biosyst 2016, 13:193-207.
2016
2016
28. Sahoo BR, Fujiwara T: Membrane Mediated Antimicrobial and Antitumor Activity of Cathelicidin 6: Structural Insights from Molecular Dynamics Simulation on Multi-Microsecond Scale.
PLoS One 2016, 11:e0158702.
27. Dikhit MR, Purkait B, Singh R, Sahoo BR, Kumar A, Kar RK, Ansari MY, Saini S, Abhishek K, Sahoo GC, et al.: Activity of a novel sulfonamide compound 2-nitro-N-(pyridin-2-ylmethyl)benzenesulfonamide against Leishmania donovani.
Drug Des Devel Ther 2016, 10:1753-1761.
26. Dikhit MR, Ansari MY, Vijaymahantesh, Kalyani, Mansuri R, Sahoo BR, Dehury B, Amit A, Topno RK, Sahoo GC, et al.: Computational prediction and analysis of potential antigenic CTL epitopes in Zika virus: A first step towards vaccine development.
Infect Genet Evol 2016, 45:187-197.
2015
2015
25. Sahoo BR, Dikhit MR, Bhoi GK, Maharana J, Lenka SK, Dubey PK, Tiwari DK: Understanding the distinguishable structural and functional features in zebrafish TLR3 and TLR22, and their binding modes with fish dsRNA viruses: an exploratory structural model analysis.
Amino Acids 2015, 47:381-400.
24. Dehury B, Maharana J, Sahoo BR, Sahu J, Sen P, Modi MK, Barooah M: Molecular recognition of avirulence protein (avrxa5) by eukaryotic transcription factor xa5 of rice (Oryza sativa L.): insights from molecular dynamics simulations.
J Mol Graph Model 2015, 57:49-61.
23. Dikhit MR, Kumar S, Vijaymahantesh, Sahoo BR, Mansuri R, Amit A, Yousuf Ansari M, Sahoo GC, Bimal S, Das P: Computational elucidation of potential antigenic CTL epitopes in Ebola virus.
Infect Genet Evol 2015, 36:369-375.
22. Maharana J, Dehury B, Sahoo JR, Jena I, Bej A, Panda D, Sahoo BR, Patra MC, Pradhan SK: Structural and functional insights into CARDs of zebrafish (Danio rerio) NOD1 and NOD2, and their interaction with adaptor protein RIP2.
Mol Biosyst 2015, 11:2324-2336
21. Maharana J, Sahoo BR, Bej A, Jena I, Parida A, Sahoo JR, Dehury B, Patra MC, Martha SR, Balabantray S, et al.: Structural models of zebrafish (Danio rerio) NOD1 and NOD2 NACHT domains suggest differential ATP binding orientations: insights from computational modeling, docking and molecular dynamics simulations.
PLoS One 2015, 10:e0121415.
20. Moharana KC, Dikhit MR, Sahoo BR, Sahoo GC, Das P: GAOPP: Operon prediction in prokaryotes using genetic algorithm.
Curr Bioinform 2015, 10: 299-305.
2014
2014
19. Sahoo BR, Maharana J, Bhoi GK, Lenka SK, Patra MC, Dikhit MR, Dubey PK, Pradhan SK, Behera BK: A conformational analysis of mouse Nalp3 domain structures by molecular dynamics simulations, and binding site analysis.
Mol Biosyst 2014, 10:1104-1116
18. Sahoo BR, Maharana J, Patra MC, Bhoi GK, Lenka SK, Dubey PK, Goyal S, Dehury B, Pradhan SK: Structural and dynamic investigation of bovine folate receptor alpha (FOLR1), and role of ultra-high temperature processing on conformational and thermodynamic characteristics of FOLR1-folate complex.
Colloids Surf B Biointerfaces 2014, 121:307-318.
17. Sahoo BR, Dubey PK, Goyal S, Bhoi GK, Lenka SK, Maharana J, Pradhan SK, Kataria RS: Exploration of the binding modes of buffalo PGRP1 receptor complexed with meso-diaminopimelic acid and lysine-type peptidoglycans by molecular dynamics simulation and free energy calculation.
Chem Biol Interact 2014, 220:255-268.
16. Bej A, Sahoo BR, Swain B, Basu M, Jayasankar P, Samanta M: LRRsearch: An asynchronous server-based application for the prediction of leucine-rich repeat motifs and an integrative database of NOD-like receptors.
Comput Biol Med 2014, 53:164-170.
15. Maharana J, Sahoo BR, Bej A, Patra MC, Dehury B, Bhoi GK, Lenka SK, Sahoo JR, Rout AK, Behera BK: Structural and functional investigation of zebrafish (Danio rerio) NOD1 leucine rich repeat domain and its interaction with iE-DAP.
Mol Biosyst 2014, 10:2942-2953.
14. Dikhit MR, Moharana KC, Sahoo BR, Sahoo GC, Das P: LeishMicrosatDB: open source database of repeat sequences detected in six fully sequenced Leishmania genomes.
Database (Oxford) 2014, 2014.
13. Maharana J, Patra MC, De BC, Sahoo BR, Behera BK, De S, Pradhan SK: Structural insights into the MDP binding and CARD-CARD interaction in zebrafish (Danio rerio) NOD2: a molecular dynamics approach.
J Mol Recognit 2014, 27:260-275.
12. Goyal S, Dubey PK, Sahoo BR, Mishra SK, Niranjan SK, Singh S, Mahajan R, Kataria RS: Sequence based structural characterization and genetic diversity analysis across coding and promoter regions of goat Toll-like receptor 5 gene.
Gene 2014, 540:238-245.
11. Samanta M, Swain B, Basu M, Mahapatra G, Sahoo BR, Paichha M, Lenka SS, Jayasankar P: Toll-like receptor 22 in Labeo rohita: molecular cloning, characterization, 3D modeling, and expression analysis following ligands stimulation and bacterial infection.
Appl Biochem Biotechnol 2014, 174:309-327.
2013
2013
10. Sahoo BR, Swain B, Dikhit MR, Basu M, Bej A, Jayasankar P, Samanta M: Activation of nucleotide-binding oligomerization domain 1 (NOD1) receptor signaling in Labeo rohita by iE-DAP and identification of ligand-binding key motifs in NOD1 by molecular modeling and docking.
Appl Biochem Biotechnol 2013, 170:1282-1309.
9. Kar RK, Ansari MY, Suryadevara P, Sahoo BR, Sahoo GC, Dikhit MR, Das P: Computational elucidation of structural basis for ligand binding with Leishmania donovani adenosine kinase.
Biomed Res Int 2013, 2013:609289
8. Sahoo BR, Basu M, Swain B, Dikhit MR, Jayasankar P, Samanta M: Elucidation of novel structural scaffold in rohu TLR2 and its binding site analysis with peptidoglycan, lipoteichoic acid and zymosan ligands, and downstream MyD88 adaptor protein.
Biomed Res Int 2013, 2013:185282.
7. Kar RK, Suryadevara P, Sahoo BR, Sahoo GC, Dikhit MR, Das P: Exploring novel KDR inhibitors based on pharmaco-informatics methodology.
SAR QSAR Environ Res 2013, 24:215-234.
6. Maharana J, Swain B, Sahoo BR, Dikhit MR, Basu M, Mahapatra AS, Jayasankar P, Samanta M: Identification of MDP (muramyl dipeptide)-binding key domains in NOD2 (nucleotide-binding and oligomerization domain-2) receptor of Labeo rohita.
Fish Physiol Biochem 2013, 39:1007-1023.
2012
2012
5. Sahoo BR, Swain B, Basu M, Panda P, Maiti NK, Samanta M: 3D modeling and molecular dynamics simulation of an immune-regulatory cytokine, interleukin-10, from the Indian major carp, Catla catla.
J Mol Model 2012, 18:1713-1722.
4. Sahoo BR, Basu M, Swain B, Maharana J, Dikhit MR, Jayasankar P, Samanta M: Structural insights of rohu TLR3, its binding site analysis with fish reovirus dsRNA, poly I:C and zebrafish TRIF.
Int J Biol Macromol 2012, 51:531-543.
3. Basu M, Swain B, Sahoo BR, Maiti NK, Samanta M: Induction of toll-like receptor (TLR) 2, and MyD88-dependent TLR- signaling in response to ligand stimulation and bacterial infections in the Indian major carp, mrigal (Cirrhinus mrigala).
Mol Biol Rep 2012, 39:6015-6028.
2. Samanta M, Swain B, Basu M, Panda P, Mohapatra GB, Sahoo BR, Maiti NK: Molecular characterization of toll-like receptor 2 (TLR2), analysis of its inductive expression and associated down-stream signaling molecules following ligands exposure and bacterial infection in the Indian major carp, rohu (Labeo rohita).
Fish Shellfish Immunol 2012, 32:411-425.
1. Swain B, Basu M, Sahoo BR, Maiti NK, Routray P, Eknath AE, Samanta M: Molecular characterization of nucleotide binding and oligomerization domain (NOD)-2, analysis of its inductive expression and down-stream signaling following ligands exposure and bacterial infection in rohu (Labeo rohita).
Dev Comp Immunol 2012, 36:93-103.
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