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Journal of Biomolecular Structure and Dynamics Volume 36, 2018 - Issue 10
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Research Article

Solvent sensitivity of protein aggregation in Cu, Zn superoxide dismutase: a molecular dynamics simulation study

Amresh PrakashSchool of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, IndiaORCID Iconhttp://orcid.org/0000-0002-4821-1654
ORCID Icon,
Vijay KumarCentre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, IndiaCorrespondence[email protected]
ORCID Iconhttp://orcid.org/0000-0002-3621-5025
ORCID Icon,
Preeti PandeySchool of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
,
Deepak R. BhartiSchool of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
,
Poonam VishwakarmaSchool of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
,
Ruhar SinghSchool of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Md. Imtaiyaz HassanCentre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, IndiaORCID Iconhttp://orcid.org/0000-0002-3663-4940
ORCID Icon &
Andrew M. LynnSchool of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, IndiaCorrespondence[email protected]
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Pages 2605-2617 | Received 12 Jun 2017, Accepted 01 Aug 2017, Published online: 20 Aug 2017

Citations (18)

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Shafiul Haque, Pawan Kumar, Darin Mansor Mathkor, Farkad Bantun, Naif A. Jalal, Ahmad Hasan Mufti, Amresh Prakash & Vijay Kumar. (2023) In silico evaluation of the inhibitory potential of nucleocapsid inhibitors of SARS-CoV-2: a binding and energetic perspective. Journal of Biomolecular Structure and Dynamics 41:19, pages 9797-9807.
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Satabdi Saha, Rakesh Srivastava, Parishmita Sarma, Tarun Kumar Bhatt, Amresh Prakash & Diwakar Kumar. (2023) Identification of potential inhibitors of Leishmania donovani Sterol 24-C- methyltransferase: in silico and in vitro studies. Molecular Simulation 49:13-14, pages 1311-1323.
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Ivan Yu. Torshin, Vladimir A. Namiot, Natalia G. Esipova & Vladimir G. Tumanyan. (2021) Numeric analysis of reversibility of classic movement equations and constructive criteria of estimating quality of molecular dynamic simulations. Journal of Biomolecular Structure and Dynamics 39:11, pages 4066-4076.
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Amresh Prakash, Vijay Kumar, Atanu Banerjee, Andrew M. Lynn & Rajendra Prasad. (2021) Structural heterogeneity in RNA recognition motif 2 (RRM2) of TAR DNA-binding protein 43 (TDP-43): clue to amyotrophic lateral sclerosis. Journal of Biomolecular Structure and Dynamics 39:1, pages 357-367.
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Hai-Long Li, Jae-Rin Lee, Myong-Joon Hahn, Jun-Mo Yang, Fan-Guo Meng, Jia-Wei Wu & Yong-Doo Park. (2020) The omics based study for the role of superoxide dismutase 2 (SOD2) in keratinocytes: RNA sequencing, antibody-chip array and bioinformatics approaches. Journal of Biomolecular Structure and Dynamics 38:10, pages 2884-2897.
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Debasish Kumar Ghosh, Akshaykumar Nanaji Shrikondawar & Akash Ranjan. (2020) Local structural unfolding at the edge-strands of beta sheets is the molecular basis for instability and aggregation of G85R and G93A mutants of superoxide dismutase 1. Journal of Biomolecular Structure and Dynamics 38:3, pages 647-659.
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Amresh Prakash, Vijay Kumar, Andrew M. Lynn & Rizwanul Haque. (2019) Insights into the DNA binding induced thermal stabilization of transcription factor FOXP3. Journal of Biomolecular Structure and Dynamics 37:9, pages 2219-2229.
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Amresh Prakash, Vijay Kumar, Naveen Kumar Meena, Md. Imtaiyaz Hassan & Andrew M. Lynn. (2019) Comparative analysis of thermal unfolding simulations of RNA recognition motifs (RRMs) of TAR DNA-binding protein 43 (TDP-43). Journal of Biomolecular Structure and Dynamics 37:1, pages 178-194.
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Articles from other publishers (10)

Shilpa Sharma, Vijay Raj Tomar, Abhilash Jayaraj & Shashank Deep. (2023) A computational strategy for therapeutic development against superoxide dismutase (SOD1) amyloid formation: effect of polyphenols on the various events in the aggregation pathway. Physical Chemistry Chemical Physics 25:8, pages 6232-6246.
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Sharad Kumar Suthar & Sang-Yoon Lee. (2023) The Role of Superoxide Dismutase 1 in Amyotrophic Lateral Sclerosis: Identification of Signaling Pathways, Regulators, Molecular Interaction Networks, and Biological Functions through Bioinformatics. Brain Sciences 13:1, pages 151.
Crossref
Ruiting Li, Ruhar Singh, Tara Kashav, ChunMin Yang, Ravi Datta Sharma, Andrew M. Lynn, Rajendra Prasad, Amresh Prakash & Vijay Kumar. (2022) Computational Insights of Unfolding of N-Terminal Domain of TDP-43 Reveal the Conformational Heterogeneity in the Unfolding Pathway. Frontiers in Molecular Neuroscience 15.
Crossref
Anil Kumar Tomar & Savita Yadav. 2022. TDP-43 and Neurodegeneration. TDP-43 and Neurodegeneration 81 95 .
Wahiduzzaman, Vijay Kumar, Farah Anjum, Alaa Shafie, Abdelbaset Mohamed Elasbali, Asimul Islam, Faizan Ahmad & Md. Imtaiyaz Hassan. (2021) Delineating the Aggregation-Prone Hotspot Regions (Peptides) in the Human Cu/Zn Superoxide Dismutase 1. ACS Omega 6:49, pages 33985-33994.
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Deeba Shamim Jairajpuri, Afzal Hussain, Khalida Nasreen, Taj Mohammad, Farah Anjum, Md. Tabish Rehman, Gulam Mustafa Hasan, Mohamed F. Alajmi & Md. Imtaiyaz Hassan. (2021) Identification of natural compounds as potent inhibitors of SARS-CoV-2 main protease using combined docking and molecular dynamics simulations. Saudi Journal of Biological Sciences 28:4, pages 2423-2431.
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Ben Niu, Brian C. Mackness, Jill A. Zitzewitz, C. Robert Matthews & Michael L. Gross. (2020) Trifluoroethanol Partially Unfolds G93A SOD1 Leading to Protein Aggregation: A Study by Native Mass Spectrometry and FPOP Protein Footprinting. Biochemistry 59:39, pages 3650-3659.
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Rashmi Dahiya, Taj Mohammad, Mohamed F. Alajmi, Md. Tabish Rehman, Gulam Mustafa Hasan, Afzal Hussain & Md. Imtaiyaz Hassan. (2020) Insights into the Conserved Regulatory Mechanisms of Human and Yeast Aging. Biomolecules 10:6, pages 882.
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Monika Sharma, Gopalakrishnan Bulusu & Abhijit Mitra. (2019) Unfolding Transitions of Peripheral Subunit Binding Domains Show Cooperative Behavior. The Journal of Physical Chemistry B 123:16, pages 3441-3451.
Crossref
Vijay Kumar, Amresh Prakash, Preeti Pandey, Andrew M. Lynn & Md. Imtaiyaz Hassan. (2018) TFE-induced local unfolding and fibrillation of SOD1: bridging the experiment and simulation studies. Biochemical Journal 475:10, pages 1701-1719.
Crossref

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