Structural discordance in HIV-1 Vpu from brain isolate alarms amyloid fibril forming behavior- a computational perspective

Patil Sneha, Pritam Kumar Panda, Fatemeh Rahimi Gharemirshamlu, Kourosh Bamdad, Seetharaman Balaji

Research output: Contribution to journalArticle

Abstract

HIV-1 being the most widespread type worldwide, its accounts for almost 95% of all infections including HIV associated dementia (HAD) that triggers neurological dysfunction and neurodegeneration in patients. The common features associated with HAD and other neurodegenerative diseases are accumulation of amyloid plaques, neuronal loss and deterioration of cognitive abilities, amongst which amyloid fibrillation is considered to be a hallmark. The success of effective therapeutics lies in the understanding of mechanisms leading to neurotoxicity. Few viral proteins like gp-120 are known to be involved in aggregation and enhancement of viral infectivity while comprehending the neurotoxic role of some other proteins is still underway. In the current study, amyloidogenic potential of HIV-1 Vpu protein from brain isolate is investigated through computational approaches. The aggregation propensity of brain derived HIV-1 Vpu was assessed by several amyloid prediction servers that projected the region 4–35 to be amyloidogenic. The protein structure was modeled and subjected to 70 ns molecular dynamics (MD) simulation to investigate the transformation of α-helical conformation of the predicted aggregate region into β-sheet, proposing the protein's ability to initiate fibril formation that is central to amyloidogenic proteins. The structural features of brain derived HIV-1 Vpu were consistent with the in silico amyloid prediction results that depicts the conformational change in the region 8–28 of which residues Ala8, Ile9, Val10, Ala19, Ile20 and Val21 constitutes β-sheet formation. The α-helix/β-sheet discordance of the predicted region was reflected in the simulation study highlighting the possible structural transition associated with HIV-1 Vpu protein of brain isolate.

Original languageEnglish
Pages (from-to)35-45
Number of pages11
JournalJournal of Theoretical Biology
Volume451
DOIs
Publication statusPublished - 14-08-2018

Fingerprint

amyloid
Human immunodeficiency virus 1
Amyloid
HIV-1
Brain
Proteins
Protein
brain
AIDS Dementia Complex
Aptitude
dementia
Dementia
proteins
Agglomeration
Neurodegenerative diseases
Aggregation
Amyloidogenic Proteins
neurotoxicity
prediction
molecular dynamics

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Modelling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics

Cite this

Sneha, Patil ; Panda, Pritam Kumar ; Gharemirshamlu, Fatemeh Rahimi ; Bamdad, Kourosh ; Balaji, Seetharaman. / Structural discordance in HIV-1 Vpu from brain isolate alarms amyloid fibril forming behavior- a computational perspective. In: Journal of Theoretical Biology. 2018 ; Vol. 451. pp. 35-45.
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Structural discordance in HIV-1 Vpu from brain isolate alarms amyloid fibril forming behavior- a computational perspective. / Sneha, Patil; Panda, Pritam Kumar; Gharemirshamlu, Fatemeh Rahimi; Bamdad, Kourosh; Balaji, Seetharaman.

In: Journal of Theoretical Biology, Vol. 451, 14.08.2018, p. 35-45.

Research output: Contribution to journalArticle

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