Conformational preferences of non-polar amino acid residues: An additional factor in amyloid formation

2010 ◽  
Vol 402 (3) ◽  
pp. 515-518 ◽  
Author(s):  
Jan Johansson ◽  
Charlotte Nerelius ◽  
Hanna Willander ◽  
Jenny Presto
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Susan M. Mitchell ◽  
Morven Graham ◽  
Xinran Liu ◽  
Ralf M. Leonhardt

AbstractThe pigment cell-specific protein PMEL forms a functional amyloid matrix in melanosomes onto which the pigment melanin is deposited. The amyloid core consists of a short proteolytic fragment, which we have termed the core-amyloid fragment (CAF) and perhaps additional parts of the protein, such as the PKD domain. A highly O-glycosylated repeat (RPT) domain also derived from PMEL proteolysis associates with the amyloid and is necessary to establish the sheet-like morphology of the assemblies. Excluded from the aggregate is the regulatory N-terminus, which nevertheless must be linked in cis to the CAF in order to drive amyloid formation. The domain is then likely cleaved away immediately before, during, or immediately after the incorporation of a new CAF subunit into the nascent amyloid. We had previously identified a 21 amino acid long region, which mediates the regulatory activity of the N-terminus towards the CAF. However, many mutations in the respective segment caused misfolding and/or blocked PMEL export from the endoplasmic reticulum, leaving their phenotype hard to interpret. Here, we employ a saturating mutagenesis approach targeting the motif at single amino acid resolution. Our results confirm the critical nature of the PMEL N-terminal region and identify several residues essential for PMEL amyloidogenesis.


Biomolecules ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1121 ◽  
Author(s):  
Brian Andrews ◽  
Shuting Zhang ◽  
Reinhard Schweitzer-Stenner ◽  
Brigita Urbanc

Conformational preferences of amino acid residues in water are determined by the backbone and side-chain properties. Alanine is known for its high polyproline II (pPII) propensity. The question of relative contributions of the backbone and side chain to the conformational preferences of alanine and other amino acid residues in water is not fully resolved. Because glycine lacks a heavy-atom side chain, glycine-based peptides can be used to examine to which extent the backbone properties affect the conformational space. Here, we use published spectroscopic data for the central glycine residue of cationic triglycine in water to demonstrate that its conformational space is dominated by the pPII state. We assess three commonly used molecular dynamics (MD) force fields with respect to their ability to capture the conformational preferences of the central glycine residue in triglycine. We show that pPII is the mesostate that enables the functional backbone groups of the central residue to form the most hydrogen bonds with water. Our results indicate that the pPII propensity of the central glycine in GGG is comparable to that of alanine in GAG, implying that the water-backbone hydrogen bonding is responsible for the high pPII content of these residues.


2020 ◽  
Vol 21 (16) ◽  
pp. 5856
Author(s):  
Davide Gentile ◽  
Virginia Fuochi ◽  
Antonio Rescifina ◽  
Pio Maria Furneri

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a severe global health crisis. In this paper, we used docking and simulation methods to identify potential targets and the mechanism of action of chloroquine (CQ) and hydroxychloroquine (HCQ) against SARS-CoV-2. Our results showed that both CQ and HCQ influenced the functionality of the envelope (E) protein, necessary in the maturation processes of the virus, due to interactions that modify the flexibility of the protein structure. Furthermore, CQ and HCQ also influenced the proofreading and capping of viral RNA in SARS-CoV-2, performed by nsp10/nsp14 and nsp10/nsp16. In particular, HCQ demonstrated a better energy binding with the examined targets compared to CQ, probably due to the hydrogen bonding of the hydroxyl group of HCQ with polar amino acid residues.


2001 ◽  
Vol 268 (17) ◽  
pp. 4674-4685 ◽  
Author(s):  
Rakhilya Murtazina ◽  
Brenda J. Booth ◽  
Bonnie L. Bullis ◽  
Dyal N. Singh ◽  
Larry Fliegel

2016 ◽  
Vol 7 ◽  
Author(s):  
Paulina Aguilera ◽  
Andrés Marcoleta ◽  
Pablo Lobos-Ruiz ◽  
Rocío Arranz ◽  
José M. Valpuesta ◽  
...  

2001 ◽  
Vol 357 (1) ◽  
pp. 1 ◽  
Author(s):  
Christine A. WIEBE ◽  
Emily R. DiBATTISTA ◽  
Larry FLIEGEL

Diabetes ◽  
1990 ◽  
Vol 39 (1) ◽  
pp. 118-122 ◽  
Author(s):  
C. Betsholtz ◽  
L. Christmanson ◽  
U. Engstrom ◽  
F. Rorsman ◽  
K. Jordan ◽  
...  

2014 ◽  
Vol 16 (41) ◽  
pp. 22527-22536 ◽  
Author(s):  
Reinhard Schweitzer-Stenner ◽  
Siobhan E. Toal

The conformational entropy of amino acid residues in unfolded peptides and proteins is estimated from conformational backbone distributions and compared with experimental and computational values.


2016 ◽  
Vol 11 (11) ◽  
pp. 3132-3139 ◽  
Author(s):  
Shinsuke Inuki ◽  
Toshihiko Aiba ◽  
Natsumi Hirata ◽  
Osamu Ichihara ◽  
Daisuke Yoshidome ◽  
...  

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