Effects of trimethylamine-N-oxide (TMAO) on aqueous N-methylacetamide solution: A comparison of different force fields of TMAO

Chand, Apramita; Chettiyankandy, Pragin; Pattanayak, Subrat Kumar; Chowdhuri, Snehasis

doi:10.1016/j.molliq.2016.05.044

Cited by 12 publications

(3 citation statements)

References 42 publications

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“…We also computed the PMFs for dimer formation using the osmotic model of TMAO to check for the model dependence (Figure S4). We do observe some differences in the PMF profiles as expected with different models . No significant stabilization of the dimer is found for the Asn side chain and Gly6 compared with the monomers (Figure S4A,C).…”

Section: Resultssupporting

confidence: 65%

“…We do observe some differences in the PMF profiles as expected with different models. 82 No significant stabilization of the dimer is found for the Asn side chain and Gly6 compared with the monomers (Figure S4A,C). The dimer of the Gln side chain is stabilized and that of the Tyr side chain is destabilized (Figure S4B,D), in agreement with the data from the Kast model (Figure 5B,D).…”

Section: ■ Results and Discussionmentioning

confidence: 95%

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Osmolyte Effects on the Growth of Amyloid Fibrils

Muttathukattil

Reddy

2016

J. Phys. Chem. B

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Understanding the role of naturally occurring protective osmolytes, such as trimethylamine N-oxide (TMAO), in the growth of amyloid fibrils implicated in neurodegenerative diseases is important to prevent fibril growth. The effect of TMAO on the growth of amyloid fibrils formed by the Sup35 prion peptide NNQQNY is studied using molecular dynamics simulations. The free-energy surface for the growth of the protofibril shows three major basins, corresponding to the free state where the peptide is in solution, the docked state where the peptide in solution interacts with the surface of the protofibril, and the locked state where the peptide is tightly bound to the protofibril, becoming a part of the fibril. The free-energy surface in the presence of TMAO shows that TMAO stabilizes the locked state of the peptide compared with the free state, indicating that TMAO aids in fibril growth. Dissecting the interaction of TMAO with individual amino acids in the peptide shows that TMAO interacts both directly and indirectly with the amino acids, depending on the nature of the side chains. The methyl groups in TMAO interact strongly with the hydrophobic aromatic ring in the Tyr residue. In the locked state, the surface area of Tyr available for interaction with TMAO decreases; as a result, the Tyr residue in the peptide flips out from the locked position, increasing the fluctuations of the peptide locked in the protofibril. Such strong direct interactions of amino acids with TMAO destabilize the folded or aggregated states of proteins. The overall increased stability of the peptide locked in the protofibril by TMAO is due to entropic or indirect interactions with the backbone Asn and Gln residues, which form major components of the NNQQNY peptide.

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Section: Resultssupporting

confidence: 65%

Section: ■ Results and Discussionmentioning

confidence: 95%

Osmolyte Effects on the Growth of Amyloid Fibrils

Muttathukattil

Reddy

2016

J. Phys. Chem. B

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“…N-Methylacetamide (NMA) is considered as a minimal part of the peptide backbone that contains a peptide linkage and, additionally, two hydrophobic methyl groups. Aqueous solutions of NMA in the presence of osmolytes have been studied mainly theoretically [14][15][16][17][18][19] and rarely experimentally [20][21][22], and they have provided information about various interactions that play a role in the protein folding process.…”

Section: Introductionmentioning

confidence: 99%

Interactions in Ternary Aqueous Solutions of NMA and Osmolytes—PARAFAC Decomposition of FTIR Spectra Series

Kaczkowska

Panuszko

Bruździak

2021

IJMS

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Intermolecular interactions in aqueous solutions are crucial for virtually all processes in living cells. ATR-FTIR spectroscopy is a technique that allows changes caused by many types of such interactions to be registered; however, binary solutions are sometimes difficult to solve in these terms, while ternary solutions are even more difficult. Here, we present a method of data pretreatment that facilitates the use of the Parallel Factor Analysis (PARAFAC) decomposition of ternary solution spectra into parts that are easier to analyze. Systems of the NMA–water–osmolyte-type were used to test the method and to elucidate information on the interactions between N-Methylacetamide (NMA, a simple peptide model) with stabilizing (trimethylamine N-oxide, glycine, glycine betaine) and destabilizing osmolytes (n-butylurea and tetramethylurea). Systems that contain stabilizers change their vibrational structure to a lesser extent than those with denaturants. Changes in the latter are strong and can be related to the formation of direct NMA–destabilizer interactions.

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