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In this study, we investigate the conformational characteristics of full-length Aβ peptide monomers in presence of Na and Zn metal ions using atomistic molecular dynamics (MD) simulations with an aim to explore the possible driving forces behind enhanced aggregation rates of the peptides in presence of salts. The calculations reveal that the presence of metal ions shifts the conformational equilibrium more towards the compact ordered Aβ structures. Such compact ordered structures stabilized by distant non-local contacts between two crucial hydrophobic segments, hp1 and hp2, primarily through two important hydrophobic aromatic residues, Phe-19 and Phe-20, are expected to trigger the aggregation process at a faster rate by populating and stabilizing the aggregation prone structures. Formation of a significant number of such distant contacts in presence of Na ions has also been found to result in breaking of the N-terminal helix. On the contrary, binding of Zn ion to Aβ peptide is highly specific, which stabilizes the N-terminal helix instead of breaking it. This explains why the aggregation rate of Aβ peptides is higher in presence of divalent Zn ions than monovalent Na ions. Relatively higher overall stability of the most populated Aβ peptide monomers in presence of Zn ions has been found to be associated with specific Zn-Aβ binding and significant free energy gain.
This article was published in the following journal.
Name: Journal of chemical information and modeling
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Metal Ions levels of cobalt, chromium, and titanium in 40 patients preoperatively and at least 1 year status post total hip replacement with the Trident II Tritatnium system using an MDM l...
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A computer simulation technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein.
A computer simulation developed to study the motion of molecules over a period of time.
A family of soluble metal binding proteins that are involved in the intracellular transport of specific metal ions and their transfer to the appropriate metalloprotein precursor.
A mass spectrometric technique that is used for the analysis of large biomolecules. Analyte molecules are embedded in an excess matrix of small organic molecules that show a high resonant absorption at the laser wavelength used. The matrix absorbs the laser energy, thus inducing a soft disintegration of the sample-matrix mixture into free (gas phase) matrix and analyte molecules and molecular ions. In general, only molecular ions of the analyte molecules are produced, and almost no fragmentation occurs. This makes the method well suited for molecular weight determinations and mixture analysis.
Proteins that have one or more tightly bound metal ions forming part of their structure. (Dorland, 28th ed)