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Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics
KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.ORCID-id: 0000-0002-1763-9383
2013 (engelsk)Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 7, s. 2069-2080Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores-acridine yellow and proflavin-located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site. The computational scheme adopted involves classical molecular dynamics simulations of the ligands bound to the protein and subsequent linear response polarizable embedding density functional theory calculations of the excitation energies. A polarizable embedding potential consisting of point charges fitted to reproduce the electrostatic potential and isotropic atomic polarizabilities computed individually for every residue of the protein was used in the linear response calculations. Comparing the calculated aqueous solution-to-protein shifts of maximum absorption energies to available experimental data, we concluded that the cationic proflavin chromophore is likely not to bind albumin at its drug binding site I nor at its heme binding site. Although agreement with experimental data could only be obtained in qualitative terms, our results clearly indicate that the difference in optical response of the two probes is due to deprotonation, and not, as earlier suggested, to different binding sites. The ramifications of this finding for design of molecular probes targeting albumin or other proteins is briefly discussed.

sted, utgiver, år, opplag, sider
2013. Vol. 117, nr 7, s. 2069-2080
Emneord [en]
Chromophores, Density functional theory, Dyes, Molecular dynamics, Porphyrins, Probes, Proteins
HSV kategori
Identifikatorer
URN: urn:nbn:se:kth:diva-120169DOI: 10.1021/jp311863xISI: 000315432200010PubMedID: 23356863Scopus ID: 2-s2.0-84874153067OAI: oai:DiVA.org:kth-120169DiVA, id: diva2:613761
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QC 20130402

Tilgjengelig fra: 2013-04-02 Laget: 2013-04-02 Sist oppdatert: 2022-06-24bibliografisk kontrollert

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