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Color modeling of protein optical probes
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0003-0185-5724
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0003-2729-0290
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0002-1763-9383
2012 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 14, no 3, 1107-1112 p.Article in journal (Refereed) Published
Abstract [en]

We present a strategy for modeling optical probes within heterogeneous environments of restricted dimension. The method is based on a multiphysics approach comprising sequential structure modeling by means of hybrid Car-Parrinello molecular dynamics and property modeling by means of quantum mechanics/molecular mechanics response theory. For demonstration we address the structural and optical properties of nile red within the beta-lacto globulin protein. We consider the cases with the probe situated on the surface or within the cavity of the protein, or embedded in a water solvent. We find the absorption properties of the probe to be highly dependent on its position relative to the protein. Structural rearrangements of the optical probe are found to contribute significantly to these environmental effects.

Place, publisher, year, edition, pages
2012. Vol. 14, no 3, 1107-1112 p.
Keyword [en]
ARLO-QUANTUM-MECHANICS, MOLECULAR DYNAMICS/QUANTUM MECHANICS, ELECTRONIC-ABSORPTION-SPECTRUM, SOLVENT POLARITY INDICATORS, GAUSSIAN-BASIS SETS, NILE-RED, SOLVATOCHROMIC PROPERTIES, MISFOLDING DISEASES, LENGTH ALTERNATION, FLUORESCENT-PROBE
National Category
Physical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-83792DOI: 10.1039/c1cp23060cISI: 000299271800003Scopus ID: 2-s2.0-84255197265OAI: oai:DiVA.org:kth-83792DiVA: diva2:513521
Funder
Swedish e‐Science Research Center
Note

QC 20120402

Available from: 2012-04-02 Created: 2012-02-13 Last updated: 2017-12-07Bibliographically approved

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Natarajan Arul, MuruganÅgren, Hans

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