Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation - Publikacja - MOST Wiedzy

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Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation

Abstrakt

EmrE protein transports positively charged aromatic drugs (xenobiotics) in exchange for two protons and thus provides bacteria resistance to variety of drugs. In order to understand how this protein may recognize ligands, the monomer and asymmetric apo-form of the EmrE dimer embedded in a heterogeneous phospholipid (POPE + POPG) membrane were studied by molecular dynamics simulations. Dimer is regarded as a functional form of the transporter, but to understand molecular aspects of its mode of action, a monomer was also included in our work. We analyzed hydrogen bonds which include inter- and intra-molecular interactions. Analyzing the long-lasting H-bond interactions, we found that water access to the internal transmembrane segments is regulated by residues with aromatic or basic side chains and fluctuating transmembrane helices. Our finding supports that GLU14 in EmrE apo-form is ready to interact or bind with substrate molecule. The analysis of distance center of masses and water entrance area indicate the feasibility of the dimer to undergo induced fit in order to accommodate a ligand. The results indicate that a binding pattern can be formed in the EmrE in such a way that GLU14 binds to the positively charged fragment of a substrate molecule, and other aromatic residues (i.e., TRP63 and TYR40) located in vicinity may accommodate other non-polar parts of substrate molecule. The results of our simulation also allow us to support experimentally testable hypotheses concerning functional inward–outward conformational changes of the protein.

Cytowania

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Informacje szczegółowe

Kategoria:
Publikacja w czasopiśmie
Typ:
artykuł w czasopiśmie wyróżnionym w JCR
Opublikowano w:
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES nr 1848, wydanie 10 ,Part: A, strony 2065 - 2074,
ISSN: 0005-2736
Język:
angielski
Rok wydania:
2015
Opis bibliograficzny:
Padariya M., Kalathiya U., Bagiński M.: Structural and dynamic changes adopted by EmrE, multidrug transporter protein—Studies by molecular dynamics simulation// BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES. -Vol. 1848, iss. 10 ,Part: A (2015), s.2065-2074
DOI:
Cyfrowy identyfikator dokumentu elektronicznego (otwiera się w nowej karcie) 10.1016/j.bbamem.2015.05.014
Weryfikacja:
Politechnika Gdańska

wyświetlono 22 razy

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