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Binding site of ABC transporter homology models confirmed by ABCB1 crystal structure.

Ravna AW, Sylte I, Sager G - Theor Biol Med Model (2009)

Bottom Line: As a quality assurance of the methodology, the ABCB1 model was compared to an ABCB1 X-ray crystal structure, and with published cross-linking and site directed mutagenesis data of ABCB1.Amino acids Ile306 (TMH5), Ile340 (TMH6), Phe343 (TMH6), Phe728 (TMH7), and Val982 (TMH12), form a putative substrate recognition site in the ABCB1 model, which is confirmed by both the ABCB1 X-ray crystal structure and the site-directed mutagenesis studies.The ABCB1, ABCC4 and ABCC5 models display distinct differences in the electrostatic properties of their drug recognition sites.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medical Pharmacology and Toxicology, Institute of Medical Biology, Faculty of Health Sciences, University of Tromsø, N-9037 Tromsø, Norway. Aina.W.Ravna@uit.no

ABSTRACT
The human ATP-binding cassette (ABC) transporters ABCB1, ABCC4 and ABCC5 are involved in resistance to chemotherapeutic agents. Here we present molecular models of ABCB1, ABCC4 and ABCC5 by homology based on a wide open inward-facing conformation of Escherichia coli MsbA, which were constructed in order to elucidate differences in the electrostatic and molecular features of their drug recognition conformations. As a quality assurance of the methodology, the ABCB1 model was compared to an ABCB1 X-ray crystal structure, and with published cross-linking and site directed mutagenesis data of ABCB1. Amino acids Ile306 (TMH5), Ile340 (TMH6), Phe343 (TMH6), Phe728 (TMH7), and Val982 (TMH12), form a putative substrate recognition site in the ABCB1 model, which is confirmed by both the ABCB1 X-ray crystal structure and the site-directed mutagenesis studies. The ABCB1, ABCC4 and ABCC5 models display distinct differences in the electrostatic properties of their drug recognition sites.

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A-C: Backbone Cα-traces of ABCB1 model (A), ABCC4 model (B) and ABCC5 model (C) viewed from intracellular side. Colour coding: blue via white to red from N-terminal to C-terminal. D-F: The water-accessible surfaces of ABCB1 model (D), ABCC4 model (E) and ABCC5 model (F) viewed from intracellular side collared coded according to the electrostatic potentials 1.4 Å outside the surface; negative (-10  kcal/mol), red to positive (+10 kcal/mol), blue. G-I: Cross sections along the inner  membrane layer of water-accessible surfaces of ABCB1 model (G), ABCC4 model (H)  and ABCC5 model (I) viewed from intracellular side, colour coding as D-F. All  illustrations are in similar view.
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Figure 4: A-C: Backbone Cα-traces of ABCB1 model (A), ABCC4 model (B) and ABCC5 model (C) viewed from intracellular side. Colour coding: blue via white to red from N-terminal to C-terminal. D-F: The water-accessible surfaces of ABCB1 model (D), ABCC4 model (E) and ABCC5 model (F) viewed from intracellular side collared coded according to the electrostatic potentials 1.4 Å outside the surface; negative (-10 kcal/mol), red to positive (+10 kcal/mol), blue. G-I: Cross sections along the inner membrane layer of water-accessible surfaces of ABCB1 model (G), ABCC4 model (H) and ABCC5 model (I) viewed from intracellular side, colour coding as D-F. All illustrations are in similar view.

Mentions: The loop connecting NBD1 and TMD2 of each transporter was abundant with charged amino acids. The loop connecting NBD1 and TMD2 of ABCB1 was in extended conformation forming a β-sheet between amino acids sections Lys645-Glu652 and Lys665-Ser671, while the loops connecting the subunits of ABCC4 and ABCC5 were α-helical. ABCB5 featured an insertion loop (as compared with the amino acid sequences of Escherichia coli MsbA) from Ile479 to His548 in NBD1, and as displayed in Figures 3C and 4C, this loop was pointing away from NBD1 parallel to the membrane. However, modelling loops of lengths as that of the connection between NBD1 and TMD2 is relatively inaccurate and consequently the modelled loop structures must be regarded as uncertain.


Binding site of ABC transporter homology models confirmed by ABCB1 crystal structure.

Ravna AW, Sylte I, Sager G - Theor Biol Med Model (2009)

A-C: Backbone Cα-traces of ABCB1 model (A), ABCC4 model (B) and ABCC5 model (C) viewed from intracellular side. Colour coding: blue via white to red from N-terminal to C-terminal. D-F: The water-accessible surfaces of ABCB1 model (D), ABCC4 model (E) and ABCC5 model (F) viewed from intracellular side collared coded according to the electrostatic potentials 1.4 Å outside the surface; negative (-10  kcal/mol), red to positive (+10 kcal/mol), blue. G-I: Cross sections along the inner  membrane layer of water-accessible surfaces of ABCB1 model (G), ABCC4 model (H)  and ABCC5 model (I) viewed from intracellular side, colour coding as D-F. All  illustrations are in similar view.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC2747915&req=5

Figure 4: A-C: Backbone Cα-traces of ABCB1 model (A), ABCC4 model (B) and ABCC5 model (C) viewed from intracellular side. Colour coding: blue via white to red from N-terminal to C-terminal. D-F: The water-accessible surfaces of ABCB1 model (D), ABCC4 model (E) and ABCC5 model (F) viewed from intracellular side collared coded according to the electrostatic potentials 1.4 Å outside the surface; negative (-10 kcal/mol), red to positive (+10 kcal/mol), blue. G-I: Cross sections along the inner membrane layer of water-accessible surfaces of ABCB1 model (G), ABCC4 model (H) and ABCC5 model (I) viewed from intracellular side, colour coding as D-F. All illustrations are in similar view.
Mentions: The loop connecting NBD1 and TMD2 of each transporter was abundant with charged amino acids. The loop connecting NBD1 and TMD2 of ABCB1 was in extended conformation forming a β-sheet between amino acids sections Lys645-Glu652 and Lys665-Ser671, while the loops connecting the subunits of ABCC4 and ABCC5 were α-helical. ABCB5 featured an insertion loop (as compared with the amino acid sequences of Escherichia coli MsbA) from Ile479 to His548 in NBD1, and as displayed in Figures 3C and 4C, this loop was pointing away from NBD1 parallel to the membrane. However, modelling loops of lengths as that of the connection between NBD1 and TMD2 is relatively inaccurate and consequently the modelled loop structures must be regarded as uncertain.

Bottom Line: As a quality assurance of the methodology, the ABCB1 model was compared to an ABCB1 X-ray crystal structure, and with published cross-linking and site directed mutagenesis data of ABCB1.Amino acids Ile306 (TMH5), Ile340 (TMH6), Phe343 (TMH6), Phe728 (TMH7), and Val982 (TMH12), form a putative substrate recognition site in the ABCB1 model, which is confirmed by both the ABCB1 X-ray crystal structure and the site-directed mutagenesis studies.The ABCB1, ABCC4 and ABCC5 models display distinct differences in the electrostatic properties of their drug recognition sites.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medical Pharmacology and Toxicology, Institute of Medical Biology, Faculty of Health Sciences, University of Tromsø, N-9037 Tromsø, Norway. Aina.W.Ravna@uit.no

ABSTRACT
The human ATP-binding cassette (ABC) transporters ABCB1, ABCC4 and ABCC5 are involved in resistance to chemotherapeutic agents. Here we present molecular models of ABCB1, ABCC4 and ABCC5 by homology based on a wide open inward-facing conformation of Escherichia coli MsbA, which were constructed in order to elucidate differences in the electrostatic and molecular features of their drug recognition conformations. As a quality assurance of the methodology, the ABCB1 model was compared to an ABCB1 X-ray crystal structure, and with published cross-linking and site directed mutagenesis data of ABCB1. Amino acids Ile306 (TMH5), Ile340 (TMH6), Phe343 (TMH6), Phe728 (TMH7), and Val982 (TMH12), form a putative substrate recognition site in the ABCB1 model, which is confirmed by both the ABCB1 X-ray crystal structure and the site-directed mutagenesis studies. The ABCB1, ABCC4 and ABCC5 models display distinct differences in the electrostatic properties of their drug recognition sites.

Show MeSH
Related in: MedlinePlus