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Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites

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Standard

Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites. / Dupont, Daniel M; Thuesen, Cathrine K; Bøtkjær, Kenneth A; Behrens, Manja A; Dam, Karen; Sørensen, Hans P.; Pedersen, Jan; Ploug, Michael; Jensen, Jan K; Andreasen, Peter A.

I: PLOS ONE, Bind 10, Nr. 4, e0119207, 2015.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Harvard

Dupont, DM, Thuesen, CK, Bøtkjær, KA, Behrens, MA, Dam, K, Sørensen, HP, Pedersen, J, Ploug, M, Jensen, JK & Andreasen, PA 2015, 'Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites', PLOS ONE, bind 10, nr. 4, e0119207. https://doi.org/10.1371/journal.pone.0119207

APA

Dupont, D. M., Thuesen, C. K., Bøtkjær, K. A., Behrens, M. A., Dam, K., Sørensen, H. P., ... Andreasen, P. A. (2015). Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites. PLOS ONE, 10(4), [e0119207]. https://doi.org/10.1371/journal.pone.0119207

Vancouver

Dupont DM, Thuesen CK, Bøtkjær KA, Behrens MA, Dam K, Sørensen HP o.a. Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites. PLOS ONE. 2015;10(4). e0119207. https://doi.org/10.1371/journal.pone.0119207

Author

Dupont, Daniel M ; Thuesen, Cathrine K ; Bøtkjær, Kenneth A ; Behrens, Manja A ; Dam, Karen ; Sørensen, Hans P. ; Pedersen, Jan ; Ploug, Michael ; Jensen, Jan K ; Andreasen, Peter A. / Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites. I: PLOS ONE. 2015 ; Bind 10, Nr. 4.

Bibtex

@article{83e407202c3b40be82bee0059110a785,
title = "Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites",
abstract = "Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126) with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA). We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A) controlling uPA activities. One of the aptamers (upanap-126) binds to the area around the C-terminal α-helix in pro-uPA, while the other aptamer (upanap-12) binds to both the β-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results suggest and highlight that the size and shape of an aptamer as well as the domain organization of a multi-domain protein such as uPA, may provide the basis for extensive sterical interference with protein ligand interactions considered distant from the aptamer binding site.",
author = "Dupont, {Daniel M} and Thuesen, {Cathrine K} and B{\o}tkj{\ae}r, {Kenneth A} and Behrens, {Manja A} and Karen Dam and S{\o}rensen, {Hans P.} and Jan Pedersen and Michael Ploug and Jensen, {Jan K} and Andreasen, {Peter A.}",
year = "2015",
doi = "10.1371/journal.pone.0119207",
language = "English",
volume = "10",
journal = "P L o S One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "4",

}

RIS

TY - JOUR

T1 - Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites

AU - Dupont, Daniel M

AU - Thuesen, Cathrine K

AU - Bøtkjær, Kenneth A

AU - Behrens, Manja A

AU - Dam, Karen

AU - Sørensen, Hans P.

AU - Pedersen, Jan

AU - Ploug, Michael

AU - Jensen, Jan K

AU - Andreasen, Peter A.

PY - 2015

Y1 - 2015

N2 - Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126) with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA). We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A) controlling uPA activities. One of the aptamers (upanap-126) binds to the area around the C-terminal α-helix in pro-uPA, while the other aptamer (upanap-12) binds to both the β-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results suggest and highlight that the size and shape of an aptamer as well as the domain organization of a multi-domain protein such as uPA, may provide the basis for extensive sterical interference with protein ligand interactions considered distant from the aptamer binding site.

AB - Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126) with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA). We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A) controlling uPA activities. One of the aptamers (upanap-126) binds to the area around the C-terminal α-helix in pro-uPA, while the other aptamer (upanap-12) binds to both the β-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results suggest and highlight that the size and shape of an aptamer as well as the domain organization of a multi-domain protein such as uPA, may provide the basis for extensive sterical interference with protein ligand interactions considered distant from the aptamer binding site.

U2 - 10.1371/journal.pone.0119207

DO - 10.1371/journal.pone.0119207

M3 - Journal article

C2 - 25793507

VL - 10

JO - P L o S One

JF - P L o S One

SN - 1932-6203

IS - 4

M1 - e0119207

ER -

ID: 133846030