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Gianotti AR, Klinke S, Ermácora MR. The structure of unliganded sterol carrier protein 2 from Yarrowia lipolytica unveils a mechanism for binding site occlusion. J Struct Biol 2020; 213:107675. [PMID: 33278583 DOI: 10.1016/j.jsb.2020.107675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/21/2020] [Accepted: 11/27/2020] [Indexed: 11/19/2022]
Abstract
Isolated or as a part of multidomain proteins, Sterol Carrier Protein 2 (SCP2) exhibits high affinity and broad specificity for different lipidic and hydrophobic compounds. A wealth of structural information on SCP2 domains in all forms of life is currently available; however, many aspects of its ligand binding activity are poorly understood. ylSCP2 is a well-characterized single domain SCP2 from the yeast Yarrowia lipolytica. Herein, we report the X-ray structure of unliganded ylSCP2 refined to 2.0 Å resolution. Comparison with the previously solved liganded ylSCP2 structure unveiled a novel mechanism for binding site occlusion. The liganded ylSCP2 binding site is a large cavity with a volume of more than 800 Å3. In unliganded ylSCP2 the binding site is reduced to about 140 Å3. The obliteration is caused by a swing movement of the C-terminal α helix 5 and a subtle compaction of helices 2-4. Previous pairwise comparisons were between homologous SCP2 domains with a uncertain binding status. The reported unliganded ylSCP2 structure allows for the first time a fully controlled comparative analysis of the conformational effects of ligand occupation dispelling several doubts regarding the architecture of SCP2 binding site.
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Affiliation(s)
- Alejo R Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Argentina; Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Mario R Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Argentina; Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina.
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Machado VB, Maróstica de Sá J, Miranda Prado AK, Alves de Toledo K, Regasini LO, Pereira de Souza F, Caruso ÍP, Fossey MA. Biophysical and flavonoid-binding studies of the G protein ectodomain of group A human respiratory syncytial virus. Heliyon 2019; 5:e01394. [PMID: 30976680 PMCID: PMC6439273 DOI: 10.1016/j.heliyon.2019.e01394] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/17/2019] [Accepted: 03/18/2019] [Indexed: 02/02/2023] Open
Abstract
The human Respiratory Syncytial Virus (hRSV) is the major causative agent of lower respiratory tract diseases in infants, young children and elderly. The membrane protein G is embedded in the viral lipid envelope and plays an adhesion function of the virus to host cells. The present study reports the production of the group A hRSV recombinant G protein ectodomain (edG) and its characterization of secondary structure and thermal unfolding by circular dichroism (CD), as well as the binding investigation of flavonoids quercetin and morin to this protein by fluorescent quenching. CD data reveal that edG is composed mostly of β-structure and its melting temperature is of 325 K. Fluorescence quenching experiments of hRSV edG show that the dissociation constants for the flavonoids binding are micromolar and the binding affinity for the edG/quercetin complex is inversely dependent on rising temperature while is directly dependent for the edG/morin interaction. The thermodynamic parameters suggest that hydrophobic contacts are important for the edG/morin association while van der Waals forces and hydrogen bonds contribute to the stabilization of the edG/quercetin complex. Thus, data reported herein may contribute to the development of new treatment strategies that prevent the viral infection by hRSV.
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Affiliation(s)
- Vitor Brassolatti Machado
- Instituto de Biociências, Letras e Ciências Exatas, UNESP, Department of Biology, São José do Rio Preto, SP, Brazil
- Instituto de Biociências, Letras e Ciências Exatas, UNESP, Multiuser Center for Biomolecular Innovation, Laboratory of Molecular Biology, São José do Rio Preto, SP, Brazil
| | - Jéssica Maróstica de Sá
- Instituto de Biociências, Letras e Ciências Exatas, UNESP, Multiuser Center for Biomolecular Innovation, Laboratory of Molecular Biology, São José do Rio Preto, SP, Brazil
- Instituto de Biociências, Letras e Ciências Exatas, UNESP, Department of Physics, São José do Rio Preto, SP, Brazil
| | - Ana Karla Miranda Prado
- Instituto de Biociências, Letras e Ciências Exatas, UNESP, Multiuser Center for Biomolecular Innovation, Laboratory of Molecular Biology, São José do Rio Preto, SP, Brazil
- Instituto de Biociências, Letras e Ciências Exatas, UNESP, Department of Physics, São José do Rio Preto, SP, Brazil
| | - Karina Alves de Toledo
- Faculdade de Ciências e Letras, UNESP, Department of Biology Sciences, Assis, SP, Brazil
| | - Luis Octávio Regasini
- Instituto de Biociências, Letras e Ciências Exatas, UNESP, Department of Chemistry and Environmental Sciences, São José do Rio Preto, SP, Brazil
| | - Fátima Pereira de Souza
- Instituto de Biociências, Letras e Ciências Exatas, UNESP, Multiuser Center for Biomolecular Innovation, Laboratory of Molecular Biology, São José do Rio Preto, SP, Brazil
- Instituto de Biociências, Letras e Ciências Exatas, UNESP, Department of Physics, São José do Rio Preto, SP, Brazil
| | - Ícaro Putinhon Caruso
- Instituto de Biociências, Letras e Ciências Exatas, UNESP, Multiuser Center for Biomolecular Innovation, Laboratory of Molecular Biology, São José do Rio Preto, SP, Brazil
- Instituto de Biociências, Letras e Ciências Exatas, UNESP, Department of Physics, São José do Rio Preto, SP, Brazil
- Corresponding author.
| | - Marcelo Andres Fossey
- Instituto de Biociências, Letras e Ciências Exatas, UNESP, Multiuser Center for Biomolecular Innovation, Laboratory of Molecular Biology, São José do Rio Preto, SP, Brazil
- Instituto de Biociências, Letras e Ciências Exatas, UNESP, Department of Physics, São José do Rio Preto, SP, Brazil
- Corresponding author.
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