Inverse Conformational Selection in Lipid–Protein Binding

Autor: Matti Javanainen, Salla I. Virtanen, Fernando Favela-Rosales, Chris Papadopoulos, Antonio Peón, Amélie Bacle, Anne M. Kiirikki, Patrick F.J. Fuchs, O. H. Samuli Ollila, Pavel Buslaev, Ángel Piñeiro, Rebeca García-Fandiño, Paula Milán Rodríguez, Tiago Mendes Ferreira, Markus S. Miettinen, Jesper J. Madsen, Josef Melcr, Ivan Gushchin, Thomas J. Piggot
Přispěvatelé: Lipotoxicity and Channelopathies - ConicMeds (LitCh), Signalisation et Transports Ioniques Membranaires (STIM), Université de Poitiers-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Nanoscience Center [Jyväskylä Univ] (NSC@JYU), University of Jyväskylä (JYU), Moscow Institute of Physics and Technology [Moscow] (MIPT), Centro de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS ), Universidade de Santiago de Compostela [Spain] (USC ), Universidade do Porto = University of Porto, Tecnológico Nacional de México (TecNM), Martin-Luther-University Halle-Wittenberg, Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), UFR Sciences du Vivant [Sciences] - Université Paris Cité (UFR SDV UPCité), Université Paris Cité (UPCité), Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB / CAS), Czech Academy of Sciences [Prague] (CAS), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Chicago, University of South Florida [Tampa] (USF), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen [Groningen], Max Planck Institute of Colloids and Interfaces, Max-Planck-Gesellschaft, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), University of Southampton, Molecular Dynamics, Institute of Biotechnology, Biophysical chemistry, Gestionnaire, Hal Sorbonne Université, Université Paris Cité - UFR Sciences du Vivant [Sciences] (UPCité - UFR SDV), Université de Poitiers-Université de Tours-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Universidade do Porto, Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Paris - UFR Sciences du Vivant [Sciences] (UP - UFR SDV), Université de Paris (UP), University of Helsinki-University of Helsinki, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Jazyk: angličtina
Rok vydání: 2021
Předmět:
DYNAMICS
ELECTRIC CHARGE
BILAYERS
PHOSPHATIDYLCHOLINE HEADGROUP
Membrane lipids
DEUTERIUM
Plasma protein binding
Molecular Dynamics Simulation
lipidit
010402 general chemistry
01 natural sciences
Biochemistry
biomolekyylit
Catalysis
03 medical and health sciences
Molecular dynamics
kemialliset sidokset
Colloid and Surface Chemistry
Protein structure
PHOSPHOLIPID-BINDING
MAGNETIC-RESONANCE
[SDV.BBM] Life Sciences [q-bio]/Biochemistry
Molecular Biology
SEGMENTAL ORDER
[SDV.BBM]Life Sciences [q-bio]/Biochemistry
Molecular Biology
Conformational ensembles
Nuclear Magnetic Resonance
Biomolecular
030304 developmental biology
chemistry.chemical_classification
0303 health sciences
Chemistry
Biomolecule
MEMBRANE-LIPIDS
Proteins
Phosphatidylglycerols
General Chemistry
computer.file_format
Protein Data Bank
Lipids
0104 chemical sciences
Biophysics
Phospholipid Binding
Phosphatidylcholines
MAS NMR
1182 Biochemistry
cell and molecular biology
lipids (amino acids
peptides
and proteins)
proteiinit
computer
Protein Binding
Zdroj: Journal of the American Chemical Society
Journal of the American Chemical Society, 2021, 143 (34), pp.13701-13709. ⟨10.1021/jacs.1c05549⟩
Journal of the American Chemical Society, 143(34), 13701-13709. AMER CHEMICAL SOC
Journal of the American Chemical Society, American Chemical Society, 2021, 143 (34), pp.13701-13709. ⟨10.1021/jacs.1c05549⟩
ISSN: 0002-7863
1520-5126
DOI: 10.1021/jacs.1c05549⟩
Popis: International audience; Interest in lipid interactions with proteins and other biomolecules is emerging not only in fundamental biochemistry but also in the field of nanobiotechnology where lipids are commonly used, for example, in carriers of mRNA vaccines. The outward-facing components of cellular membranes and lipid nanoparticles, the lipid headgroups, regulate membrane interactions with approaching substances, such as proteins, drugs, RNA, or viruses. Because lipid headgroup conformational ensembles have not been experimentally determined in physiologically relevant conditions, an essential question about their interactions with other biomolecules remains unanswered: Do headgroups exchange between a few rigid structures, or fluctuate freely across a practically continuous spectrum of conformations? Here, we combine solid-state NMR experiments and molecular dynamics simulations from the NMRlipids Project to resolve the conformational ensembles of headgroups of four key lipid types in various biologically relevant conditions. We find that lipid headgroups sample a wide range of overlapping conformations in both neutral and charged cellular membranes, and that differences in the headgroup chemistry manifest only in probability distributions of conformations. Furthermore, the analysis of 894 protein-bound lipid structures from the Protein Data Bank suggests that lipids can bind to proteins in a wide range of conformations, which are not limited by the headgroup chemistry. We propose that lipids can select a suitable headgroup conformation from the wide range available to them to fit the various binding sites in proteins. The proposed inverse conformational selection model will extend also to lipid binding to targets other than proteins, such as drugs, RNA, and viruses.
Databáze: OpenAIRE
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