ArticleProtein science : a publication of the Protein Society2020
Ligand binding and global adaptation of the GlnPQ substrate binding domain 2 revealed by molecular dynamics simulations.
Article in Protein science : a publication of the Protein Society, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 9 citations in OpenAlex.
- Dissecting mechanisms of ligand binding and conformational changes in the glutamine-binding protein.eLife · 2026Article
- Exploring the Ligand Binding and Conformational Dynamics of the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ.The journal of physical chemistry. B · 2024Article
- How arginine inhibits substrate-binding domain 2 elucidated using molecular dynamics simulations.Protein science : a publication of the Protein Society · 2024Article
- The role of C-terminal helix in the conformational transition of an arginine binding protein.Journal of structural biology: X · 2022Article
- Ligand binding and global adaptation of the GlnPQ substrate binding domain 2 revealed by molecular dynamics simulations.Protein science : a publication of the Protein Society · 2020Article
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Substrate-binding domains (SBD) are important structural elements of substrate transporters mediating the transport of essential molecules across the cell membrane. The SBD2 domain of the glutamine (GLN) transporter from bacteria consists of two domains D1 and D2 that bind GLN in the space between the domains in a closed conformation. In the absence of ligand, SBD2 adopts an open conformation with increased domain distance. In molecular dynamics (MD) simulations in the absence of ligands, no closing of the open conformation was observed on the MD time scale. Addition of GLN resulted in several reversible binding and unbinding events of GLN at the binding site on the D1 domain but did not induce domain closing indicating that binding and global domain closing do not occur simultaneously. The SBD2 structure remained in a closed state when starting from the GLN-bound closed crystal structure and opened quickly to reach the open state upon removal of the GLN ligand. Free energy simulations to induce opening to closing indicated a barrier for closing in the absence and presence of ligand and a significant penalty for closing without GLN in the binding pocket. Simulations of a Leu480Ala mutation also indicate that an interaction of a C-terminal D1-tail
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