In silico Description of LAT1 Transport Mechanism at an Atomistic Level

Palazzolo, Luca; Parravicini, Chiara; Laurenzi, Tommaso; Guerrini, Uliano; Indiveri, Cesare; Gianazza, Elisabetta; Eberini, Ivano

doi:10.3389/fchem.2018.00350

Cited by 15 publications

(13 citation statements)

References 61 publications

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“…6). This correlates with the finding that this helical domain most probably moves during the conformational changes necessary for translocation as also recently proposed 45,51 . The stimulation by ATP may have a biological significance linked to the metabolic state of the cells.…”

Section: Discussionsupporting

confidence: 91%

ATP modulates SLC7A5 (LAT1) synergistically with cholesterol

Cosco

Scalise

Colas

et al. 2020

Sci Rep

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The plasma membrane transporter hLAT1 is responsible for providing cells with essential amino acids. hLAT1 is over-expressed in virtually all human cancers making the protein a hot-spot in the fields of cancer and pharmacology research. However, regulatory aspects of hLAT1 biology are still poorly understood. A remarkable stimulation of transport activity was observed in the presence of physiological levels of cholesterol together with a selective increase of the affinity for the substrate on the internal site, suggesting a stabilization of the inward open conformation of hLAT1. A synergistic effect by ATP was also observed only in the presence of cholesterol. The same phenomenon was detected with the native protein. Altogether, the biochemical assays suggested that cholesterol and ATP binding sites are close to each other. The computational analysis identified two neighboring regions, one hydrophobic and one hydrophilic, to which cholesterol and ATP were docked, respectively. The computational data predicted interaction of the ϒ-phosphate of ATP with Lys 204, which was confirmed by site-directed mutagenesis. The hLAT1-K204Q mutant showed an impaired function and response to ATP. Interestingly, this residue is conserved in several members of the SLC7 family.

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Section: Discussionsupporting

confidence: 91%

ATP modulates SLC7A5 (LAT1) synergistically with cholesterol

Cosco

Scalise

Colas

et al. 2020

Sci Rep

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“…In the absence of protein structure information, different methods can be used to identify putative hit compounds. Two prominent approaches include (1) structure-based design using homology modeling and molecular docking ( Schmidt et al, 2014 ; Louet et al, 2017 ; Palazzolo et al, 2018 ; Singh et al, 2019a ; Singh et al, 2019b ; Singh et al, 2020c ) and (2) ligand-based modeling ( Chaput et al, 2020 ) using the structure-activity relationships ( Kubinyi, 1998 ) (SARs) information derived from experimentally validated compound libraries. Notably, homology modeling, in conjunction with molecular docking, is widely used in virtual screening ( Spyrakis and Cavasotto, 2015 ; Slater and Kontoyianni, 2019 ; Singh et al, 2020b ).…”

Section: Introductionmentioning

confidence: 99%

Demystifying the Molecular Basis of Pyrazoloquinolinones Recognition at the Extracellular α1+/β3- Interface of the GABAA Receptor by Molecular Modeling

Singh

Villoutreix

2020

Front. Pharmacol.

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GABA A receptors are pentameric ligand-gated ion channels that serve as major inhibitory neurotransmitter receptors in the mammalian brain and the target of numerous clinically relevant drugs interacting with different ligand binding sites. Here, we report an in silico approach to investigate the binding of pyrazoloquinolinones (PQs) that mediate allosteric effects through the extracellular a+/binterface of GABA A receptors. First, we docked a potent prototype of PQs into the a1+/b3site of a homology model of the human a1b3g2 subtype of the GABA A receptor. Next, for each docking pose, we computationally derived protein-ligand complexes for 18 PQ analogs with known experimental potency. Subsequently, binding energy was calculated for all complexes using the molecular mechanics-generalized Born surface area method. Finally, docking poses were quantitatively assessed in the light of experimental data to derive a binding hypothesis. Collectively, the results indicate that PQs at the a1+/b3site likely exhibit a common binding mode that can be characterized by a hydrogen bond interaction with b3Q64 and hydrophobic interactions involving residues a1F99, b3Y62, b3M115, a1Y159, and a1Y209. Importantly, our results are in good agreement with the recently resolved cryo-Electron Microscopy structures of the human a1b3g2 and a1b2g2 subtypes of GABA A receptors.

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“…From a structural point of view, this particular aromatic amino acid seems to assume the same function of Trp202, the gating residue of the arginine/agmatine antiporter AdiC. This gating mechanism is also supposed to be conserved for the SLC6 family (Pramod et al 2013) and it was simulated for LAT1 (SLC7A5) via target molecular dynamics (Palazzolo et al 2018). To evaluate the gating arrangement, we compared the placement of Phe319 in two DAT crystallographic structures in OF conformation, with gate open (Pdb ID: 4M48 ) (Penmatsa, Wang, and Gouaux 2015) and closed (Pdb ID: 4XPA) (Wang, Penmatsa, and Gouaux 2015), via a structural superposition.…”

Section: Figurementioning

confidence: 99%

SLC6A14, a Pivotal Actor on Cancer Stage: When Function Meets Structure

et al. 2019

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SLC6A14 (ATB0,+) is a sodium- and chloride-dependent neutral and dibasic amino acid transporter that regulates the distribution of amino acids across cell membranes. The transporter is overexpressed in many human cancers characterized by an increased demand for amino acids; as such, it was recently acknowledged as a novel target for cancer therapy. The knowledge on the molecular mechanism of SLC6A14 transport is still limited, but some elegant studies on related transporters report the involvement of the 12 transmembrane α-helices in the transport mechanism, and describe structural rearrangements mediated by electrostatic interactions with some pivotal gating residues. In the present work, we constructed a SLC6A14 model in outward-facing conformation via homology modeling and used molecular dynamics simulations to predict amino acid residues critical for substrate recognition and translocation. We docked the proteinogenic amino acids and other known substrates in the SLC6A14 binding site to study both gating regions and the exposed residues involved in transport. Interestingly, some of these residues correspond to those previously identified in other LeuT-fold transporters; however, we could also identify a novel relevant residue with such function. For the first time, by combined approaches of molecular docking and molecular dynamics simulations, we highlight the potential role of these residues in neutral amino acid transport. This novel information unravels new aspects of the human SLC6A14 structure–function relationship and may have important outcomes for cancer treatment through the design of novel inhibitors of SLC6A14-mediated transport.

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In silico Description of LAT1 Transport Mechanism at an Atomistic Level

Cited by 15 publications

References 61 publications

ATP modulates SLC7A5 (LAT1) synergistically with cholesterol

ATP modulates SLC7A5 (LAT1) synergistically with cholesterol

Demystifying the Molecular Basis of Pyrazoloquinolinones Recognition at the Extracellular α1+/β3- Interface of the GABAA Receptor by Molecular Modeling

SLC6A14, a Pivotal Actor on Cancer Stage: When Function Meets Structure

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