Biology subjects

Prince, S. M.

Publications and source records attributed to Prince, S. M..

7 recordsLinked to original sources

bioRxiv2025

Outward-facing P-glycoprotein bound to drug displays nucleotide-dependent drug egress mechanism

ABCB1/P-glycoprotein requires coordination between ligand movement in the trans-membrane cavity and ATP binding and hydrolysis at the nucleotide binding domains, yet the sequence of these events remains incompletely resolved. Here, atomistic simulations with paclitaxel and verapamil across outward facing P-glycoprotein ensembles in various nucleotide states were integrated with analysis of transmembrane domain contacts, geometric solvent/ligand pathways, extracellular gating distances, and nucleotide coordi-nation characterization. Collectively, our simulations delineate a mechanistic framework for P-glycoprotein in which ATP binding organizes an outward-facing ensemble and sequential hydrolysis at the two nucleotide-binding sites drives substrate progression toward egress. Asymmetry in the nucleotide state is correlated to distinct motions within the transmembrane domains, which suggests a possible transient extracellular gating mechanism that enables staged release and limits re-entry of the ligand. The resulting model connects nucleotide chemistry to transmembrane domain motions that regulate gate dynamics and may guide experiments and development of modulators for ABC exporter activity in physiological and pharmacological contexts.

molecular biology↗

bioRxiv2025

Drug-bound P-glycoprotein reveals nucleotide-dependent ligand pockets and ingress channels

P-glycoprotein, an ATP-binding cassette exporter, coordinates drug recognition in a central cavity with nucleotide handling at nucleotide binding domains, yet the sequence and coupling of these events remain incompletely defined. Here, we report an integrated computational analysis of inward facing P-glycoprotein ensembles across varying drug locations, nucleotide states, and starting conformations. The sampled inward-facing ensembles of P-glycoprotein display continuous ligand cavity, reshaped by nucleotide occupancy, which enables polyspecific ligand recognition while transmitting allosteric signals to the nucleotide binding domains through intracellular coupling loops. Asymmetry between the two nucleotide binding sites follows from this communication, which alters the nucleotide coordination to potentially affect the catalytic progression. Our simulations reveal dynamic cavity access routes from cytosol and inner membrane, together with transient secondary structure within the interdomain flexible linker. Overall, our study gives insights into how ligand redistribution, asymmetric nucleotide coordination, and linker flexibility may correlate to form a unified view of early transport steps, yielding hypotheses for mutational and kinetic evaluation and informing strategies for small-molecule modulation of transporter function in cellular contexts where multidrug transport affects therapeutic response.

molecular biology↗

bioRxiv2025

Insights into the linker domain in ABCB1/P-glycoprotein

ABCB1/P-glycoprotein(P-gp) is one of the best-known ABC transporters and its involvement in the clearance of chemotherapy agents in cancer cells can lead to multidrug resistance. The N- and C-terminal halves of P-gp are joined by a flexible linker region. Linker regions in ABC transporters often play pivotal roles (i.e. CFTR), however, there is no consensus on the importance of the role of the linker, the complete 3D-structure of which has not yet been determined. Prior studies on linker length showed major effects on P-gp function. In this work, we combined microsecond simulations ({approx}50{micro}s) on mouse and human P-glycoprotein, cryo-EM and other computational methods to trace a profile of the linker region. Different experimentally verified conditions involving the linker region were simulated, analysed and compared. Attachment of the linker to the membrane was spontaneously and occasionally encountered via a recurrent series of amino-acids, despite random starting conformations, suggesting that the lipid bilayer might be involved in linker regulation. As carried out in previous experiments, shortening the linker could potentially disconnect the ATPase activity from the substrate transport by interfering with one ATP site while introducing a short partially-structured linker shows remarkable stability in accelerated MD. Finally, we investigated the linker region by positioning it in specific quadrants of the 3D space, with simulations suggesting 1) a possible influence on protein flexibility, 2) selective tightening and opening of the two halves of P-gp, and a 3) possible stabilization of the inward-facing/occluded-state. The interaction between the linker and ATPs was investigated using protein-protein docking, simulations and a re-refined cryo-EM map where medium-low resolution and weak Coulomb density was found between the nucleotide binding domains.

biochemistry↗

bioRxiv2025

Nucleotide Asymmetry and Flexible Linker Dynamics Modulate Drug Efflux Cycle of P-glycoprotein, a Computational Study

Despite advancements in oncology, multidrug resistance (MDR) mediated by P-glycoprotein (P-gp/ABCB1) remains a major barrier to chemotherapy. P-gp is an ATP-binding cassette transporter that undergoes nucleotide-driven structural rearrangements to efflux chemotherapeutics, but the mechanistic details of the substrate transport remain poorly resolved. Here, we performed high-throughput molecular dynamics to simulate P-gp in a lipid bilayer (totaling [~]110 {micro}s) to dissect nucleotide-dependent conformational changes across the transport cycle. Our adaptive sampling strategy reveals asymmetric nucleotide coordination at nucleotide-binding sites (NBS), which correlates with transmembrane domain (TMD) restructuring for substrate efflux. The experimentally unresolved flexible linker transiently forms up to five turn -helix that affects nucleotide binding domain (NBD) dimerization process. We identified conformation-dependent substrate/allocrite pathways including nucleotide-specific access routes, while TMD-linker interaction facilitates substrate access tunnel formation. Together, these pathways reveal that the concerted interplay of nucleotide occupancy, linker dynamics, and overall protein conformation governs the structural plasticity and broad substrate promiscuity of the substrate binding cavity in P-gp. By integrating these findings, this work bridges static structural data with dynamic functional insights to further our understanding of the P-gp substrate translocation cycle.

biochemistry↗

bioRxiv2023

New information triggers prospective codes to adapt for flexible navigation

Navigating a dynamic world requires rapidly updating choices by integrating past experiences with new information. In hippocampus and prefrontal cortex, neural activity representing future goals is theorized to support planning. However, it remains unknown how prospective goal representations incorporate new, pivotal information. Accordingly, we designed a novel task that precisely introduces new information using virtual reality, and we recorded neural activity as mice flexibly adapted their planned destinations. We found that new information triggered increased hippocampal prospective representations of both possible goals; while in prefrontal cortex, new information caused prospective representations of choices to rapidly shift to the new choice. When mice did not flexibly adapt, prefrontal choice codes failed to switch, despite relatively intact hippocampal goal representations. Prospective code updating depended on the commitment to the initial choice and degree of adaptation needed. Thus, we show how prospective codes update with new information to flexibly adapt ongoing navigational plans.

neuroscience↗

bioRxiv2021

Structure of ABCB1/P-glycoprotein bound to the CFTR potentiator ivacaftor.

ABCB1 (P-glycoprotein) is an ATP binding cassette transporter that is involved in the clearance of xenobiotics and it affects the disposition of many drugs in the body. Here we have studied ABCB1 in the drug-bound and drug-free states, simultaneously, using high contrast cryo-electron microscopy imaging and a Volta phase plate. The binding of the potent CFTR potentiator, ivacaftor, at a site in the central aqueous cavity is mediated by transmembrane -helices 3,6,10,11 & 12. Binding is associated with a wider separation of the two halves of the transporter in the inward-facing state. Induced-fit changes the nucleotide binding domains in a way that may explain their increased affinity for ATP when drug is bound. Comparison of ivacaftor-bound structures of CFTR and ABCB1 suggests common features in the binding modes.

biochemistry↗

bioRxiv2019

How the dual PDZ domain from Postsynaptic density protein 95 clusters ion channels and receptors.

PSD-95 is a member of Membrane Associated Guanylate Kinase class of proteins which form scaffolding interactions with partner proteins including ion and receptor channels. PSD-95 is directly implicated in modulating the electrical responses of excitable cells. The first two PSD-95/Disks Large/Zona Occludens domains of PSD-95 have been shown to be the key component in the formation of channel clusters. We report crystal structures of the dual domain in both in apo and ligand-bound form; thermodynamic analysis of ligand association and Small Angle X-ray Scattering of the dual domain in the absence and presence of ligands. These experiments reveal that the ligated double domain forms a scaffold in the complete sense of the word. The concentration of the components in this study is comparable to those found in compartments of excitable cells such as the postsynaptic density and juxta-paranodes of Ranvier. The properties of the dual domain explain the basis of the scaffolding function of PSD-95, and provide a more detailed understanding of the integration of key components of neuronal specializations involved in nervous signal transmission.

biophysics↗