A functional NMR for membrane proteins: dynamics, ligand binding, and allosteric modulation

Abstract

By nature of conducting ions, transporting substrates and transducing signals, membrane channels, transporters and receptors are expected to exhibit intrinsic conformational dynamics. It is therefore of great interest and importance to understand the various properties of conformational dynamics acquired by these proteins, for example, the relative population of states, exchange rate, conformations of multiple states, and how small molecule ligands modulate the conformational exchange. Because small molecule binding to membrane proteins can be weak and/or dynamic, structural characterization of these effects is very challenging. This review describes several NMR studies of membrane protein dynamics, ligand-induced conformational rearrangements, and the effect of ligand binding on the equilibrium of conformational exchange. The functional significance of the observed phenomena is discussed.

Solution NMR Studies of Anesthetic Interactions with Ion Channels

“…OuYang et al, 2013; Oxenoid & Chou, 2016; Schnell & Chou, 2008). With an increased molecular mass, both the sensitivity and resolution of NMR spectra worsen dramatically; NMR signals broaden significantly due to slower rotational tumbling of the larger protein.…”

“…Nuclear magnetic resonance (NMR) spectroscopy has a wide range of applications, including the determination of protein structures, characterization of protein-ligand interactions, and detection of changes in protein conformations and dynamics upon ligand binding (Kay, 2016; Kim, Howell, Van Horn, Jeon, & Sanders, 2009; Kitevski-LeBlanc & Prosser, 2012; Liang & Tamm, 2016; Liu, Horst, Katritch, Stevens, & Wuthrich, 2012; Oxenoid & Chou, 2013, 2016; Rosenzweig & Kay, 2016; Ye, Van Eps, Zimmer, Ernst, & Prosser, 2016; Zhuang et al, 2013). For the specific purpose of understanding anesthetic interactions with proteins, NMR has been used to determine the structures of anesthetic targets (Bondarenko et al, 2012; Bondarenko et al, 2014; Bondarenko, Tillman, Xu, & Tang, 2010; Cui et al, 2012; Ma, Brandon, et al, 2008; Ma, Liu, Li, Tang, & Xu, 2005; Ma, Tillman, et al, 2008; Mowrey, Cui, et al, 2013; Mowrey, Kinde, Xu, & Tang, 2015; Tang, Mandal, & Xu, 2002), identify anesthetic binding sites in proteins (Bondarenko, Mowrey, Liu, Xu, & Tang, 2013; Bondarenko et al, 2014; Bondarenko, Yushmanov, Xu, & Tang, 2008; Kinde, Bondarenko, et al, 2016; Kinde, Bu, et al, 2016; Mowrey, Liu, et al, 2013; Tang, Eckenhoff, & Xu, 2000), characterize the direct interactions between proteins and anesthetics over a broad range of binding affinities (Bondarenko et al, 2013; Bondarenko et al, 2008; Canlas, Cui, Li, Xu, & Tang, 2008; Cui et al, 2008; Ma, Brandon, et al, 2008; Tang et al, 2000; Tang, Hu, Liachenko, & Xu, 1999; Xu, Seto, Tang, & Firestone, 2000; Xu, Tang, Firestone, & Zhang, 1996), and determine how anesthetic binding affects protein structures and dynamics (Canlas et al, 2008; Cui et al, 2008; Cui, Canlas, Xu, & Tang, 2010; Mowrey, Liu, et al, 2013).…”

Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport

“…Spectroscopic approaches have long complemented static structural methods, providing information on protein allostery, ligand binding, and other dynamic processes [40, 41]. A prominent example is nuclear magnetic resonance (NMR) spectroscopy, which can be used to characterize individual atoms in a molecule based on variations in local magnetic fields around isotope labeled nuclei (e.g.…”

Effect of OATP1B1 genetic polymorphism on the uptake of tamoxifen and its metabolite, endoxifen

“…Drugs enter into hepatocytes through influx transporters in addition to the diffusion into blood flow, and will be metabolized by hepatic enzymes and then be transported from hepatocytes into blood flow or into bile to complete the process of drug clearance (1). The absorption, distribution, excretion and transportation of drugs by cell membranes are inseparable from drug transporters (2).…”