Protein conformational dynamics dictate the binding affinity for a ligand

Seo, Myung Won; Park, Jeongbin; Kim, Eunkyung; Hohng, Sungchul; Kim, Kwang Ho

doi:10.1038/ncomms4724

Cited by 121 publications

(134 citation statements)

References 38 publications

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“…To verify proper reconstitution, we observed the time duration of fluorescence bursts in a confocal microscope with McjD in detergent and in proteoliposomes and found the expected increase for proteoliposomes to about 10–20 ms (Fig EV3A) compared to ~1 ms for McjD in detergent micelles. These values are similar to reported ones for other diffusing liposome systems (Seo et al , 2014). Finally, we verified random insertion (inside‐out and inside‐in) of McjD into the proteoliposomes with a ratio of ca.…”

Section: Resultssupporting

confidence: 92%

Conformational dynamics of the ABC transporter McjD seen by single‐molecule FRET

et al. 2018

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ABC transporters utilize ATP for export processes to provide cellular resistance against toxins, antibiotics, and harmful metabolites in eukaryotes and prokaryotes. Based on static structure snapshots, it is believed that they use an alternating access mechanism, which couples conformational changes to ATP binding (outward‐open conformation) and hydrolysis (inward‐open) for unidirectional transport driven by ATP. Here, we analyzed the conformational states and dynamics of the antibacterial peptide exporter McjD from Escherichia coli using single‐molecule Förster resonance energy transfer (smFRET). For the first time, we established smFRET for an ABC exporter in a native‐like lipid environment and directly monitor conformational dynamics in both the transmembrane‐ (TMD) and nucleotide‐binding domains (NBD). With this, we unravel the ligand dependences that drive conformational changes in both domains. Furthermore, we observe intrinsic conformational dynamics in the absence of ATP and ligand in the NBDs. ATP binding and hydrolysis on the other hand can be observed via NBD conformational dynamics. We believe that the progress made here in combination with future studies will facilitate full understanding of ABC transport cycles.

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Section: Resultssupporting

confidence: 92%

Conformational dynamics of the ABC transporter McjD seen by single‐molecule FRET

et al. 2018

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“…It has been frequently observed that enzymes in their free unliganded state sample 3D conformations that consist of those visited in the presence of the ligand (7). Differences in intrinsic conformational dynamics in the wild type and the mutant maltose-binding proteins have been shown to be related to association and dissociation of ligand and thereby to affect dissociation constants (8). Enzyme dynamics in Cyclophilin A (CypA), a peptidyl prolyl cis-trans isomerase, have been demonstrated to occur on the same millisecond timescale as the catalytic turnover (9).…”

mentioning

confidence: 99%

Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation

Doshi

Holliday

Eisenmesser

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

152

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Detailed understanding of how conformational dynamics orchestrates function in allosteric regulation of recognition and catalysis remains ambiguous. Here, we simulate CypA using multiple-microsecond-long atomistic molecular dynamics in explicit solvent and carry out NMR experiments. We analyze a large amount of time-dependent multidimensional data with a coarse-grained approach and map key dynamical features within individual macrostates by defining dynamics in terms of residue-residue contacts. The effects of substrate binding are observed to be largely sensed at a location over 15 Å from the active site, implying its importance in allostery. Using NMR experiments, we confirm that a dynamic cluster of residues in this distal region is directly coupled to the active site. Furthermore, the dynamical network of interresidue contacts is found to be coupled and temporally dispersed, ranging over 4 to 5 orders of magnitude. Finally, using network centrality measures we demonstrate the changes in the communication network, connectivity, and influence of CypA residues upon substrate binding, mutation, and during catalysis. We identify key residues that potentially act as a bottleneck in the communication flow through the distinct regions in CypA and, therefore, as targets for future mutational studies. Mapping these dynamical features and the coupling of dynamics to function has crucial ramifications in understanding allosteric regulation in enzymes and proteins, in general.allostery | enzyme dynamics | residue-residue contacts | Cyclophilin A | molecular dynamics

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“…The ability of the pocket to close around different ligands can contribute to specificity (5). Switching to the inactive state of the receptor dramatically increases the dissociation rate, so pocket dynamics controls the residence time of ligands (4,12), and thus the catalytic rate of most enzymes (3). The importance of the inactive state to association rates is less clear; inactive states have been shown have lower (4,12), similar (13), or higher (14) association rates relative to the active state, and the functional importance of the differences is unclear.…”

mentioning

confidence: 99%

Inactive conformation enhances binding function in physiological conditions

Yakovenko

Tchesnokova

Sokurenko

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Many receptors display conformational flexibility, in which the binding pocket has an open inactive conformation in the absence of ligand and a tight active conformation when bound to ligand. Here we study the bacterial adhesin FimH to address the role of the inactive conformation of the pocket for initiating binding by comparing two variants: a wild-type FimH variant that is in the inactive state when not bound to its target mannose, and an engineered activated variant that is always in the active state. Not surprisingly, activated FimH has a longer lifetime and higher affinity, and bacteria expressing activated FimH bound better in static conditions. However, bacteria expressing wild-type FimH bound better in flow. It is now known that few proteins recognize ligands through a lock and key mechanism, in which the binding pocket is in essentially the same conformation whether or not ligand is bound. Instead, the conformation of the binding pocket is usually dynamic. Conformational dynamics have many functions for receptors as well as enzymes, so for simplicity, we will use the term ligand to describe substrates and products as well as molecules that are not changed by binding. For allosteric proteins, an obvious function of conformational changes in the pocket is to allow regulation of ligand binding by an allosteric effector. For other proteins, flexibility in the binding pocket allows proteins to bind structurally distinct ligands (1), which may in turn facilitate evolution of new structures and functions (2, 3). In many cases, the inactive conformation of the pocket is relatively loose, and the active conformation tightens around the ligand, often due to the closing of a hinge (4) between two domains, or loops that are described as a gate (e.g., refs. 5-7) or a lid (e.g., refs. 8-11) because they close over the ligand in binding pocket. The ability of the pocket to close around different ligands can contribute to specificity (5). Switching to the inactive state of the receptor dramatically increases the dissociation rate, so pocket dynamics controls the residence time of ligands (4, 12), and thus the catalytic rate of most enzymes (3). The importance of the inactive state to association rates is less clear; inactive states have been shown have lower (4, 12), similar (13), or higher (14) association rates relative to the active state, and the functional importance of the differences is unclear.We hypothesize that inactive states can have faster ligand association rates, and that this is important for nonequilibrium processes, where the kinetics, or rates, of individual steps are more important than overall affinity because the process does not reach equilibrium. An example of a nonequilibrium process is cell adhesion. Because adhesive receptors bind to ligands that are anchored to other cells or surfaces, the adhesive bonds are subjected to tensile mechanical force due to cytoskeletal contraction, fluidflow-induced drag forces, or other stresses. This tensile force can only be applied between receptor and lig...

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Protein conformational dynamics dictate the binding affinity for a ligand

Cited by 121 publications

References 38 publications

Conformational dynamics of the ABC transporter McjD seen by single‐molecule FRET

Conformational dynamics of the ABC transporter McjD seen by single‐molecule FRET

Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation

Inactive conformation enhances binding function in physiological conditions

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