Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions

Liu, Xu; Speckhard, David C.; Shepherd, Tyson R.; Sun, Young Joo; Hengel, Sarah R; Yu, Liping; Fowler, Audrée V.; Gakhar, Lokesh; Fuentes, Ernesto J.

doi:10.1016/j.str.2016.08.019

Cited by 23 publications

(26 citation statements)

References 63 publications

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“…Altogether these data uphold the view that the affinity of MnmEG and its homologs to ammonium, glycine and taurine in the presence of different substrate tRNAs may be a key factor for regulating the modification reaction. In this respect, the conformational dynamics of MnmG could play a relevant role in the interaction with the reaction substrates [23], as conformational dynamics can be crucial in tuning the affinity and specificity of molecular interactions [24]. …”

Section: Resultsmentioning

confidence: 99%

Bacillus subtilis exhibits MnmC-like tRNA modification activities

et al. 2018

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The MnmE-MnmG complex of Escherichia coli uses either ammonium or glycine as a substrate to incorporate the 5-aminomethyl or 5-carboxymethylaminomethyl group into the wobble uridine of certain tRNAs. Both modifications can be converted into a 5-methylaminomethyl group by the independent oxidoreductase and methyltransferase activities of MnmC, which respectively reside in the MnmC(o) and MnmC(m) domains of this bifunctional enzyme. MnmE and MnmG, but not MnmC, are evolutionarily conserved. Bacillus subtilis lacks genes encoding MnmC(o) and/or MnmC(m) homologs. The glycine pathway has been considered predominant in this typical gram-positive species because only the 5-carboxymethylaminomethyl group has been detected in tRNALysUUU and bulk tRNA to date. Here, we show that the 5-methylaminomethyl modification is prevalent in B. subtilis tRNAGlnUUG and tRNAGluUUC. Our data indicate that B. subtilis has evolved MnmC(o)- and MnmC(m)-like activities that reside in non MnmC homologous protein(s), which suggests that both activities provide some sort of biological advantage.

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Section: Resultsmentioning

confidence: 99%

Bacillus subtilis exhibits MnmC-like tRNA modification activities

et al. 2018

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“…PGC1a Binding Rigidifies Local Dynamics around AF-2 Site of AncGR2 LBD. Protein dynamics are crucial for enzyme catalysis, ligand recognition, protein allostery, and molecular evolution (Henzler-Wildman and Kern, 2007;Tokuriki and Tawfik, 2009;Motlagh et al, 2014;Liu et al, 2016). Solution-based studies, including nuclear magnetic resonance spectroscopy and HDX coupled with mass spectrometry, allow for measuring protein motions to probe conformational fluctuations that are not readily observed in static crystal structures.…”

Section: Structural Analyses Of Gr Lbd-ligand-pgc1a Complexesmentioning

confidence: 99%

First High-Resolution Crystal Structures of the Glucocorticoid Receptor Ligand-Binding Domain–Peroxisome Proliferator-Activated γ Coactivator 1-α Complex with Endogenous and Synthetic Glucocorticoids

2019

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Both synthetic and endogenous glucocorticoids are important pharmaceutic drugs known to bind to the ligand-binding domain (LBD) of glucocorticoid receptor (GR), a member of the nuclear receptor (NR) superfamily. Ligand binding induces conformational changes within GR, resulting in subsequent DNA binding and differential coregulator recruitment, ultimately activating or repressing target gene expression. One of the most crucial coregulators is peroxisome proliferator-activated g coactivator 1-a (PGC1a), which acts to regulate energy metabolism by directly interacting with GR to modulate gene expression. However, the mechanisms through which PGC1a senses GR conformation to drive transcription are not completely known. Here, an ancestral variant of the GR (AncGR2) LBD was used as a tool to produce stable protein for biochemical and structural studies. PGC1a is found to interact more tightly and form a more stable complex with AncGR2 LBD than nuclear receptor coactivator 2. We report the first high-resolution X-ray crystal structures of AncGR2 LBD in complex with PGC1a and dexamethasone (DEX) or hydrocortisone (HCY). Structural analyses reveal how distinct steroid drugs bind to GR with different affinities by unique hydrogen bonds and hydrophobic interactions. Important charge clamps are formed between the activation function 2 and PGC1a to mediate their specific interactions. These interactions lead to a high level of protection from hydrogen-deuterium exchange at the coregulator interaction site and strong intramolecular allosteric communication to ligand binding site. This is the first structure detailing the GR-PGC1a interaction providing a foundation for future design of specific therapeutic agents targeting these critical metabolic regulators. SIGNIFICANCE STATEMENT High-resolution structures of AncGR2 LBD bound to DEX and HCY in complex with PGC1a reveal the molecular mechanism of PGC1a binding to AncGR2 LBD as well as the distinct affinities between DEX and HCY binding. Identifying the structural mechanisms that drive drug affinity is of pharmacologic interest to the glucocorticoid receptor field as an avenue to guide future drug design targeting GR-PGC1a signaling, which plays a crucial role in controlling hepatic glucose output.

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“…However, eight PDZ complexes in the PDB that have Val at the peptide C-terminus all have a different orientation of their α 2 helix, which may increase slightly the volume of the P0 binding pocket. The structure of the QM:Neurexin complex supports this idea, as the Neurexin peptide contains Val at position 0 and the α 2 helix orientation is changed relative to that in WT Tiam1 PDZ (Liu et al, 2016 ). With the larger Met0 side chain, WT:Sdc1-A0M also binds very weakly, ΔΔ G = 1.56 kcal/mol.…”

Section: Resultsmentioning

confidence: 93%

“…The peptides were bound to either the wildtype Tiam1 PDZ domain (WT) or a variant containing four amino acid changes (quadruple mutant or QM). The four complexes are WT:Sdc1 (PDB 4GVD) (Liu et al, 2013 ), WT:consensus (PDB 3KZE) (Shepherd et al, 2010 ), QM:Caspr4 (PDB 4NXQ) (Liu et al, 2016 ), and QM:Neurexin (PDB 4NXR) (Liu et al, 2016 ). Ten other complexes involving Caspr4 or its F0A mutant were modeled starting from QM:Caspr4.…”

Section: Methodsmentioning

confidence: 99%

A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain

Panel

Sun

Fuentes

et al. 2017

Front. Mol. Biosci.

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PDZ domains generally bind short amino acid sequences at the C-terminus of target proteins, and short peptides can be used as inhibitors or model ligands. Here, we used experimental binding assays and molecular dynamics simulations to characterize 51 complexes involving the Tiam1 PDZ domain and to test the performance of a semi-empirical free energy function. The free energy function combined a Poisson-Boltzmann (PB) continuum electrostatic term, a van der Waals interaction energy, and a surface area term. Each term was empirically weighted, giving a Linear Interaction Energy or “PB/LIE” free energy. The model yielded a mean unsigned deviation of 0.43 kcal/mol and a Pearson correlation of 0.64 between experimental and computed free energies, which was superior to a Null model that assumes all complexes have the same affinity. Analyses of the models support several experimental observations that indicate the orientation of the α2 helix is a critical determinant for peptide specificity. The models were also used to predict binding free energies for nine new variants, corresponding to point mutants of the Syndecan1 and Caspr4 peptides. The predictions did not reveal improved binding; however, they suggest that an unnatural amino acid could be used to increase protease resistance and peptide lifetimes in vivo. The overall performance of the model should allow its use in the design of new PDZ ligands in the future.

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Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions

Cited by 23 publications

References 63 publications

Bacillus subtilis exhibits MnmC-like tRNA modification activities

Bacillus subtilis exhibits MnmC-like tRNA modification activities

First High-Resolution Crystal Structures of the Glucocorticoid Receptor Ligand-Binding Domain–Peroxisome Proliferator-Activated γ Coactivator 1-α Complex with Endogenous and Synthetic Glucocorticoids

A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain

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