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DIRECT-ID: An automated method to identify and quantify conformational variations--application to ?2 -adrenergic GPCR.

ABSTRACT: The conformational dynamics of a macromolecule can be modulated by a number of factors, including changes in environment, ligand binding, and interactions with other macromolecules, among others. We present a method that quantifies the differences in macromolecular conformational dynamics and automatically extracts the structural features responsible for these changes. Given a set of molecular dynamics (MD) simulations of a macromolecule, the norms of the differences in covariance matrices are calculated for each pair of trajectories. A matrix of these norms thus quantifies the differences in conformational dynamics across the set of simulations. For each pair of trajectories, covariance difference matrices are parsed to extract structural elements that undergo changes in conformational properties. As a demonstration of its applicability to biomacromolecular systems, the method, referred to as DIRECT-ID, was used to identify relevant ligand-modulated structural variations in the ?2 -adrenergic (?2 AR) G-protein coupled receptor. Micro-second MD simulations of the ?2 AR in an explicit lipid bilayer were run in the apo state and complexed with the ligands: BI-167107 (agonist), epinephrine (agonist), salbutamol (long-acting partial agonist), or carazolol (inverse agonist). Each ligand modulated the conformational dynamics of ?2 AR differently and DIRECT-ID analysis of the inverse-agonist vs. agonist-modulated ?2 AR identified residues known through previous studies to selectively propagate deactivation/activation information, along with some previously unidentified ligand-specific microswitches across the GPCR. This study demonstrates the utility of DIRECT-ID to rapidly extract functionally relevant conformational dynamics information from extended MD simulations of large and complex macromolecular systems.

SUBMITTER: Lakkaraju SK

PROVIDER: S-EPMC4756637 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature

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DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR.

Lakkaraju Sirish Kaushik SK Lemkul Justin A JA Huang Jing J MacKerell Alexander D AD

Journal of computational chemistry 20151112 4

The conformational dynamics of a macromolecule can be modulated by a number of factors, including changes in environment, ligand binding, and interactions with other macromolecules, among others. We present a method that quantifies the differences in macromolecular conformational dynamics and automatically extracts the structural features responsible for these changes. Given a set of molecular dynamics (MD) simulations of a macromolecule, the norms of the differences in covariance matrices are c ...[more]

PMID: 26558323

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Project description:PurposeG protein-coupled receptors (GPCRs) are a superfamily of membrane proteins of vast pharmaceutical interest. Here, we describe a graph theory-based analysis of the structure of the β2 adrenergic receptor (β2 AR), a prototypical GPCR. In particular, we illustrate the network of direct and indirect interactions that link each amino acid residue to any other residue of the receptor.MethodsNetworks of interconnected amino acid residues in proteins are analogous to social networks of interconnected people. Hence, they can be studied through the same analysis tools typically employed to analyze social networks - or networks in general - to reveal patterns of connectivity, influential members, and dynamicity. We focused on the analysis of closeness-centrality, which is a measure of the overall connectivity distance of the member of a network to all other members.ResultsThe residues endowed with the highest closeness-centrality are located in the middle of the seven transmembrane domains (TMs). In particular, they are mostly located in the middle of TM2, TM3, TM6 or TM7, while fewer of them are located in the middle of TM1, TM4 or TM5. At the cytosolic end of TM6, the centrality detected for the active structure is markedly lower than that detected for the corresponding residues in the inactive structures. Moreover, several residues acquire centrality when the structures are analyzed in the presence of ligands. Strikingly, there is little overlap between the residues that acquire centrality in the presence of the ligand in the blocker-bound structures and the agonist-bound structures.ConclusionsOur results reflect the fact that the receptor resembles a bow tie, with a rather tight knot of closely interconnected residues and two ends that fan out in two opposite directions: one toward the extracellular space, which hosts the ligand binding cavity, and one toward the cytosol, which hosts the G protein binding cavity. Moreover, they underscore how interaction network is by the conformational rearrangements concomitant with the activation of the receptor and by the presence of agonists or blockers.

Project description:Glucose metabolism is under the cooperative regulation of both insulin receptor (IR) and β(2)-adrenergic receptor (β(2)AR), which represent the receptor tyrosine kinases (RTKs) and seven transmembrane receptors (7TMRs), respectively. Studies demonstrating cross-talk between these two receptors and their endogenous coexpression have suggested their possible interactions. To evaluate the effect of IR and prospective heteromerization on β(2)AR properties, we showed that IR coexpression had no effect on the ligand binding properties of β(2)AR; however, IR reduced β(2)AR surface expression and accelerated its internalization. Additionally, both receptors displayed a similar distribution pattern with a high degree of colocalization. To test the possible direct interaction between β(2)AR and IR, we employed quantitative BRET(2) saturation and competition assays. Saturation assay data suggested constitutive β(2)AR and IR homo- and heteromerization. Calculated acceptor/donor (AD50) values as a measure of the relative affinity for homo- and heteromer formation differed among the heteromers that could not be explained by a simple dimer model. In heterologous competition assays, a transient increase in the BRET(2) signal with a subsequent hyperbolical decrease was observed, suggesting higher-order heteromer formation. To complement the BRET(2) data, we employed the informational spectrum method (ISM), a virtual spectroscopy method to investigate protein-protein interactions. Computational peptide scanning of β(2)AR and IR identified intracellular domains encompassing residues at the end of the 7th TM domain and C-terminal tail of β(2)AR and a cytoplasmic part of the IR β chain as prospective interaction domains. ISM further suggested a high probability of heteromer formation and homodimers as basic units engaged in heteromerization. In summary, our data suggest direct interaction and higher-order β(2)AR:IR oligomer formation, likely comprising heteromers of homodimers.

Dataset Information

DIRECT-ID: An automated method to identify and quantify conformational variations--application to ?2 -adrenergic GPCR.

Publications

DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR.

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