Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors.

Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD) simulations. We introduce a computational framework that provides a compact representation of the dynamic conformational space of biomolecular simulations. This method presents a systematic approach designed to reduce the large MD simulation spatiotemporal datasets into a manageable set in order to guide our understanding of how protein mechanics emerge from side chain organization and dynamic reorganization. We focus on the detection of side chain interactions that undergo rearrangements mediating global domain motions and vice versa. Side chain rearrangements are extracted from side chain interactions that undergo well-defined abrupt and persistent changes in distance time series using Gaussian mixture models, whereas global domain motions are detected using dynamic cross-correlation. Both side chain rearrangements and global domain motions represent the dynamic components of the protein MD simulation, and are both mapped into a network where they are connected based on their degree of coupling. This method allows for the study of allosteric communication in proteins by mapping out the protein dynamics into an intramolecular network to reduce the large simulation data into a manageable set of communities composed of coupled side chain rearrangements and global domain motions. This computational framework is suitable for the study of tightly packed proteins, such as G protein-coupled receptors, and we present an application on a seven microseconds MD trajectory of CC chemokine receptor 7 (CCR7) bound to its ligand CCL21

Syndrome des antisynthétases compliqué d’une myocardite sévère

Le syndrome des antisynthétases correspond à l'association d'une myosite, une polyarthrite, un phénomène de Raynaud, une atteinte pulmonaire interstitielle et une hyperkératose fissurée des mains. Des anticorps de type «antisynthétases», en particulier l'anticorps anti-Jo1caractérise ce syndrome. L'atteinte cardiaque est rare, pouvant être parfois fatale. Patient âgé de 42 ans, hospitalisé pour des myalgies diffuses évoluant depuis un mois, une polyarthrite des genoux et des poignets, une dyspnée récente et un phénomène de Raynaud. L'examen physique a révélé une tachycardie sinusale à 110 battements /minute, un déficit musculaire prédominant aux ceintures, une hyperkératose fissurée des paumes des mains et des râles sous crépitants aux deux bases pulmonaires. L'examen biologique a montré un taux élevé des enzymes musculaires à 5 fois la normale, un syndrome inflammatoire, un bilan hépatique et rénal sans anomalies. L'électromyogramme a confirmé un tracé de type myogène. Le bilan immunologique a révélé la présence d'anticorps anti-Jo1. Les explorations fonctionnelles respiratoires ont conclut à un syndrome restrictif sévère. Le scanner thoracique a retrouvé un aspect en rayon de miel évocateur d'une fibrose pulmonaire. Un syndrome des antisynthétases a été évoqué. Le traitement s'est basé sur une corticothérapie associée aux boli de cyclophosphamide. L'évolution était marquée par l'amélioration des signes musculaires et articulaires. Devant la persistance de la tachycardie inexpliquée et l'aggravation de la dyspnée, des explorations cardiaques ont été réalisées montrant une myocardite compliquée d'une insuffisance cardiaque sévère. Le patient était rapidement décédé dans un tableau de défaillance cardiaque compliqué d'un état de choc.Le syndrome des antisynthétases correspond à l'association d'une myosite, une polyarthrite, un phénomène de Raynaud, une atteinte pulmonaire interstitielle et une hyperkératose fissurée des mains. Des anticorps de type «antisynthétases», en particulier l'anticorps anti-Jo1caractérise ce syndrome. L'atteinte cardiaque est rare, pouvant être parfois fatale. Patient âgé de 42 ans, hospitalisé pour des myalgies diffuses évoluant depuis un mois, une polyarthrite des genoux et des poignets, une dyspnée récente et un phénomène de Raynaud. L'examen physique a révélé une tachycardie sinusale à 110 battements /minute, un déficit musculaire prédominant aux ceintures, une hyperkératose fissurée des paumes des mains et des râles sous crépitants aux deux bases pulmonaires. L'examen biologique a montré un taux élevé des enzymes musculaires à 5 fois la normale, un syndrome inflammatoire, un bilan hépatique et rénal sans anomalies. L'électromyogramme a confirmé un tracé de type myogène. Le bilan immunologique a révélé la présence d'anticorps anti-Jo1. Les explorations fonctionnelles respiratoires ont conclut à un syndrome restrictif sévère. Le scanner thoracique a retrouvé un aspect en rayon de miel évocateur d'une fibrose pulmonaire. Un syndrome des antisynthétases a été évoqué. Le traitement s'est basé sur une corticothérapie associée aux boli de cyclophosphamide. L'évolution était marquée par l'amélioration des signes musculaires et articulaires. Devant la persistance de la tachycardieinexpliquée et l'aggravation de la dyspnée, des explorations cardiaques ont été réalisées montrant une myocardite compliquée d'une insuffisance cardiaque sévère. Le patient était rapidement décédé dans un tableau de défaillance cardiaque compliqué d'un état de choc

Dissecting Distinct Roles of NEDDylation E1 Ligase Heterodimer APPBP1 and UBA3 Reveals Potential Evolution Process for Activation of Ubiquitin-related Pathways.

Despite the similar enzyme cascade in the Ubiquitin and Ubiquitin-like peptide(Ubl) conjugation, the involvement of single or heterodimer E1 activating enzyme has been a mystery. Here, by using a quantitative Förster Resonance Energy Transfer (FRET) technology, aided with Analysis of Electrostatic Similarities Of Proteins (AESOP) computational framework, we elucidate in detail the functional properties of each subunit of the E1 heterodimer activating-enzyme for NEDD8, UBA3 and APPBP1. In contrast to SUMO activation, which requires both subunits of its E1 heterodimer AOS1-Uba2 for its activation, NEDD8 activation requires only one of two E1 subunits, UBA3. The other subunit, APPBP1, only contributes by accelerating the activation reaction rate. This discovery implies that APPBP1 functions mainly as a scaffold protein to enhance molecular interactions and facilitate catalytic reaction. These findings for the first time reveal critical new mechanisms and a potential evolutionary pathway for Ubl activations. Furthermore, this quantitative FRET approach can be used for other general biochemical pathway analysis in a dynamic mode

Beyond Shielding: The Roles of Glycans in the SARS-CoV‑2 Spike Protein

The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 28,000,000 infections and 900,000 deaths worldwide to date. Antibody development efforts mainly revolve around the extensively glycosylated SARS-CoV-2 spike (S) protein, which mediates host cell entry by binding to the angiotensin-converting enzyme 2 (ACE2). Similar to many other viral fusion proteins, the SARS-CoV-2 spike utilizes a glycan shield to thwart the host immune response. Here, we built a full-length model of the glycosylated SARS-CoV-2 S protein, both in the open and closed states, augmenting the available structural and biological data. Multiple microsecond-long, all-atom molecular dynamics simulations were used to provide an atomistic perspective on the roles of glycans and on the protein structure and dynamics. We reveal an essential structural role of N-glycans at sites N165 and N234 in modulating the conformational dynamics of the spike’s receptor binding domain (RBD), which is responsible for ACE2 recognition. This finding is corroborated by biolayer interferometry experiments, which show that deletion of these glycans through N165A and N234A mutations significantly reduces binding to ACE2 as a result of the RBD conformational shift toward the “down” state. Additionally, end-to-end accessibility analyses outline a complete overview of the vulnerabilities of the glycan shield of the SARS-CoV-2 S protein, which may be exploited in the therapeutic efforts targeting this molecular machine. Overall, this work presents hitherto unseen functional and structural insights into the SARS-CoV-2 S protein and its glycan coat, providing a strategy to control the conformational plasticity of the RBD that could be harnessed for vaccine development

The Groebke-Blackburn-Bienayme Reaction

Imidazo[1,2a]pyridine is a well‐known scaffold in many marketed drugs, such as Zolpidem, Minodronic acid, Miroprofen and DS‐1 and it also serves as a broadly applied pharmacophore in drug discovery. The scaffold revoked a wave of interest when Groebke, Blackburn and Bienaymé reported independently a new three component reaction resulting in compounds with the imidazo[1,2‐a]‐heterocycles as a core structure. During the course of two decades the Groebke Blackburn Bienaymé (GBB‐3CR) reaction has emerged as a very important multicomponent reaction (MCR), resulting in over a hundred patents and a great number of publications in various fields of interest. Now two compounds derived from GBB‐3CR chemistry received FDA approval. To celebrate the first 20 years of GBB‐chemistry , we present an overview of the chemistry of the GBB‐3CR, including an analysis of each of the three starting material classes, solvents and catalysts. Additionally, a list of patents and their applications and a more in‐depth summary of the biological targets that were addressed, including structural biology analysis, is given

In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR

A plethora of databases exist online that can assist in in silico chemical or drug safety assessment. However, a systematic review and grouping of databases, based on purpose and information content, consolidated in a single source has been lacking. To resolve this issue, this review provides a comprehensive listing of the key in silico data resources relevant to: chemical identity and properties, drug action, toxicology (including nano-material toxicity), exposure, omics, pathways, Absorption, Distribution, Metabolism and Elimination (ADME) properties, clinical trials, pharmacovigilance, patents-related databases, biological (genes, enzymes, proteins, other macromolecules etc.) databases, protein-protein interactions (PPIs), environmental exposure related, and finally databases relating to animal alternatives in support of 3Rs policies. More than nine hundred databases were identified and reviewed against criteria relating to accessibility, data coverage, interoperability or application programming interface (API), appropriate identifiers, types of in vitro-in vivo -clinical data recorded and suitability for modelling, read-across or similarity searching. This review also specifically addresses the need for solutions for mapping and integration of databases into a common platform for better translatability of preclinical data to clinical data

Molecular Switches Coordinate Dynamically Coupled Allosteric Networks in Protein Complexes

Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational transitions, which are typically captured by molecular dynamics (MD) simulations. Conformational state transitions in a protein involve shifts in its equilibrium conformations that occur either independently or as a response to external perturbations. In this work, we describe the effect of ligand binding and post-translational modifications (PTMs) to proteins as an external perturbation responsible for conformational changes in chemokine receptor 7 (CCR7) and the KU70-KU80 protein complex, respectively. In both systems, we isolate specific side chain rearrangements that act as molecular switches, and mediate the allosteric communication between distant functional sites in a protein, as a mechanism to regulate conformational state transitions and sampling. Specifically, in CCR7, we focus on the role of allostery in regulating the information transduced from the ligand-binding site to the intracellular region of the receptor to allow discrimination in binding intracellular effectors. This phenomenon is known as biased activation and is critical to G protein-coupled receptor function. In our work, we detect a series of molecular switches in CCR7 that are coupled to various ligand-induced allosteric events. Although these molecular switches mediate the transitioning between different states, the receptor remains inactive (absence of the canonical TM6 outward movement), illustrating loose coupling between the extracellular ligand-binding site and the intracellular effector-binding site. This finding might justify the existence of a novel hybrid model in CCR7, consisting of a “rhodopsin-like” sequential network of allosteric events (mediated by molecular switches) and a “β2-adrenergic-like” loose coupling between the extracellular and intracellular regions of the receptor. Furthermore, MD simulations of the ligand-free receptor highlight the importance of the ligand in coordinating the receptor’s side-chain fluctuations. We also focus on developing new methods to systematically detect coupled molecular switches and large domain motions in membrane proteins. Finally, we used MD simulations and electrostatic calculations to identify the role of PTMs, such as acetylation and methylation, on KU70-KU80’s dynamics. Such PTMs are shown to regulate conformational changes within several of KU70’s functional domains through acetylation-dependent alteration of the electrostatic profile of the DNA-binding and linker-SAP domains, and methylation-dependent molecular switching that is responsible for regulating a “pendulum-like” motion in linker-SAP domain