Vibrational anisotropy decay resolves rare earth binding induced conformational change in DTPA.

Elucidating the relationship between metal-ligand interactions and the associated conformational change of the ligand is critical for understanding the separation of lanthanides ion binding. Here we examine DTPA, a multidentate ligand that binds lanthanides, in its free and metal bound conformations using ultrafast polarization dependent vibrational spectroscopy. The polarization dependent pump-probe spectra were analyzed to extract the isotropic and anisotropic response of DTPA's carbonyl groups in the 1550-1650 cm spectral region.

SARS-CoV-2 seroprevalence in French 9-year-old children and their parents after the first lockdown in 2020.

Introduction: Children have been significantly less affected by COVID-19 than adults and presented with milder and less symptomatic forms of the disease. However, there has been suggestion that children older than 10 years and adolescents exhibits features closer to that of young adults. Most studies combine children in different age-groups and lack sufficient numbers to explore in detail age specificities.

Parents' depression and anxiety associated with hyperactivity-inattention and emotional symptoms in children during school closure due to COVID-19 in France.

Several risk factors of children's mental health issues have been identified during the pandemic of COronaVIrus Disease first appeared in 2019 (COVID-19). This study aims to fill the knowledge gap regarding the association between parents' and children's mental health issues during the COVID-19 school closure in France. We conducted a cross-sectional analysis of data collected in the SAPRIS-ELFE study during the COVID-19 pandemic in France.

Pre- and post-natal exposure of children to organophosphate flame retardants: A nationwide survey in France.

The use of organophosphate flame retardants (OPFRs) has been on the rise ever since many brominated flame retardants were banned, back in the 2000 s. The objectives of this study are to describe the pre- and post-natal exposure of children to OPFRs, and to explore their possible determinants. A total of 259 children aged 3.

Longitudinal impact of psychosocial status on children's mental health in the context of COVID-19 pandemic restrictions.

Emerging research suggests that the prevalence of child and adolescent mental health problems has increased considerably during the COVID-19 crisis. However, there have been few longitudinal studies on children's mental health issues according to their social determinants in this context, especially in Europe. Our aim was to investigate the association between family socioeconomic status (SES) and children' mental health during the period of school closure due to COVID-19.

Children's mental and behavioral health, schooling, and socioeconomic characteristics during school closure in France due to COVID-19: the SAPRIS project.

COVID-19 limitation strategies have led to widespread school closures around the world. The present study reports children's mental health and associated factors during the COVID-19 school closure in France in the spring of 2020. We conducted a cross-sectional analysis using data from the SAPRIS project set up during the COVID-19 pandemic in France.

MoMA-LoopSampler: a web server to exhaustively sample protein loop conformations.

Summary: MoMA-LoopSampler is a sampling method that globally explores the conformational space of flexible protein loops. It combines a large structural library of three-residue fragments and a novel reinforcement-learning-based approach to accelerate the sampling process while maintaining diversity. The method generates a set of statistically likely loop states satisfying geometric constraints, and its ability to sample experimentally observed conformations has been demonstrated.

Protein loops with multiple meta-stable conformations: A challenge for sampling and scoring methods.

Flexible regions in proteins, such as loops, cannot be represented by a single conformation. Instead, conformational ensembles are needed to provide a more global picture. In this context, identifying statistically meaningful conformations within an ensemble generated by loop sampling techniques remains an open problem.

A reinforcement-learning-based approach to enhance exhaustive protein loop sampling.

Motivation: Loop portions in proteins are involved in many molecular interaction processes. They often exhibit a high degree of flexibility, which can be essential for their function. However, molecular modeling approaches usually represent loops using a single conformation.

Conformational changes in antibody Fab fragments upon binding and their consequences on the performance of docking algorithms.

Background: The existence of conformational changes in antibodies upon binding has been previously established. However, existing analyses focus on individual cases and no quantitative study provides a more global view of potential moves and repacking, especially on recent data. The present study focuses on analyzing the conformational changes in various antibodies upon binding, providing quantitative observations to be exploited for antibody-related modeling.

Segmenting Proteins into Tripeptides to Enhance Conformational Sampling with Monte Carlo Methods.

This paper presents an approach to enhance conformational sampling of proteins employing stochastic algorithms such as Monte Carlo (MC) methods. The approach is based on a mechanistic representation of proteins and on the application of methods originating from robotics. We outline the general ideas of our approach and detail how it can be applied to construct several MC move classes, all operating on a shared representation of the molecule and using a single mathematical solver.

Characterizing Energy Landscapes of Peptides Using a Combination of Stochastic Algorithms.

Obtaining accurate representations of energy landscapes of biomolecules such as proteins and peptides is central to the study of their physicochemical properties and biological functions. Peptides are particularly interesting, as they exploit structural flexibility to modulate their biological function. Despite their small size, peptide modeling remains challenging due to the complexity of the energy landscape of such highly-flexible dynamic systems.

Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods.

Background: Obtaining atomic-scale information about large-amplitude conformational transitions in proteins is a challenging problem for both experimental and computational methods. Such information is, however, important for understanding the mechanisms of interaction of many proteins.

Methods: This paper presents a computationally efficient approach, combining methods originating from robotics and computational biophysics, to model protein conformational transitions.

Structure and electronic spectra of purine-methyl viologen charge transfer complexes.

The structure and properties of the electron donor-acceptor complexes formed between methyl viologen and purine nucleosides and nucleotides in water and the solid state have been investigated using a combination of experimental and theoretical methods. Solution studies were performed using UV-vis and (1)H NMR spectroscopy. Theoretical calculations were performed within the framework of density functional theory (DFT).

Nature of noncovalent interactions in catenane supramolecular complexes: calibrating the MM3 force field with ab initio, DFT, and SAPT methods.

The design and assembly of mechanically interlocked molecules, such as catenanes and rotaxanes, are dictated by various types of noncovalent interactions. In particular, [C-H···O] hydrogen-bonding and π-π stacking interactions in these supramolecular complexes have been identified as important noncovalent interactions. With this in mind, we examined the [3]catenane 2·4PF6 using molecular mechanics (MM3), ab initio methods (HF, MP2), several versions of density functional theory (DFT) (B3LYP, M0X), and the dispersion-corrected method DFT-D3.

MoMA-LigPath: a web server to simulate protein-ligand unbinding.

Protein-ligand interactions taking place far away from the active site, during ligand binding or release, may determine molecular specificity and activity. However, obtaining information about these interactions with experimental or computational methods remains difficult. The computational tool presented in this article, MoMA-LigPath, is based on a mechanistic representation of the molecular system, considering partial flexibility, and on the application of a robotics-inspired algorithm to explore the conformational space.

Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase.

Dynamics is a key feature of enzyme catalysis. Unfortunately, current experimental and computational techniques do not yet provide a comprehensive understanding and description of functional macromolecular motions. In this work, we have extended a novel computational technique, which combines molecular modeling methods and robotics algorithms, to investigate functional motions of protein loops.

Enhancing systematic protein-protein docking methods using ray casting: application to ATTRACT.

Systematic protein-protein docking methods need to evaluate a huge number of different probe configurations, thus leading to high computational cost. We present an efficient filter-ray casting filter (RCF)-that enables a notable speed-up of systematic protein-protein docking. The high efficiency of RCF is the outcome of the following factors: (i) extracting of pockets and protrusions on the surfaces of the proteins using visibilities; (ii) a ray casting method that finds aligned receptor pocket/probe protrusion pairs without explicit similarity computations.

Theoretical investigation into the structural, thermochemical, and electronic properties of the decathio[10]circulene.

For the first time, a theoretical study has been performed on the prototypical decathio[10]circulene (C(20)S(10)) species, which is an analogue of the novel octathio[8]circulene "Sulflower" molecule (C(16)S(8)). Examinations of the singlet and triplet states of C(20)S(10) were made at the B3LYP/6-311G(d) level. Local minima of C(2) and C(s) symmetry were found for the lowest singlet and triplet states, respectively.

A mixed molecular modeling-robotics approach to investigate lipase large molecular motions.

Large-scale conformational rearrangement of a lid subdomain is a key event in the interfacial activation of many lipases. We present herein a study in which the large-scale "open-to-closed" movement of Burkholderia cepacia lipase lid has been simulated at the atomic level using a hybrid computational method. The two-stage approach combines path-planning algorithms originating from robotics and molecular mechanics methods.

Simulating ligand-induced conformational changes in proteins using a mechanical disassembly method.

Simulating protein conformational changes induced or required by the internal diffusion of a ligand is important for the understanding of their interaction mechanisms. Such simulations are challenging for currently available computational methods. In this paper, the problem is formulated as a mechanical disassembly problem where the protein and the ligand are modeled like articulated mechanisms, and an efficient method for computing molecular disassembly paths is described.