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Instruments / Technical Area	Publication Details	Published
	DNET: A graph-based tool and workflow for dynamic hydrogen-bond networks and applications for visual rhodopsins Éva Bertalan , Matthew J. Rodrigues , Deborah Walter , Gebhard F. X. Schertler , Ana-Nicoleta Bondar Journal Of Chemical Theory And Computation DOI: 10.1021/acs.jctc.5c01366 Show Abstract ▼ Abstract: G Protein-Coupled Receptors (GPCRs) mediate signal transduction across cellular membranes and are major drug targets. Activation of these receptors upon binding of an extracellular ligand involves propagation of structural change across the transmembrane domain to the cytoplasmic G protein partner, a process generally thought to involve dynamic hydrogen(H)-bond networks. Here we present DNET, a graph-based tool and workflow that enables efficient computations of dynamic protein–water H-bond networks. DNET is a fully portable Python tool that reads simulation trajectories, computes graphs of the dynamic protein–water H-bond networks, and generates, for each H-bonding residue, a residue summary that includes water interactions, H-bond time series, histograms, potential of mean force estimates, and the number of conformations of the H-bond. To facilitate estimates of pKa fluctuations within the H-bond network, DNET calls PROPKA and computes, for each titratable residue that is part of the H-bond network, time series and analyses of the pKa estimates. To illustrate the usefulness of DNET we apply it to study the wild-type and two mutations of jumping spider rhodopsin 1, JSR-1, a visual rhodopsin GPCR activated by the photoisomerization of the covalently bound retinal chromophore. The UV–vis data we present here demonstrate that the mutated JSR-1 proteins express, but both have an altered electrostatic environment of the retinal Schiff base. The DNET analyses indicate a highly complex dynamics of the retinal H-bond network, with some H-bonds that have only one conformational mode, and other H-bonds with multiple conformational modes separated by small energy barriers, and pKa fluctuations that associate with the H-bond dynamics. The mutations associate with an altered H-bond network of the retinal Schiff base.	Jan 2026
	Accurate estimation of diffusion coefficients and their uncertainties from computer simulation Andrew R. Mccluskey , Samuel W. Coles , Benjamin J. Morgan Journal Of Chemical Theory And Computation 45 DOI: 10.1021/acs.jctc.4c01249 Open Access Show Abstract ▼ Abstract: Self-diffusion coefficients, D, are routinely estimated from molecular dynamics simulations by fitting a linear model to the observed mean squared displacements (MSDs) of mobile species. MSDs derived from simulations exhibit statistical noise that causes uncertainty in the resulting estimate of D. An optimal scheme for estimating D* minimizes this uncertainty, i.e., it will have high statistical efficiency, and also gives an accurate estimate of the uncertainty itself. We present a scheme for estimating D* from a single simulation trajectory with a high statistical efficiency and accurately estimating the uncertainty in the predicted value. The statistical distribution of MSDs observable from a given simulation is modeled as a multivariate normal distribution using an analytical covariance matrix for an equivalent system of freely diffusing particles, which we parametrize from the available simulation data. We use Bayesian regression to sample the distribution of linear models that are compatible with this multivariate normal distribution to obtain a statistically efficient estimate of D* and an accurate estimate of the associated statistical uncertainty.	Dec 2024
B21-High Throughput SAXS	Accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for molecular simulations Federico Ballabio , Cristina Paissoni , Michela Bollati , Matteo De Rosa , Riccardo Capelli , Carlo Camilloni Journal Of Chemical Theory And Computation DOI: 10.1021/acs.jctc.3c00864 Diamond Proposal Number(s): [20221] Open Access Show Abstract ▼ Abstract: Small-angle X-ray and neutron scattering (SAXS/SANS) provide valuable insights into the structure and dynamics of biomolecules in solution, complementing a wide range of structural techniques, including molecular dynamics simulations. As contrast-based methods, they are sensitive not only to structural properties but also to solvent–solute interactions. Their use in molecular dynamics simulations requires a forward model that should be as fast and accurate as possible. In this work, we demonstrate the feasibility of calculating SAXS and SANS intensities using a coarse-grained representation consisting of one bead per amino acid and three beads per nucleic acid, with form factors that can be corrected on the fly to account for solvation effects at no additional computational cost. By coupling this forward model with molecular dynamics simulations restrained with SAS data, it is possible to determine conformational ensembles or refine the structure and dynamics of proteins and nucleic acids in agreement with the experimental results. To assess the robustness of this approach, we applied it to gelsolin, for which we acquired SAXS data on its closed state, and to a UP1-microRNA complex, for which we used previously collected measurements. Our hybrid-resolution small-angle scattering (hySAS) implementation, being distributed in PLUMED, can be used with atomistic and coarse-grained simulations using diverse restraining strategies.	Nov 2023
I19-Small Molecule Single Crystal Diffraction	Gas transport in mixed matrix membranes: Two methods for time lag determination Alessio Fuoco , Marcello Monteleone , Elisa Esposito , Rosaria Bruno , Jesus Ferrando-Soria , Emilio Pardo , Donatella Armentano , Johannes Carolus Jansen Computation 8(2), 28 DOI: 10.3390/computation8020028 Diamond Proposal Number(s): [18768] Open Access Show Abstract ▼ Abstract: The most widely used method to measure the transport properties of dense polymeric membranes is the time lag method in a constant volume/pressure increase instrument. Although simple and quick, this method provides only relatively superficial, averaged data of the permeability, diffusivity, and solubility of gas or vapor species in the membrane. The present manuscript discusses a more sophisticated computational method to determine the transport properties on the basis of a fit of the entire permeation curve, including the transient period. The traditional tangent method and the fitting procedure were compared for the transport of six light gases (H2, He, O2, N2, CH4, and CO2) and ethane and ethylene in mixed matrix membranes (MMM) based on Pebax®1657 and the metal–organic framework (MOF) CuII2(S,S)-hismox·5H2O. Deviations of the experimental data from the theoretical curve could be attributed to the particular MOF structure, with cavities of different sizes. The fitting procedure revealed two different effective diffusion coefficients for the same gas in the case of methane and ethylene, due to the unusual void morphology in the MOFs. The method was furthermore applied to mixed gas permeation in an innovative constant-pressure/variable-volume setup with continuous analysis of the permeate composition by an on-line mass-spectrometric residual gas analyzer. This method can provide the diffusion coefficient of individual gas species in a mixture, during mixed gas permeation experiments. Such information was previously inaccessible, and it will greatly enhance insight into the mixed gas transport in polymeric or mixed matrix membranes.	Apr 2020
B21-High Throughput SAXS	Phosphorylation of a disordered peptide – structural effects and force field inconsistencies Ellen Rieloff , Marie Skepö Journal Of Chemical Theory And Computation DOI: 10.1021/acs.jctc.9b01190 Diamond Proposal Number(s): [24294] Open Access Show Abstract ▼ Abstract: Phosphorylation is one of the most abundant types of post-translational modifications of intrinsically disordered proteins (IDPs). This study examines the conformational changes in the 15 residue long N-terminal fragment of the IDP Statherin upon phosphorylation, using computer simulations with two different force fields: AMBER ff99SB-ILDN and CHARMM36m. The results from the simulations are compared with experimental small-angle X-ray scattering and circular dichroism data. In the unphosphorylated state, the two force fields are in excellent agreement regarding global structural properties such as size and shape, however, they exhibit some differences in the extent and type of secondary structure. In the phosphorylated state, neither of the force fields performs well compared to the experimental data. Both force fields show a compaction of the peptide upon phosphorylation, greater than what is seen in SAXS experiments, although they differ in local structure. While the CHARMM force field increases the fraction of bends in the peptide as a response to strong interactions between the phosphorylated residues and arginines, the AMBER force field shows an increase of helical content in the N-terminal part of the peptide, where the phosphorylated residues reside, in better agreement with circular dichroism results.	Feb 2020

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