Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of biomolecules and ...their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food sciences. Since 2010, the WeNMR project (
www.wenmr.eu
) has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field, using the high throughput computing infrastructure provided by EGI. These services have been further developed in subsequent initiatives under H2020 projects and are now operating as Thematic Services in the European Open Science Cloud portal (
www.eosc-portal.eu
), sending >12 millions of jobs and using around 4,000 CPU-years per year. Here we review 10 years of successful e-infrastructure solutions serving a large worldwide community of over 23,000 users to date, providing them with user-friendly, web-based solutions that run complex workflows in structural biology. The current set of active WeNMR portals are described, together with the complex backend machinery that allows distributed computing resources to be harvested efficiently.
Classical molecular dynamics (MD) simulations are widely used to inspect the behavior of zinc(II)-proteins at the atomic level, hence the need to properly model the zinc(II) ion and the interaction ...with its ligands. Different approaches have been developed to represent zinc(II) sites, with the bonded and nonbonded models being the most used. In the present work, we tested the well-known zinc AMBER force field (ZAFF) and a recently developed nonbonded force field (NBFF) to assess how accurately they reproduce the dynamic behavior of zinc(II)-proteins. For this, we selected as benchmark six zinc-fingers. This superfamily is extremely heterogenous in terms of architecture, binding mode, function, and reactivity. From repeated MD simulations, we computed the order parameter (S
) of all backbone N-H bond vectors in each system. These data were superimposed to heteronuclear Overhauser effect measurements taken by NMR spectroscopy. This provides a quantitative estimate of the accuracy of the FFs in reproducing protein dynamics, leveraging the information about the protein backbone mobility contained in the NMR data. The correlation between the MD-computed S
and the experimental data indicated that both tested FFs reproduce well the dynamic behavior of zinc(II)-proteins, with comparable accuracy. Thus, along with ZAFF, NBFF represents a useful tool to simulate metalloproteins with the advantage of being extensible to diverse systems such as those bearing dinuclear metal sites.
We investigated the kinetics of the release of iron(II) ions from the internal cavity of human H-ferritin as a function of pH. Extensive molecular dynamics simulations of the entire 24-mer ferritin ...provided atomic-level information on the release mechanism. Double protonation of His residues at pH 4 facilitates the removal of the iron ligands within the C3 channel through the formation of salt bridges, resulting in a significantly lower release energy barrier than pH 9.
Intrinsically disordered proteins (IDPs) are involved in a wide variety of physiological and pathological processes and are best described by ensembles of rapidly interconverting conformers. Using ...fast field cycling relaxation measurements we here show that the IDP α-synuclein as well as a variety of other IDPs undergoes slow reorientations at time scales comparable to folded proteins. The slow motions are not perturbed by mutations in α-synuclein, which are related to genetic forms of Parkinson’s disease, and do not depend on secondary and tertiary structural propensities. Ensemble-based hydrodynamic calculations suggest that the time scale of the underlying correlated motion is largely determined by hydrodynamic coupling between locally rigid segments. Our study indicates that long-range correlated dynamics are an intrinsic property of IDPs and offers a general physical mechanism of correlated motions in highly flexible biomolecular systems.
A comprehensive understanding of the dynamic behavior of a tree can play a key role in the tree stability analysis. Indeed, through an engineering approach, the living tree can be modeled as a ...mechanical system and monitored observing its dynamic properties. In the current work, procedures of dynamic identification used in civil engineering are applied to the case study of a black locust (Robinia pseudoacacia L.). The tree was instrumented with 13 seismic, high-sensitivity accelerometers. Time histories of the tree response under ambient vibration were recorded. Three representative sections of the trunk (the collar, the diameter at breast height, and the tree fork) were equipped with three accelerometers, in order to obtain lateral and torsional vibrations. Moreover, two pairs of accelerometers were fixed on the two main branches. The results show that it is possible to identify the natural frequencies of a tree under ambient vibrations, thanks also to the support of a preliminary finite element model. Even though the optimal position is under the tree fork, the sensors fixed at the diameter at breast height allow a clear identification of the main peaks in the frequency domain.
The concept of maximum occurrence (MO), i.e., the maximum percent of time that flexible proteins can spend in any given conformation, is introduced, and a rigorous method is developed to extensively ...sample the conformational space and to construct MO maps from experimental data. The method is tested in a case study, the flexible two-domain protein calmodulin (CaM), using SAXS and NMR data (i.e., pseudocontact shifts and self-orientation residual dipolar couplings arising from the presence of paramagnetic lanthanide ions), revealing that the “closed” and “fully extended” conformations trapped in the crystalline forms of CaM have MOs of only 5 and 15%, respectively. Compact conformations in general have small MOs, whereas some extended conformations have MO as high as 35%, strongly suggesting these conformations to be most abundant in solution. The method is universally applicable as it requires only standard SAXS data and specific NMR data on lanthanide derivatives of the protein (using native metal sites or lanthanide tagging). The computer program is publicly available using the grid computing infrastructure through the authors’ Web portal.
Biogenesis of iron–sulfur cluster proteins is a highly regulated process that requires complex protein machineries. In the cytosolic iron–sulfur protein assembly machinery, two human key ...proteins—NADPH-dependent diflavin oxidoreductase 1 (Ndor1) and anamorsin—form a stable complex in vivo that was proposed to provide electrons for assembling cytosolic iron–sulfur cluster proteins. The Ndor1–anamorsin interaction was also suggested to be implicated in the regulation of cell survival/death mechanisms. In the present work we unravel the molecular basis of recognition between Ndor1 and anamorsin and of the electron transfer process. This is based on the structural characterization of the two partner proteins, the investigation of the electron transfer process, and the identification of those protein regions involved in complex formation and those involved in electron transfer. We found that an unstructured region of anamorsin is essential for the formation of a specific and stable protein complex with Ndor1, whereas the C-terminal region of anamorsin, containing the 2Fe-2S redox center, transiently interacts through complementary charged residues with the FMN-binding site region of Ndor1 to perform electron transfer. Our results propose a molecular model of the electron transfer process that is crucial for understanding the functional role of this interaction in human cells.
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Protein assemblies are involved in many important biological processes. Solid-state NMR (SSNMR) spectroscopy is a technique suitable for the structural characterization of samples ...with high molecular weight and thus can be applied to such assemblies. A significant bottleneck in terms of both effort and time required is the manual identification of unambiguous intermolecular contacts. This is particularly challenging for homo-oligomeric complexes, where simple uniform labeling may not be effective. We tackled this challenge by exploiting coevolution analysis to extract information on homo-oligomeric interfaces from NMR-derived ambiguous contacts. After removing the evolutionary couplings (ECs) that are already satisfied by the 3D structure of the monomer, the predicted ECs are matched with the automatically generated list of experimental contacts. This approach provides a selection of potential interface residues that is used directly in monomer–monomer docking calculations. We validated the protocol on tetrameric L-asparaginase II and dimeric Sod1.
In this paper we introduce a novel framework for 3D object retrieval that relies on tree-based shape representations (TreeSha) derived from the analysis of the scale-space of the Auto Diffusion ...Function (ADF) and on specialized graph kernels designed for their comparison. By coupling maxima of the Auto Diffusion Function with the related basins of attraction, we can link the information at different scales encoding spatial relationships in a graph description that is isometry invariant and can easily incorporate texture and additional geometrical information as node and edge features. Using custom graph kernels it is then possible to estimate shape dissimilarities adapted to different specific tasks and on different categories of models, making the procedure a powerful and flexible tool for shape recognition and retrieval. Experimental results demonstrate that the method can provide retrieval scores similar or better than state-of-the-art on textured and non textured shape retrieval benchmarks and give interesting insights on effectiveness of different shape descriptors and graph kernels.
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