Biology subjects

Antes, I.

Publications and source records attributed to Antes, I..

4 recordsLinked to original sources

bioRxiv2021

SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations

Computational methods play a key role for investigating allosteric mechanisms in proteins, with the potential of generating valuable insights for innovative drug design. Here we present the SenseNet ("Structure ENSEmble NETworks") framework for analysis of protein structure networks, which differs from established network models by focusing on interaction timelines obtained by molecular dynamics simulations. This approach is evaluated by predicting allosteric residues reported by NMR experiments in the PDZ2 domain of hPTP1e, a reference system for which previous computational predictions have shown considerable variance. We applied two models based on the mutual information between interaction timelines to estimate the conformational influence of each residue on its local environment. In terms of accuracy our prediction model is comparable to the top performing model published for this system, but by contrast benefits from its independence from NMR structures. Our results are complementary to experimental data and the consensus of previous predictions, demonstrating the potential of our new analysis tool SenseNet. Biochemical interpretation of our model suggests that allosteric residues in the PDZ2 domain form two distinct clusters of contiguous sidechain surfaces. SenseNet is provided as a plugin for the network analysis software Cytoscape, allowing for ease of future application and contributing to a system of compatible tools bridging the fields of system and structural biology. Author SummaryRegulation and signal transduction processes in proteins are often correlated to structural changes induced by ligand binding, which can lead to suppression or enhancement of protein function. A common method to investigate such changes are numerical simulations of protein dynamics. We developed the analysis software SenseNet for predicting how protein dynamics and function is affected by e.g. ligand binding events based on molecular dynamics simulations. Our model estimates which structural elements of the protein confer the most information about their local environment, reasoning that these elements are essential for signal propagation. Applying this method on the PDZ2 domain of the hPTP1e protein, we were able to accurately predict structure elements with known signaling roles as determined by previous experiments. Integrating these experimental data with the consensus of other computational models and our predictions, we find two separate pathways which may transmit information through the PDZ2 protein structure. In addition to deepening our insight into the behavior of this particular protein, these results demonstrate the usefulness of our methods for other systems, such as potential drug targets. To make this analysis available to a broad audience, we implemented it as a plugin for the popular network analysis software Cytoscape.

bioinformatics↗

bioRxiv2021

Assessment of Molecular Mechanics-based Zn2+ Models in Mono- and Bimetallic Ligand Binding Sites

Zn2+ ions play an important role in biology, but accurate sampling of metalloproteins using Molecular Mechanics remains challenging. Several models have been proposed to describe Zn2+ in biomolecular simulations, ranging from nonbonded models, employing classical 12-6 Lennard-Jones (LJ) potentials or extended LJ-potentials, to dummy-atom models and bonded models. We evaluated the performance of a large variety of these Zn2+ models in two challenging environments for which little is known about the performance of these methods, namely in a monometallic (Carbonic Anhydrase II) and a bimetallic ligand binding site (metallo-{beta}-lactamase VIM-2). We focused on properties which are important for a stable, correct binding site description during molecular dynamics (MD) simulations, because a proper treatment of the metal coordination and forces are here essential. We observed that the strongest difference in performance of these Zn2+ models can be found in the description of interactions between Zn2+ and non-charged ligating atoms, such as the imidazole nitrogen in histidine residues. We further show that the nonbonded (12-6 LJ) models struggle most in the description of Zn2+-biomolecule interactions, while the inclusion of ion-induced dipole effects strongly improves the description between Zn2+ and non-charged ligating atoms. The octahedral dummy-atom models result in highly stable simulations and correct Zn2+ coordination, and are therefore highly suitable for binding sites containing an octahedral coordinated Zn2+ ion. The results from this evaluation study in ligand binding sites can guide structural studies of Zn2+ containing proteins, such as MD-refinement of docked ligand poses and long-term MD simulations.

bioinformatics↗

bioRxiv2021

Spatial and temporal plasticity of neoantigen-specific T-cell responses bases on characteristics associated to antigen and TCR

Neoantigens derived from somatic mutations have been demonstrated to correlate with therapeutic responses mediated by treatment with immune checkpoint inhibitors. Neoantigens are therefore highly attractive targets for the development of personalized medicine approaches although their quality and associated immune responses is not yet well understood. In a case study of metastatic malignant melanoma, we performed an in-depth characterization of neoantigens and respective T-cell responses in the context of immunotherapy with Ipilimumab. Three neoantigens identified either by immunopeptidomics or in silico prediction were investigated using binding affinity analyses and structural simulations. We isolated seven T-cell receptors (TCRs) from the patient immune repertoire recognizing these antigens. TCRs were compared in-vitro and in-vivo with multi-parametric analyses. Identified immunogenic peptides showed similar binding affinities to the human leukocyte antigen (HLA) complex and comparable differences to their wildtype counterparts in molecular dynamic simulations. Nevertheless, isolated TCRs differed substantially in functionality and frequency. In fact, TCRs with comparably lower functional avidity and higher potential for cross-reactivity provided at least equal anti-tumor immune responses in vivo. Of note, these TCRs showed a reduced activation pattern upon primary in vitro stimulation. Exploration of the TCR-{beta} repertoire in blood and in different tumor-related tissues over three years, offered insights on the high frequency and particular long-term persistence of low-avidity TCRs. These data indicate that qualitative differences of neoantigen-specific TCRs and their impact on function and longevity need to be considered for neoantigen targeting by adoptive T-cell therapy using TCR-transgenic T cells. Statement of translational relevanceImmunotherapy has demonstrated high efficacy in diverse malignancies. Neoantigens derived from mutations provide promising targets for safe and highly tumor-specific therapeutic approaches. Yet, single determinants of an effective and enduring T-cell mediated tumor rejection are still not well understood. We analyzed in detail seven neoantigen-specific T-cell receptors (TCRs) derived from a melanoma patient targeting three different altered peptide ligands identified by mass spectrometry and prediction analyses. Functional characterization of these TCRs revealed potent anti-tumor reactivity of all TCRs. Of special interest, TCRs with comparably lower affinity demonstrated effective in vivo activity as well as dominant spatial and temporal distribution in blood and tissue. Functional differences of TCR may require further T-cell and/or TCR engineering and should be considered for future clinical trial designs.

immunology↗

bioRxiv2019

Broad spectrum antibiotic-degrading metallo-β-lactamases are phylogenetically diverse and widespread in the environment.

Antibiotic resistance has emerged as a major global health threat. The Zn2+-dependent metallo-{beta}-lactamases (MBLs) are of particular concern as they act on the most widely prescribed class of antibiotics, the {beta}-lactams, and are largely unaffected by commonly used {beta}-lactamase antagonists such as clavulanic acid. MBLs are subdivided into three groups (B1 to B3); despite low overall sequence similarity, their catalytic centers are conserved with two closely spaced Zn2+ binding sites ( and {beta} site). We recovered almost 1500 B3 MBLs from >100,000 public microbial genomes representing a wide range of habitats including pristine sites not impacted by human activity. Although homologs were predominantly identified in members of the bacterial phylum Proteobacteria, the recovered B3 MBLs represent a much broader phylogenetic diversity than is currently appreciated based on the study of model pathogens. This includes three active site variants inferred to have arisen from the ancestral B3 enzyme. One of these variants, B3-RQK, is noteworthy for being broadly sensitive to clavulanic acid. Through targeted mutations we demonstrate that the presence of a lysine residue (Lys263) in the {beta} site of the catalytic center of this variant confers sensitivity to this compound. Replacing this lysine with the canonical histidine (His263) found in all other MBLs restored resistance. Crystallographic and computational data reveal that clavulanic acid inhibits B3-RQK MBLs by displacing the Zn2+ ion in the {beta} site. Therefore, modifying clavulanic acid to effectively interact with His263 may increase the therapeutic range of this widely used antibiotic resistance drug.\n\nSignificanceThis study surveys the environmental and phylogenetic diversity of the B3 subgroup of antibiotic-degrading metallo-{beta}-lactamases (MBLs). B3-like MBLs are more widespread in the environment than previously appreciated suggesting multiple unrecognized reservoirs of antibiotic resistance. Three variants of the canonical active site were identified, including B3-RQK, which amongst the B3 MBLs is uniquely inhibited by the antibiotic resistance drug clavulanic acid. We demonstrate that the mode of inhibition involves the displacement of a catalytically essential Zn2+ ion from the active site. It may thus be possible to modify clavulanic acid so that it can compete with the Zn2+ ions in other MBLs as well, increasing the therapeutic range of this compound.

biochemistry↗