Solvent sensitivity of protein aggregation in Cu, Zn superoxide dismutase: a molecular dynamics simulation study

Comprehensive mapping of mutations in TDP-43 and α-Synuclein that affect stability and binding

Abnormal aggregation and amyloid inclusions of TAR DNA-binding protein 43 (TDP-43) and α-Synuclein (α-Syn) are frequently co-observed in amyotrophic lateral sclerosis, Parkinson's disease, and Alzheimer's disease. Several reports showed TDP-43 C-terminal domain (CTD) and α-Syn interact with each other and the aggregates of these two proteins colocalized together in different cellular and animal models. Molecular dynamics simulation was conducted to elucidate the stability of the TDP-43 and Syn complex structure. The interfacial mutations in protein complexes changes the stability and binding affinity of the protein that may cause diseases. Here, we have utilized the computational saturation mutagenesis approach including structure-based stability and binding energy calculations to compute the systemic effects of missense mutations of TDP-43 CTD and α-Syn on protein stability and binding affinity. Most of the interfacial mutations of CTD and α-Syn were found to destabilize the protein and reduced the protein binding affinity. The results thus shed light on the functional consequences of missense mutations observed in TDP-43 associated proteinopathies and may provide the mechanisms of co-morbidities involving these two proteins.Communicated by Ramaswamy H. Sarma.

In silico evaluation of the inhibitory potential of nucleocapsid inhibitors of SARS-CoV-2: a binding and energetic perspective

The COVID-19 outbreak brought on by the SARS-CoV-2 virus continued to infect a sizable population worldwide. The SARS-CoV-2 nucleocapsid (N) protein is the most conserved RNA-binding structural protein and is a desirable target because of its involvement in viral transcription and replication. Based on this aspect, this study focused to repurpose antiviral compounds approved or in development for treating COVID-19. The inhibitors chosen are either FDA-approved or are currently being studied in clinical trials against COVID-19. Initially, they were designed to target stress granules and other RNA biology. We have utilized structure-based molecular docking and all-atom molecular dynamics (MD) simulation approach to investigate in detail the binding energy and binding modes of the different anti-N inhibitors to N protein. The result showed that five drugs including Silmitasterib, Ninetanidinb, Ternatin, Luteolin, Fedratinib, PJ34, and Zotatafin were found interacting with RNA binding sites as well as to predicted protein interface with higher binding energy. Overall, drug binding increases the stability of the complex with maximum stability found in the order, Silmitasertib > PJ34 > Zotatatafin. In addition, the frustration changes due to drug binding brings a decrease in local frustration and this decrease is mainly observed in α-helix, β3, β5, and β6 strands and are important for drug binding. Our in-silico data suggest that an effective interaction occurs for some of the tested drugs and prompt their further validation to reduce the rapid outspreading of SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

A computational strategy for therapeutic development against superoxide dismutase (SOD1) amyloid formation: effect of polyphenols on the various events in the aggregation pathway

Pathology of superoxide dismutase 1 (SOD1) aggregation is linked to a neurodegenerative disease known as amyotrophic lateral sclerosis (ALS). Without suitable post-translational modifications (PTMs), the protein structure tends to become aggregation-prone. Understanding the role of PTMs and targeting the aggregation-prone SOD1 with small molecules can be used to design a strategy to inhibit its aggregation. Microsecond long molecular dynamics (MD) simulations followed by free energy surface (FES) analyses show that the loss of structure in the apo monomer happens locally and stepwise. Removing the disulfide bond from apoprotein leads to further instability in the zinc-binding loop, giving rise to non-native protein conformations. Further, it was found that these non-native conformations have a higher propensity to form a non-native dimer. We chose three structurally similar polyphenols based on their binding energies and investigated their impact on SOD1 aggregation kinetics. MD simulations of apo-SOD1^SH/corkscrew fibril-polyphenol complexes were also carried out. The effect of polyphenols was seen on fibril elongation as well. Based on the experiments and MD simulation results, it can be inferred that the choice of inhibitors is influenced not only by the binding energy but also by dimer interface stabilization, the proclivity to form non-native dimers, the propensity to break fibrils, and the propensity to decrease the rate of elongation. The polyphenols with 3' and 4' hydroxyl groups are better inhibitors of SOD1 aggregation.

The Role of Superoxide Dismutase 1 in Amyotrophic Lateral Sclerosis: Identification of Signaling Pathways, Regulators, Molecular Interaction Networks, and Biological Functions through Bioinformatics

Mutations in superoxide dismutase 1 (SOD1) result in misfolding and aggregation of the protein, causing neurodegenerative amyotrophic lateral sclerosis (ALS). In recent years, several new SOD1 variants that trigger ALS have been identified, making it increasingly crucial to understand the SOD1 toxicity pathway in ALS. Here we used an integrated bioinformatics approach, including the Ingenuity Pathway Analysis (IPA) tool to analyze signaling pathways, regulators, functions, and network molecules of SOD1 with an emphasis on ALS. IPA toxicity analysis of SOD1 identified superoxide radicals' degradation, apelin adipocyte, ALS, NRF2-mediated oxidative stress response, and sirtuin signaling as the key signaling pathways, while the toxicity of SOD1 is exerted via mitochondrial swelling and oxidative stress. IPA listed CNR1, APLN, BTG2, MAPK, DRAP1, NFE2L2, SNCA, and CG as the upstream regulators of SOD1. IPA further revealed that mutation in SOD1 results in hereditary disorders, including ALS. The exploration of the relationship between SOD1 and ALS using IPA unveiled SOD1-ALS pathway molecules. The gene ontology (GO) analysis of SOD1-ALS pathway molecules with ShinyGO reaffirmed that SOD1 toxicity results in ALS and neurodegeneration. The GO analysis further identified enriched biological processes, molecular functions, and cellular components for SOD1-ALS pathway molecules. The construction of a protein-protein interaction network of SOD1-ALS pathway molecules using STRING and further analysis of that network with Cytoscape identified ACTB followed by TP53, IL6, CASP3, SOD1, IL1B, APP, APOE, and VEGFA as the major network hubs. Taken together, our study provides insight into the molecular underpinning of SOD1's toxicity in ALS.

Computational Insights of Unfolding of N-Terminal Domain of TDP-43 Reveal the Conformational Heterogeneity in the Unfolding Pathway

TDP-43 proteinopathies is a disease hallmark that characterizes amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). The N-terminal domain of TDP-43 (NTD) is important to both TDP-43 physiology and TDP-43 proteinopathy. However, its folding and dimerization process is still poorly characterized. In the present study, we have investigated the folding/unfolding of NTD employing all-atom molecular dynamics (MD) simulations in 8 M dimethylsulfoxide (DMSO) at high temperatures. The MD results showed that the unfolding of the NTD at high temperature evolves through the formation of a number of conformational states differing in their stability and free energy. The presence of structurally heterogeneous population of intermediate ensembles was further characterized by the different extents of solvent exposure of Trp80 during unfolding. We suggest that these non-natives unfolded intermediate ensembles may facilitate NTD oligomerization and subsequently TDP-43 oligomerization, which might lead to the formation of irreversible pathological aggregates, characteristics of disease pathogenesis.

Delineating the Aggregation-Prone Hotspot Regions (Peptides) in the Human Cu/Zn Superoxide Dismutase 1

Amyotrophic lateral sclerosis (ALS) is a fatal, incurable neurodegenerative disease described by progressive degeneration of motor neurons. The most common familial form of ALS (fALS) has been associated with mutations in the Cu/Zn superoxide dismutase (SOD1) gene. Mutation-induced misfolding and aggregation of SOD1 is often found in ALS patients. In this work, we probe the aggregation properties of peptides derived from the SOD1. To examine the source of SOD1 aggregation, we have employed a computational algorithm to identify four peptides from the SOD1 protein sequence that aggregates into a fibril. Aided by computational algorithms, we identified four peptides likely involved in SOD1 fibrillization. These four aggregation-prone peptides were 14VQGIINFE21, 30KVWGSIKGL38, 101DSVISLS107, and 147GVIGIAQ153. In addition, the formation of fibril propensities from the identified peptides was investigated through different biophysical techniques. The atomic structures of two fibril-forming peptides from the C-terminal SOD1 showed that the steric zippers formed by 101DSVISLS107 and 147GVIGIAQ153 vary in their arrangement. We also discovered that fALS mutations in the peptide 147GVIGIAQ153 increased the fibril-forming propensity and altered the steric zipper's packing. Thus, our results suggested that the C-terminal peptides of SOD1 have a central role in amyloid formation and might be involved in forming the structural core of SOD1 aggregation observed in vivo.

Identification of natural compounds as potent inhibitors of SARS-CoV-2 main protease using combined docking and molecular dynamics simulations

Coronavirus disease 2019 (COVID-19) has emerged from China and globally affected the entire population through the human-to-human transmission of a newly emerged virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genome of SARS-CoV-2 encodes several proteins that are essential for multiplication and pathogenesis. The main protease (Mpro or 3CLpro) of SARS-CoV-2 plays a central role in its pathogenesis and thus is considered as an attractive drug target for the drug design and development of small-molecule inhibitors. We have employed an extensive structure-based high-throughput virtual screening to discover potential natural compounds from the ZINC database which could inhibit the Mpro of SARS-CoV-2. Initially, the hits were selected on the basis of their physicochemical and drug-like properties. Subsequently, the PAINS filter, estimation of binding affinities using molecular docking, and interaction analyses were performed to find safe and potential inhibitors of SARS-CoV-2 Mpro. We have identified ZINC02123811 (1-(3-(2,5,9-trimethyl-7-oxo-3-phenyl-7H-furo[3,2-g]chromen-6-yl)propanoyl)piperidine-4-carboxamide), a natural compound bearing appreciable affinity, efficiency, and specificity towards the binding pocket of SARS-CoV-2 Mpro. The identified compound showed a set of drug-like properties and preferentially binds to the active site of SARS-CoV-2 Mpro. All-atom molecular dynamics (MD) simulations were performed to evaluate the conformational dynamics, stability and interaction mechanism of Mpro with ZINC02123811. MD simulation results indicated that Mpro with ZINC02123811 forms a stable complex throughout the trajectory of 100 ns. These findings suggest that ZINC02123811 may be further exploited as a promising scaffold for the development of potential inhibitors of SARS-CoV-2 Mpro to address COVID-19.

Trifluoroethanol Partially Unfolds G93A SOD1 Leading to Protein Aggregation: A Study by Native Mass Spectrometry and FPOP Protein Footprinting

Misfolding of Cu, Zn superoxide dismutase (SOD1) variants may lead to protein aggregation and ultimately amyotrophic lateral sclerosis (ALS). The mechanism and protein conformational changes during this process are complex and remain unclear. To study SOD1 variant aggregation at the molecular level and in solution, we chemically induced aggregation of a mutant variant (G93A SOD1) with trifluoroethanol (TFE) and used both native mass spectrometry (MS) to analyze the intact protein and fast photochemical oxidation of proteins (FPOP) to characterize the structural changes induced by TFE. We found partially unfolded G93A SOD1 monomers prior to oligomerization and identified regions of the N-terminus, C-terminus, and strands β5, β6 accountable for the partial unfolding. We propose that exposure of hydrophobic interfaces of these unstructured regions serves as a precursor to aggregation. Our results provide a possible mechanism and molecular basis for ALS-linked SOD1 misfolding and aggregation.

Insights into the Conserved Regulatory Mechanisms of Human and Yeast Aging

Aging represents a significant biological process having strong associations with cancer, diabetes, and neurodegenerative and cardiovascular disorders, which leads to progressive loss of cellular functions and viability. Astonishingly, age-related disorders share several genetic and molecular mechanisms with the normal aging process. Over the last three decades, budding yeast Saccharomyces cerevisiae has emerged as a powerful yet simple model organism for aging research. Genetic approaches using yeast RLS have led to the identification of hundreds of genes impacting lifespan in higher eukaryotes. Numerous interventions to extend yeast lifespan showed an analogous outcome in multi-cellular eukaryotes like fruit flies, nematodes, rodents, and humans. We collected and analyzed a multitude of observations from published literature and provide the contribution of yeast in the understanding of aging hallmarks most applicable to humans. Here, we discuss key pathways and molecular mechanisms that underpin the evolutionarily conserved aging process and summarize the current understanding and clinical applicability of its trajectories. Gathering critical information on aging biology would pave the way for future investigation targeted at the discovery of aging interventions.

Unfolding Transitions of Peripheral Subunit Binding Domains Show Cooperative Behavior

Characterization of native, intermediate, and denatured states is crucial for understanding the factors influencing the stability of proteins. We have carried out molecular dynamics simulations to study the unfolding of three peripheral subunit binding domains (PSBDs): E. coli BBL, Bacillus stearothermophilus E3BD, and human hbSBD, at three different temperatures: 300, 330, and 400 K, and in the presence of two solvents: water and 5 M guanidinium hydrochloride (GndCl) solution. These proteins share similar folds, with two parallel helices, maintained via a hydrophobic core comprising residues from their interconnecting loop. BBL is more sensitive to thermal and chemical denaturation in comparison to hbSBD, and E3BD is the most stable of all of the three proteins. The effect of temperature on the stability of these proteins is more pronounced in "water-only" simulations compared to that in the presence of guanidium hydrochloride in high concentrations. Our results show cooperative unfolding transitions of these proteins, which are triggered by an initial melting of the C-terminal helix H2. The consequent loss of interhelical interactions or native contacts, as observed, leads to the subsequent melting of the N-terminal helix H1.

TFE-induced local unfolding and fibrillation of SOD1: bridging the experiment and simulation studies

Misfolding and aggregation of Cu, Zn Superoxide dismutase (SOD1) is involved in the neurodegenerative disease, amyotrophic lateral sclerosis. Many studies have shown that metal-depleted, monomeric form of SOD1 displays substantial local unfolding dynamics and is the precursor for aggregation. Here, we have studied the structure and dynamics of different apo monomeric SOD1 variants associated with unfolding and aggregation in aqueous trifluoroethanol (TFE) through experiments and simulation. TFE induces partially unfolded β-sheet-rich extended conformations in these SOD1 variants, which subsequently develops aggregates with fibril-like characteristics. Fibrillation was achieved more easily in disulfide-reduced monomeric SOD1 when compared with wild-type and mutant monomeric SOD1. At higher concentrations of TFE, a native-like structure with the increase in α-helical content was observed. The molecular dynamics simulation results illustrate distinct structural dynamics for different regions of SOD1 variants and show uniform local unfolding of β-strands. The strands protected by the zinc-binding and electrostatic loops were found to unfold first in 20% (v/v) TFE, leading to a partial unfolding of β-strands 4, 5, and 6 which are prone to aggregation. Our results thus shed light on the role of local unfolding and conformational dynamics in SOD1 misfolding and aggregation.