Epitope region identification challenges of intrinsically disordered proteins in neurodegenerative diseases: Secondary structure dependence of α‐synuclein on simulation techniques and force field parameters

Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study

α-Synuclein (α-syn) is a 140 amino acid intrinsically disordered protein (IDP) and the primary component of cytotoxic oligomers implicated in the etiology of Parkinson's disease (PD). While IDPs lack a stable three-dimensional structure, they sample a heterogeneous ensemble of conformations that can, in principle, be assessed through molecular dynamics simulations. However, describing the structure and aggregation of large IDPs is challenging due to force field (FF) accuracy and sampling limitations. To cope with the latter, coarse-grained (CG) FFs emerge as a potential alternative at the expense of atomic detail loss. Whereas CG models can accurately describe the structure of the monomer, less is known about aggregation. The latter is key for assessing aggregation pathways and designing aggregation inhibitor drugs. Herein, we investigate the structure and dynamics of α-syn using different resolution CG (Martini3 and Sirah2) and all-atom (Amber99sb and Charmm36m) FFs to gain insight into the differences and resemblances between these models. The dependence of the magnitude of protein-water interactions and the putative need for enhanced sampling (replica exchange) methods in CG simulations are analyzed to distinguish between force field accuracy and sampling limitations. The stability of the CG models of an α-syn fibril was also investigated. Additionally, α-syn aggregation was studied through umbrella sampling for the CG models and CG/all-atom models for an 11-mer peptide (NACore) from an amyloidogenic domain of α-syn. Our results show that despite the α-syn structures of Martini3 and Sirah2 with enhanced protein-water interactions being similar, major differences exist concerning aggregation. The Martini3 fibril is not stable, and the binding free energy of α-syn and NACore is positive, opposite to Sirah2. Sirah2 peptides in a zwitterionic form, in turn, display termini interactions that are too strong, resulting in end-to-end orientation. Sirah2, with enhanced protein-water interactions and neutral termini, provides, however, a peptide aggregation free energy profile similar to that found with all-atom models. Overall, we find that Sirah2 with enhanced protein-water interactions is suitable for studying protein-protein and protein-drug aggregation.

Complex Conformational Space of the RNA Polymerase II C-Terminal Domain upon Phosphorylation

Intrinsically disordered proteins (IDPs) have been closely studied during the past decade due to their importance in many biological processes. The disordered nature of this group of proteins makes it difficult to observe its full span of the conformational space using either experimental or computational studies. In this article, we explored the conformational space of the C-terminal domain (CTD) of RNA polymerase II (Pol II), which is also an intrinsically disordered low complexity domain, using enhanced sampling methods. We provided a detailed conformational analysis of model systems of CTD with different lengths; first with the last 44 residues of the human CTD sequence and finally the CTD model with 2-heptapeptide repeating units. We then investigated the effects of phosphorylation on CTD conformations by performing simulations at different phosphorylated states. We obtained broad conformational spaces in nonphosphorylated CTD models, and phosphorylation has complex effects on the conformations of the CTD. These complex effects depend on the length of the CTD, spacing between the multiple phosphorylation sites, ion coordination, and interactions with the nearby residues.

GaMD simulations as an alternative in the TFE-water mixture description

CONTEXT

2,2,2-Trifluoroethanol has been widely used to study the structure and dynamic properties of intrinsically disordered proteins. Experimentally, it is known that TFE-water mixtures stabilize secondary structures of IDPs, and therefore, it allows the studying of conformational ensembles of these proteins. In the last decades, molecular dynamic simulations have helped study the IDPs' conformational ensemble. Unfortunately, conventional MD requires very long simulation times to describe the properties of IDPs. Therefore, a variety of accelerated sampling techniques have been developed and employed. The TFE-water mixture arrangement description through MD has faced substantial difficulties since emulating the TFE nanocrowding at certain TFE:H[Formula: see text]O ratios (around 15-40% of TFE). In this work, we determine the most suitable conditions that reproduce experimentally reported properties of TFE-water mixtures. We compared the employment of conventional MD and GaMD simulations and various water parameters. Our results show that the combination of parameters that better reproduce the experimental information is the combination of the TIP4PD water model and GaMD simulations. Therefore, these conditions help accurately describe the structural ensemble of IDPs in TFE-water mixtures.

METHODS

Conventional MD and GaMD simulations were performed under AMBER 18 software. The TFE and water molecules were described using GAFF2 and a variety of water models, such as TIP3P, TIP4P2005, TIP4PD, and TIP5P, respectively. The systems were simulated a 100 ns at 298 K.

How Cu(II) binding affects structure and dynamics of α-synuclein revealed by molecular dynamics simulations

We report accelerated molecular dynamics simulations of α-Synuclein and its complex with two Cu(II) ions bound to experimentally determined binding sites. Adding two Cu(II) ions, one bound to the N-terminal region and one to the C-terminus, decreases size and flexibility of the peptide while introducing significant new contacts within and between N-terminus and non-Aβ component (NAC). Cu(II) ions also alter the pattern of secondary structure within the peptide, inducing more and longer-lasting elements of secondary structure such as β-strands and hairpins. Free energy surfaces, obtained from reweighting the accelerated molecular dynamics boost potential, further demonstrate the restriction on size and flexibility that results from binding of copper ions.

Evaluation of implicit solvent models in molecular dynamics simulation of α-Synuclein

We report conventional and accelerated molecular dynamics simulations of α-Synuclein, designed to assess performance of using different starting conformation, solvation environment and force field combination. Backbone and sidechain chemical shifts, radius of gyration, presence of β-hairpin structures in KTK(E/Q)GV repeats and secondary structure percentages were used to evaluate how variations in forcefield, solvation model and simulation protocol provide results that correlate with experimental findings. We show that with suitable choice of forcefield and solvent, ff03ws and OBC implicit model, respectively, acceptable reproduction of experimental data on size and secondary structure is obtained by both conventional and accelerated MD. In contrast to the implicit solvent model, simulations in explicit TIP4P/2005 solvent do not properly represent size or secondary structure of α-Synuclein.Communicated by Ramaswamy H. Sarma.

Structures of the Wild-Type and S59L Mutant CHCHD10 Proteins Important in Amyotrophic Lateral Sclerosis-Frontotemporal Dementia

The S59L genetic mutation of the mitochondrial coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10) is involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The wild-type and mutant forms of this protein contain intrinsically disordered regions, and their structural characterization has been facing challenges. Here, for the first time in the literature, we present the structural ensemble properties of the wild-type and S59L mutant form of CHCHD10 in an aqueous solution environment at the atomic level with dynamics. Even though available experiments suggested that the S59L mutation may not change the structure of the CHCHD10 protein, our structural analysis clearly shows that the structure of this protein is significantly affected by the S59L mutation. We present here the secondary structure components with their abundances per residue, the tertiary structure properties, the free energy surfaces based on the radius of gyration and end-to-end distance values, the Ramachandran plots, the quantity of intramolecular hydrogen bonds, and the principal component analysis results. These results may be crucial in designing more efficient treatment for ALS and FTD diseases.

Peptide-Based Vaccines for Neurodegenerative Diseases: Recent Endeavors and Future Perspectives

The development of peptide-based vaccines for treating human neurodegenerative diseases has been the eventual aim of many research endeavors, although no active immunotherapies have been approved for clinical use till now. A typical example of such endeavors is the effort to develop vaccines for Alzheimer’s disease based on the beta-amyloid peptide, which continues to be intensively investigated despite previous setbacks. In this paper, recent developments in peptide-based vaccines which target beta-amyloid as well as tau protein and α-synuclein are presented. Particular focus has been directed toward peptide epitopes and formulation systems selected/developed and employed to enhance vaccine efficacy and safety. Results from both, human clinical trials and animal preclinical studies conducted mainly in transgenic mice have been included. Future perspectives on the topic are also briefly discussed.

Secondary structure dependence of amyloid-β(1-40) on simulation techniques and force field parameters

Our recent studies revealed that none of the selected widely used force field parameters and molecular dynamics simulation techniques yield structural properties for the intrinsically disordered α-synuclein that are in agreement with various experiments via testing different force field parameters. Here, we extend our studies on the secondary structure properties of the disordered amyloid-β(1-40) peptide in aqueous solution. For these purposes, we conducted extensive replica exchange molecular dynamics simulations and obtained extensive molecular dynamics simulation trajectories from David E. Shaw group. Specifically, these molecular dynamics simulations were conducted using various force field parameters and obtained results are compared to our replica exchange molecular dynamics simulations and experiments. In this study, we calculated the secondary structure abundances and radius of gyration values for amyloid-β(1-40) that were simulated using varying force field parameter sets and different simulation techniques. In addition, the intrinsic disorder propensity, as well as sequence-based secondary structure predisposition of amyloid-β(1-40) and compared the findings with the results obtained from molecular simulations using various force field parameters and different simulation techniques. Our studies clearly show that the epitope region identification of amyloid-β(1-40) depends on the chosen simulation technique and chosen force field parameters. Based on comparison with experiments, we find that best computational results in agreement with experiments are obtained using the a99sb*-ildn, charmm36m, and a99sb-disp parameters for the amyloid-β(1-40) peptide in molecular dynamics simulations without parallel tempering or via replica exchange molecular dynamics simulations.

Unraveling diverse action of triton X-100 and methimazole on lysozyme fibrillation/aggregation: Physicochemical insights

Identification of functionalities responsible for prevention of fibrillation in proteins is important to design effective drugs in addressing neurodegenerative diseases. We have used nonionic surfactant triton X-100 (TX-100) and antithyroid drug methimazole (MMI) to understand mechanistic aspects of action of these molecules having different functionalities on hen egg-white lysozyme at different stages of fibrillation. After establishing the nucleation, elongation and maturation stages of fibrillation of protein at 57 °C, energetics of interactions with these molecules have been determined by using isothermal titration calorimetry. Differential scanning calorimetry has permitted assessment of thermal stability of the protein at these stages, with or without these molecular entities. The enthalpies of interaction of TX-100 and MMI with protein fibrils suggest importance of hydrogen bonding and polar interactions in their effectiveness towards prevention of fibrils. TX-100, in spite of several polar centres, is unable to prevent fibrillation, rather it promotes. MMI is able to establish polar interactions with interacting strands of the protein and disintegrate fibrils. A rigorous comparison with inhibitors reported in literature highlights importance -OH and >CO functionalities in fibrillation prevention. Even though MMI has hydrogen bonding centres, its efficiency as inhibitor falls after the inhibited lysozyme fibrils further interact and form amorphous aggregates.

Current Challenges and Limitations in the Studies of Intrinsically Disordered Proteins in Neurodegenerative Diseases by Computer Simulations

Experiments face challenges in the analysis of intrinsically disordered proteins in solution due to fast conformational changes and enhanced aggregation propensity. Computational studies complement experiments, being widely used in the analyses of intrinsically disordered proteins, especially those positioned at the centers of neurodegenerative diseases. However, recent investigations - including our own - revealed that computer simulations face significant challenges and limitations themselves. In this review, we introduced and discussed some of the scientific challenges and limitations of computational studies conducted on intrinsically disordered proteins. We also outlined the importance of future developments in the areas of computational chemistry and computational physics that would be needed for generating more accurate data for intrinsically disordered proteins from computer simulations. Additional theoretical strategies that can be developed are discussed herein.

Structures of the intrinsically disordered Aβ, tau and α-synuclein proteins in aqueous solution from computer simulations

Intrinsically disordered proteins (IDPs) play many biological roles in the human proteome ranging from vesicular transport, signal transduction to neurodegenerative diseases. The Aβ and tau proteins, and the α-synuclein protein, key players in Alzheimer's and Parkinson's diseases, respectively are fully disordered at the monomer level. The structural heterogeneity of the monomeric and oligomeric states and the high self-assembly propensity of these three IDPs have precluded experimental structural determination. Simulations have been used to determine the atomic structures of these IDPs. In this article, we review recent computer models to capture the equilibrium ensemble of Aβ, tau and α-synuclein proteins at different association steps in aqueous solution and present new results of the PEP-FOLD framework on α-synuclein monomer.