SPC Water Model Research Articles

Multitargeted Docking, DFT-Based Optimisation, Pharmacokinetics, and MD Simulation Reveal 6-Oxidopamine HBr as a Multitargeted Inhibitor of Cervical Cancer Proteins.

Cervical cancer originates in the cervix, the lower part of the uterus, and results from the uncontrolled growth of abnormal cervical cells, forming malignant tumours. It poses a major global health challenge, calling for innovative drug design strategies to enhance treatment outcomes. In this study, we have screened the FDA-approved drug library against four proteins, MCM10, MCM6, DNA polymerase epsilon subunit-2, and TBK1, which are essential for DNA replication, DNA repair, and cellular signalling pathways, which are dysregulated in cervical cancer cells, leading to uncontrolled growth. We have used the multisampling algorithms for screening using HTVS, SP, and XP docking; identified 6- oxidopamine HBr (C8H12BrNO3), which is used to create a model of Parkinson's disease in animals, and obtained the docking score ranging from -5.057 to -8.871 Kcal/mol. The poses were filtered with MM\GBSA score ranging from -21.67 to -27.63 Kcal/mol. We performed QM-based DFT and pharmacokinetics studies and compared them with the standard values, suggesting that the compound can be used in cervical cancer proteins. The P-L complex's interaction fingerprints have resulted in the most interacting residues, 4THR, 4SER, and 4LYS, showing the compound's interaction pattern. Further, the stability of 6-oxidopamine HBr in complex with each protein was evaluated with 100ns MD simulation in the SPC water model in a neutralised state to analyse the deviation, fluctuations, and intermolecular interactions that have proven the compound to have a better inhibitory effect against each protein and that it can be used for cervical cancer; however, experimental validation is suggested before human use.

The Study of the Binding Ability of Antimicrobial Peptides to Spike Protein of the Coronavirus by Docking and Molecular Dynamics Simulation

Introduction: Since the start of 2020, SARS -CoV-2 has infected a significant number of individuals, prompting extensive research. Antimicrobial peptides can be considered as a promising treatment for emerging viral pathogens due to their safety, efficacy, and specificity. Method: In this study, first, 104 natural antiviral peptides were chosen from APD databases. Then, the third structure of proteins was modeled by PEP -FOLD 3 server. The structures were refined and optimized for docking operation. Subsequently, peptide -protein docking was performed using AutoDock Vina. The most favorable peptide -protein complex, chosen based on binding energy, was employed for molecular simulation using GROMACS. The simulation was carried out for 100 ns at 310° K and pH=7. Gromos54a7 force field was used in this study and the SPC water model was used as solvent. Results: The obtained results from molecular dynamics examine the stability of complex structure and energy calculations. RMSD, RMSF, radius of gyration, and SASA analyses indicate the stability of the peptide -protein complex during the simulation. Additionally, LJ, CL, HBond, and ΔG analyses were conducted to calculate the energy interactions between the peptide and the Spike protein. Conclusion: The results indicate that antimicrobial peptides can effectively bind to the SARS -CoV-2 spike protein, acting as inhibitors with a favorable binding energy. Consequently, these peptides can be employed for therapeutic and experimental studies of COVID -19.

Insights into the binding mechanism of 2,5‐substituted 4‐pyrone derivatives as therapeutic agents for fused dimeric interactions: A computational study using QTAIM, dynamics and docking simulations of protein–ligand complexes

AbstractThe study is focused on examining 2,5‐Substituted 4‐Pyrone based compounds through quantum chemical and topological analysis techniques, evaluating the properties of these compounds, including their geometrical structure, intermolecular interactions and assess their possible applications. Additionally, the molecular stability, charge delocalization and UV‐Visible data was investigated and compared with the calculated energy and oscillator strength using the TD‐DFT approach. The researchers observed that charge transfer occurred within the molecule, indicated by the HOMO and LUMO energies. It was also found that the compound exhibited planarity and higher chemical reactivity. The calculated Mulliken charges and molecular electrostatic potential were used to interpret the Fukui index data that help predict reactive sites and understand the reactivity patterns of specific atoms in a compound. The study is aimed to understand the role of NCI in the molecule under investigation using electron localization functions and localized orbit locator methods. Molecular docking and ADMET studies were conducting involving a detailed MD simulation of a protein‐ligand complex using the OPLS3e force field and the SPC water model. These findings could prove to be beneficial in developing new therapeutic agents with various pharmacological effects and potential toxicities.

Delineated 3-1-BenCarMethInYlPro-Phosphonic Acid's Adroit Activity against Lung Cancer through Multitargeted Docking, MM\GBSA, QM-DFT and Multiscale Simulations.

Lung cancer is a pervasive and challenging disease with limited treatment options, with global health challenges often present with complex molecular profiles necessitating the exploration of innovative therapeutic strategies. Single-target drugs have shown limited success due to the heterogeneity of this disease. Multitargeted drug designing is imperative to combat this complexity by simultaneously targeting multiple target proteins and pathways, which can enhance treatment efficacy and overcome resistance by addressing the dynamic nature of the disease and stopping tumour growth and spread. In this study, we performed the molecular docking studies of Drug Bank compounds with a multitargeted approach against crucial proteins of lung cancer such as heat shock protein 5 (BIP/GRP78) ATPase, myosin 9B RhoGAP, EYA2 phosphatase inhibitor, RSK4 N-terminal kinase, and collapsin response mediator protein-1 (CRMP-1) using HTVS, SP with XP algorithms, and poses were filtered using MM\GBSA which identified [3-(1-Benzyl-3-Carbamoylmethyl-2-Methyl-1h-Indol-5-Yloxy)-Propyl-]-Phosphonic Acid (3-1-BenCarMethIn YlPro-Phosphonic Acid) (DB02504) as multitargeted drug candidate with docking and MM\GBSA score ranges from -5.83 to -10.66 and -7.56 to -50.14 Kcal/mol, respectively. Further, the pharmacokinetic and QM-based DFT studies have shown complete acceptance results, and interaction fingerprinting reveals that ILE, GLY, VAL, TYR, LEU, and GLN were among the most interacting residues. The 100 ns MD simulation in the SPC water model with NPT ensemble showed stable performance with deviation and fluctuations <2 Å with huge interactions, making it a promising multitargeted drug candidate; however, experimental studies are needed before use.

Unrevealing the multitargeted potency of 3-1-BCMIYPPA against lung cancer structural maintenance and suppression proteins through pharmacokinetics, QM-DFT, and multiscale MD simulation studies.

Lung cancer, a relentless and challenging disease, demands unwavering attention in drug design research. Single-target drugs have yielded limited success, unable to effectively address this malignancy's profound heterogeneity and often developed resistance. Consequently, the clarion call for lung cancer drug design echoes louder than ever, and multitargeted drug design emerges as an imperative approach in this landscape, which is done by concurrently targeting multiple proteins and pathways and offering a beacon of hope. This study is focused on the multitargeted drug designing approach by identifying drug candidates against human cyclin-dependent kinase-2, SRC-2 domains of C-ABL, epidermal growth factor and receptor extracellular domains, and insulin-like growth factor-1 receptor kinase. We performed the multitargeted molecular docking studies of Drug Bank compounds using HTVS, SP and XP algorithms and poses filter with MM\GBSA against all proteins and identified DB02504, namely [3-(1-Benzyl-3-Carbamoylmethyl-2-Methyl-1h-Indol-5-Yloxy)-Propyl-]-Phosphonic Acid (3-1-BCMIYPPA) as multitargeted lead with docking and MM\GBSA score range from -8.242 to -6.274 and -28.2 and -44.29 Kcal/mol, respectively. Further, the QikProp-based pharmacokinetic computations and QM-based DFT showed acceptance results against standard values, and interaction fingerprinting reveals that THR, MET, GLY, VAL, LEU, GLU and ASP were among the most interacting residues. The NPT ensemble-based 100ns MD simulation in a neutralised state with an SPC water model has also shown a stable performance and produced deviation and fluctuations <2Å with huge interactions, making it a promising multitargeted drug candidate-however, experimental studies are suggested.

Multidisciplinary characterization of potential inhibitors of the MSUT‐2 protein using molecular dynamics, mechanosensation assays, and deep AI‐based hit optimization for the treatment of Alzheimer’s disease

AbstractBackgroundAlzheimer’s disease is a type of tauopathy, which is a broad category of diseases marked by abnormal aggregation and hyperphosphorylation of the tau protein. The MSUT‐2 protein has gained traction as a promising target for the treatment of tauopathies, given the protein’s RNA‐binding activity linked to tau aggregation. Previously in this research endeavor, using techniques like Quantum Machine Learning and Virtual Screening, 5 potential MSUT‐2 inhibitors have been identified from an initial set of 500,000 candidate compounds. The primary research aim is to further analyze these 5 potential hits using a new combination of computational methodologies and laboratory characterization.MethodA myriad of tests were performed with strains of C. elegans (microscopic roundworms that are established models for neurodegeneration) to validate previous computational indications. A series of motion evaluations, mechanosensation assays, and behavioral assessments were performed with CL2319 C. elegans (mutated to overexpress neuronal tau) with all 5 compounds. One of the compounds, named R128, was found to improve the health and behavior of tau mutant worms across experimental assessments at increasing doses of the compound. A 100 nanosecond simulation of the MSUT2‐R128 complex using the GROMOS96 43a1 force field and SPC Water Model was used to computationally validate protein‐ligand stability based on RMSD fluctuation values. DeepFrag, a fragment‐based lead optimization tool with a deep convolutional neural network backend, was then used to generate 20 potential optimized compounds, nine of which were found to retain R128’s druglikeliness profile yet have improved binding affinities to MSUT‐2.ResultThis multidisciplinary workflow has uncovered a promising hit for the MSUT‐2 protein, named R128, with 9 optimized derivatives with improved drug‐like qualities. This methodology can be used to efficiently identify promising treatment candidates for new protein targets involved in neurodegenerative diseases, with the prospect of expediting the drug discovery process significantly.ConclusionTo conclude, a translational approach, combining molecular dynamics, mechanosensation assessments with C. elegans, and an AI‐based hit optimization strategy has been used to identify new treatment candidates for Alzheimer’s disease. R128, a promising inhibitor for MSUT‐2 (an understudied target for Alzheimer’s disease), has also been identified in this study.

SPP1, a potential therapeutic target and biomarker for lung cancer: functional insights through computational studies

NIH reported 128 different types of cancer of which lung cancer is the leading cause of mortality. Globally, it is estimated that on average one in every seventeen hospitalized patients was deceased. There are plenty of studies that have been reported on lung cancer draggability and therapeutics, but yet a protein that plays a central specific to cure the disease remains unclear. So, this study is designed to identify the possible therapeutic targets and biomarkers that can be used for the potential treatment of lung cancers. In order to identify differentially expressed genes, 39 microarray datasets of lung cancer patients were obtained from various demographic regions of the GEO database available at NCBI. After annotating statistically, 6229 up-regulated genes and 10324 down-regulated genes were found. Out of 17 up-regulated genes and significant genes, we selected SPP1 (osteopontin) through virtual screening studies. We found functional interactions with the other cancer-associated genes such as VEGF, FGA, JUN, EGFR, and TGFB1. For the virtual screening studies,198 biological compounds were retrieved from the ACNPD database and docked with SPP1 protein (PDBID: 3DSF). In the results, two highly potential compounds secoisolariciresinol diglucoside (-12.9 kcal/mol), and Hesperidin (-12.0 kcal/mol) showed the highest binding affinity. The stability of the complex was accessed by 100 ns simulation in an SPC water model. From the functional insights obtained through these computational studies, we report that SPP1 could be a potential biomarker and successive therapeutic protein target for lung cancer treatment.

Molecular dynamics calculations of partial molar volumes of amino acids in aqueous solutions

Partial molar volumes of amino acids in their zwitterionic and molecular forms were calculated using molecular dynamics simulations of these systems in aqueous solutions. Calculations performed with the TIP4P, SPC (rigid and flexible), SPC/E, and polarizable water models showed that the choice of water model can have a significant impact on the calculated volumes. The effect of treatment of long-range electrostatic interactions on the calculated results was also investigated. The volumes obtained in simulations with a properly chosen water model fit well the experimental data for both molecular and zwitterionic forms of amino acids.

MOLECULAR DYNAMICS STUDY OF OLEIC ACID-BASED SURFACTANTS FOR ENHANCED OIL RECOVERY

Surfactants have been intensively used for Enhanced Oil Recovery (EOR). Nevertheless, environmental issues cause some surfactants to become unfavored in EOR application. Biodegradable surfactants are the suitable choice to make the environment safer. However, screening surfactants that have a good performance for EOR are time-consuming and costly. Molecular Dynamics (MD) simulation is an alternative solution to reduce cost and time. In the present study, oleic acid-based surfactants that combined with the various length of polyethylene glycol were studied. The potential surfactants were screened by MD simulation to evaluate their ability to reduce the Interfacial Tension (IFT) between oil and water layers, which is the by GROMACS software with Gromos force field and SPC water model. Carboxyl-terminal of the oleic acid was substituted by a different length of polyethylene glycol. All MD simulations were prepared in octadecanewater mixture with temperature ranges of 303-363 K. Our simulations found that the increasing number of polyethylene glycol was not always followed by the decreasing of IFT value between octadecane and water layers. These results were validated with the experimental data and found the similar IFT profile. The simulation of oil emulsification showed that all surfactant samples have good performance and stability as exhibited by their emulsification rate and emulsion stability in different temperatures. The last test to get the best surfactant was the wetability test. The simulation gave the result that both PEG100-oleic and PEG400-oleic were able to change wetability of rocks from oil-wet to water-wet. Accordingly, PEG400-oleic is the best nonionic surfactant candidate due to its performance in each simulation test.

Investigation of Chitosan, Quercetin and Water Interactions using Free Energy Calculations and Molecular Docking

Predicting the preferred orientation of a ligand to a receptor and the free energy (ΔG AB ) of these molecules in a solution is very useful for pharmaceutical applications. In this work, ΔG AB between chitosan and quercetin molecules with water were obtained by the thermodynamic integration (TI) method and the chitosan+quercetin complex was investigated by Molecular Docking (MDK). The topology of the molecules was compatible with the CHARMM force-field. Both molecules were solvated with the GROMACS SPC water model. The ΔG AB values of the molecule+water systems with the thermodynamic integration (TI) method was done in a 10 ns simulation. The complex was achieved in a 2.5 nm x 2.5 nm x 2.5 nm box. The ΔG AB values for the molecules+water systems were 14.36 +/- 0.46 and 0.19 +/- 0.53 kJ/mol, respectively. For the complex, nine conformations were obtained for the quercetin around the chitosan. The best conformation showed an affinity energy of -3.8 kcal/mol. The ΔG AB results for the systems confirm the low or no solubility of the molecules in the water under normal conditions, as already demonstrated experimentally. The docking showed that the interaction between chitosan and quercetin molecules involves hydrogen bonds in a specific position. DOI: http://dx.doi.org/10.17807/orbital.v11i2.1344

Calculation of the water-octanol partition coefficient of cholesterol for SPC, TIP3P, and TIP4P water.

We present a numerical study of the relative solubility of cholesterol in octanol and water. Our calculations allow us to compare the accuracy of the computed values of the excess chemical potential of cholesterol for several widely used water models (SPC, TIP3P, and TIP4P). We compute the excess solvation free energies by means of a cavity-based method [L. Li et al., J. Chem. Phys. 146(21), 214110 (2017)] which allows for the calculation of the excess chemical potential of a large molecule in a dense solvent phase. For the calculation of the relative solubility ("partition coefficient," log10 ) of cholesterol between octanol and water, we use the OPLS/AA force field in combination with the SPC, TIP3P, and TIP4P water models. For all water models studied, our results reproduce the experimental observation that cholesterol is less soluble in water than in octanol. While the experimental value for the partition coefficient is log10 = 3.7, SPC, TIP3P, and TIP4P give us a value of log10 = 4.5, 4.6, and 2.9, respectively. Therefore, although the results for the studied water models in combination with the OPLS/AA force field are acceptable, further work to improve the accuracy of current force fields is needed.

Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm.

To perform computationally efficient concurrent multiscale simulations of biological macromolecules in solution, where the all-atom (AT) models are coupled to supramolecular coarse-grained (SCG) solvent models, previous studies resorted to modified AT water models, such as the bundled-simple point charge (SPC) models, that use semiharmonic springs to restrict the relative movement of water molecules within a cluster. Those models can have a significant impact on the simulated biomolecules and can lead, for example, to a partial unfolding of a protein. In this work, we employ the recently developed alternative approach with a dynamical clustering algorithm, SWINGER, which enables a direct coupling of original unmodified AT and SCG water models. We perform an adaptive resolution molecular dynamics simulation of a Trp-Cage miniprotein in multiscale water, where the standard SPC water model is interfaced with the widely used MARTINI SCG model, and demonstrate that, compared to the corresponding full-blown AT simulations, the structural and dynamic properties of the solvated protein and surrounding solvent are well reproduced by our approach.

Shape matters: The case for Ellipsoids and Ellipsoidal Water11This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form

We describe the shape potentials used for the van der Waals interactions between soft-ellipsoids used to coarse-grain molecular moieties in Metropolis Monte-Carlo simulation software. The morphologies resulting from different expressions for these van der Waals interaction potentials are discussed for the case of a prolate spheroid system with a strong dipole at the center. We also show that the calculation of ellipsoids is, at worst, only about fivefold more expensive computationally when compared to a simple Lennard-Jones sphere. Finally, as an application of the ellipsoidal shape we parametrize water from the original SPC water model and observe – just through the difference in shape alone – a significant improvement of the O-O radial distribution function when compared to experimental data.

Effect of Sodium and Chloride Binding on a Lecithin Bilayer. A Molecular Dynamics Study.

The effect of ion binding on the structural, mechanical, dynamic and electrostatic properties of a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer in a 0.5 M aqueous NaCl solution is investigated using classical atomistic molecular dynamics simulation with different force-field descriptions for ion-ion and ion-lipid interactions. Most importantly, the repulsive Lennard–Jones parameters for the latter were modified, such that approximately similar binding of cations and anions to the lipid membrane is achieved. This was done to qualitatively improve the apparent ion-lipid binding constants obtained from simulations with the original force field (Berger lipids and GROMOS87 ions in combination with the SPC water model) in comparison to experimental data. Furthermore, various parameters characterizing membrane structure, elasticity, order and dynamics are analyzed. It is found that ion binding as observed in simulations involving the modified in comparison to the original force-field description leads to: (i) a smaller salt-induced change in the area per lipid, which is in closer agreement with the experiment; (ii) a decrease in the area compressibility and bilayer thickness to values comparable to a bilayer in pure water; (iii) lipid deuterium order parameters and lipid diffusion coefficients on nanosecond timescales that are very similar to the values for a membrane in pure water. In general, salt effects on the structural properties of a POPC bilayer in an aqueous sodium-chloride solution appear to be reproduced reasonably well by the new force-field description. An analysis of membrane-membrane disjoining pressure suggests that the smaller salt-induced change in area per lipid induced by the new force-field description is not due to the alteration of membrane-associated net charge, but must rather be understood as a consequence of ion-specific effects on the arrangement of lipid molecules.

Base sequence specificity of counterion binding to DNA: what can MD simulations tell us?

Nucleic acids are highly charged biopolymers whose secondary structure is strongly dependent on electrostatic interactions. Solvent molecules and ions are also believed to play an important role in mediating and directing both sequence recognition and interactions with other molecules, such as proteins and a variety of ligands. Therefore, to fully understand the biological functions of DNA, it is necessary to understand the interactions with the surrounding counterions. It is well known that monovalent counterions can bind to the minor groove of DNA with consecutive sequences of four, or more, adenine and thymine (A-tracts) with relatively long residence times. However, much less is known about their binding to the backbone and to the major groove. In this work, we used molecular dynamics simulations to both investigate the interactions between the backbone and major groove of DNA and one of its physiological counterions (Na+) and evaluate the relationship between these interactions and the nucleotide sequence. Three dodecamers, namely CGAAAATTTTCG, CGCTCTAGAGCG, and CGCGAATTCGCG, were simulated using the Toukan–Rahman flexible SPC water model and Smith and Dang parameters for Na+, revealing a significant sequence dependence on the ion binding to both backbone and major groove. In the absence of experimental data on the atomistic details of the studied interactions, the reliability of the results was evaluated performing the simulations with additional sets of potential parameters for ions and solvent, namely the Ȧqvist or the Joung and Cheatham ion parameters and the TIP3P water model. This allowed us to evaluate the results by verifying which features are preserved independently from the parameters adopted.

Wetting and nanodroplet contact angle of the clay 2:1 surface: The case of Na-montmorillonite (001)

Molecular dynamics simulation method is performed to study the wetting and contact angle between a water nanodroplet and a surface of Na-montmorillonite (Na-MMT). The nanodroplet of 256, 500 and 1000 water molecules, based on SPC and TIP4P water models, is handled by means of Monte Carlo and Molecular Dynamics simulation methods The spreading of water molecules on Na-MMT’s surface is not uniform. In fact, the contact line is not perfectly circlar; it depends on the distribution of cations on clay’s surface. The average contact angle of air/water/clay corresponds to 25° for all cases of nanodroplets studied here, which reveals that Na-MMT is definitely hydrophilic. In the nanodroplet, most of water molecules remain at a distance between 3.5 and ∼4Å to the clay’s surface. However, at the edge of nanodroplet, water molecules are caught by the clay’s surface oxygen and thus enter into the 0–3Å zone, which blocks the spreading of nanodroplet.

Effect of solvent composition on the structural and dynamical properties of sodium chloride solutions in water-methanol mixtures

Molecular dynamics (MD) simulations have been performed on sodium chloride solutions in water-methanol mixtures under ambient conditions with methanol mole fractions (xm) ranging from 0.09 to 0.87. MD simulations are performed with the flexible SPC water model and the flexible six-site model for methanol. The ions are modeled as charged Lennard–Jones spheres. The structural properties of the solutions are discussed on the basis of radial distribution functions. A chain cluster of methanol is predominant in the mixture where xm exceeds 0.7. The number of methanol molecules are higher than water molecules in the first coordination shell of sodium and chloride ions beyond xm=0.5 and 0.48 respectively. With increasing xm, the diffusion coefficients for water (DH2O) and for methanol (DCH3OH) initially decrease. From xm=0.29 DCH3OH increases while DH2O rises only from about 0.7. The two diffusion coefficients are equal at xm=0.8. The deduced first and second reorientational correlation times for the OH and the dipole moment vectors for water speed up with increasing xm. Through the τ1/τ2 ratio, the reorientational motion of water molecules can be entirely ascribed to a jump. OH methanol vector reorientational occurs by a mechanism similar to that of water.

Effects of Translational and Rotational Degrees of Freedom on the Hydration of Ionic Solutes as Seen by the Popular Water Models.

We employed molecular dynamics simulations with separate thermostats for translational and rotational temperatures in order to study the effects of these degrees of freedom on the hydration of ions. In this work we examine how water models, differing in charge distribution, respond to the rise of rotational temperature. The study shows that, with respect to the distribution of negative charge, popular water models lead to different responses upon an increase of the rotational temperature. The differences arise in hydration of cations, as the negative charge distribution on the model solvent represents the determining factor in such cases. The cation-water correlation increases with the increasing rotational temperature if negative charge is placed in (or close to) the centre of the water molecule (a typical example is the SPC water model) and decreases, when the negative charge is shifted from the centre (as in the TIP5P model of water). Because all the water models examined here have similar distributions of positive charge, they all exhibit similar trends in solvation of anions. In contrast to above, the effect of translational temperature variation is similar for all water-solute pairs; any increase in translational temperature decreases the solute-water correlations.

On the compatibility of polarisable and non-polarisable models for liquid water

The properties of water at physiological conditions can be modelled at different levels of resolution: (1) sub-atomic models that take into account electronic degrees of freedom, (2) atomic models that only account for atomic degrees of freedom and (3) supra-molecular models that only involve some supra-molecular degrees of freedom. To enhance the computational efficiency of molecular simulation, models at different levels of resolution should be simultaneously usable for different parts of a system for which the level of detail of interest is different. This requires these different types of models to be compatible with each other. In the present study, the compatibility of two polarisable models for liquid water, COS/G2 and COS/D, with a non-polarisable model for liquid water, SPC, is investigated. It is shown that these models are compatible. The polarisable models can thus be used to solvate biomolecules described by a biomolecular force field that is compatible with the SPC water model.

The Impact of Molecular Dynamics Methods on the Accuracy of Simulations of the Disordered Protein Sic1

Intrinsically disordered proteins (IDPs), proteins that lack a uniquely folded structure, comprise a significant portion of eukaryotic proteomes and play essential roles in signal transduction and cell cycle control. Mapping the dynamics and conformational ensembles of these proteins is essential to understanding their function. IDPs are generally thought to bind via coupled folding and binding. Sic1, however, even in its bound state with Cdc4, remains largely disordered and ‘ultrasensitive’. The lack of static structure and dynamic nature of this process poses challenges for many traditional biophysical techniques, highlighting the importance of computational methods for its characterization. Molecular dynamics (MD) simulations of IDPs are often complicated by biases introduced by force fields originally optimized to simulate folded proteins. Often simulations oversample secondary structure and lead to collapsed protein conformations. This study aims to consider canonical MD force fields and simulation methods and how accurately these techniques are able to reproduce experimental results. We carried out simulations in both implicit and explicit (with varying salt concentration) solvents with the force fields Amber12, Charmm27, OPLS-AA and Gromos at multiple temperatures. Simulations in implicit solvent were not able to recapitulate experimental structural data and always led to collapsed structures. Simulations in explicit solvents (TIP3P, TIP4P and SPC water models were used where appropriate for force field) achieved more native-like states, however some still led to collapse. Salt concentration had a strong impact on the compactness of the protein providing clues into the source of non-native compactness in MD simulations of IDPs.