Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics

In silico design of antiviral peptides targeting the spike protein of SARS-CoV-2

An outbreak caused by 2019 novel coronavirus (2019-nCoV) was first identified in Wuhan City, Hubei Province, China. The new virus was later named SARS-CoV-2. The virus has affected tens of thousands of patients in the world. The infection of SARS-CoV-2 causes severe pneumonia and even death. It is urgently needed to find a therapeutic method to treat patients with SARS-CoV-2 infection. Studies showed that the surface spike (S) protein is essential for the coronavirus binding and entry of host cells. The heptad repeats 1 and 2 (HR1 and HR2) in the S protein play a decisive role in the fusion of the viral membrane with the host cell membrane. We predicted the HR1 and HR2 regions in S protein by sequence alignment. We simulated a computational model of HR1/2 regions and the fusion core. The binding energy of HR1 and HR2 of the fusion core was -33.4 kcal/mol. We then designed antivirus peptides by molecular dynamics simulation of the fusion core. The binding energy of HR2-based antiviral peptide to HR1 was -43.0 kcal/mol, which was stronger than the natural stage of the fusion core, suggesting that the predicted antiviral peptide can competitively bind with HR1 to prevent forming of the fusion core. The antiviral peptides can prevent SARS-CoV-2 membrane fusion and can potentially be used for the prevention and treatment of infections.

Structure of aqueous sodium acetate solutions by X-Ray scattering and density functional theory

The structure of aq. sodium acetate solution (CH3COONa, NaOAc) was studied by X-ray scattering and density function theory (DFT). For the first hydrated layer of Na+, coordination number (CN) between Na+ and O(W, I) decreases from 5.02 ± 0.85 at 0.976 mol/L to 3.62 ± 1.21 at 4.453 mol/L. The hydration of carbonyl oxygen (OC) and hydroxyl oxygen (OOC) of CH3COO− were investigated separately and the OC shows a stronger hydration bonds comparing with OOC. With concentrations increasing, the hydration shell structures of CH3COO− are not affected by the presence of large number of ions, each CH3COO− group binds about 6.23 ± 2.01 to 7.35 ± 1.73 water molecules, which indicates a relatively strong interaction between CH3COO− and water molecules. The larger uncertainty of the CN of Na+ and OC(OOC) reflects the relative looseness of Na-OC and Na-OOC ion pairs in aq. NaOAc solutions, even at the highest concentration (4.453 mol/L), suggesting the lack of contact ion pair (CIP) formation. In aq. NaOAc solutions, the so called “structure breaking” property of Na+ and CH3COO− become effective only for the second hydration sphere of bulk water. The DFT calculations of CH3COONa (H2O)n=5–7 clusters suggest that the solvent-shared ion pair (SIP) structures appear at n = 6 and become dominant at n = 7, which is well consistent with the result from X-ray scattering.

Structure-based designing efficient peptides based on p53 binding site residues to disrupt p53-MDM2/X interaction

MDM2 and MDMX are known as overexpressed oncoproteins in several wild-type p53 cancer cells. The development of potent and dual antagonist peptides for p53-MDM2/X is a continuous challenge. In this study, we intended to investigate the pivotal structural points respecting the development of potent and dual inhibitors of MDM2/X. Correspondingly, MD simulation was performed on the experimentally confirmed peptides, comprising p53, pDI, pDIQ, PMI, and computationally screened mutant pDI and pDIQ. A follow-up secondary structure analysis showed the last three C-terminal residues provide the helicity reservation of peptides bound to MDM2/X. Furthermore, a delicate residue-residue examination displayed Met 11 and Ser12 in the modified peptides contribute significantly to dual inhibition of MDM2/X. Additionally, the peptides_MDM2/X complexes' ΔG_binding extracted by the umbrella sampling method were in agreement with the pattern of their experimental affinity values. It was concluded the screened pDI mutants were considered as suitable anti-MDM2/X peptides, and the data obtained could be exploited as the theoretical structure-based guide for rational peptide design. Taking account of results, the suitable C-terminal residues of p53-based peptides especially Met11, and Ser12, as well as higher umbrella sampling, generated ΔG_binding to MDM2/X would be considered as the positive structural markers of a promising anti-cancer agent.

Computationally predicting binding affinity in protein-ligand complexes: free energy-based simulations and machine learning-based scoring functions

Accurately predicting protein-ligand binding affinities can substantially facilitate the drug discovery process, but it remains as a difficult problem. To tackle the challenge, many computational methods have been proposed. Among these methods, free energy-based simulations and machine learning-based scoring functions can potentially provide accurate predictions. In this paper, we review these two classes of methods, following a number of thermodynamic cycles for the free energy-based simulations and a feature-representation taxonomy for the machine learning-based scoring functions. More recent deep learning-based predictions, where a hierarchy of feature representations are generally extracted, are also reviewed. Strengths and weaknesses of the two classes of methods, coupled with future directions for improvements, are comparatively discussed.

An insight into the role of riboflavin ligand in the self-assembly of poly(lactic-co-glycolic acid)-based nanoparticles - a molecular simulation and experimental approach

Nanoparticles (NPs) used for targeted delivery purposes are rapidly gaining importance in diagnostic and therapeutic fields. These agents have been studied extensively so far to reveal their optimal physicochemical properties including the effects of ligands and their density on the surface of NPs. This article was conducted through a computational approach (all-atom molecular dynamics simulations) to predict the stability of NPs based on a poly-lactic-co-glycolic acid (PLGA) hydrophobic core with a poly-ethylene glycol (PEG) hydrophilic shell and varying numbers of riboflavin (RF) molecules as ligands. Depending on the molecular weight of the polymers, the most stable composition of NPs was achieved at 20 wt% and 10 wt% PLGA-PEG-RF for PLGA3kDa-PEG2kDa and PLGA4.5kDa-PEG2kDa polymers, respectively. According to the simulations, riboflavin molecules were located on the surface of the NPs, which would indicate that riboflavin-bound PLGA-PEG NPs could be efficiently utilized for active targeting purposes. To scrutinize the simulation results, NPs with riboflavin ligands were synthesized and put into in vitro experiments. Outstandingly, the empirical outcomes revealed that the hydrodynamic sizes of NPs also met minimum points at 20 and 10 wt% for PLGA3kDa-PEG2kDa and PLGA4.5kDa-PEG2kDa, respectively. Moreover, similar trends in the gyration radius as a function of riboflavin content were observed in the simulation analysis and the experimental results, which would indicate that the method of molecular dynamics (MD) simulation is a reliable mathematical technique and could be applied for predicting the physicochemical properties of NPs.

Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions

Thermodynamic integration (TI), a powerful formalism for computing Gibbs free energy, has been implemented for many biophysical processes with alchemical schemes that require delicate human efforts to choose/design biasing potentials for sampling the desired biophysical events and to remove their artifactitious consequences afterwards. Theoretically, an alchemical scheme is exact but practically, an unsophisticated implementation of this exact formula can cause error amplifications. Small relative errors in the input parameters can be amplified many times in their propagation into the computed free energy [due to subtraction of similar numbers such as (105 ± 5)‒(100 ± 5) = 5 ± 7]. In this paper, we present an unsophisticated implementation of TI in 3n dimensions (3nD) (n=1,2,3…) for the potential of mean force along a 3nD path connecting one state in the bound state ensemble to one state in the unbound state ensemble. Fluctuations in these 3nD are integrated in the bound and unbound state ensembles but not along the 3nD path. Using TI3nD, we computed the standard binding free energies of three protein complexes: trometamol in Salmonella effector SpvD (n=1), biotin-avidin (n=2), and Colicin E9 endonuclease with cognate immunity protein Im9 (n=3). We employed three different protocols in three independent computations of E9-Im9 to show TI3nD's robustness. We also computed the hydration energies of ten biologically relevant compounds (n=1 for water, acetamide, urea, glycerol, trometamol, ammonium and n=2 for erythritol, 1,3-propanediol, xylitol, biotin). Each of the 15 computations is accomplishable within one (for hydration) to ten (for E9-Im9) days on an inexpensive GPU workstation. The computed results all agree with the available experimental data.

A molecular dynamics investigation on transporting mechanism of glucose through a cyclic peptide nanotube

Cyclic peptide nanotubes (CPNTs) are open-ended, hollow, and tubular structures that are made of several cyclic peptide rings. These structures can act as a transmembrane channel and transport ions or small molecules. In this work, we studied the stability of a cyclic peptide nanotube 8 × [(Trp-D-Leu)4-Gln-D-Leu] into a fully hydrated membrane composed of DPPC/POPC/POPS/cholesterol and also the transport mechanism of β-D-glucose through this nanotube was investigated. Our findings revealed that the CPNT was stable in the lipid bilayer during the simulation time and non-bonded interactions, especially hydrogen bonding have an important role to form a stable CPNT in the membrane. The glucose jumps from a Cα-region into the mid-Cα region and spends more time in this region because of its more desirable interactions with water molecules and the CPNT. In the transport pathway, non-bonded interactions between glucose, water molecules and the CPNT facilitate the transport of the glucose through the CPNT. The collaboration of hydrogen bonds, electrostatic and van der Waals interactions change the pulling force and lead to transport glucose through the CPNT. Potential of mean force (PMF) calculations revealed that the glucose has a minimum value of binding free energy and maximum configurational entropy in MPR regions. These findings can be used to design more CPNTs with different goals such as drug delivery.Communicated by Ramaswamy H. Sarma.

Efficient Estimation of Absolute Binding Free Energy for a Homeodomain-DNA Complex from Nonequilibrium Pulling Simulations

Estimation of binding free energies is one of the central aims of simulations of biomolecular complexes. We explore the accuracy and efficiency of setups based on nonequilibrium pulling simulations applied to the estimation of binding affinities of DNA-binding proteins. Absolute binding free energies are calculated over a range of temperatures and compared to results obtained previously using an equilibrium method. We show that realistic binding affinities can be obtained with the presented nonequilibrium approach, which also entails lower computational requirements. Errors of the binding free energy estimates are investigated and are shown to be comparable to those observed previously. Bounds are provided on the convergence of the errors with respect to the number of pulling simulations performed and with respect to the applied pull rate.

FKBP12 dimerization mutations effect FK506 binding and differentially alter calcineurin inhibition in the human pathogen Aspergillus fumigatus

The 12-kDa FK506-binding protein (FKBP12) is the target of the commonly used immunosuppressive drug FK506. The FKBP12-FK506 complex binds to calcineurin and inhibits its activity, leading to immunosuppression and preventing organ transplant rejection. Our recent characterization of crystal structures of FKBP12 proteins in pathogenic fungi revealed the involvement of the 80's loop residue (Pro90) in the active site pocket in self-substrate interaction providing novel evidence on FKBP12 dimerization in vivo. The 40's loop residues have also been shown to be involved in reversible dimerization of FKBP12 in the mammalian and yeast systems. To understand how FKBP12 dimerization affects FK506 binding and influences calcineurin function, we generated Aspergillus fumigatus FKBP12 mutations in the 40's and 50's loop (F37 M/L; W60V). Interestingly, the mutants exhibited variable FK506 susceptibility in vivo indicating differing dimer strengths. In comparison to the 80's loop P90G and V91C mutants, the F37 M/L and W60V mutants exhibited greater FK506 resistance, with the F37M mutation showing complete loss in calcineurin binding in vivo. Molecular dynamics and pulling simulations for each dimeric FKBP12 protein revealed a two-fold increase in dimer strength and significantly higher number of contacts for the F37M, F37L, and W60V mutations, further confirming their varying degree of impact on FK506 binding and calcineurin inhibition in vivo.

Pulling Simulations and Hydrogen Sorption Modelling on Carbon Nanotube Bundles

Recent progress in molecular simulation technology has developed an interest in modernizing the usual computational methods and approaches. For instance, most of the theoretical work on hydrogen adsorption on carbon nanotubes was conducted a decade ago. It should be insightful to reinvestigate the field and take advantage of code improvements and features implemented in contemporary software. One example of such features is the pulling simulation modules now available in many molecular dynamics programs. We conduct pulling simulations on pairs of carbon nanotubes and measure the inter-tube distance before they dissociate in water. We use this distance to set the interval size between adjacent nanotubes as we arrange them in bundle configurations. We consider bundles with triangular, intermediate and honeycomb patterns, and armchair nanotubes with a chiral index from n = 5 to n = 10. Then, we simulate low pressure hydrogen adsorption isotherms at 77 K, using the grand canonical Monte Carlo method. The different bundle configurations adsorb great hydrogen amounts that may exceed 2% wt at ambient pressures. The computed hydrogen capacities are considered large for physisorption on carbon nanostructures and attributed to the ultra-microporous network and extraordinary high surface area of the configured models.

Enhanced sampling and free energy calculations for protein simulations

Molecular dynamics simulation is a powerful computational technique to study biomolecular systems, which complements experiments by providing insights into the structural dynamics relevant to biological functions at atomic scale. It can also be used to calculate the free energy landscapes of the conformational transitions to better understand the functions of the biomolecules. However, the sampling of biomolecular configurations is limited by the free energy barriers that need to be overcome, leading to considerable gaps between the timescales reached by MD simulation and those governing biological processes. To address this issue, many enhanced sampling methodologies have been developed to increase the sampling efficiency of molecular dynamics simulations and free energy calculations. Usually, enhanced sampling algorithms can be classified into methods based on collective variables (CV-based) and approaches which do not require predefined CVs (CV-free). In this chapter, the theoretical basis of free energy estimation is briefly reviewed first, followed by the reviews of the most common CV-based and CV-free methods including the presentation of some examples and recent developments. Finally, the combination of different enhanced sampling methods is discussed.

Design and development of high affinity dual anticancer peptide-inhibitors against p53-MDM2/X interaction

AIMS

Inhibition of P53-MDM2/X interaction is known as an effective cancer therapy strategy. In this regard, pDI peptide was introduced previously with the potential of targeting MDM2. In this research, the large-scale peptide mutation screening was used to achieve the best sequence of pDI with the highest affinity for inhibition activity against MDM2/X.

MAIN METHODS

Three mutant peptides of pDI as dual inhibitor peptides including single mutations of pDIm/4W, pDIm/11M and double mutations of pDIdm/4W11M were presented with the high affinities to inhibit both MDM2/X. The selected mutants were then evaluated comprehensively to confirm their ability as potent MDM2/X inhibitors, using a theoretical simulation approach.

KEY FINDINGS

MD simulations analyses confirmed their dual inhibition potential against both MDM2/X interactions with p53 protein. The developed pDIm and mainly pDIdm peptides showed stable conformations over the simulation time with conserved secondary structure and effective interaction with MDM2/X by physical binding such as hydrogen bonding. Besides, umbrella sampling free energy calculation indicated higher binding energy, ΔG_binding, of pDIm-MDM2/X and pDIdm-MDM2/X compared to pDI-MDM2/X.

SIGNIFICANCE

The optimized and improved mutant pDI, pDIdm, with more effective ΔG_binding values of -30 and -25 kcal/mol to MDMX and MDM2, respectively, is recommended as a promising anticancer agent and suitable candidate for experimental evaluations.

Growth Mechanism of Gold Nanorods: the Effect of Tip-Surface Curvature As Revealed by Molecular Dynamics Simulations

An understanding of the anisotropic growth mechanism of gold nanorods (AuNRs) during colloidal synthesis is critical for controlling the nanocrystal size and shape and thus has implications in tuning the properties for applications in a wide range of research and technology fields. In order to investigate the role of the cetyltrimethylammonium bromide (CTAB) coating in the anisotropic growth mechanism of AuNRs, we used molecular dynamics (MD) simulations and built a computational model that considered explicitly the effect of the curvature of the gold surface on CTAB adsorption and therefore differentiated between the CTAB arrangements on flat and curved surfaces, representing the lateral and tip facets of growing AuNRs, respectively. We verified that on a curved surface, a lower CTAB coverage density and larger intermicellar channels are generated compared to those on a flat surface. Using umbrella sampling simulations, we measured the free energy profile and verified that the environment around a curved surface corresponds to an easier migration from the solution to the gold surface for the [AuBr₂]^- species than does a flat surface. Long unbiased molecular dynamics simulations also corroborated the umbrella sampling results. Therefore, the [AuBr₂]^- diffusion through the environment of the tips is much more favorable than that in the case of lateral facets. This shows that the surface curvature is an essential component of the anisotropic growth mechanism.

Identifying the key residues instrumental in imparting stability to amyloid beta protofibrils - a comparative study using MD simulations of 17-42 residues

Extracellular plaques, the hallmark of Alzheimer's disease brains, consist of insoluble amyloid fibrils that result from the aggregation of amyloid beta peptides. None of the few therapeutic options currently adopted, address the cause of the disease. Instead, they reduce symptom of the disease. Inhibition of aggregation or destabilization of aggregates therefore, emerges as a preferable therapeutic approach. Designing inhibitors or destabilizers demands comprehensive knowledge of the residues of amyloid beta responsible for the phenomenal structural stability of the aggregate. For the purpose, we have compared the effect on structural destabilization of 13 in silico mutations (single and double) with the wild type counterpart of beta-strand-turn-beta-strand motif of the amyloid beta protofibrils by molecular dynamics simulation. Besides the already known salt bridge interaction between K28 and D23, our analyses expose more significant role of K28 as the only positive charge present in the vicinity. Amongst the two consecutive aromatic residues, F19 is involved in stacking interaction; although effect of F20 mutation is more pronounced. Face to face arrangement of A21 and V36 acts as a pillar maintaining the necessary optimum distance between consecutive chains to promote stabilizing interactions. In addition to providing stability to the first beta-strand, large sized negatively charged E22 facilitates salt bridge formation by ensuring fixed relative position of D23 and in turn K28. Likewise, the hydrophobic residues I32 and L34 pack the protofibril core, once again fostering salt bridge interaction. Prospectively, these findings may be compiled for efficient identification or design of scaffolds accountable for protofibril destabilization.Communicated by Ramaswamy H. Sarma.

Novel Disassembly Mechanisms of Sigmoid Aβ42 Protofibrils by Introduced Neutral and Charged Drug Molecules

Alzheimer's disease (AD) is characterized by fibrillar deposits of amyloid-β (Aβ) peptides and neurofibrillary tangles of Tau proteins. Aβ peptides are composed of 37-49 residues, among which the Aβ₄₂ isoform is particularly toxic and aggregation-prone and is enriched in the plaques of AD brains and thus considered central to the development of AD. Therefore, disaggregation and disruption provide potential therapeutic approaches to reduce, inhibit, and even reverse Aβ aggregation. Here we capture the atomic-level details of the interactions between sigmoid Aβ₄₂ fibril 2MXU or 5KK3 and either natural tanshinone compounds TS1 or TS0 or negatively charged ER, proposing two unprecedented disassembly mechanisms. Natural TS1 or TS0 prefers to insert into the cavity together with part at the surface of the 2MXU to open up the mouth and twist the conformation, destroying the ordered growth of subsequent monomers along the fibril axis. For the more compact two-fold 5KK3 , attachment of TS1 or TS0 at the surface including some inserted in cavity results in the separation of the two folds. In the two sigmoid fibril systems, it is no longer applicable for the routine criteria to assess Aβ₄₂ fibril disassembly by introduction of these drugs, such as either reduced H-bond number, decreased β-sheet contents, or both. ER, like-charged to Aβ₄₂ fibril, is especially exceptional, and departs utterly from the neutral ones to disassemble Aβ₄₂ fibril. Besides the inapplicable routine criteria, positive binding energy between ER and Aβ₄₂ fibril also deviates from the hypotheses of "ligands exhibiting greater affinity for the β-amyloid peptide are effective at altering its aggregation and inhibiting cell toxicity" ( Cairo et al. , Biochemistry 2002 , 41 , 8620 - 8629 ) but results in stronger disassembly effect on the two kinds of sigmoid Aβ₄₂ fibrils than neutral TS0 or TS1. The disassembly power of charged ER molecules derives from its stronger deformation ability to the conformation of Aβ₄₂ fibril than the neutral ones, twisting the one-fold 2MXU into tapered-shape and separating two-fold 5KK3 in two parts further, which is in great agreement with experimental observations ( Irwin et al. Biomacromolecules 2013 , 14 ( 1 ), 264 - 274 ). The unusual disassembly mechanisms fill the gaps and offer an alternative direction in engineering new inhibitors to treat AD.

Molecular dynamics simulations of loading and unloading of drug molecule bortezomib on graphene nanosheets

Graphene-drug complexes can enter the lipid bilayer and then drug molecules release from graphene surface.

Hot Spots and Their Contribution to the Self-Assembly of the Viral Capsid: In Silico Prediction and Analysis

The viral capsid is a macromolecular complex formed by a defined number of self-assembled proteins, which, in many cases, are biopolymers with an identical amino acid sequence. Specific protein-protein interactions (PPI) drive the capsid self-assembly process, leading to several distinct protein interfaces. Following the PPI hot spot hypothesis, we present a conservation-based methodology to identify those interface residues hypothesized to be crucial elements on the self-assembly and thermodynamic stability of the capsid. We validate the predictions through a rigorous physical framework which integrates molecular dynamics simulations and free energy calculations by Umbrella sampling and the potential of mean force using an all-atom molecular representation of the capsid proteins of an icosahedral virus in an explicit solvent. Our results show that a single mutation in any of the structure-conserved hot spots significantly perturbs the quaternary protein-protein interaction, decreasing the absolute value of the binding free energy, without altering the protein's secondary nor tertiary structure. Our conservation-based hot spot prediction methodology can lead to strategies to rationally modulate the capsid's thermodynamic properties.

In silico assessment of human Calprotectin subunits (S100A8/A9) in presence of sodium and calcium ions using Molecular Dynamics simulation approach

Calprotectin is a heterodimeric protein complex which consists of two subunits including S100A8 and S100A9. This protein has a major role in different inflammatory disease and various types of cancers. In current study we aimed to evaluate the structural and thermodynamic changes of the subunits and the complex in presence of sodium and calcium ions using molecular dynamics (MD) simulation. Therefore, the residue interaction network (RIN) was visualized in Cytoscape program. In next step, to measure the binding free energy, the potential of mean force (PMF) method was performed. Finally, the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method was applied as an effective tool to calculate the molecular model affinities. The MD simulation results of the subunits represented their structural changes in presence of Ca2+. Moreover, the RIN and Hydrogen bond analysis demonstrated that cluster interactions between Calprotectin subunits in presence of Ca2+ were greater in comparison with Na+. Our findings indicated that the binding free energy of the subunits in presence of Ca2+ was significantly greater than Na+. The results revealed that Ca2+ has the ability to induce structural changes in subunits in comparison with Na+ which lead to create stronger interactions between. Hence, studying the physical characteristics of the human proteins could be considered as a powerful tool in theranostics and drug design purposes.

Investigation of Drug for Pulmonary Administration-Model Pulmonary Surfactant Monolayer Interactions Using Langmuir-Blodgett Monolayer and Molecular Dynamics Simulation: A Case Study of Ketoprofen

Pulmonary administration is widely used for the treatment of lung diseases. The interaction between drug molecules and pulmonary surfactants affects the efficacy of the drug directly. The location and distribution of drug molecules in a model pulmonary surfactant monolayer under different surface pressures can provide vivid information on the interaction between drug molecules and pulmonary surfactants during the pulmonary administration. Ketoprofen is a nonsteroidal anti-inflammatory drug for pulmonary administration. The effect of ketoprofen molecules on the lipid monolayer containing 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) and 1,2-dipalmitoyl-sn-glycero-3-phospho-rac-glycerol (DPPG) is studied by surface pressure (π)-area (A) isotherms and compressibility modulus (C_s^-1)-surface pressure (π) isotherms. The location and distribution of ketoprofen molecules in a lipid monolayer under different surface pressures are explored by surface tension, density profile, radial distribution function (RDF), and the potential of mean force (PMF) simulated by molecular dynamics (MD) simulation. The introduction of ketoprofen molecules affects the properties of DPPC/DPPG monolayers and the location and distribution of ketoprofen molecules in monolayers with various surface pressures. The existence of ketoprofen molecules hinders the formation of liquid-condensed (LC) films and decreases the compressibility of DPPC/DPPG monolayers. The location and distribution of ketoprofen molecules in the lipid monolayer are affected by cation-π interaction between the choline group of lipids and the benzene ring of ketoprofen, the steric hindrance of the lipid head groups, and the hydrophobicity of ketoprofen molecule itself, comprehensively. The contact state of lipid head group with water is determined by surface pressure, which affects the interaction between drug molecules and lipids and further dominates the location and distribution of ketoprofen in the lipid monolayer. This work confirms that ketoprofen molecules can affect the property and the inner structure of DPPC/DPPG monolayers during breathing. Furthermore, the results obtained using a mixed monolayer containing two major pulmonary surfactants DPPC/DPPG and ketoprofen molecules will be helpful for the in-depth understanding of the mechanism of inhaled administration therapy.

Structural Mechanism of Barriers to Interspecies Seeding Transmissibility of Full-Length Prion Protein Amyloid

A puzzling feature of prion diseases is the cross-species barriers. The detailed molecular mechanisms underlying these interspecies barriers remain poorly understood because of a lack of high-resolution structural information on the scrapie isoform of the prion protein (PrP^Sc ). In this study we identified the critical role of the residues 165/167 in the barrier to seeding mouse PrP (mPrP) fibril seeds to human cellular prion protein (PrP^C ). Solid-state NMR revealed a C-terminal β-sheet core spanning residues 165-230 and the packing arrangement of mPrP fibrils. Residues 165/167 are located on one end of the fibril core. Molecular dynamics simulations demonstrated that the stabilities of the seeding-induced β-strand structures are significantly impacted by hydrogen bonds involving the side chain of residue 167 and steric resistance involving residue 165. These findings suggest that the α2-β2 loop containing residues 165/167 could be the initial site of seed-template conformational conversion.

Carbon Nanotubes Translocation through a Lipid Membrane and Transporting Small Hydrophobic and Hydrophilic Molecules

Carbon nanotubes (CNTs) are extensively adopted in the applications of biotechnology and biomedicine. Their interactions with cell membranes are of great importance for understanding the toxicity of CNTs and the application of drug delivery. In this paper, we use atomic molecular dynamics simulations to study the permeation and orientation of pristine and functionalized CNTs in a lipid bilayer. Pristine CNT (PCNT) can readily permeate into the membrane and reside in the hydrophobic region without specific orientation. The insertion of PCNTs into the lipid bilayer is robust and independent on the lengths of PCNTs. Due to the presence of hydroxyl groups on both ends of the functionalized CNT (FCNT), FCNT prefers to stand upright in the lipid bilayer center. Compared with PCNT, FCNT is more suitable to be a bridge connecting the inner and outer lipid membrane. The inserted CNTs have no distinct effects on membrane structure. However, they may block the ion channels. In addition, preliminary explorations on the transport properties of CNTs show that the small hydrophobic molecule carbon dioxide can enter both PCNT and FCNT hollow channels. However, hydrophilic molecule urea is prone to penetrate the PCNT but finds it difficult to enter the FCNT. These results may provide new insights into the internalization of CNT in the lipid membrane and the transport properties of CNTs when embedded therein.

Polyproline chains destabilize the Alzheimer's amyloid-β protofibrils: A molecular dynamics simulation study

Alzheimer's is a fatal neurodegenerative disease for which there is no cure at present. The disease is characterized by the presence of plaques, principally comprising the amyloid-β peptide (viz., β-sheet) in the brains of a patient. In our present work, we study the interaction of these β-sheets with a different number of repeating units of proline (β-sheet breaker) by docking and all atom molecular dynamics simulations. Our results indicate that proline can break the amyloid protofibrils apart, cause them to break their β-sheet structure, and in some cases even induce the formation of 3₁₀ helices, which may be intermediates in the unfolding of these β-sheets. We have also observed that some of the important hydrogen bonds and salt bridges between chains were disrupted by proline and the tight interatomic packing of atoms in the fibrils was made relatively loose. Proline chains had a tendency to make several contacts with charged residues. Proline chains binded well to the fibrils by strong electrostatic interactions while hydrophobic interactions played a less important role. This leads to the conclusion that proline can break the amyloid fibrils apart and can be considered in the design of novel peptide-based drugs to treat Alzheimer's disease and potentially other diseases caused by the misfolding of proteins into β-sheets.

A de novo substitution in BCL11B leads to loss of interaction with transcriptional complexes and craniosynostosis

Craniosynostosis, the premature ossification of cranial sutures, is a developmental disorder of the skull vault, occurring in approximately 1 in 2250 births. The causes are heterogeneous, with a monogenic basis identified in ~25% of patients. Using whole-genome sequencing, we identified a novel, de novo variant in BCL11B, c.7C>A, encoding an R3S substitution (p.R3S), in a male patient with coronal suture synostosis. BCL11B is a transcription factor that interacts directly with the nucleosome remodelling and deacetylation complex (NuRD) and polycomb-related complex 2 (PRC2) through the invariant proteins RBBP4 and RBBP7. The p.R3S substitution occurs within a conserved amino-terminal motif (RRKQxxP) of BCL11B and reduces interaction with both transcriptional complexes. Equilibrium binding studies and molecular dynamics simulations show that the p.R3S substitution disrupts ionic coordination between BCL11B and the RBBP4-MTA1 complex, a subassembly of the NuRD complex, and increases the conformational flexibility of Arg-4, Lys-5 and Gln-6 of BCL11B. These alterations collectively reduce the affinity of BCL11B p.R3S for the RBBP4-MTA1 complex by nearly an order of magnitude. We generated a mouse model of the BCL11B p.R3S substitution using a CRISPR-Cas9-based approach, and we report herein that these mice exhibit craniosynostosis of the coronal suture, as well as other cranial sutures. This finding provides strong evidence that the BCL11B p.R3S substitution is causally associated with craniosynostosis and confirms an important role for BCL11B in the maintenance of cranial suture patency.

Influence of charge sequence on the adsorption of polyelectrolytes to oppositely-charged polyelectrolyte brushes

When a solution of polyanionic chains is placed in contact with a polycationic brush, the polyanions adsorb into the brush. We investigate the influence of the charge sequences of the free and bound species on the thermodynamics of polyelectrolyte adsorption. As model systems, we consider free and brush polyelectrolytes with either block or alternating charge sequences, and study the adsorption process using coarse-grained Langevin dynamics with implicit solvent, explicit counterions, and excess salt. Free energy, internal energy, and entropy of adsorption are computed using umbrella sampling methods. When the number of polyanions exceed the number of polycations, the brush becomes overcharged. Free chains adsorb most strongly when both free and tethered chains have a block charge sequence, and most weakly when both species have an alternating sequence. Adsorption is stronger when the free polyanion has a block sequence and the tethered polycation is alternating than in the reverse case of an alternating free polymer and a tethered block copolymer. Sequence-dependent effects are shown to be largely energetic, rather than entropic, in origin.

C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ11-42 Tetramer in Solution: Intensive MD Study

Amyloid beta (Aβ) peptides are characterized as the major factors associated with neuron death in Alzheimer's disease, which is listed as the most common form of neurodegeneration. Disordered Aβ peptides are released from proteolysis of the amyloid precursor protein. The Aβ self-assembly process roughly takes place via five steps: disordered forms → oligomers → photofibrils → mature fibrils → plaques. Although Aβ fibrils are often observed in patient brains, oligomers were recently indicated to be major neurotoxic elements. In this work, the neurotoxic compound S-shape Aβ11-42 tetramer (S4Aβ11-42) was investigated over 10 μs of unbiased MD simulations. In particular, the S4Aβ11-42 oligomer adopted a high dynamics structure, resulting in unsuccessful determination of their structures in experiments. The C-terminal was suggested as the possible nucleation of the Aβ42 aggregation. The sequences 27-35 and 39-40 formed rich β-content, whereas other residues mostly adopted coil structures. The mean value of the β-content over the equilibrium interval is ∼42 ± 3%. Furthermore, the dissociation free energy of the S4Aβ11-42 peptide was predicted using a biased sampling method. The obtained free energy is ΔG US = -58.44 kcal/mol which is roughly the same level as the corresponding value of the U-shape Aβ17-42 peptide. We anticipate that the obtained S4Aβ11-42 structures could be used as targets for AD inhibitor screening over the in silico study.

The interactions of an Aβ protofibril with a cholesterol-enriched membrane and involvement of neuroprotective carbazolium-based substances

Recent studies have shown that the aggregation of the amyloid-beta peptide (Aβ) in the brain cell membrane is responsible for the emergence of Alzheimer's disease (AD); the exploration of effective factors involved in the extension of the aggregation process and alternatively the examination of an effective inhibitor via theoretical and experimental tools are among the main research topics in the field of AD treatment. Therefore, in this study, we used all-atom molecular dynamics (MD) simulations to clarify the impact of cell membrane cholesterol on the interaction of Aβ with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) as a membrane model. Moreover, the effect of the P7C3-S243 molecule on the abovementioned process was investigated. The simulation results disclosed the neuroprotective property of the P7C3-S243 molecule. The MD simulation results indicate that the interaction of cholesterol molecules with the Aβ oligomer is negligible and cannot enhance membrane rupture. However, strong hydrogen bonding between the POPC molecules and the oligomers led to membrane perturbation. According to our modellings, the P7C3-S243 molecular layer can protect the cell membrane by inhibiting the direct interaction between the bilayer and Aβ. In addition, free-energy calculations were conducted to determine the possible penetration of Aβ fibrils into the cholesterol-enriched membrane.

Site-specific glycation of Aβ1-42 affects fibril formation and is neurotoxic

Aβ1-42 is involved in Alzheimer's disease (AD) pathogenesis and is prone to glycation, an irreversible process where proteins accumulate advanced glycated end products (AGEs). N ^ϵ-(Carboxyethyl)lysine (CEL) is a common AGE associated with AD patients and occurs at either Lys-16 or Lys-28 of Aβ1-42. Methyglyoxal is commonly used for the unspecific glycation of Aβ1-42, which results in a complex mixture of AGE-modified peptides and makes interpretation of a causative AGE at a specific amino acid residue difficult. We address this issue by chemically synthesizing defined CEL modifications on Aβ1-42 at Lys-16 (Aβ-CEL16), Lys-28 (Aβ-CEL28), and Lys-16 and -28 (Aβ-CEL16&28). We demonstrated that double-CEL glycations at Lys-16 and Lys-28 of Aβ1-42 had the most profound impact on the ability to form amyloid fibrils. In silico predictions indicated that Aβ-CEL16&28 had a substantial decrease in free energy change, which contributes to fibril destabilization, and a increased aggregation rate. Single-CEL glycations at Lys-28 of Aβ1-42 had the least impact on fibril formation, whereas CEL glycations at Lys-16 of Aβ1-42 delayed fibril formation. We also tested these peptides for neuronal toxicity and mitochondrial function on a retinoic acid-differentiated SH-SY5Y human neuroblastoma cell line (RA-differentiated SH-SY5Y). Only Aβ-CEL16 and Aβ-CEL28 were neurotoxic, possibly through a nonmitochondrial pathway, whereas Aβ-CEL16&28 showed no neurotoxicity. Interestingly, Aβ-CEL16&28 had depolarized the mitochondrial membrane potential, whereas Aβ-CEL16 had increased mitochondrial respiration at complex II. These results may indicate mitophagy or an alternate route of metabolism, respectively. Therefore, our results provides insight into potential therapeutic approaches against neurotoxic CEL-glycated Aβ1-42.

Insights into the Molecular Mechanisms of Eg5 Inhibition by (+)-Morelloflavone

(+)-Morelloflavone (MF) is an antitumor biflavonoid that is found in the Garcinia species. Recently, we reported MF as a novel inhibitor of ATPase and microtubules-gliding activities of the kinesin spindle protein (Eg5) in vitro. Herein, we provide dynamical insights into the inhibitory mechanisms of MF against Eg5, which involves binding of the inhibitor to the loop5/α2/α3 allosteric pocket. Molecular dynamics simulations were carried out for 100 ns on eight complexes: Eg5-Adenosine diphosphate (Eg5-ADP), Eg5-ADP-S-trityl-l-cysteine (Eg5-ADP-STLC), Eg5-ADP-ispinesib, Eg5-ADP-MF, Eg5-Adenosine triphosphate (Eg5-ATP), Eg5-ATP-STLC, Eg5-ATP-ispinesib, and Eg5-ATP-MF complexes. Structural and energetic analyses were done using Umbrella sampling, Molecular Mechanics Poisson–Boltzmann Surface Area (MM/PBSA) method, GROMACS analysis toolkit, and virtual molecular dynamics (VMD) utilities. The results were compared with those of the known Eg5 inhibitors; ispinesib, and STLC. Our data strongly support a stable Eg5-MF complex, with significantly low binding energy and reduced flexibility of Eg5 in some regions, including loop5 and switch I. Furthermore, the loop5 Trp127 was trapped in a downward position to keep the allosteric pocket of Eg5 in the so-called “closed conformation”, comparable to observations for STLC. Altered structural conformations were also visible within various regions of Eg5, including switch I, switch II, α2/α3 helices, and the tubulin-binding region, indicating that MF might induce modifications in the Eg5 structure to compromise its ATP/ADP binding and conversion process as well as its interaction with microtubules. The described mechanisms are crucial for understanding Eg5 inhibition by MF.

Oxidation destabilizes toxic amyloid beta peptide aggregation

The aggregation of insoluble amyloid beta (Aβ) peptides in the brain is known to trigger the onset of neurodegenerative diseases, such as Alzheimer’s disease. In spite of the massive number of investigations, the underlying mechanisms to destabilize the Aβ aggregates are still poorly understood. Some studies indicate the importance of oxidation to destabilize the Aβ aggregates. In particular, oxidation induced by cold atmospheric plasma (CAP) has demonstrated promising results in eliminating these toxic aggregates. In this paper, we investigate the effect of oxidation on the stability of an Aβ pentamer. By means of molecular dynamics simulations and umbrella sampling, we elucidate the conformational changes of Aβ pentamer in the presence of oxidized residues, and we estimate the dissociation free energy of the terminal peptide out of the pentamer form. The calculated dissociation free energy of the terminal peptide is also found to decrease with increasing oxidation. This indicates that Aβ pentamer aggregation becomes less favorable upon oxidation. Our study contributes to a better insight in one of the potential mechanisms for inhibition of toxic Aβ peptide aggregation, which is considered to be the main culprit to Alzheimer’s disease.

Amyloidogenicity and Cytotoxicity of a Recombinant C-Terminal His6-Tagged Aβ1-42

Aggregation of amyloid β peptide (Aβ) is closely associated with the occurrence and development of Alzheimer's disease (AD). Reproducible and detailed studies on the aggregation kinetics and structure of various aggregates have been conducted using recombinant Aβ peptides. While the His₆-tag is commonly used in the purification of recombinant proteins due to its great simplicity and affinity, there is little information on the aggregation of His₆-tagged Aβ and its corresponding cytotoxicity. Moreover, it is also unclear whether there is an effect of the His₆-tag on the amyloidogenicity and cytotoxicity of recombinant Aβ_1-42. Herein, a method to express and purify a mutant C-terminally His₆-tagged Aβ_1-42 (named as Aβ_1-42-His₆) from Escherichia coli was described. Aβ_1-42-His₆ aggregated into β-sheet-rich fibrils as shown by thioflavin T fluorescence, atomic force microscopy and circular dichroism spectroscopy. Moreover, the fibrillar recombinant Aβ_1-42-His₆ showed strong toxicity toward PC12 cells in vitro. Molecular dynamics simulations revealed that the His₆-tag contributed little to the secondary structure and intermolecular interactions, including hydrophobic interactions, salt bridges, and hydrogen bonding of the fibrillar pentamer of Aβ_1-42. This highlights the biological importance of modification on the molecular structure of Aβ. Thus, the easily purified high-quality Aβ_1-42-His₆ offers great advantages for screening aggregation inhibitors or in vitro confirmation of rationally designed drugs for the treatment of AD.

Can All-Atom Molecular Dynamics Simulations Quantitatively Describe Homeodomain-DNA Binding Equilibria?

We systematically investigate the applicability of a molecular dynamics-based setup for the calculations of standard binding free energies of biologically relevant protein-DNA complexes. The free energies are extracted from a potential of mean force calculated using umbrella sampling simulations. Two protein-DNA systems derived from a homeodomain transcription factor complex are studied in order to investigate the binding of both disordered and globular proteins. Free energies and trajectories obtained using two modern molecular mechanical force fields are compared to each other and to experimental data. The temperature dependence of the calculated standard binding free energies is investigated by performing all simulations over a range of temperatures. We show that the values of standard binding free energies obtained from these simulations are overestimated compared to experimental results. Significant differences are observed between the two protein-DNA systems and between the two force fields, which are explained by different propensities to form inter- and intramolecular contacts. The number of protein-DNA contacts increases with increasing temperature, in agreement with the experimentally known temperature dependence of enthalpies of binding. However, conclusions about the temperature dependence of the standard binding free energies cannot be made with confidence, as the differences among the values are on the order of statistical uncertainty.

Exploration of Catalytic Selectivity for Aminotransferase (BtrR) Based on Multiple Molecular Dynamics Simulations

The aminotransferase from Bacillus circulans (BtrR), which is involved in the biosynthesis of butirosin, catalyzes the pyridoxal phosphate (PLP)-dependent transamination reaction to convert valienone to β-valienamine (a new β-glycosidase inhibitor for the treatment of lysosomal storage diseases) with an optical purity enantiomeric excess value. To explore the stereoselective mechanism of valienamine generated by BtrR, multiple molecular dynamics (MD) simulations were performed for the BtrR/PLP/valienamine and BtrR/PLP/β-valienamine complexes. The theoretical results showed that β-valienamine could make BtrR more stable and dense than valienamine. β-valienamine could increase the hydrogen bond probability and decrease the binding free energy between coenzyme PLP and BtrR by regulating the protein structure of BtrR, which was conducive to the catalytic reaction. β-valienamine maintained the formation of cation-p interactions between basic and aromatic amino acids in BtrR, thus enhancing its stability and catalytic activity. In addition, CAVER 3.0 analysis revealed that β-valienamine could make the tunnel of BtrR wider and straight, which was propitious to the removal of products from BtrR. Steered MD simulation results showed that valienamine interacted with more residues in the tunnel during dissociation compared with β-valienamine, resulting in the need for a stronger force to be acquired from BtrR. Taken together, BtrR was more inclined to catalyze the substrates to form β-valienamine, either from the point of view of the catalytic reaction or product removal.

Effective Estimation of Ligand-Binding Affinity Using Biased Sampling Method

The binding between two biomolecules is one of the most critical factors controlling many bioprocesses. Therefore, it is of great interest to derive a reliable method to calculate the free binding energy between two biomolecules. In this work, we have demonstrated that the binding affinity of ligands to proteins can be determined through biased sampling simulations. The umbrella sampling (US) method was applied on 20 protein-ligand complexes, including the cathepsin K (CTSK), type II dehydroquinase (DHQase), heat shock protein 90 (HSP90), and factor Xa (FXa) systems. The ligand-binding affinity was evaluated as the difference between the largest and smallest values of the free-energy curve, which was obtained via a potential of mean force analysis. The calculated affinities differ sizably from the previously reported experimental values, with an average difference of ∼3.14 kcal/mol. However, the calculated results are in good correlation with the experimental data, with correlation coefficients of 0.76, 0.87, 0.96, and 0.97 for CTSK, DHQase, HSP90, and FXa, respectively. Thus, the binding free energy of a new ligand can be reliably estimated using our US approach. Furthermore, the root-mean-square errors (RMSEs) of binding affinity of these systems are 1.13, 0.90, 0.37, and 0.25 kcal/mol, for CTSK, DHQase, HSP90, and FXa, respectively. The small RMSE values indicate the good precision of the biased sampling method that can distinguish the ligands exhibiting similar binding affinities.

Host-Guest Interactions between Candesartan and Its Prodrug Candesartan Cilexetil in Complex with 2-Hydroxypropyl-β-cyclodextrin: On the Biological Potency for Angiotensin II Antagonism

Renin-angiotensin aldosterone system inhibitors are for a long time extensively used for the treatment of cardiovascular and renal diseases. AT1 receptor blockers (ARBs or sartans) act as antihypertensive drugs by blocking the octapeptide hormone Angiotensin II to stimulate AT1 receptors. The antihypertensive drug candesartan (CAN) is the active metabolite of candesartan cilexetil (Atacand, CC). Complexes of candesartan and candesartan cilexetil with 2-hydroxylpropyl-β-cyclodextrin (2-HP-β-CD) were characterized using high-resolution electrospray ionization mass spectrometry and solid state ¹³C cross-polarization/magic angle spinning nuclear magnetic resonance (CP/MAS NMR) spectroscopy. The ¹³C CP/MAS results showed broad peaks especially in the aromatic region, thus confirming the strong interactions between cyclodextrin and drugs. This experimental evidence was in accordance with molecular dynamics simulations and quantum mechanical calculations. The synthesized and characterized complexes were evaluated biologically in vitro. It was shown that as a result of CAN's complexation, CAN exerts higher antagonistic activity than CC. Therefore, a formulation of CC with 2-HP-β-CD is not indicated, while the formulation with CAN is promising and needs further investigation. This intriguing result is justified by the binding free energy calculations, which predicted efficient CC binding to 2-HP-β-CD, and thus, the molecule's availability for release and action on the target is diminished. In contrast, CAN binding was not favored, and this may allow easy release for the drug to exert its bioactivity.

P152R Mutation Within MeCP2 Can Cause Loss of DNA-Binding Selectivity

MeCP2 is a protein highly expressed in the brain that participates in the genetic expression and RNA splicing regulation. MeCP2 binds preferably to methylated DNA and other nuclear corepressors to alter chromatin. MECP2 gene mutations can cause rett syndrome (RTT), a severe neurological disorder that affects around one in ten thousand girls. In this paper, Molecular Dynamics (MD) simulations were performed to scrutinize how the MeCP2 P152R mutation influences the protein binding to DNA. Also, the Umbrella Sampling technique was used to obtain the potential mean forces (PMFs) of both wild-type and mutated MeCP2 Methyl-CpG-binding domain (MBD) binding to both non-methylated and methylated DNA. P152R is a common missense mutation in MBD associated with RTT; however, there are no studies that explain how it causes protein dysfunction. The results from this study hypothesize that P152R mutation leads to MBD binding more strongly to DNA, while selectively decreasing binding affinity to methylated DNA. These provide an explanation for previous not conclusive experimental results regarding the mechanism of how this mutation affects the binding of the protein to DNA, and subsequently its effects on RTT. Furthermore, the results of this research-in-progress can be used as the basis for further investigations into the molecular basis of RTT and to potentially reveal a target for therapy in the future.