The luciferase-based in vivo protein-protein interaction assay revealed that CHK1 promotes PP2A and PME-1 interaction.

Protein phosphatase 2A (PP2A) is an essential serine/threonine protein phosphatase, and its dysfunction is involved in the onset of cancer and neurodegenerative disorders. PP2A functions as a trimeric holoenzyme whose composition is regulated by the methyl-esterification (methylation) of the PP2A catalytic subunit (PP2Ac). Protein phosphatase methylesterase-1 (PME-1) is the sole PP2Ac methylesterase, and the higher PME-1 expression is observed in various cancer and neurodegenerative diseases. Apart from serving as a methylesterase, PME-1 acts as a PP2A inhibitory protein, binding directly to PP2Ac and suppressing its activity. The intricate function of PME-1 hinders drug development by targeting the PME-1/PP2Ac axis. This study applied the NanoBiT system, a bioluminescence-based protein interaction assay, to elucidate the molecular mechanism that modulates unknown PME-1/PP2Ac protein-protein interaction (PPI). Compound screening identified that the CHK1 inhibitors inhibited PME-1/PP2Ac association without affecting PP2Ac methylation levels. CHK1 directly phosphorylates PP2Ac to promote PME-1 association. Phospho-mass spectrometry identified multiple phospho-sites on PP2Ac, including the Thr219, that affect PME-1 interaction. An anti-phospho-Thr219 PP2Ac antibody was generated and showed that CHK1 regulates the phosphorylation levels of this site in cells. On the contrary, in vitro phosphatase assay showed that CHK1 is the substrate of PP2A, and PME-1 hindered PP2A-mediated dephosphorylation of CHK1. Our data provides novel insights into the molecular mechanisms governing the PME-1/PP2Ac PPI and the triad relationship between PP2A, PME-1, and CHK1.

Constant pH molecular dynamics of porcine circovirus 2 capsid protein reveals a mechanism for capsid assembly.

Spatiotemporal regulation of viral capsid assembly ensures the selection of the viral genome for encapsidation. The porcine circovirus 2 is the smallest autonomously replicating pathogenic virus, yet how PCV2 capsid assembly is regulated to occur within the nucleus remains unknown. We report that pure PCV2 capsid proteins, in the absence of nucleic acids, require acidic conditions to assemble into empty capsids in vitro. By employing constant pH replica exchange molecular dynamics, we unveil the atomistic mechanism of pH-dependency for capsid assembly. The results show that an appropriate protonation configuration for a cluster of acidic amino acids is necessary to appropriately position the GH-loop for driving the capsid assembly. We demonstrate that assembly is prohibited at neutral pH because deprotonation of these residues results in their electrostatic repulsion, shifting the GH-loop to a position incompatible with capsid assembly. We propose that encapsulation of nucleic acids overcomes this repulsion to suitably position the GH-loop. Our findings provide the first atomic resolution mechanism of capsid assembly regulation. These findings are useful for the development of therapeutics that inhibit PCV2 self-assembly.

Single-molecule motions of MHC class II rely on bound peptides.

The major histocompatibility complex (MHC) class II protein can bind peptides of different lengths in the region outside the peptide-binding groove. Peptide-flanking residues (PFRs) contribute to the binding affinity of the peptide for MHC and change the immunogenicity of the peptide/MHC complex with regard to T cell receptor (TCR). The mechanisms underlying these phenomena are currently unknown. The molecular flexibility of the peptide/MHC complex may be an important determinant of the structures recognized by certain T cells. We used single-molecule x-ray analysis (diffracted x-ray tracking (DXT)) and fluorescence anisotropy to investigate these mechanisms. DXT enabled us to monitor the real-time Brownian motion of the peptide/MHC complex and revealed that peptides without PFRs undergo larger rotational motions than peptides with PFRs. Fluorescence anisotropy further revealed that peptides without PFRs exhibit slightly larger motions on the nanosecond timescale. These results demonstrate that peptides without PFRs undergo dynamic motions in the groove of MHC and consequently are able to assume diverse structures that can be recognized by T cells.

Assessment and acceleration of binding energy calculations for protein-ligand complexes by the fragment molecular orbital method.

In the field of drug discovery, it is important to accurately predict the binding affinities between target proteins and drug applicant molecules. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics-based force fields, although they cannot fully describe protein-ligand interactions. A noteworthy computational method in development involves large-scale electronic structure calculations. Fragment molecular orbital (FMO) method, which is one of such large-scale calculation techniques, is applied in this study for calculating the binding energies between proteins and ligands. By testing the effects of specific FMO calculation conditions (including fragmentation size, basis sets, electron correlation, exchange-correlation functionals, and solvation effects) on the binding energies of the FK506-binding protein and 10 ligand complex molecule, we have found that the standard FMO calculation condition, FMO2-MP2/6-31G(d), is suitable for evaluating the protein-ligand interactions. The correlation coefficient between the binding energies calculated with this FMO calculation condition and experimental values is determined to be R = 0.77. Based on these results, we also propose a practical scheme for predicting binding affinities by combining the FMO method with the quantitative structure-activity relationship (QSAR) model. The results of this combined method can be directly compared with experimental binding affinities. The FMO and QSAR combined scheme shows a higher correlation with experimental data (R = 0.91). Furthermore, we propose an acceleration scheme for the binding energy calculations using a multilayer FMO method focusing on the protein-ligand interaction distance. Our acceleration scheme, which uses FMO2-HF/STO-3G:MP2/6-31G(d) at R(int) = 7.0 Å, reduces computational costs, while maintaining accuracy in the evaluation of binding energy.

A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.

The Poisson-Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N- and C-terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules.

Molecular Dynamics Study of Conformational Changes of Tankyrase 2 Binding Subsites upon Ligand Binding.

The interactions between proteins and ligands are involved in various biological functions. While experimental structures provide key static structural information of ligand-unbound and ligand-bound proteins, dynamic information is often insufficient for understanding the detailed mechanism of protein-ligand binding. Here, we studied the conformational changes of the tankyrase 2 binding pocket upon ligand binding using molecular dynamics simulations of the ligand-unbound and ligand-bound proteins. The ligand-binding pocket has two subsites: the nicotinamide and adenosine subsite. Comparative analysis of these molecular dynamics trajectories revealed that the conformational change of the ligand-binding pocket was characterized by four distinct conformations of the ligand-binding pocket. Two of the four conformations were observed only in molecular dynamics simulations. We found that the pocket conformational change on ligand binding was based on the connection between the nicotinamide and adenosine subsites that are located adjacently in the pocket. From the analysis, we proposed the protein-ligand binding mechanism of tankyrase 2. Finally, we discussed the computational prediction of the ligand binding pose using the tankyrase 2 structures obtained from the molecular dynamics simulations.

Molecular mechanisms of how mercury inhibits water permeation through aquaporin-1: understanding by molecular dynamics simulation.

Aquaporin (AQP) functions as a water-conducting pore. Mercury inhibits the water permeation through AQP. Although site-directed mutagenesis has shown that mercury binds to Cys189 during the inhibition process, it is not fully understood how this inhibits the water permeation through AQP1. We carried out 40 ns molecular dynamics simulations of bovine AQP1 tetramer with mercury (Hg-AQP1) or without mercury (Free AQP1). In Hg-AQP1, Cys191 (Cys189 in human AQP1) is converted to Cys-SHg+ in each monomer. During each last 10 ns, we observed water permeation events occurred 23 times in Free AQP1 and never in Hg-AQP1. Mercury binding did not influence the whole structure, but did induce a collapse in the orientation of several residues at the ar/R region. In Free AQP1, backbone oxygen atoms of Gly190, Cys191, and Gly192 lined, and were oriented to, the surface of the water pore channel. In Hg-AQP1, however, the SHg+ of Cys191-SHg+ was oriented toward the outside of the water pore. As a result, the backbone oxygen atoms of Gly190, Cys191, and Gly192 became disorganized and the ar/R region collapsed, thereby obstructing the permeation of water. We suggest that mercury disrupts the water pore of AQP1 through local conformational changes in the ar/R region.

High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations.

Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design. However, this method is not completely reliable and therefore unsatisfactory. In this study, we used massive molecular dynamics simulations of protein-ligand conformations obtained by molecular docking in order to improve the enrichment performance of molecular docking. Our screening approach employed the molecular mechanics/Poisson-Boltzmann and surface area method to estimate the binding free energies. For the top-ranking 1,000 compounds obtained by docking to a target protein, approximately 6,000 molecular dynamics simulations were performed using multiple docking poses in about a week. As a result, the enrichment performance of the top 100 compounds by our approach was improved by 1.6-4.0 times that of the enrichment performance of molecular dockings. This result indicates that the application of molecular dynamics simulations to virtual screening for lead discovery is both effective and practical. However, further optimization of the computational protocols is required for screening various target proteins.

Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH.

Following the discovery of cryptochrome-DASH (CRYD) as a new type of blue-light receptor cryptochrome, theoretical and experimental findings on CRYD have been reported. Early studies identified CRYD as highly homologous to the DNA repair enzyme photolyases (PLs), suggesting the involvement of CRYD in DNA repair. However, an experimental study reported that CRYD does not exhibit DNA repair activity in vivo. Successful PL-mediated DNA repair requires: (i) the recognition of UV-induced DNA lesions and (ii) an electron transfer reaction. If either of them is inefficient, the DNA repair activity will be low. To elucidate the functional differences between CRYD and PL, we theoretically investigated the electron transfer reactivity and DNA binding affinity of CRYD and also performed supplementary experiments. The average electronic coupling matrix elements value for Arabidopsis thaliana CRYD (AtCRYD) was estimated to be 5.3 meV, comparable to that of Anacystis nidulans cyclobutane pyrimidine dimer PLs (AnPL) at 4.5 meV, indicating similar electron transfer reactivities. We also confirmed the DNA repair activity of AtCRYD for UV-damaged single-stranded DNA by the experimental analysis. In addition, we investigated the dynamic behavior of AtCRYD and AnPL in complex with double-stranded DNA using molecular dynamics simulations and observed the formation of a transient salt bridge between protein and DNA in AtCRYD, in contrast to AnPL in which it was formed stably. We suggested that the instability of the salt bridge between protein and DNA will lead to reduced DNA binding affinity for AtCRYD.

Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation.

We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (Mpro) to examine the binding dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir, were used as the potential lead drugs to investigate access to the drug binding sites in Mpro. The frequently accessed sites on Mpro were classified based on contacts between the ligands and the protein, and the differences in site distributions of the encounter complex were observed among the ligands. All seven ligands showed binding to the active site at least twice in 28 simulations of 200 ns each. We further investigated the variations in the complex structure of the active site with the ligands, using microsecond order simulations. Results revealed a wide variation in the shapes of the binding sites and binding poses of the ligands. Additionally, the C-terminal region of the other chain often interacted with the ligands and the active site. Collectively, these findings indicate the importance of dynamic sampling of protein-ligand complexes and suggest the possibilities of further drug optimisations.

Use of the Multilayer Fragment Molecular Orbital Method to Predict the Rank Order of Protein-Ligand Binding Affinities: A Case Study Using Tankyrase 2 Inhibitors.

In computational drug discovery, ranking a series of compound analogues in the order that is consistent with the experimental binding affinities remains a challenge. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics (MM)-based force fields, although they cannot completely describe protein-ligand interactions. By contrast, quantum mechanics (QM) calculations play an important role in understanding the protein-ligand interactions; however, their huge computational costs hinder their application in drug discovery. In this study, we have evaluated the ability to rank the binding affinities of tankyrase 2 ligands by combining both MM and QM calculations. Our computational approach uses the protein-ligand binding energies obtained from a cost-effective multilayer fragment molecular orbital (MFMO) method combined with the solvation energy obtained from the MM-Poisson-Boltzmann/surface area (MM-PB/SA) method to predict the binding affinity. This approach enabled us to rank tankyrase 2 inhibitor analogues, outperforming several MM-based methods, including rescoring by molecular docking and the MM-PB/SA method alone. Our results show that this computational approach using the MFMO method is a promising tool for predicting the rank order of the binding affinities of inhibitor analogues.

Evaluation of protein-ligand affinity prediction using steered molecular dynamics simulations.

In computational drug design, ranking a series of compound analogs in a manner that is consistent with experimental affinities remains a challenge. In this study, we evaluated the prediction of protein-ligand binding affinities using steered molecular dynamics simulations. First, we investigated the appropriate conditions for accurate predictions in these simulations. A conic harmonic restraint was applied to the system for efficient sampling of work values on the ligand unbinding pathway. We found that pulling velocity significantly influenced affinity predictions, but that the number of collectable trajectories was less influential. We identified the appropriate pulling velocity and collectable trajectories for binding affinity predictions as 1.25 Å/ns and 100, respectively, and these parameters were used to evaluate three target proteins (FK506 binding protein, trypsin, and cyclin-dependent kinase 2). For these proteins using our parameters, the accuracy of affinity prediction was higher and more stable when Jarzynski's equality was employed compared with the second-order cumulant expansion equation of Jarzynski's equality. Our results showed that steered molecular dynamics simulations are effective for predicting the rank order of ligands; thus, they are a potential tool for compound selection in hit-to-lead and lead optimization processes.

All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid's Stability.

Present experimental methods do not have sufficient resolution to investigate all processes in virus particles at atomistic details. We report the results of molecular dynamics simulations and analyze the connection between the number of ions inside an empty capsid of PCV2 virus and its stability. We compare the crystallographic structures of the capsids with unresolved N-termini and without them in realistic conditions (room temperature and aqueous solution) and show that the structure is preserved. We find that the chloride ions play a key role in the stability of the capsid. A low number of chloride ions results in loss of the native icosahedral symmetry, while an optimal number of chloride ions create a neutralizing layer next to the positively charged inner surface of the capsid. Understanding the dependence of the capsid stability on the distribution of the ions will help clarify the details of the viral life cycle that is ultimately connected to the role of packaged viral genome inside the capsid.

A pre-metazoan origin of the CRK gene family and co-opted signaling network.

CRK and CRKL adapter proteins play essential roles in development and cancer through their SRC homology 2 and 3 (SH2 and SH3) domains. To gain insight into the origin of their shared functions, we have investigated their evolutionary history. We propose a term, crk/crkl ancestral (crka), for orthologs in invertebrates before the divergence of CRK and CRKL in the vertebrate ancestor. We have isolated two orthologs expressed in the choanoflagellate Monosiga brevicollis, a unicellular relative to the metazoans. Consistent with its highly-conserved three-dimensional structure, the SH2 domain of M. brevicollis crka1 can bind to the mammalian CRK/CRKL SH2 binding consensus phospho-YxxP, and to the SRC substrate/focal adhesion protein BCAR1 (p130CAS) in the presence of activated SRC. These results demonstrate an ancient origin of the CRK/CRKL SH2-target recognition specificity. Although BCAR1 orthologs exist only in metazoans as identified by an N-terminal SH3 domain, YxxP motifs, and a C-terminal FAT-like domain, some pre-metazoan transmembrane proteins include several YxxP repeats in their cytosolic region, suggesting that they are remotely related to the BCAR1 substrate domain. Since the tyrosine kinase SRC also has a pre-metazoan origin, co-option of BCAR1-related sequences may have rewired the crka-dependent network to mediate adhesion signals in the metazoan ancestor.

A leukotriene C4 synthase inhibitor with the backbone of 5-(5-methylene-4-oxo-4,5-dihydrothiazol-2-ylamino) isophthalic acid.

The cysteinyl leukotrienes (cys-LTs), leukotriene C4 (LTC4) and its metabolites, LTD4 and LTE4, are proinflammatory lipid mediators in asthma and other inflammatory diseases. They are generated through the 5-lipoxygenase/LTC4 synthase (LTC4S) pathway and act via at least two distinct G protein-coupled receptors. The inhibition of human LTC4S will make a simple way to treat the cys-LT relevant inflammatory diseases. Here, we show that compounds having 5-(5-methylene-4-oxo-4,5-dihydrothiazol-2-ylamino) isophthalic acid moiety suppress LTC4 synthesis, glutathione conjugation to the precursor LTA4, in both an enzyme assay and a whole-cell assay. Hierarchical in silico screenings of 6 million compounds provided 300,000 dataset for docking, and after energy minimization based on the crystal structure of LTC4S, 111 compounds were selected as candidates for a competitive inhibitor to glutathione. One of those compounds showed significant inhibitory activity, and subsequently, its derivative 5-((Z)-5-((E)-2-methyl-3-phenylallylidene)-4-oxo-4,5-dihydrothiazol-2-ylamino) isophthalic acid (compound 1) was found to be the most potent inhibitor. The enzyme assay showed the IC50 was 1.9 µM and the corresponding 95% confidence interval was from 1.7 to 2.2 µM. The whole-cell assay showed that compound 1 was cell permeable and inhibited LTC4 synthesis in a concentration dependent manner.

Ligand Diffusion on Protein Surface Observed in Molecular Dynamics Simulation.

The process of binding of small ligands to dihydrofolate reductase protein has been investigated using all-atom molecular dynamics simulations. The existence of a mechanism that facilitates the search of the binding site by the ligand is demonstrated. The mechanism consists of ligand diffusing on the protein's surface. It has been discussed in the literature before, but has not been explicitly confirmed for realistic molecular systems. The strength of this nonspecific binding is roughly estimated and found to be essential for the binding kinetics.

An efficient computational method for calculating ligand binding affinities.

Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design. However, the docking scores are not sufficiently precise to represent the protein-ligand binding affinity. Here, we developed an efficient computational method for calculating protein-ligand binding affinity, which is based on molecular mechanics generalized Born/surface area (MM-GBSA) calculations and Jarzynski identity. Jarzynski identity is an exact relation between free energy differences and the work done through non-equilibrium process, and MM-GBSA is a semimacroscopic approach to calculate the potential energy. To calculate the work distribution when a ligand is pulled out of its binding site, multiple protein-ligand conformations are randomly generated as an alternative to performing an explicit single-molecule pulling simulation. We assessed the new method, multiple random conformation/MM-GBSA (MRC-MMGBSA), by evaluating ligand-binding affinities (scores) for four target proteins, and comparing these scores with experimental data. The calculated scores were qualitatively in good agreement with the experimental binding affinities, and the optimal docking structure could be determined by ranking the scores of the multiple docking poses obtained by the molecular docking process. Furthermore, the scores showed a strong linear response to experimental binding free energies, so that the free energy difference of the ligand binding (ΔΔG) could be calculated by linear scaling of the scores. The error of calculated ΔΔG was within ≈ ± 1.5 kcal.mol(-1) of the experimental values. Particularly, in the case of flexible target proteins, the MRC-MMGBSA scores were more effective in ranking ligands than those generated by the MM-GBSA method using a single protein-ligand conformation. The results suggest that, owing to its lower computational costs and greater accuracy, the MRC-MMGBSA offers efficient means to rank the ligands, in the post-docking process, according to their binding affinities, and to compare these directly with the experimental values.

Free-energy landscapes of protein domain movements upon ligand binding.

The conformation and functions of proteins are closely linked, and many proteins undergo conformational changes upon ligand binding. The X-ray crystallographic studies have revealed conformational differences in proteins between the liganded and unliganded states. Currently, the conformational transitions that originate in the ligand binding are explained on the basis of two representative models, the induced-fit and preexisting equilibrium dynamics models. However, the actual dynamics of the proteins remain ambiguous. Though these two models are the extreme ones, it is important to understand the difference between these two, particularly in structural biology and medicinal chemistry studies. Here, we clarified the difference in the mechanisms responsible for the conformational changes induced in two proteins upon ligand binding by examining computationally determined free-energy profiles of the apo- and holoproteins. The lysine/arginine/ornithine-binding protein and maltose/maltodextrin-binding protein were chosen as the target proteins, and the energy profiles were generated by a molecular simulation approach. Our results revealed that fluctuations in the apo state and protein-ligand interactions both play important roles in conformational transition, and the mechanism is highly influenced by the fluctuations in the apo state, which are unique to a particular structure.

FGF9 monomer-dimer equilibrium regulates extracellular matrix affinity and tissue diffusion.

The spontaneous dominant mouse mutant, Elbow knee synostosis (Eks), shows elbow and knee joint synosotsis, and premature fusion of cranial sutures. Here we identify a missense mutation in the Fgf9 gene that is responsible for the Eks mutation. Through investigation of the pathogenic mechanisms of joint and suture synostosis in Eks mice, we identify a key molecular mechanism that regulates FGF9 signaling in developing tissues. We show that the Eks mutation prevents homodimerization of the FGF9 protein and that monomeric FGF9 binds to heparin with a lower affinity than dimeric FGF9. These biochemical defects result in increased diffusion of the altered FGF9 protein (FGF9(Eks)) through developing tissues, leading to ectopic FGF9 signaling and repression of joint and suture development. We propose a mechanism in which the range of FGF9 signaling in developing tissues is limited by its ability to homodimerize and its affinity for extracellular matrix heparan sulfate proteoglycans.

Prediction of the Structure of Complexes Comprised of Proteins and Glycosaminoglycans Using Docking Simulation and Cluster Analysis.

A typical docking simulation provides information on the structure of ligand-receptor complexes and their binding affinity in terms of a docking energy. We have developed a potent method combining a docking simulation with cluster analysis to extract adequate docking structures from the many possible output structures of the simulation. First, we tried to predict the structure of basic fibroblast growth factor (bFGF) bound to heparin, using the docking simulation program AutoDock 3.0. Two X-ray crystal structures had already been obtained for bFGF. One was a complex of the protein and heparin, a kind of glycosaminoglycan, and the other, only the protein itself, hereafter called a simplex. We docked a heparin molecule onto the protein simplex and generated many trial structures for the bFGF-heparin complex. The structures of those docked complexes were optimized through energy minimization by AMBER8. Although neither the docking energy calculated by AMBER8 nor that calculated by AutoDock 3.0 could be used satisfactorily by themselves to select a proper heparin-binding complex from the output structures, the majority of the structures generated by AutoDock 3.0 were fairly close to each other in atom geometry, and the averaged geometry over these structures was also close to that of the crystal. Hence, we utilized only the atom geometry for evaluation and carried out cluster analysis with the collection of geometries. This procedure enabled selection of a structure considerably close to the crystal's. We applied this approach to two other heparin-binding proteins: antithrombin and annexin V. Two crystal structures, a complex and a simplex, had been elucidated for these proteins as well as for bFGF. Our trials gave an exact prediction of the heparin-binding structures of these proteins, showing the approach in this study is effective in studying the docking of ligands that have a variety of docking conformations due to the presence of multiple rotatable bonds and charged chemical groups.