Influence of the R823W mutation on the interaction of the ANKS6–ANKS3: insights from molecular dynamics simulation and free energy analysis

The sterile alpha motif (SAM) domain of the protein ANKS6, a protein–protein interaction domain, is responsible for autosomal dominant polycystic kidney disease. Although the disease is the result of the R823W point mutation in the SAM domain of the protein ANKS6, the molecular details are still unclear. We applied molecular dynamics simulations, the principal component analysis, and the molecular mechanics Poisson–Boltzmann surface area binding free energy calculation to explore the structural and dynamic effects of the R823W point mutation on the complex ANKS6–ANKS3 (PDB ID: 4NL9) in comparison to the wild proteins. The energetic analysis presents that the wild type has a more stable structure than the mutant. The R823W point mutation not only disrupts the structure of the ANKS6 SAM domain but also negatively affects the interaction of the ANKS6–ANKS3. These results further clarify the previous experiments to understand the ANKS6–ANKS3 interaction comprehensively. In summary, this study would provide useful suggestions to understand the interaction of these proteins and their fatal action on mediating kidney function.     

Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations

Designing selective protein kinase B (PKB/Akt) inhibitor is an area of intense research to develop potential anticancer drugs. In the present study, the molecular basis governing PKB-selective inhibition has been investigated using molecular dynamics simulation. The binding free energies calculated by MM/PBSA gave a good correlation with the experimental biological activity and a good explanation of the activity difference of the studied inhibitors. The decomposition of free energies by MM/GBSA indicates that the ethyl group on pyrrolo[2,3-d]pyrimidine ring of inhibitor Lig1 (N-{[(3S)-3-amino-1-(5-ethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)pyrrolidin-3-yl]-methyl}-2,4-difluoro-benzamide) is an important contributor to its PKBα selectivity due to its hydrophobic interaction with the side chain of Thr291 in PKBα. The substituted groups on the pyrrolidine ring of Lig1 also show a strong tendency to mediate protein-ligand interactions through the hydrogen bonds formed between the amino or amide groups of Lig1 and the carboxyl O atoms of Glu234, Glu278, and Asp292 of PKBα. It was reported that there are only three key amino acid differences between PKBα (Thr211, Ala230, Met281) and PKA (Val104, Val123, Leu173) within the clefts of ATP-binding sites. These differences propel a drastic conformational change in PKA, weakening its binding interactions with inhibitor. The impact was also confirmed by MD simulated interaction modes of inhibitor binding to PKBα mutants with the in silico mutations of the three key amino acids, respectively. We expect that the results obtained here could be useful for future rational design of specific ATP-competitive inhibitors of PKBα.     

Investigations of Takeout proteins’ ligand binding and release mechanism using molecular dynamics simulation

Takeout (To) proteins exist in a diverse range of insect species. They are involved in many important processes of insect physiology and behaviors. As the ligand carriers, To proteins can transport the small molecule to the target tissues. However, ligand release mechanism of To proteins is unclear so far. In this contribution, the process and pathway of the ligand binding and release are revealed by conventional molecular dynamics simulation, steered molecular dynamics simulation and umbrella sampling methods. Our results show that the α4-side of the protein is the unique gate for the ligand binding and release. The structural analysis confirms that the internal cavity of the protein has high rigidity, which is in accordance with the recent experimental results. By using the potential of mean force calculations in combination with residue cross correlation calculation, we concluded that the binding between the ligand and To proteins is a process of conformational selection. Furthermore, the conformational changes of To proteins and the hydrophobic interactions both are the key factors for ligand binding and release.     

Insight into TPMT∗23 mutation mis-folding using molecular dynamics simulation and protein structure analysis

Thiopurine S-methyltransferase (TPMT) is an important enzyme that metabolizes thiopurine drugs. This enzyme exhibits a large number of interindividual polymorphism. TPMT^?23 polymorphism has been reported in a few cases in the world in co-dominance with TPMT^?3A. The phenotype has been reported to affect enzyme activity in vivo and in vitro. Its underlying structural basis is not clarified yet. In our study, the wild type (WT) protein structure was analyzed and the amino acids bordering water channels in thiopurine sites were identified. Molecular dynamics of both the WT and TPMT^?23 mutation was carried out. In addition, the effects of this mutation, especially on the thiopurine site which is closed with a pincer like mechanism, were investigated. We focused on explaining how a locally occurred A167G substitution propagated through hydrogen bonds alteration to induce structural modification which affects both thiopurine and S-adenosylmethionine receptors. Finally, a genetic prediction of mutation functional consequences has been conducted confirming altered activity.

An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:20     

Understanding the molecular basis of MK2-p38α signaling complex assembly: insights into protein-protein interaction by molecular dynamics and free energy studies

The formation of a p38 MAPK and MAPK-activated protein kinase 2 (MK2) signaling complex is physiologically relevant to cellular responses such as the proinflammatory cytokine production. The interaction between p38α isoform and MK2 is of great importance for this signaling. In this study, molecular dynamics simulation and binding free energy calculation were performed on the MK2-p38α signaling complex to investigate the protein-protein interaction between the two proteins. Dynamic domain motion analyses were performed to analyze the conformational changes between the unbound and bound states of proteins during the interaction. The activation loop, αF-I helices, and loops among α helices in the C-lobe of MK2 are found to be highly flexible and exhibit significant changes upon p38α binding. The results also show that after the binding of p38α, the N- and C-terminal domains of MK2 display an opening and twisting motion centered on the activation loop. The molecular mechanics Poisson-Boltzmann and generalized-Born surface area (MM-PB/GBSA) methods were used to calculate binding free energies between MK2 and p38α. The analysis of the components of binding free energy calculation indicates that the van der Waals interaction and the nonpolar solvation energy provide the driving force for the binding process, while the electrostatic interaction contributes critically to the specificity, rather than to MK2-p38α binding affinity. The contribution of each residue at the interaction interface to the binding affinity of MK2 with p38α was also analyzed by free energy decomposition. Several important residues responsible for the protein-protein interaction were also identified.     

The mechanism of the effect of U18666a on blocking the activity of 3β-hydroxysterol Δ-24-reductase (DHCR24): molecular dynamics simulation study and free energy analysis

DHCR24 encodes 3β-hydroxysterol-Δ²⁴-reductase (DHCR24) catalyzing the cholesterol synthesis from desmosterol using the flavin adenine dinucleotide (FAD) as a co-factor. It is generally accepted that U18666a inhibits the reductase activity of DHCR24, but the detailed mechanism remains elusive. To explore the mechanism of the inhibitory effect of U18666a on DHCR24, we performed molecular dynamics (MD) simulations of two complexes including complexes of DHCR24-FAD-desmosterol enzymatic reactive components with and without the inhibitor U18666a. We found that the U18666a bound into the hydrophobic package near the FAD package of DHCR24. Furthermore, binding free energy of DHCR24 and desmosterol without U18666a is ?54.86 kcal/mol, while the system with U18666a is ?62.23 kcal/mol, suggesting that the affinity of the substrate desmosterol to DHCR24 was increased in response to the U18666a. In addition, U18666a interacts with FAD by newly forming three hydrogen bonds with Lys292, Lys367, and Gly438 of DHCR24. Finally, secondary structural analysis data obtained from the surrounding hot spots showed that U18666a induced dramatic secondary structural changes around the key residues in the interaction of DHCR24, FAD, and desmosterol. Taken together, these results for the first time demonstrate at the molecular structure level that U18666a blocks DHCR24 activity through an allosteric inhibiting mechanism, which may provide new insight into the development of a new type of cholesterol-lowering drug targeting to block the activity of DHCR24.     

Unraveling the molecular effects of mutation L270P on Wiskkot–Aldrich syndrome protein: insights from molecular dynamics approach

Missense mutation L270P disrupts the auto-inhibited state of “Wiskkot–Aldrich syndrome protein” (WASP), thereby constitutively activating the mutant structure, a key event for pathogenesis of X-linked neutropenia (XLN). In this study, we comprehensively deciphered the molecular feature of activated mutant structure by all atom molecular dynamics (MD) approach. MD analysis revealed that mutant structure exposed a wide variation in the spatial environment of atoms, resulting in enhanced residue flexibility. The increased flexibility of residues favored to decrease the number of intra-molecular hydrogen bonding interactions in mutant structure. The reduction of hydrogen bonds in the mutant structure resulted to disrupt the local folding of secondary structural elements that eventually affect the proper folding of mutants. The unfolded state of mutant structure established more number of inter-molecular hydrogen bonding interaction at interface level due to the conformational variability, thus mediated high binding affinity with its interacting partner, Cdc42.     

Interaction of narcissoside with α-amylase from Bacillus subtilis and Porcine pancreatic by multi-spectral analysis and molecular dynamics simulation

In this work, interaction mechanism of narcissoside with two α-amylase from Bacillus subtilis (BSA) and Porcine pancreatic (PPA) are comparatively studied by multi-spectral analysis, molecular docking and molecular dynamics simulation. The results prove that narcissoside can statically quench fluorescence of BSA/PPA. Two complexes are mainly formed by hydrogen bond and van der Waals force. With the increase of temperature, the two complexes formed by narcissoside and two enzymes become unstable. At the same experimental temperature, the binding force of narcissoside to PPA is higher than that of BSA. The binding of narcissoside to PPA/BSA increases the hydrophobicity of microenvironment. Moreover, the secondary structure of PPA/BSA is mainly changed by decreasing the α-helix. The optimal binding modes of narcissoside with BSA/PPA are predicted by molecular docking, and the stability of the two complexes is evaluated by molecular dynamics simulations.     

Fluorescent membrane probes’ behavior in lipid bilayers: insights from molecular dynamics simulations

Fluorescence spectroscopy and microscopy have been used as tools to study membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Two major points of concern arise regarding this matter, namely the incomplete understanding of the probe behavior inside the bilayer and the perturbation of the latter resulting from probe incorporation. To this effect, molecular dynamics (MD) simulations, by providing detailed atomic-scale information, represent a valuable way to characterize the location and dynamics of bilayer-inserted membrane probes, as well as the magnitude of perturbation they induce on the host lipid structure, and several important classes of reporter molecules have been studied in recent years. This article reviews the state of the art of MD simulations of bilayer-inserted fluorescent probes, focusing on the information that has been obtained from previous studies and hinting at future perspectives in this rapidly emerging field.     

Characterization,inhibitory activity and mechanism of polyphenols from faba bean (gallic-acid and catechin) on α-glucosidase: insights from molecular docking and simulation study

Abstract

The chemo-profiling of ethanolic extract of faba beans seeds was performed and explored as an α-glucosidase inhibitor. The inhibition of α-glucosidase is one of the alternatives approach to control postprandial hyperglycemia by, resulting in the delay of the carbohydrate digestion of absorbable monosaccharides. Ethanolic seed extract showed phenolic compounds, flavonoid such as gallic acid (m/z [M–?H]?=?169.0124,C₇H₆O₅) ellagic acid derivatives epigallocatechin (m/z [M–?H?=?305.0644,C₁₅H₁₄O₇),catechin (m/z [M–?H]?=?289.0656,C₁₅H₁₄O₆), epigallocatechin gallate (m/z [M–?H]?=?457.0578,C₂₂H₁₈O₁₁) and epicatechin monogallate (m/z [M–?H]?=?441.081, C₂₂H₁₈O₁₀). The extract was found to exert inhibitory activity (88.28?±?2.67%) (IC₅₀ value of 2.30?±?0.032?mg/mL) with a mixed mode of inhibition (Km, apparent = 0.54?±?0.020?mM and Vmax, apparent 0.136?±?0.04?mM/min). Molecular docking studies of gallic acid and catechin on α-glucosidase proposed productive binding modes having binding energy (?6.58?kcal/mol and ?7.25?kcal/mol) with an effective number of hydrogen bonds and binding energy. Tyr63, Arg197, Asp198, Glu 233, Asn324, Asp 326 of α-glucosidase participated in binding events with gallic acid and catechin. Molecular dynamics simulation studies were performed for both complexes i.e. gal:α-glucosidase and cat:α-glucosidase along with apo state of α-glucosidase, which revealed stable systems during the simulation. These findings of the present study may give an insight into the further development of the novel antidiabetic drug from the seeds of faba beans.     

Effect of double mutations K214/A–E215/Q of FRATide on GSK3β: insights from molecular dynamics simulation and normal mode analysis

Glycogen synthase kinase 3β (GSK3β) is a multifunctional serine/threonine protein kinase that is involved in several biological processes including insulin and Wnt signaling pathways. The Wnt signaling via FRAT-mediated displacement of axin inhibits GSK3β activity toward non-primed substrates without affecting its activity toward primed substrates. Herein, molecular dynamics simulation, molecular mechanics generalized Born/surface area (MM_GBSA) calculation, and normal mode analysis are performed to explore the structural influence of the double mutations K214/A-E215/Q of FRATide on the GSK3β-FRATide complex. The results reveal that the priming phosphate-binding site, the primed substrate-binding site, the alignment of the critical active site residues in the ATP-binding site, as well as the periodic open-closed conformational change of the ATP-binding site, which are critical for the catalytic activity of GSK3β, are negligibly influenced in the mutated system compared with the wild-type (WT) system. This indicates that FRATide does not inhibit the GSK3β activity toward primed substrates. Additionally, MM_GBSA calculation indicates that the less energy-favorable GSK3β-FRATide complex is observed in the mutant than in the WT complex.     

Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β42 monomer: insights from molecular dynamics simulations

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder that is characterized by loss of intellectual functioning of brain and memory loss. According to amyloid cascade hypothesis, aggregation of amyloid-β₄₂ (Aβ₄₂) peptide can generate toxic oligomers and their accumulation in the brain is responsible for the onset of AD. In spite of carrying out a large number of experimental studies on inhibition of Aβ₄₂ aggregation by small molecules, the detailed inhibitory mechanism remains elusive. In the present study, comparable molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a sulfonamide inhibitor C1 (2,5-dichloro-N-(4-piperidinophenyl)-3-thiophenesulfonamide), reported for its in vitro and in vivo anti-aggregation activity against Aβ₄₂. MD simulations reveal that C1 stabilizes native α-helix conformation of Aβ₄₂ by interacting with key residues in the central helix region (13–26) with hydrogen bonds and π–π interactions. C1 lowers the solvent-accessible surface area of the central hydrophobic core (CHC), KLVFF (16–20), that confirms burial of hydrophobic residues leading to the dominance of helical conformation in the CHC region. The binding free energy analysis with MM–PBSA demonstrates that Ala2, Phe4, Tyr10, Gln15, Lys16, Leu17, Val18, Phe19, Phe20, Glu22, and Met35 contribute maximum to binding free energy (?43.1 kcal/mol) between C1 and Aβ₄₂ monomer. Overall, MD simulations reveal that C1 inhibits Aβ₄₂ aggregation by stabilizing native helical conformation and inhibiting the formation of aggregation-prone β-sheet conformation. The present results will shed light on the underlying inhibitory mechanism of small molecules that show potential in vitro anti-aggregation activity against Aβ₄₂.     

Partial activation of α7 nicotinic acetylcholine receptors: insights from molecular dynamics simulations

Nicotinic acetylcholine receptors (nAChRs) are drug targets for neuronal disorders and diseases. Partial agonists for nAChRs are currently being developed as drugs for the treatment of neurological diseases for their relative safety originated from reduced excessive stimulation. In the current study, molecular docking, molecular dynamics simulations and binding energy calculations were performed to theoretically investigate the interactions between the partial agonists, 4-OH-DMXBA and tropisetron with α7-nAChR. The results suggest that the partial agonists 4-OH-DMXBA and tropisetron bind with α7-nAChR in a binding mode similar to that with AChBP. The non-conserved residues in the binding sites contribute to the orientation deviation of these partial agonists from their orientation in AChBP. Energy calculation and decomposition using MM-GB/SA suggests that the van der Waals term (ΔE_VDW) is the main driving force for the binding of the partial agonists to α7-nAChR. The molecular dynamics simulations showed that the opening of the C-loop binding with the partial agonists is in-between the openings for the binding with the full agonist and in the apo state. This conformation difference for the C-loop sheds light on the partial agonism of nAChR.     

Investigation of the ‘double cross’ splitting mechanism of single-crystal diamond under nanoindentation via molecular dynamics simulation

Elucidating the mechanical response of diamond is a difficult task due to its ultrahard nature. Here, we applied a molecular dynamics (MD) method to investigate the mechanical response of single-crystal diamond under nanoindentation. There was no obvious “pop in” phenomenon on the load–depth curve, and the elastic modulus deduced from the curve was 1128 GPa, which was similar to the value obtained from experimental measurements. Results from computed tomography (CT) and the coordination number showed that the distribution of the mismatched C atoms around the deformation zone took the form of a ‘double cross.’ The atoms around the indenter tip could be divided into two zones, a translation zone and a lattice distortion zone, based on their movements. Subsequent first-principles calculations revealed that the C-atom displacement barrier varied significantly with direction, which resulted in shear stress between the two zones and the formation of the double-cross splitting.

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Graphical Abstract The displacement of the atoms around the indenter tip

     

212 Shifting interfaces: changes in protein–protein and protein–DNA interfaces probed via molecular dynamics

Over the past decade, there has been a growing interest in studying the binding of DNA to the MutSalpha protein complex. This heterodimeric protein complex, the Msh2/Msh6 complex in humans, is the initial complex that binds mismatched DNA and other DNA defects that occur during replication. This complex has also been shown to bind at least some types of damaged DNA, such as the cross-linked adducts due to the chemotherapeutics cisplatin and carboplatin, or the incorporation of the chemotherapeutic, FdU. As a result of this interest, multiple studies have contrasted the interactions of MutSalpha with its normal mismatched substrate and with the interactions of MutsSalpha with the DNA damaged by chemotherapeutic cisplatin. To complement these studies, we examine the interaction between MutSalpha and the DNA damaged by carboplatin via all-atom molecular dynamics simulations. These simulations provide evidence for subtle changes in the protein–DNA and protein–protein interfaces. The interfaces shifts found are broadly similar to those found in binding with adduct from cis-platin, but have distinct differences. These subtle differences may play a role in the way of the different damages and mismatched DNA are signaled by MutSalpha, and suggest a signaling mechanism for DNA damage that chiefly involves shifts in protein–protein interactions as opposed to changes in protein conformation.     

Unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations

Alzheimer's disease (AD) pathogenesis is associated with formation of amyloid fibrils caused by polymerization of the amyloid β-peptide (Aβ), which is a process that requires unfolding of the native helical structure of Aβ. According to recent experimental studies, stabilization of the Aβ central helix is effective in preventing Aβ polymerization into toxic assemblies. To uncover the fundamental mechanism of unfolding of the Aβ central helix, we performed molecular dynamics simulations for wild-type (WT), V18A/F19A/F20A mutant (MA), and V18L/F19L/F20L mutant (ML) models of the Aβ central helix. It was quantitatively demonstrated that the stability of the α-helical conformation of both MA and ML is higher than that of WT, indicating that the α-helical propensity of the three nonpolar residues (18, 19, and 20) is the main factor for the stability of the whole Aβ central helix and that their hydrophobicity plays a secondary role. WT was found to completely unfold by a three-step mechanism: 1) loss of α-helical backbone hydrogen bonds, 2) strong interactions between nonpolar sidechains, and 3) strong interactions between polar sidechains. WT did not completely unfold in cases when any of the three steps was omitted. MA and ML did not completely unfold mainly due to the lack of the first step. This suggests that disturbances in any of the three steps would be effective in inhibiting the unfolding of the Aβ central helix. Our findings would pave the way for design of new drugs to prevent or retard AD.     

A molecular dynamics simulation study of polyamine– and sodium–DNA. Interplay between polyamine binding and DNA structure

Four different molecular dynamics (MD) simulations have been performed for infinitely long ordered DNA molecules with different counterions, namely the two natural polyamines spermidine(3+) (Spd³⁺) and putrescine(2+) (Put²⁺), the synthetic polyamine diaminopropane(2+) (DAP²⁺), and the simple monovalent cation Na⁺. All systems comprised a periodical hexagonal cell with three identical DNA decamers, 15 water molecules per nucleotide, and counterions balancing the DNA charge. The simulation setup mimics the DNA state in oriented DNA fibers, previously studied using NMR and other experimental methods. In this paper the interplay between polyamine binding and local DNA structure is analyzed by investigating how and if the minor groove width of DNA depends on the presence and dynamics of the counterions. The results of the MD simulations reveal principal differences in the polyamine–DNA interactions between the natural [spermine(4+), Spd³⁺, Put²⁺] and the synthetic (DAP²⁺) polyamines.Abbreviations DAP diaminopropane - DDD Drew–Dickerson dodecamer - MD molecular dynamics - Put putrescine - RDF radial distribution function - Spd spermidine - Spm spermine