Molecular Dynamics Simulation

Hydroxynitrile lyases (HNLs) defend plants from herbivores and microbial attack by releasing cyanide from hydroxynitriles. The reverse process has been productively applied to bioorganic syntheses of pharmaceuticals and agrochemicals. To improve our understanding of the catalytic mechanism of HNLs, extensive ab initio QM/MM and classical MM molecular dynamics simulations have been performed to explore the catalytic conversion of cyanohydrins into aldehyde (or ketone) and HCN by hydroxynitrile lyases from Hevea brasiliensis (HbHNLs). It was found that the catalytic reaction approximately follows a two-stage mechanism. The first stage involves two fast processes including the proton abstraction of the substrate through a double-proton transfer and the C-CN bond cleavage, while the second stage concerns HCN formation and is rate-determining. The complete free energy profile exhibits a peak of ∼18 kcal mol(-1). Interestingly, the protonation state of Lys236 influences the efficiency of ...

Oil palm shell (OPS) and palm oil clinker (POC) is a waste from palm industries which is excess from .a process where electricity was generated in palm oil factories. The use of this POC material as partial sand replacement material in concrete will help lower the pollution to the environment. This thesis presents an experimental study on effect of POC content towards mechanical properties of OPS LWAC Two types of mixes that has been used in this study that is plain OPS LWAC containing 100% natural river sand and another mix containing POC as partial sand replacement. POC used as partial sand replacement from ranges from 0% to 20%. All specimens were cast and subjected to water curing until the testing date. Specimens were tested for compressive strength and flexural strength up to 28 days. The highest compressive strength and flexural strength achieved reaching up to 34.4 MPa and 3.42 MPa respectively at age 28 days with 20% POC as partial sand replacement. Conclusively use of POC ...

Despite some success for small molecules, elucidating structure-function relationships for biologically active peptides - the ligands for various targets in the organism - remains a great challenge and calls for the development of novel approaches. Some of us recently proposed the Protein Surface Topography (PST) approach, which benefits from a simplified representation of biomolecules' surface as projection maps, which enables the exposure of the structure-function dependencies. Here, we use PST to uncover the "activity pattern" in α-conotoxins - neuroactive peptides that effectively target nicotinic acetylcholine receptors (nAChRs). PST was applied in order to design several variants of the α-conotoxin PnIA, which were synthesized and thoroughly studied. Among the best was PnIA[R9, L10], which exhibits nanomolar affinity for the α7 nAChR, selectivity and a slow wash-out from this target. Importantly, these mutations could hardly be delineated by "standard" ...

Peptide/protein hormones could be stored as non-toxic amyloid-like structures in pituitary secretory granules. ACTH and β-endorphin are two of the important peptide hormones that get co-stored in the pituitary secretory granules. Here, we study molecular interactions between ACTH and β-endorphin and their colocalization in the form of amyloid aggregates. Although ACTH is known to be a part of ACTH-β-endorphin aggregate, ACTH alone cannot aggregate into amyloid under various plausible conditions. Using all atom molecular dynamics simulation we investigate the early molecular interaction events in the ACTH-β-endorphin system, β-endorphin-only system and ACTH-only system. We find that β-endorphin and ACTH formed an interacting unit, whereas negligible interactions were observed between ACTH molecules in ACTH-only system. Our data suggest that ACTH is not only involved in interaction with β-endorphin but also enhances the stability of mixed oligomers of the entire system.

BRAF gene mutations are frequently seen in both inherited and somatic diseases. However, the harmful mutations for BRAF gene have not been predicted in silico. Owing to the importance of BRAF gene in cell division, differentiation and secretion processes, the functional analysis was carried out to explore the possible association between genetic mutations and phenotypic variations. Genomic analysis of BRAF was initiated with SIFT followed by PolyPhen and SNPs&GO servers to retrieve the 85 deleterious non-synonymous SNPs (nsSNPs) from dbSNP. A total of 5 mutations i.e. c.406T>G (S136A), c.1446G>T (R462I), c.1556 A>G (K499E), c.1860 T>A (V600E) and c.2352 C>T (P764L) that are found to exert benign effects on the BRAF protein structure and function were chosen for further analysis. Protein structural analysis with these amino acid variants was performed by using I-Mutant, FOLD-X, HOPE, NetSurfP, Swiss PDB viewer, Chimera and NOMAD-Ref servers to check their solvent accessibility, molecular dynamics and energy minimization calculations. Our in silico analysis suggested that S136A and P764L variants of BRAF could directly or indirectly destabilize the amino acid interactions and hydrogen bond networks thus explain the functional deviations of protein to some extent. Screening for BRAF, S136A and P764Lvariants may be useful for disease molecular diagnosis and also to design the molecular inhibitors of BRAF pathways.

In meiotic DNA recombination, the Hop2-Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex by a yet-unclear mechanism. Here, the crystal structure of Hop2-Mnd1 reveals that it forms a curved rod-like structure consisting of three leucine zippers and two kinked junctions. One end of the rod is linked to two juxtaposed winged-helix domains, and the other end is capped by extra α-helices to form a helical bundle-like structure. Deletion analysis shows that the helical bundle-like structure is sufficient for interacting with the Dmc1-ssDNA nucleofilament, and molecular modeling suggests that the curved rod could be accommodated into the helical groove of the nucleofilament. Remarkably, the winged-helix domains are juxtaposed at fixed relative orientation, and their binding to DNA is likely to perturb the base pairing according to molecular simulations. These findings allow us to propose a model explaining how Ho...

Lectins from different sources have been shown to interfere with HIV infection by binding to the sugars of viral-envelope glycoproteins. Three-dimensional atomic structures of a number of HIV-inactivating lectins have been determined, both as free proteins and in glycan-bound forms. However, details on the mechanism of recognition and binding to sugars are elusive. Herein we focus on the anti-HIV lectin OAA from Oscillatoria agardhii: We show that in the absence of sugars in solution, both the sugar-free and sugar-bound protein conformations that were observed in the X-ray crystal structures exist as conformational substates. Our results suggest that glycan recognition occurs by conformational selection within the ground state; this model differs from the popular "excited-state" model. Our findings provide further insight into molecular recognition of the major receptor on the HIV virus by OAA. These details can potentially be used for the optimization and/or development o...

HIV-1 passage in cell culture in the presence of chemokine receptor antagonists can result in selection of viruses with env mutations that confer resistance to these inhibitors. In the present study, we examined the effect of HIV-1 env mutations that confer resistance to CXCR4 antagonists on envelope (Env) sensitivity to neutralizing antibodies (NAbs). Serial passage of CXCR4-tropic HIV-1 NL4-3 in PM1/CCR5 cells under CXCR4 antagonists KRH-3955, AMD3100 and AMD070 yielded two KRH-3955-resistant, one AMD3100-resistant and one AMD070-resistant viruses. These viruses had multiple env mutations including the Env gp120 V3 region. The majority of viruses having these CXCR4 antagonist-resistant Envs showed higher sensitivity to NAbs 447-52D, b12 and 2F5 targeting the V3 region, the gp120 CD4-binding site and the gp41 membrane proximal region, respectively, compared to NL4-3 WT virus. Recombinant NL4-3 viruses with the V3-coding region replaced with those derived from the CXCR4 antagonist-resistant viruses showed increased sensitivity to NAbs b12, 2F5 and 447-52D. Molecular dynamics simulations of Env gp120 outer domains predicted that the V3 mutations increased levels of fluctuations at the tip and stem of the V3 loop. These results indicate that mutations in the V3-coding region that result in loss of viral sensitivity to CXCR4 antagonists increase viral sensitivity to NAbs, providing insights into our understanding of the interplay of viral Env accessibility to chemokine receptors and sensitivity to NAbs.

The structural changes of water upon deep supercooling were studied through wide-angle x-ray scattering at SwissFEL. The experimental setup had a momentum transfer range of 4.5 Å-1 , which covered the principal doublet of the x-ray structure factor of water. The oxygen-oxygen structure factor was obtained for temperatures down to 228.5 ± 0.6 K. Similar to previous studies, the second diffraction peak increased strongly in amplitude as the structural change accelerated toward a local tetrahedral structure upon deep supercooling. We also observed an anomalous trend for the second peak position of the oxygen-oxygen structure factor (q 2). We found that q 2 exhibits an unprecedented positive partial derivative with respect to temperature for temperatures below 236 K. Based on Fourier inversion of our experimental data combined with reference data, we propose that the anomalous q 2 shift originates from that a repeat spacing in the tetrahedral network, associated with all peaks in the oxygen-oxygen pair-correlation function, gives rise to a less dense local ordering that resembles that of low-density amorphous ice. The findings are consistent with that liquid water consists of a pentamer-based hydrogen-bonded network with low density upon deep supercooling.

Molecular dynamics calculations of pressure effects on mStrawberry and mCherry fluorescent proteins are reported. The simulations reveal that mStrawberry has much floppier structure at atmospheric pressure, as evidenced by larger backbone fluctuations and the coexistence of two conformers that differ by Ser146 orientation. Consequently, pressure increase has a larger effect on mStrawberry, making its structure more rigid and reducing the population of one of the conformers. The most significant effect of pressure increase is in the hydrogen-bonding network between the chromophore and the nearby residues. The quantum-mechanics/molecular mechanics calculations of excitation energies in mStrawberry explain the observed blue shift and identify Lys70 as the residue that has the most pronounced effect on the spectra. The results suggest that pressure increase causes an initial increase of fluorescence yield only for relatively floppy fluorescent proteins, whereas the fluorescent proteins that have more rigid structures have quantum yields close to their maximum. The results suggest that a low quantum yield in fluorescent proteins is dynamic in nature and depends on the range of thermal motions of the chromophore and fluctuations in the H-bonding network rather than on their average structure.

Several neurodegenerative diseases, like Alzheimer's (AD), are characterized by amyloid fibrillar deposition of misfolded proteins, and this feature can be exploited for both diagnosis and therapy design. In this paper, structural modifications of curcumin scaffold were examined in order to improve its bioavailability and stability in physiological conditions, as well as its ability to interfere with β-amyloid fibrils and aggregates. The acid-base behaviour of curcumin derivatives, their pharmacokinetic stability in physiological conditions, and in vitro ability to interfere with Aβ fibrils at different incubation time were investigated. The mechanisms governing these phenomena have been studied at atomic level by means of molecular docking and dynamic simulations. Finally, biological activity of selected curcuminoids has been investigated in vitro to evaluate their safety and efficiency in oxidative stress protection on hippocampal HT-22 mouse cells. Two aromatic rings, π-conju...

In 2012, it was reported that anti-cancer drug bexarotene reduced amyloid plaque and improved mental functioning in a small sample of mice engineered to exhibit Alzheimer's like symptoms. It has been suggested that bexarotene stimulates expression of apolipoprotein E (ApoE) leading to intracellular clearance of amyloid beta (Aβ). However the effect of bexarotene on clearance of plaques has not been seen in some mouse models. Two interesting questions that emerge are: can bexarotene destroy Aβ fibrils via direct interaction with them and how this compound impacts the lag phase in the fibril growth process. By the Thioflavin T fluorescence assay and atomic force microscopy we have shown that bexarotene prolongs the lag phase but it does not degrade Aβ fibrils. The impotence of bexarotence in destroying fibrils means that this compound is weakly bound to Aβ. On the other hand, the weak binding would prevent bexarotene from prolonging the lag phase. Thus our two main in vitro observ...

A two‐component recombinant fusion protein antigen was re‐engineered and tested as a medical counter measure against the possible biological threat of aerosolized Yersinia pestis. The active component of the proposed subunit vaccine combines the F1 capsular protein and V virulence antigen of Y. pestis and improves upon the design of an earlier histidine‐tagged fusion protein. In the current study, different production strains were screened for suitable expression and a purification process was optimized to isolate an F1‐V fusion protein absent extraneous coding sequences. Soluble F1‐V protein was isolated to 99% purity by sequential liquid chromatography including capture and refolding of urea‐denatured protein via anion exchange, followed by hydrophobic interaction, concentration, and then transfer into buffered saline for direct use after frozen storage. Protein identity and primary structure were verified by mass spectrometry and Edman sequencing, confirming a purified product of...

Significance An important challenge has been to develop computer methods that can predict protein native structures from their sequences and satisfy the thermodynamic principle of Boltzmann's Law, which requires that the sampling method obey detailed balance. The latter is needed to study mechanisms and dynamics, which require an understanding of relative populations of states. These dual goals are met by atomistic model simulations, but they have been too expensive computationally. Here, we join together molecular dynamics (MD) with Bayesian inferences derived from loose insights (proteins have “hydrophobic cores” and “secondary structures”). We show that this method can speed up MD simulations by up to five orders of magnitude, allowing for the accurate predictions of small native protein structures with only atomistic potentials.

become irreversible on a macroscopic scale when they are sheared beyond the yield strain and begin flowing. Using computer simulations of oscillatory shear, we investigate atomic scale reversibility. We employ molecular dynamics simulations to cool binary Lennard-Jones liquids to zero temperature over a wide range of cooling rates. We then apply oscillatory quasistatic shear at constant pressure to the zero-temperature glasses and identify neighborswitching atomic rearrangement events. We determine the critical strain γ * , beyond which atoms in the system do not return to their original positions upon reversing the strain. We show that for more slowly cooled glasses, the average potential energy is lower and the typical size of atomic rearrangements is smaller, which correlates with larger γ * . Finally, we connect atomic-and macro-scale reversibility by determining the number of and correlations between the atomic rearrangements that occur as the system reaches the yield strain.

The response of amorphous solids to applied shear has several distinct regimes: quasi-elastic, yielding, and plastic flow regimes in the absence of fracture. Both non-affine particle motion and particle rearrangement events give rise to the strong nonlinear behavior of the stress versus strain curve. Here, we focus on computational studies of the mechanical behavior of binary Lennard-Jones glasses in three spatial dimensions that are prepared over a wide range of cooling rates. We apply athermal quasistatic pure shear to the glasses and uniquely identify each particle rearrangement event. We then determine the frequency of rearrangements and the energy drop after each event. We also quantify ductility by measuring the critical strain at which the material fractures during tensile tests. We find that more rapidly cooled glasses undergo more frequent particle rearrangements with larger energy drops on average. In contrast, rearrangements are much less frequent and dissipate less energy in more slowly cooled glasses, and thus are more susceptible to fracture than rapidly cooled glasses. In fact, we can predict the ductility of amorphous solids by measuring the total energy loss per strain in the putative linear stress versus strain regime before fracture occurs.

Micro- and nanoresonators have important applications including sensing, navigation, and biochemical detection. Their performance is quantified using the quality factor Q, which gives the ratio of the energy stored to the energy dissipated per cycle. Metallic glasses are a promising material class for micro- and nanoscale resonators since they are amorphous and can be fabricated precisely into complex shapes on these length scales. To understand the intrinsic dissipation mechanisms that ultimately limit large Q-values in metallic glasses, we perform molecular dynamics simulations to model metallic glass resonators subjected to bending vibrations at low temperatures. We calculate the power spectrum of the kinetic energy, redistribution of energy from the fundamental mode of vibration, and Q vs the kinetic energy per atom K of the excitation. In the harmonic and anharmonic response regimes where there are no atomic rearrangements, we find that Q → ∞ over the time periods we consider (...

This is the third part of a series of fictional conversations taking place among Descartes' hypothetical characters (Eudoxius, Epistemon and Polyander) [1,2]. As usual, the three friends meet at their favorite place to spend the afternoon exchanging their thoughts about different scientific topics. In this occasion, the discussion revolves around the concepts of equilibrium and steady state. While Epistemon presents an encyclopedic knowledge on the topic, Eudoxius insists on the importance of models to understand these concepts. Polyander pays careful attention and learns a lot, meanwhile Karsoni, the waiter, brings the drinks.

MicroRNAs (miRNAs) are endogenous small RNAs of ∼21 nt that regulate multiple biological pathways in multicellular organisms. They derive from longer transcripts that harbor an imperfect stem-loop structure. In plants, the ribonuclease type III DICER-LIKE1 assisted by accessory proteins cleaves the precursor to release the mature miRNA. Numerous studies highlight the role of the precursor secondary structure during plant miRNA biogenesis; however, little is known about the relevance of the precursor sequence. Here, we analyzed the sequence composition of plant miRNA primary transcripts and found specifically located sequence biases. We show that changes in the identity of specific nucleotides can increase or abolish miRNA biogenesis. Most conspicuously, our analysis revealed that the identity of the nucleotides at unpaired positions of the precursor plays a crucial role during miRNA biogenesis in Arabidopsis.

Raman optical activity (ROA) spectroscopy is used to investigate the backbone conformation of valinomycin in methanol and dioxane solution. Experimental Raman and ROA spectral differences are interpreted by using density functional calculations, molecular dynamics, and Cartesian tensor transfer. Of the several conformers with different numbers of intramolecular hydrogen bonds which were preselected by calculations of relative energies, the dominant ones are identified on the basis of ROA. To separate the backbone signal from that of the side chains, conformational search for the isopropyl residues is performed for each backbone conformer. In dioxane, the most populated conformer does not exhibit C3 symmetry, but adopts a distorted “bracelet” structure, similar to a crystal structure. This complements previous NMR spectroscopic results that could not distinguish the nonsymmetric structures. In methanol, a different, “propeller” conformer is indicated by ROA, which has three loops res...

Background and objectives: Cyclophilin A (CypA) is involved in various human biological processes. Its role in many pathological conditions makes it a promising target for treating human diseases, such as viral infections. The aim of the present study was to investigate docking of CypA mutants with its potential inhibitors using molecular dynamic simulation ((MDS). Methods: The crystallographic structure of CypA was extracted from the protein database (PDB). Important CypA substitutions were obtained from the literature. CypA inhibitors were taken from chemical databases. The affinity and binding sites of the compounds to CypA and its mutants were also scaled through Autodock Vina. Root-mean-square deviation (RMSD), radios gyration, Lenard-jones potential, and hydrogen bonding were investigated by using MDS for 600 ps. The findings revealed that SangfA and HBF-0259 had more affinity to the CypA (-7.8Kcal/mol and -7.5Kcal/mol, respectively). Conformational changes were observed in CypA W121A/F mutants. SangfA complexed with CypA and its mutants had relatively stable RMSD. Higher Lenard-Jones potential has been observed in the interaction of SangfA to W121A, HBF-0259 to M61, and SCY-635 to H70F. The SangfA had a higher HBs ratio with CypA. Conclusion: Given the higher affinity of SangfA and HBF-0259 to CypA and its mutants, they would influence the stability of the protein. RMSD analysis revealed that SangfA is probably ligated to CypA and its mutants, which are relatively stable. Substitution at W121 residue would reduce inhibitor binding to CypA.

The presence in the mRNA of premature stop codons (PTCs) results in protein truncation responsible for several inherited (genetic) diseases. A well-known example of these diseases is cystic fibrosis (CF), where approximately 10% (worldwide) of patients have nonsense mutations in the CF transmembrane regulator (CFTR) gene. PTC124 (3-(5-(2fluorophenyl)-1,2,4-oxadiazol-3-yl)-benzoic acid), also known as Ataluren, is a small molecule that has been suggested to allow PTC readthrough even though its target has yet to be identified. In the lack of a general consensus about its mechanism of action, we experimentally tested the ability of PTC124 to promote the readthrough of premature termination codons by using a new reporter. The reporter vector was based on a plasmid harboring the H2B histone coding sequence fused in frame with the green fluorescent protein (GFP) cDNA, and a TGA stop codon was introduced in the H2B-GFP gene by sitedirected mutagenesis. Additionally, an unprecedented computational study on the putative supramolecular interaction between PTC124 and an 11-codon (33-nucleotides) sequence corresponding to a CFTR mRNA fragment containing a central UGA nonsense mutation showed a specific interaction between PTC124 and the UGA codon. Altogether, the H2B-GFP-opal based assay and the molecular dynamics (MD) simulation support the hypothesis that PTC124 is able to promote the specific readthrough of internal TGA premature stop codons.

Desmin is a muscle-specific intermediate filament protein which forms a network connecting the sarcomere, T tubules, sarcolemma, nuclear membrane, mitochondria and other organelles. Mutations in the gene coding for desmin (DES) cause skeletal myopathies often combined with cardiomyopathy, or isolated cardiomyopathies. The molecular pathomechanisms of the disease remain ambiguous. Here, we describe and comprehensively characterize two DES mutations found in Polish patients with a clinical diagnosis of desminopathy. The study group comprised 16 individuals representing three families. Two mutations were identified: a novel missense mutation (Q348P) and a small deletion of nine nucleotides (A357_E359del), previously described by us in the Polish population. A common ancestry of all the families bearing the A357_E359del mutation was confirmed. Both mutations were predicted to be pathogenic using a bioinformatics approach, including molecular dynamics simulations which helped to rational...

A challenge in the treatment of Staphylococcus aureus infections is the high prevalence of methicillin-resistant S. aureus (MRSA) strains and the formation of non-growing, dormant 'persister' subpopulations that exhibit high levels of tolerance to antibiotics and have a role in chronic or recurrent infections. As conventional antibiotics are not effective in the treatment of infections caused by such bacteria, novel antibacterial therapeutics are urgently required. Here we used a Caenorhabditis elegans-MRSA infection screen to identify two synthetic retinoids, CD437 and CD1530, which kill both growing and persister MRSA cells by disrupting lipid bilayers. CD437 and CD1530 exhibit high killing rates, synergism with gentamicin, and a low probability of resistance selection. All-atom molecular dynamics simulations demonstrated that the ability of retinoids to penetrate and embed in lipid bilayers correlates with their bactericidal ability. An analogue of CD437 was found to reta...

The Marburg virus (MARV), a member of the family Filoviridae, is a highly pathogenic virus causing severe hemorrhagic fever with extremely high mortality in humans and non-human primates. The MARV exhibits clinical and epidemiological features almost identical to those of the Ebola virus, no licensed vaccines or antiviral treatments have been developed yet for MARV. However, only a few treatments that remain uncertain of the disease are available to help bring a case for a new therapeutic approach. Considering the non-availability of any standard drug we have planned to identify potential inhibi tors of VP24 (PDB ID: 4OR8) through a computational drug repurposing process. The workflow includes: identifying a druggable pocket on VP24, screening of FDA-approved antivirals via molecular docking, assessing the stability using molecular dynamics simulations, and estimating binding affinity through MM-PBSA calculations. After going through the analysis, the compound Bictegravir manifests as a hit compound which will undergo in vitro and in vivo validation to confirm its efficacy against MARV.

Streptococcus pneumoniae is a major cause of community-acquired pneumonia (CAP), particularly affecting children, the elderly, and immunocompromised individuals. Its polysaccharide capsule helps it evade immune defenses, leading to lung infections characterized by fever, cough, and respiratory distress. The bacteria spread through respiratory droplets, posing a significant public health risk. Although pneumococcal vaccines have reduced the incidence of pneumonia, non-vaccine serotypes and antibiotic resistance continue to challenge prevention and treatment efforts. This study aimed to utilize computational methods and tools to predict, analyze, and understand the potential antipneumonial effects of phytochemical compounds derived from Curcuma longa on the bacterium responsible for causing pneumonia. To accomplish this, a target protein of Streptococcus pneumoniae was selected from the Protein Data Bank for further analysis. The receptor (4IVV) was prepared using Chimera-1.10.1, PyMOL-2.3.0, and Autodock Tools-1.5.6, with the same preparation process applied to the reference ligand (EDO). Phytochemicals were selected from Drug Bank and PubChem database, then screened using Data Warrior based on Lipinski's Rule of Five and toxicity criteria. The screened phytochemicals were subsequently extracted and prepared with Autodock Tools-1.5.6. The docking protocol was validated, followed by molecular docking using autodock-vina. The docking results were then analyzed and visualized using PyMOL-2.3.0. After completing the procedures, the reference ligand exhibited a mean binding energy of-2.5 Kcal/mol. In comparison, the 105 phytoconstituents, including the top 10 candidates, showed lower binding energies, ranging from-8.1 Kcal/mol to-6.5 Kcal/mol, indicating a stronger binding affinity than the reference ligand.

A theory for the analytical prediction of microstructure of concentrated Brownian suspensions of spheres in simple-shear flow is developed. The computed microstructure is used in a prediction of the suspension rheology. A near-hard-sphere suspension is studied for solid volume fraction φ 0.55 and Péclet number P e = 3πη γa 3 /k b T 100; a is the particle radius, η is the suspending Newtonian fluid viscosity, γ is the shear rate, k b is the Boltzmann constant and T is absolute temperature. The method developed determines the steady pair distribution function g(r), where r is the pair separation vector, from a solution of the Smoluchowski equation (SE) reduced to pair level. To account for the influence of the surrounding bath of particles on the interaction of a pair, an integrodifferential form of the pair SE is developed; the integral portion represents the forces due to the bath which drive the pair interaction. Hydrodynamic interactions are accounted in a pairwise fashion, based on the dominant influence of pair lubrication interactions for concentrated suspensions. The SE is modified to include the influence of shear-induced relative diffusion, and this is found to be a crucial for success of the theory; a simple model based on understanding of the shear-induced self-diffusivity is used for this property. The computation of the microstructure is split into two parts, one specific to near-equilibrium (P e 1), where a regular perturbation expansion of g in P e is applied, and a general-

ELIC, the pentameric ligand-gated ion channel from Erwinia chrysanthemi, is a prototype for Cys-loop receptors. Here we show that acetylcholine is a competitive antagonist for ELIC. We determine the acetylcholine-ELIC cocrystal structure to a 2.9-Å resolution and find that acetylcholine binding to an aromatic cage at the subunit interface induces a significant contraction of loop C and other structural rearrangements in the extracellular domain. The side chain of the pore-lining residue F247 reorients and the pore size consequently enlarges, but the channel remains closed. We attribute the inability of acetylcholine to activate ELIC primarily to weak cation-π and electrostatic interactions in the pocket, because an acetylcholine derivative with a simple quaternary-to-tertiary ammonium substitution activates the channel. This study presents a compelling case for understanding the structural underpinning of the functional relationship between agonism and competitive antagonism in the ...

In LeuT, a prokaryotic homolog of neurotransmitter transporters, Na(+) stabilizes outward-open conformational states. We examined how each of the two LeuT Na(+) binding sites contributes to Na (+)-dependent closure of the cytoplasmic pathway using biochemical and biophysical assays of conformation. Mutating either of two residues that contribute to the Na2 site completely prevented cytoplasmic closure in response to Na(+), suggesting that Na2 is essential for this conformational change, whereas Na1 mutants retained Na(+) responsiveness. However, mutation of Na1 residues also influenced the Na+-dependent conformational change in ways that varied depending on the position mutated. Computational analyses suggest those mutants influence the ability of Na1 binding to hydrate the substrate pathway and perturb an interaction network leading to the extracellular gate. Overall, the results demonstrate that occupation of Na2 stabilizes outward-facing conformations presumably through a direct ...

Представлена феноменологическая модель, интерпретирующая крупномасштабные структуры галактического гало — Пузыри Ферми, eROSITA и Microwave Haze — как проекции единой фазовой сверхструктуры. Модель основана на геометрическом подходе конус-фильтра в рамках теории функций комплексного пространственного переменного и Σ-алгебры. Численные эксперименты демонстрируют морфологическое соответствие наблюдениям в гамма, рентгеновском и микроволновом диапазонах. Обсуждаются физические механизмы синхротронного излучения и фарадеевского вращения в рамках модели, её ограничения и перспективы развития в сторону самосогласованных 3D-MHD расчётов.

The field of nanotechnology has made remarkable advancements in drug delivery systems, enabling improved drug penetration and direct delivery to specific areas. These systems, known as drug delivery systems (DDSs), aim to enhance drug efficacy and safety by controlling release rate, timing, and targeted location within the body. Carbon nanotubes (CNTs) have emerged as promising materials due to their ability to target specific sites and regulate molecule release. In this study, molecular dynamics simulation was used to compare the interactions between commonly used drugs such as mitoxantrone (MTX) and doxorubicin (DOX) and singlewalled carbon nanotubes (SWCNTs). The adsorption process of these drugs was observed in a non-aqueous simulation box to evaluate their compatibility with nanocarriers for biomedical applications. The results demonstrated positive energetic interactions between anti-cancer drugs and SWCNTs, driven by π-π interactions and significant interaction energies. According to the RDF results, it was observed that mitoxantrone and doxorubicin drugs had π-π interactions with the carbon nanotube with approximately 3.5 Å-4.0 Å. Additionally, interaction energy values were calculated as-92.43 kJ/mol and-105.42 kJ/mol for SWCNT-MTX and SWCNT-DOX systems, respectively. While MTX and DOX interacted effectively with the carbon nanotube, doxorubicin showed a more efficient interaction.

The design of new biocatalysts is a target that is receiving increasing attention. One of the most popular reactions in this regard is the Diels-Alder cycloaddition due to its applications in organic synthesis and the absence of efficient natural enzymes that catalyze it. In this paper, the possibilities of using the highly promiscuous Candida Antarctica lipase B (CALB) as a protein scaffold to re-design a Diels-Alderase has been explored by means of theoretical quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. Free energy surfaces have been computed for two reactions in the wild-type and in several mutants with hybrid AM1/MM potentials with corrections at M06-2X/MM level. The study of the counterpart reactions in solution has allowed performing comparative analysis that render interesting conclusion. Since the dienophile anchors very well in the oxyanion hole of all tested protein variants, the slight electronic changes from reactant complex to the transition state suggest that mutations should be focused in favoring the formation of reactive conformations of reactant complex that, in turn, would reduce the energy barrier.

Cruzain, a cysteine protease of the papain family, is essential in the development of the protozoan Trypanosoma cruzi, the etiologic agent of Chagas disease, making it an attractive target for developing new drugs. The present paper is aimed at the study of the catalytic mechanism of the cruzain by first exploring the different protonation states of the active site Cys25 and His159 in the Michaelis complex and the effect on the full catalytic mechanism of this enzyme. The exploration of the equilibrium between these two states has been performed with alchemical free energy perturbation methods with molecular mechanics (MM) force fields and by generating the free energy surfaces in terms of the potential of mean force computed at two levels of theory: AM1d/MM and M06-2X/6-31+G(d,p):AM1d/MM. Alternative mechanisms for the acylation step have been identified on the free energy surfaces and the results suggest the existence of three new reaction mechanisms starting from the peptide binding to the apoenzyme in its neutral Cys25S/His159 dyad state. The mechanism starting with the protonation of the nitrogen atom of the peptide followed by the attack of Cys25S -was revealed as the most favorable one, but it can be competitive with its counterpart mechanism initiated in the Cys25S -/His159H + ion pair Michaelis complex. Analysis of energetic and average geometries will allow continuing improvement of our knowledge on this enzyme at the molecular level, which can be crucial to the design of new inhibitors based on the structures of the transition states (transition states analogues) or stable intermediates.

The design of new biocatalysts is a target that is receiving increasing attention. One of the most popular reactions in this regard is the Diels-Alder cycloaddition because of its applications in organic synthesis and the absence of efficient natural enzymes that catalyze it. In this paper, the possibilities of using the highly promiscuous Candida Antarctica lipase B as a protein scaffold to redesign a Diels-Alderase has been explored by means of theoretical quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations. Free energy surfaces have been computed for two reactions in the wild-type and in several mutants with hybrid AM1/MM potentials with corrections at M06-2X/MM level. The study of the counterpart reactions in solution has allowed performing comparative analysis that render interesting conclusions. Since the dienophile anchors very well in the oxyanion hole of all tested protein variants, the slight electronic changes from reactant complex to the transiti...

The hydride transfer from C6 of tetrahydrofolate to the reaction's exocyclic methylene-dUMP intermediate is the rate limiting step in thymidylate synthase (TSase) catalysis. This step has been studied by means of QM/MM molecular dynamics simulations to generate the corresponding free energy surfaces. The use of two different initial X-ray structures has allowed exploring different conformational spaces and the existence of chemical paths with not only different reactivities but also different reaction mechanisms. The results confirm that this chemical conversion takes place preferentially via a concerted mechanism where the hydride transfer is conjugated to thiol-elimination from the product. The findings also confirm the labile character of the substrate-enzyme covalent bond established between the C6 of the nucleotide substrate and a conserved cysteine residue. The calculations also reproduce and rationalize a normal H/T 2° kinetic isotope effect measured for that step. From a...

Molecular dynamics simulations were performed on E. coli wild type (WT) Trp repressor and the AV77 mutant in interaction with DNA. Alanine to valine mutation at position 77 results in a repressor with enhanced activity at low concentrations of the L-Trp co-repressor. However, WT and AV77 mutant show an identical crystallographic structure, preventing to devise a clear structure-function correlation and suggesting that the different activity could be ascribed to a varied dynamical behavior. Root mean square deviations, dynamical cross correlation and hydrogen bond analysis have been performed to detect specific differences between the two repressor forms, showing that both ligand and DNA binding is different in the two complexes.

Diabetes mellitus (DM) affects over 77 million adults in India, with cases expected to reach 134 million by 2045. Current treatments, including sulfonylureas and thiazolidinediones, are inadequate, underscoring the need for novel therapeutic strategies. This study investigates marine natural products (MNPs) as alternative therapeutic agents targeting SIK2, a key enzyme involved in DM. The structural stability of the predicted SIK2 model was validated using computational methods and subsequently employed for structure based virtual screening (SBVS) of over 38,000 MNPs. This approach identified five promising candidates: CMNPD21753 and
CMNPD13370 from the Comprehensive Marine Natural Product Database, MNPD10685 from the Marine Natural Products Database, and SWMDRR053 and SWMDRR052 from the Seaweed Metabolite Database. The identified compounds demonstrated docking scores ranging from −7.64 to −11.95 kcal/mol and MMGBSA binding scores between −33.29 and −68.29 kcal/mol, with favourable predicted pharmacokinetic and toxicity profiles. Molecular dynamics simulations (MDS) revealed stronger predicted binding affinity for these compounds compared to ARN-3236,
a known SIK2 inhibitor. Principal component (PC)-based free energy landscape (FEL) analysis further supported the stable binding of these compounds to SIK2. These computational findings highlight the potential of these leads as novel SIK2 inhibitors, warranting future in vitro and in vivo validation.

Diabetes mellitus (DM) affects over 77 million adults in India, with cases expected to reach 134 million by 2045. Current treatments, including sulfonylureas and thiazolidinediones, are inadequate, underscoring the need for novel therapeutic strategies. This study investigates marine natural products (MNPs) as alternative therapeutic agents targeting SIK2, a key enzyme involved in DM. The structural stability of the predicted SIK2 model was validated using computational methods and subsequently employed for structure based virtual screening (SBVS) of over 38,000 MNPs. This approach identified five promising candidates: CMNPD21753 and
CMNPD13370 from the Comprehensive Marine Natural Product Database, MNPD10685 from the Marine Natural Products Database, and SWMDRR053 and SWMDRR052 from the Seaweed Metabolite Database. The identified compounds demonstrated docking scores ranging from −7.64 to −11.95 kcal/mol and MMGBSA binding scores between −33.29 and −68.29 kcal/mol, with favourable predicted pharmacokinetic and toxicity profiles. Molecular dynamics simulations (MDS) revealed stronger predicted binding affinity for these compounds compared to ARN-3236,
a known SIK2 inhibitor. Principal component (PC)-based free energy landscape (FEL) analysis further supported the stable binding of these compounds to SIK2. These computational findings highlight the potential of these leads as novel SIK2 inhibitors, warranting future in vitro and in vivo validation.

Purpose To investigate the mechanistic basis of the antitumor effect of the compound ITB-301. Methods Chemical modifications of genistein have been introduced to improve its solubility and efficacy. The antitumor effects were tested in ovarian cancer cells using proliferation assays, cell cycle analysis, immunofluorescence, and microscopy. In this work, we show that a unique glycoside of genistein, ITB-301, inhibits the proliferation of SKOv3 ovarian cancer cells. We found that the 50% growth inhibitory concentration of ITB-301 in SKOv3 cells was 0.5 lM. Similar results were obtained in breast cancer, ovarian cancer, and acute myelogenous leukemia cell lines. ITB-301 induced significant time-and dose-dependent microtubule depolymerization. This depolymerization resulted in mitotic arrest and inhibited proliferation in all ovarian cancer cell lines examined including SKOv3, ES2, HeyA8, and HeyA8-MDR cells. The cytotoxic effect of ITB-301 was dependent on its induction of mitotic arrest as siRNA-mediated depletion of BUBR1 significantly reduced the cytotoxic effects of ITB-301, even at a concentration of 10 lM. Importantly, efflux-mediated drug resistance did not alter the cytotoxic effect of ITB-301 in two independent cancer cell models of drug resistance. Conclusion These results identify ITB-301 as a novel anti-tubulin agent that could be used in cancers that are multidrug resistant. We propose a structural model for the binding of ITB-301 to aand b-tubulin dimers on the basis of molecular docking simulations. This model provides a rationale for future work aimed at designing of more potent analogs.

To accelerate the logical drug design procedure, we created the program "NAGARA," a plugin for PyMOL, and applied it to the discovery of small compounds called medical chaperones (MCs) that stabilize the cellular form of a prion protein (PrP(C)). In NAGARA, we constructed a single platform to unify the docking simulation (DS), free energy calculation by molecular dynamics (MD) simulation, and interfragment interaction energy (IFIE) calculation by quantum chemistry (QC) calculation. NAGARA also enables large-scale parallel computing via a convenient graphical user interface. Here, we demonstrated its performance and its broad applicability from drug discovery to lead optimization with full compatibility with various experimental methods including Western blotting (WB) analysis, surface plasmon resonance (SPR), and nuclear magnetic resonance (NMR) measurements. Combining DS and WB, we discovered anti-prion activities for two compounds and tegobuvir (TGV), a non-nucleoside no...

Bacterial enhancer binding proteins (bEBPs) are a subclass of the AAA + (ATPases Associated with various cellular Activities) protein family. They are responsible for σ 54 -dependent transcription activation during infection and function under many stressful growth conditions. The majority of bEBPs are regulated in their formation of ring-shaped hexameric self-assemblies via an amino-terminal domain through its phosphorylation or ligand binding. In contrast, the Escherichia coli phage shock protein F (PspF) is negatively regulated in trans by phage shock protein A (PspA). Up to six PspA subunits suppress PspF hexamer action. Here, we present biochemical evidence that PspA engages across the side of a PspF hexameric ring. We identify three key binding determinants located in a surface-exposed 'W56 loop' of PspF, which form a tightly packed hydrophobic cluster, the 'YLW' patch. We demonstrate the profound impact of the PspF W56 loop residues on ATP hydrolysis, the σ 54 binding loop 1, and the self-association interface. We infer from single-chain studies that for complete PspF inhibition to occur, more than three PspA subunits need to bind a PspF hexamer with at least two binding to adjacent PspF subunits. By structural modelling, we propose that PspA binds to PspF via its first two helical domains. After PspF binding-induced conformational changes, PspA may then share structural similarities with a bEBP regulatory domain.

We employ atomic-scale simulation methods to investigate bulk and surface properties of an analytic Tersoff-Abell type potential for describing interatomic interactions in GaAs. The potential is a modified form of that proposed by Albe and colleagues [Phys. Rev. B 66, 035205 (2002)] in which the cut-off parameters for the As-As interaction have been shortened. With this modification, many bulk properties predicted by the potential for solid GaAs are the same as those in the original potential, but properties of the GaAs(001) surface better match results from first-principles calculations with density-functional theory (DFT). We tested the ability of the potential to reproduce the phonon dispersion and heat capacity of bulk solid GaAs by comparing it to experiment and the overall agreement is good. In the modified potential, the GaAs(001) β2(2 × 4) reconstruction is favored under As-rich growth conditions in agreement with DFT calculations. Additionally, the binding energies and diffusion barriers for a Ga adatom on the β2(2 × 4) reconstruction generally match results from DFT calculations. These studies indicate that the potential is suitable for investigating aspects of GaAs(001) homoepitaxy.

Drilling fluid performance is vital for operational efficiency, as it enhances the rate of penetration and ensures wellbore stability by preventing wellbore collapse. However, in harsh conditions (HPHT), the drilling efficiency and equipment longevity face significant threats. Specifically, the viscosity of drilling fluids decreases at high temperatures, exacerbating fluid loss. Mitigating fluid loss necessitates the deployment of temperature-stable additives, such as sawdust charcoal nanoparticles. These additives contribute to increased viscosity, fluid loss control, and improved filtration efficiency. The main objective of this study was to examine the rheological properties and filtration of bentonite, potassium chloride (KCl), and oil-based drilling fluids in the presence of sawdust charcoal nanoparticles using molecular dynamics (MD) simulations. First, the designed atomic samples were equilibrated, followed by an investigation into their structural evolution using the NVE ensemble. Throughout the MD simulation, to examine the rheological behavior of the target atomic structure, the changes in physical quantities, such as mean square displacement (MSD), shear stress, interaction energy, and viscosity, were analyzed. The main qualitative finding was that an increase in the initial temperature of the atomic sample enhanced atomic mobility within the simulation box; however, adding an additive to the initial structure reduced the sample's mobility due to an increase in attractive interatomic forces. Key quantitative findings included MSD increase to 2.39 Å, indicating enhanced atomic oscillation, and the absorption of 28 atoms into the porous material, suggesting improved fluid penetration. Shear stress reached 69.92 Pa, reflecting interatomic forces, while the interaction energy converged to -14.85 kcal/mol, highlighting its role in penetration thresholds. Overall, the study emphasized the need to balance fluidity and penetration efficiency to optimize drilling fluids for practical applications. The findings contributed to cost-effective and efficient drilling practices in the oil industry while addressing challenges in fluid behavior at the nanoscale.

A comprehensive effort in photodynamical ab initio simulations of the ultrafast deactivation pathways for all five nucleobases adenine, guanine, cytosine, thymine, and uracil is reported. These simulations are based on a complete nonadiabatic surface-hopping approach using extended multiconfigurational wave functions. Even though all five nucleobases share the basic internal conversion mechanisms, the calculations show a distinct grouping into purine and pyrimidine bases as concerns the complexity of the photodynamics. The purine bases adenine and guanine represent the most simple photodeactivation mechanism with the dynamics leading along a diabatic ππ* path directly and without barrier to the conical intersection seam with the ground state. In the case of the pyrimidine bases, the dynamics starts off in much flatter regions of the ππ* energy surface due to coupling of several states. This fact prohibits a clear formation of a single reaction path. Thus, the photodynamics of the py...