Conformational Modifications Research Articles

Electrochemical characterization of shikonin and in-situ evaluation of interaction with DNA

• Shikonin, a natural compound with pharmaceutical properties; • Shikonin reduction results in semiquinone radical and superoxide; • Shikonin induces DNA conformational modification. • In-situ shikonin reduction leads to occurrence 8-oxo-guanine. • Shikonin-DNA interaction mechanism proposed. Shikonin, a natural compound with pharmaceutical properties, has attracted interest due to its anti-oxidant properties, potential anti-cancer activity and activity over several biological pathways, such as dsDNA transcription/replication of cancer cells and inhibition of pyruvate kinase M2. The electrochemical behavior of shikonin in aqueous media was investigated at glassy carbon electrodes by cyclic and differential pulse voltammetry. The reduction involves the quinone moiety and formation of a semiquinone intermediate. In the absence of dissolved oxygen, the reduction is reversible while in normal atmosphere leads to formation of superoxide cation. The oxidation occurs at the dihydroxy moiety and reversibility was only observed in acid electrolytes. A redox mechanism was proposed. The interaction between shikonin and ds DNA was evaluated in incubated solutions and in situ with the dsDNA-electrochemical biosensor. The mechanism of interaction is time-dependent and follows an initial binding step at the grooves of the double strand leading to conformational modifications recognized through the variation of guanine and adenine oxidation peaks. The in-situ electrochemical production of the semiquinone intermediate leads to a preferential interaction with guanine residues, promoting their oxidation and consequently occurrence 8-oxo-guanine. An interaction mechanism was proposed.

Classification of finite irreducible conformal modules for K4′

We classify finite irreducible modules over the conformal superalgebra K4′ by their correspondence with finite conformal modules over the associated annihilation superalgebra A(K4′). This is achieved by a complete classification of singular vectors in generalized Verma modules for A(K4′). We also show that morphisms between generalized Verma modules can be arranged in infinitely many bilateral complexes.

Pharmacophore Modeling of Targets Infested with Activity Cliffs via Molecular Dynamics Simulation Coupled with QSAR and Comparison with other Pharmacophore Generation Methods: KDR as Case Study.

Activity cliffs (ACs) are defined as pairs of structurally similar compounds with large difference in their potencies against certain biotarget. We recently proposed that potent AC members induce significant entropically-driven conformational modifications of the target that unveil additional binding interactions, while their weakly-potent counterparts are enthalpically-driven binders with little influence on the protein target. We herein propose to extract pharmacophores for ACs-infested target(s) from molecular dynamics (MD) frames of purely "enthalpic" potent binder(s) complexed within the particular target. Genetic function algorithm/machine learning (GFA/ML) can then be employed to search for the best possible combination of MD pharmacophore(s) capable of explaining bioactivity variations within a list of inhibitors. We compared the performance of this approach with established ligand-based and structure-based methods. Kinase inserts domain receptor (KDR) was used as a case study. KDR plays a crucial role in angiogenic signalling and its inhibitors have been approved in cancer treatment. Interestingly, GFA/ML selected, MD-based, pharmacophores were of comparable performances to ligand-based and structure-based pharmacophores. The resulting pharmacophores and QSAR models were used to capture hits from the national cancer institute list of compounds. The most active hit showed anti-KDR IC50 of 2.76 μM.

Classification of Finite Irreducible Conformal Modules over N = 2 Lie Conformal Superalgebras of Block Type

We introduce the N = 2 Lie conformal superalgebras \({\frak {K}}(p)\) of Block type, and classify their finite irreducible conformal modules for any nonzero parameter p. In particular, we show that such a conformal module admits a nontrivial extension of a finite conformal module M over K2 if p = − 1 and M has rank (2 + 2), where K2 is an N = 2 conformal subalgebra of \({\frak {K}}(p)\). As a byproduct, we obtain the classification of finite irreducible conformal modules over a series of finite Lie conformal superalgebras \({\frak k}(n)\) for n ≥ 1. Composition factors of all the involved reducible conformal modules are also determined.

Plasmonic hot spots reveal local conformational transitions induced by DNA double-strand breaks

DNA double-strand breaks (DSBs) are typical DNA lesions that can lead to cell death, translocations, and cancer-driving mutations. The repair process of DSBs is crucial to the maintenance of genomic integrity in all forms of life. However, the limitations of sensitivity and special resolution of analytical techniques make it difficult to investigate the local effects of chemotherapeutic drugs on DNA molecular structure. In this work, we exposed DNA to the anticancer antibiotic bleomycin (BLM), a damaging factor known to induce DSBs. We applied a multimodal approach combining (i) atomic force microscopy (AFM) for direct visualization of DSBs, (ii) surface-enhanced Raman spectroscopy (SERS) to monitor local conformational transitions induced by DSBs, and (iii) multivariate statistical analysis to correlate the AFM and SERS results. On the basis of SERS results, we identified that bands at 1050 cm−1 and 730 cm−1 associated with backbone and nucleobase vibrations shifted and changed their intensities, indicating conformational modifications and strand ruptures. Based on averaged SERS spectra, the PLS regressions for the number of DSBs caused by corresponding molar concentrations of bleomycin were calculated. The strong correlation (R2 = 0.92 for LV = 2) between the predicted and observed number of DSBs indicates, that the model can not only predict the number of DSBs from the spectra but also detect the spectroscopic markers of DNA damage and the associated conformational changes.

The dynamics of t1 adenosine binding on human Argonaute 2: Understanding recognition with conformational selection.

The control of expression in genetic regulation is a fundamental process for cell life. In RNA‐mediated silencing, human Argonaute‐2 protein (hAgo2) uses sequence information encoded in small RNAs (guide) to identify complementary sites in messenger RNAs (target) for repression. The specificity of this molecular recognition lies at the basis of the mechanisms that control the expression of thousands of genes, which necessarily requires a fine tuning of complex events. Among these, the binding of the first nucleotide of the target RNA (t1) is emerging as an important modulator of hAgo2‐mediated machinery. Using atomistic molecular dynamics‐derived analyses, we address the mechanism behind t1‐dependent regulation and study the impact of different t1 nucleotides (t1A, t1C, t1G, t1U) on the conformational dynamics of both hAgo2 and guide–target RNAs. Only when an adenine is found at this position, t1 directly interacts with a specific hAgo2 binding pocket, favoring the stabilization of target binding. Our findings show that hAgo2 exploits a dynamic recognition mechanism of the t1‐target thanks to a modulation of RNA conformations. Here, t1‐adenine is the only nucleobase endowed with a dual binding mode: a T‐shape and a co‐planar conformation, respectively, orthogonal and parallel to the following base‐pairs of guide–target duplex. This triggers a composite set of molecular interactions that stabilizes distinctive conformational ensembles. Our comparative analyses show characteristic traits of local and global dynamic interplay between hAgo2 and the RNA molecules and highlight how t1A binding acts as a molecular switch for target recognition and complex stabilization. Implications for future mechanistic studies are discussed.

Potential Roles of PTEN on Longevity in Two Closely Related Argopecten Scallops With Distinct Lifespans.

Phosphatase and tensin homolog deleted on chromosome ten (PTEN) has been found to regulate longevity through the PI3K/Akt/FoxO pathway and maintenance of genome integrity in worms, flies, and mammals. However, limited information is available on the roles of PTEN in longevity of aquatic animals. Here we extended this paradigm using two closely related Argopecten scallops, Argopecten purpuratus, and Argopecten irradians, with significantly distinct life spans, which are commercially important bivalve species for fishery and aquaculture in China, United States, Peru, and Chile. The ORFs of the ApPTEN and AiPTEN were 1,476 and 1,473 bp, which encoded 491 and 490 amino acids, respectively. There were 48 synonymous and 16 non-synonymous SNPs and one InDel of three nucleotides between ApPTEN and AiPTEN, resulting in variations in 15 amino acids and lack of S453 in AiPTEN. Differences in conformation and posttranslational modification were predicted between ApPTEN and AiPTEN, which may indicate different activities of ApPTEN and AiPTEN. When the animals were subjected to nutrition restriction, the expression of both ApPTEN and AiPTEN was upregulated, with AiPTEN responded faster and more robust than ApPTEN. Ionizing radiation induced significantly elevated expression of ApPTNE but not AiPTEN in the adductor muscle, and the mortality rate of A. purpuratus was significantly lower than that of A. irradians, indicating that ApPTNE may play a protective role by maintaining the genome integrity. RNAi of ApPTNE significantly downregulated the expression of its downstream regulated genes known to favor longevity, such as FoxO, Mn-SOD, and CAT. These results indicated that PTEN may contribute to the longevity of A. purpuratus through regulation of nutrient availability and genomic stability, probably via PI3K/Akt/FoxO pathway. Our study may provide new evidence for understanding of the conservative functions of PTEN in regulation of lifespan in animals and human, and it may also benefit the selection of scallops strains with long lifespan and thus larger size.

Structure-based virtual screening for identification of potential non-steroidal LXR modulators against neurodegenerative conditions

Liver X Receptors (LXRs) are members of the nuclear receptor superfamily that regulate cholesterol metabolism. LXRs have been suggested as promising targets against many neurodegenerative diseases (NDDs). The present study was aimed to identify novel non-steroidal molecules that may potentially modulate LXR activity. The structure-based virtual screening (SBVS) was used to search for suitable compounds from the Asinex library. The top hits were selected and filtered based on their binding affinity for LXR α and β isoforms. Based on molecular docking and scoring results, 24 compounds were selected that had binding energy in the range of − 13.9 to − 12 for LXRα and − 12.5 to − 11 for LXRβ, which were higher than the reference ligands (GW3965 and TO901317). Further, the five hits referred to as model 29, 64, 202, 250, 313 were selected by virtue of their binding interactions with amino acid residues at the active site of LXRs. The selected hits were then subjected to absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis and blood-brain permeability prediction. It was observed that the selected hits had better pharmacokinetic properties with no toxicity and could cross blood-brain barrier. Further, the selected hits were analysed for dynamic evolution of the system with LXRs by molecular dynamics (MD) simulation at 100 ns using GROMACS. The MD simulation results validated that selected hits possess a remarkable amount of flexibility, stability, compactness, binding energy and exhibited limited conformational modification. The root mean square deviation (RMSD) values of the top-scoring hits complexed with LXRα and LXRβ were 0.05–0.6 nm and 0.05–0.45 nm respectively, which is greater than the protein itself. Altogether the study identified potential non-steroidal LXR modulators that appear to be effective against various neurodegenerative conditions involving perturbed cholesterol and lipid homeostasis.

Radioterapi Linac Energi 6 MV Terhadap Kanker Serviks Pada Organ Rektum Menggunakan Teknik 3DCRT dan IMRT Di RSUP Sanglah Denpasar

Cervical cancer radiotherapy on the Linac aircraft uses a 6 MV energy photon beam with 3 Dimension Conformal Radiotherapy (3DCRT) and Intensity Modulation Radiation Therapy (IMRT) techniques. Radiotherapy planning on the 3DCRT and IMRT techniques is then compared by analyzing the dose distribution or planning target volume (PTV) coverage through the Conformity Index (CI) and Homogeneity Index (HI) and Organ At Risk (OAR) where the risk organ that is considered is the rectum. In this study, 30 data on cervical cancer patients were used at the Radiotherapy Installation at Sanglah Hospital Denpasar with a plan using a box system on the 3DCRT technique and the IMRT technique with rotation angles of 00, 900, 1800, and 2700 and a radiation dose of 5000 cGy. Comparison of these two techniques is done by analyzing the Dose Volume Histogram (DVH) curve on PTV coverage on the Treatment Planning System (TPS) computer. The results of this study indicate that the average CI value in the 3DCRT technique is 1.017542 while the IMRT technique is 1.019668, with the Mann Whitney test (Asymp.Sig = 0.492). Likewise, the HI value, where the 3DCRT technique averaged 0.089494 while the IMRT technique was 0.093126 with Mann Whitney test (Asymp.Sig = 0.487), both CI and HI values were not significant. While the percentage of the average dose of the rectum on both the 3DCRT and IMRT irradiation techniques are 96% and 87%, respectively. Cervical cancer radiotherapy using IMRT technique can minimize the absorbed dose in OAR (rectum).

ST6Gal1 in plasma is dispensable for IgG sialylation.

The glycosylation of immunoglobulin G (IgG) has attracted increased attention due to the impact of N-glycan modifications at N297 on IgG function, acting primarily through modulation of Fc domain conformation and Fcγ receptor-binding affinities and signaling. However, the mechanisms regulating IgG glycosylation and especially α2,6-sialylation of its N-glycan remain poorly understood. We observed previously that IgG is normally sialylated in mice with B cells lacking the sialyltransferase ST6Gal1. This supported the hypothesis that IgG may be sialylated outside of B cells, perhaps through the action of hepatocyte-released plasma ST6Gal1. Here, we demonstrate that this model is incorrect. Animals lacking hepatocyte expressed ST6Gal1 retain normal IgG α2,6-sialylation despite the lack of detectable ST6Gal1 in plasma. Moreover, we confirmed that B cells were not a redundant source of IgG sialylation. Thus, while α2,6-sialylation is lacking in IgG from mice with germline ablation of ST6Gal1, IgG α2,6-sialylation is normal in mice lacking ST6Gal1 in either hepatocytes or B cells. These results indicate that IgG α2,6-sialylation arises after release from a B cell but is not dependent on plasma-localized ST6Gal1 activity.

Substoichiometric Hsp104 regulates the genesis and persistence of self-replicable amyloid seeds of Sup35 prion domain

Prion-like self-perpetuating conformational conversion of proteins is involved in both transmissible neurodegenerative diseases in mammals and non-Mendelian inheritance in yeast. The transmissibility of amyloid-like aggregates is dependent on the stoichiometry of chaperones such as heat shock proteins (Hsps), including disaggregases. To provide the mechanistic underpinnings of the formation and persistence of prefibrillar amyloid seeds, we investigated the role of substoichiometric Hsp104 on the in vitro amyloid aggregation of the prion domain (NM-domain) of Saccharomyces cerevisiae Sup35. At low substoichiometric concentrations, we show Hsp104 exhibits a dual role: it considerably accelerates the formation of prefibrillar species by shortening the lag phase but also prolongs their persistence by introducing unusual kinetic halts and delaying their conversion into mature amyloid fibers. Additionally, Hsp104-modulated amyloid species displayed a better seeding capability compared to NM-only amyloids. Using biochemical and biophysical tools coupled with site-specific dynamic readouts, we characterized the distinct structural and dynamical signatures of these amyloids. We reveal that Hsp104-remodeled amyloidogenic species are compositionally diverse in prefibrillar aggregates and are packed in a more ordered fashion compared to NM-only amyloids. Finally, we show these Hsp104-remodeled, conformationally distinct NM aggregates display an enhanced autocatalytic self-templating ability that might be crucial for phenotypic outcomes. Taken together, our results demonstrate that substoichiometric Hsp104 promotes compositional diversity and conformational modulations during amyloid formation, yielding effective prefibrillar seeds that are capable of driving prion-like Sup35 propagation. Our findings underscore the key functional and pathological roles of substoichiometric chaperones in prion-like propagation.

Pharmacophore-Based Discovery of Viral RNA Conformational Modulators.

New RNA-binding small-molecule scaffolds are needed to unleash the pharmacological potential of RNA targets. Here we have applied a pharmacophore-based virtual screening approach, seldom used in the RNA recognition field, to identify novel conformational inhibitors of the hepatitis C virus internal ribosome entry site. The conformational effect of the screening hits was assessed with a fluorescence resonance energy transfer assay, and the affinity, specificity, and binding site of the ligands were determined using a combination of fluorescence intensity and NMR spectroscopy experiments. The results indicate that this strategy can be successfully applied to discover RNA conformational inhibitors bearing substantially less positive charge than the reference ligands. This methodology can potentially be accommodated to other RNA motifs of pharmacological interest, facilitating the discovery of novel RNA-targeted molecules.

Switching charge states in quasi-2D molecular conductors.

2D molecular entities build next-generation electronic devices, where abundant elements of organic molecules are attractive due to the modern synthetic and stimuli control through chemical, conformational, and electronic modifications in electronics. Despite its promising potential, the insufficient control over charge states and electronic stabilities must be overcome in molecular electronic devices. Here, we show the reversible switching of modulated charge states in an exfoliatable 2D-layered molecular conductor based on bis(ethylenedithio)tetrathiafulvalene molecular dimers. The multiple stimuli application of cooling rate, current, voltage, and laser irradiation in a concurrent manner facilitates the controllable manipulation of charge crystal, glass, liquid, and metal phases. The four orders of magnitude switching of electric resistance are triggered by stimuli-responsive charge distribution among molecular dimers. The tunable charge transport in 2D molecular conductors reveals the kinetic process of charge configurations under stimuli, promising to add electric functions in molecular circuitry.

Benzimidazole Derivatives in Identifying Novel Acetylcholinesterase Inhibitors: A Combination of 3D-QSAR, Docking and Molecular Dynamics Simulation

Acetylcholinesterase is a promising therapeutic candidate for the treatment of neurodegenerative disorders, acetylcholine dysfunction and other cognitive problems. In the current study, a 3D-QSAR approach was applied to a series of benzimidazole derivatives to reveal the key influencing factors contributing to their acetylcholinesterase inhibition activity and selectivity. The developed two models, CoMFA and CoMSIA, were found to be internally validated using a training set of compounds, and both models demonstrated significant statistical reliability. Contour maps of developed models were employed to examine the main structural characteristics of inhibitors that affected their potency. It was found that electrostatic and hydrophobic interactions are significantly important for improving inhibitory activities, leading to the design of four novel acetylcholinesterase inhibitors. Among the newly designed compounds, compound A1 with the highest predicted activity was subjected to detailed molecular docking and compared to the most active compound. Further, 100 ns molecular dynamics (MD) simulation was conducted to explore the binding modes and conformational modifications throughout the interaction of compound A1 and acetylcholinesterase. The docking and MD simulation findings showed that the newly designed compound A1 remained stable within the active site of the identified acetylcholinesterase receptor, demonstrating its promise as a new potential acetylcholinesterase drug candidate.

Evaluation of storage quality of vacuum-packaged silver Pomfret (Pampus argenteus) treated with combined ultrasound and plasma functionalized liquids hurdle technology

The effects of the treatment (UPFL) combining ultrasound (US) with plasma functionalized liquids (PFL) were evaluated on the quality of vacuum-packaged silver Pomfret stored at 4 ℃ for 15 days. Conformational modifications in myofibrillar proteins, improvements in nutritional value and biomedical index of fatty acids and lipids, reduced pH of 5.70, increased K-value, TBARS, and TVB-N at values of 12.05%, 0.576 mg MDA/kg, and 9.15 mg N/100 g, respectively, and 1.99 log reductions in spoilage microorganisms were evident immediately after treatments. UPFL presented better quality preservative effects when compared with individual applications of US or PFL, and vacuum packaging ensured optimal quality enhancement effects such as stability of myofibril fragmentation, inhibition of physicochemical quality degradation, and microbial growth control. The results also revealed the predominant cultivable spoilage microbiota of vacuum-packaged silver Pomfret treated with UPFL, providing valuable information towards developing broad-spectrum sanitisers and hurdle technology for the seafood industry.

The Heisenberg-Virasoro Lie conformal superalgebra

In this paper, we introduce a finite Lie conformal superalgebra called the Heisenberg-Virasoro Lie conformal superalgebra s by using a class of Heisenberg-Virasoro Lie conformal modules. The super Heisenberg-Virasoro algebra of Ramond type S is defined by the formal distribution Lie superalgebra of s. Then we construct a class of simple S-modules, which are induced from simple modules of some finite dimensional solvable Lie superalgebras. These modules are isomorphic to simple restricted S-modules, and include the highest weight modules, Whittaker modules and high order Whittaker modules. As a byproduct, we present a subalgebra of S, which is isomorphic to the super Heisenberg-Virasoro algebra of Neveu-Schwarz type.

Photophysical and Computational Insights into Ag(I) Complexation of Porphyrinic Covalent Cages Equipped with Triazoles-Incorporating Linkers.

The photophysical characterization of four supramolecular complexes based on covalent cages 2H-S-2H, 2H-L-2H, Zn-S-2H, and Zn-L-2H, consisting in either two free-base porphyrins or one Zn(II) porphyrin and one free-base porphyrin connected by four flexible linkers of different lengths incorporating triazole binding sites, and their Ag(I) complexation are reported. The complexation processes have been followed by means of absorption and emission spectroscopies, and a comprehensive computational study explains the behavior of the free-base porphyrin-containing cages. Absorption and emission features have been interpreted on the bases of conformational changes, metalation processes, and modification of energy transfer efficiencies occurring in the different cases. In all cages, except 2H-L-2H, the coordination of four Ag(I) ions to the lateral triazole groups of the linkers leads to the enlargement of their cavity. Only for 2H-L-2H is a different behavior observed, where the process of silver metalation of the porphyrins’ core prevails.

Physicochemical Insights on Terahertz Wave Diminished Side Effects of Drugs from Slow Dissociation.

Dopamine D2 receptors (D2Rs) are one of the most intensely investigated and well-established drug targets for neuropsychiatric disorders. Selective D2R antagonists have been developed as efficacious antipsychotic drugs. Nevertheless, the potent drugs with necessarily high affinity are prone to slow dissociation, which invokes a plethora of severe side effects such as extrapyramidal symptoms, substantial weight gain, associated diabetes, etc. This has become a major barrier in treating psychiatric patients. In this work, we propose a physical method, terahertz wave modulation, to promote the dissociation of high-affinity antipsychotics and thus diminish the side effects. We have proven that a 4.0 THz wave could reduce the affinity by 71% between the D2R and a risperidone ligand and meanwhile expand the exit via conformation modulation, which promises an accelerated dissociation of risperidone. In addition, it is estimated that the enhancement of the dissociation rate due to lowered binding by terahertz irritation could constitute up to 8 orders of magnitude, which is fairly impressive and resembles the enzyme's catalysis. Also, acceleration of the dissociation rate could be adjusted by the irritation strength. This work elaborates the terahertz wave-modulated noncovalent interactions critical in cell signaling pathways. Most importantly, it demonstrates the feasibility of terahertz technologies intervening in receptor-ligand complex regulated diseases such as neurodegenerative disorders, metabolic diseases, etc.

Monoclonal Antibodies as Probes to Study Ligand-Induced Conformations of Troponin Subunits.

Striated muscle contraction and relaxation is regulated by Ca2+ at the myofilament level via conformational modulations of the troponin complex. To understand the structure–function relationship of troponin in normal muscle and in myopathies, it is necessary to study the functional effects of troponin isoforms and mutations at the level of allosteric conformations of troponin subunits. Traditional methodologies assessing such conformational studies are laborious and require significant amounts of purified protein, while many current methodologies require non-physiological conditions or labeling of the protein, which may affect their physiological conformation and function. To address these issues, we developed a novel approach using site-specific monoclonal antibodies (mAb) as molecular probes to detect and monitor conformational changes of proteins. Here, we present examples for its application in studies of two subunits of troponin: the Ca2+-binding subunit, TnC, and the tropomyosin-binding/thin filament-anchoring subunit, TnT. Studies using a high-throughput microplate assay are compared with that using localized surface plasmon resonance (LSPR) to demonstrate the effectiveness of using mAb probes to assess ligand-induced conformations of troponin subunits in physiological conditions. The assays utilize relatively small amounts of protein and are free of protein modification, which may bias results. Detailed methodologies using various monoclonal antibodies (mAbs) are discussed with considerations for the optimization of assay conditions and the broader application in studies of other proteins as well as in screening of therapeutic reagents that bind a specific target site with conformational and functional effects.

Molecular Insight into the Extracellular Chaperone Serum Albumin in Modifying the Folding Free Energy Landscape of Client Proteins.

Serum albumin (SA) is the most abundant extracellular chaperone protein presenting in various bodily fluids. Recently, several studies have revealed molecular mechanisms of SA in preventing the amyloid formation of amyloidogenic proteins. However, our insight into the mechanism SA employed to sense and regulate the folding states of full-length native proteins is still limited. Addressing this question is technically challenging due to the intrinsic dynamic nature of both chaperones and clients. Here using nuclear magnetic resonance spectroscopy, we show SA modifies the folding free energy landscape of clients and subsequently alters the equilibria between different compact conformations of its clients, resulting in the increased populations of excited states of client proteins. This modulation of client protein conformation by SA can change the client protein activity in a way that cannot be interpreted on the basis of its ground state structure; therefore, our work provides an alternative insight of SA in retaining a balanced functional proteome.