Laccase/caffeic acid-catalyzed crosslinking coupled with galactomannan alters the conformational structure of ovalbumin and alleviates Th2-mediated allergic asthma

Ovalbumin(OVA)is the major allergenic protein that can induce T helper 2(Th2)-allergic reactions,for which current treatment options are inadequate.In this study,we developed a polymerized hypoallergenic OVA product via laccase/caffeic acid(Lac/CA)-catalyzed crosslinking in conjunction with galactomannan(Man).The formation of high molecular weight crosslinked polymers and the Ig G-binding were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis(SDS-PAGE)and Western blotting.The study indicated that Lac/CA-catalyzed crosslinking plus Man conjugation substantially altered secondary and tertiary structures of OVA along with the variation in surface hydrophobicity.Gastrointestinal digestion stability assay indicated that crosslinked OVA exhibited less resistance in simulated gastric fluid(SGF)and simulated intestinal fluid(SIF).Mouse model study indicated that Lac-Man/OVA ameliorated eosinophilic airway inflammatory response and efficiently downregulated the expression of Th2-related cytokines(interleukin(IL)-4,IL-5,and IL-13),and upregulated IFN-γand IL-10 expression.Stimulation of bone marrow-derived dendritic cells with Lac-Man/OVA suppressed the expression of phenotypic maturation markers(CD80 and CD86)and MHC class II molecules,and suppressed the expression levels of proinflammatory cytokines.The knowledge obtained in the present study offers an effective way to acquire a hypoallergenic OVA product that can have a therapeutic effect in alleviating OVA-induced allergic asthma.

Modeling and analysis of Schistosoma Argonaute protein molecular spatial conformation

Objective:To analyze the amino acid sequence composition,secondary structure,the spatial conformation of its domain and other characteristics of Argonaute protein.Methods:Bioinformatics tools and the internet server were used.Firstly,the amino acid sequence composition features of the Argonaute protein were analyzed,and the phylogenetic tree was constructed.Secondly,Argonaute protein's distribution of secondary structure and its physicochemical properties were predicted.Lastly,the protein functional expression form of the domain group was established through the Phyre-based analysis on the spatial conformation of Argonaute protein domains.Results:593 amino acids were encoded by Argonaute protein,the phylogenetic tree was constructed,and Argonaute protein's distribution of secondary structure and its physicochemical properties were obtained through analysis.In addition,the functional expression form which comprised the N-terminal PAZ domain and C-terminal Piwi domain for the Argonaute protein was obtained with Phyre.Conclusions:The information relationship between the structure and function of the Argonaute protein can be initially established with bioinformatics tools and the internet server,and this provides the theoretical basis for further clarifying the function of Schistosoma Argonaute protein.

Recent advances in protein conformation sampling by combining machine learning with molecular simulation

The rapid advancement and broad application of machine learning(ML)have driven a groundbreaking revolution in computational biology.One of the most cutting-edge and important applications of ML is its integration with molecular simulations to improve the sampling efficiency of the vast conformational space of large biomolecules.This review focuses on recent studies that utilize ML-based techniques in the exploration of protein conformational landscape.We first highlight the recent development of ML-aided enhanced sampling methods,including heuristic algorithms and neural networks that are designed to refine the selection of reaction coordinates for the construction of bias potential,or facilitate the exploration of the unsampled region of the energy landscape.Further,we review the development of autoencoder based methods that combine molecular simulations and deep learning to expand the search for protein conformations.Lastly,we discuss the cutting-edge methodologies for the one-shot generation of protein conformations with precise Boltzmann weights.Collectively,this review demonstrates the promising potential of machine learning in revolutionizing our insight into the complex conformational ensembles of proteins.

Synthesis and Conformational Studies on [3.3.3]Metacyclophane Oligoketone Derivatives, and Their Metal Ion Recognition

Chemical reactions were used to synthesize 2,11,20-tris(ethanedithia)-9,18,27-trimethoxy-6,15, 24-tri-tert-butyl[3.3.3]metacyclophane 2 and 2,11-bis(ethanedithia)-9,18,27-trimethoxy-6,15,24-tri-tert-butyl[3.3.3]metacyclophane 4 from 6,15,24-tri-tert-butyl-9,18,27-trimethoxy[3.3.3]meta-cyclophane-2,11,20-trione 1 and -2,11-dione 3. The yields of 2 and 4 were 70% and 81% respectively. The conformations of the synthesized compounds 2 and 4 were studied using mainly solution Proton Nuclear Magnetic Resonance (1H NMR) spectroscopic methods. Compounds 2 and 4 were found to have a partial-cone conformation. Detailed variable temperature Proton Nuclear Magnetic Resonance studies further confirmed the partial-cone conformation for the two products, 2, 4. During the variable temperature nuclear magnetic resonance spectroscopic studies, compound 2 was found to have a coalescence temperature of about 0?C. Extraction of silver ions with compound 2 gave an extractability of 82% while the parent compound 1 showed zero (0) silver affinity. A 1:1 mol/mol mixture of compound 2 and silver ions studied by solution 1H NMR revealed a novel “Molecular Roulette” type of motion.

Conformational behavior of stereo regular substituted polyglycolides is side chain dependent

Substituted polyglycolides having two asymmetric centers are attractive alternatives to materials derived from petroleum because of their biocompatibility and biodegradability. The conformational behavior of various substituted polyglycolides has been investigated by both quantum mechanical and molecular dynamics approaches. Polymethylglycolide (polylactide) and polyphenylmethylglycolide in RS or SR forms are predicted to adopt 27 ribbon type structures with φ, ψ values of ±30, ±50 or +30 or +50 respectively stabilised by carbonyl-carbonyl interactions. Isopropylglycolide and isobutyl-glycolide having branching at β & γ positions respectively in their side chains can be realized in all SS form with φ, ψ values lying in right handed helical region. In addition to carbonyl-carbonyl interactions, the hydrophobic interactions between the side chains in isopropylgly-colide the C-H-O interactions also contributes to the stability. With cyclic side chains directly attached to Cα of backbone, polyphenylglycolide (polymandelide) and polycyclohexylglycolide are found to adopt left handed helical structure without hydrogen bonds in RR form, stabilised by stacking interactions and hydrophobic interactions respectively. In all the forms of polyphenylglycolide & polycyclohexylglycolide, the cyclic side chains are found to be locked into unfavourable gauche plus conformation. The stability of substituted polyglycolides has been analyzed in terms of various interactions. The carbonyl-carbonyl interactions in all the conformations of all forms of substituted polyglycolides are found to be of highly shielded parallel motif with only one short carbon-oxygen interaction. Simulation studies of substituted polyglycolides in water give a good insight of the approach of water molecules to the backbone.

Illuminating β-arrestin conformational dynamics by fluorine NMR

In a recent paper, solution-state ^(19)F NMR spectroscopy was used to probe the conformational dynamics of β-arrestin-1, an essential adaptor and signaling component of the G-protein couple receptor (GPCR) signaling pathway. This work reveals a highly complex conformational energy landscape of β-arrestin-1, and illuminates the molecular mechanism of the membrane phosphoinositide PIP2-induced β-arrestin-1 activation at residue level.(https://doi.org/10.1038/s41467-023-43694-1).

Synthesis and Conformational Studies of Some Metacyclophane Compounds

Various [3.3.3]metacyclophane derivatives were synthesized from 6,15,24-tri-tert-butyl-9,18,27-trimethoxy [3.3.3] metacyclophane-2,11,20-trione 1 using simple chemical reactions. The conformations of the synthesized compounds were studied using mainly solution Proton Nuclear Magnetic Resonance (1H NMR) spectroscopic methods. Two of the synthesized compounds 5, 6, were found to have a partial cone conformation with the third, 4, having the cone conformation. Detailed variable temperature Proton Nuclear Magnetic Resonance studies further confirmed the partialcone conformation for the two products, 5, 6. During the variable temperature nuclear magnetic resonance spectroscopic studies, 6,15,24-tri-tert-butyl-9,18,27-trimethoxy[3.3.3]metacyclophane-2,11,20-triol was found to have a coalescence temperature of about 0?C.

Spectroscopic studies reveal conformational flexibility of intrinsically unstructured protein HYPK

The chaperone-like huntingtin-interacting protein, HYPK, has unusual biophysical behavior like an intrinsically unstructured protein (IUP). The protein exists as a (pre-) molten globule with ~37% residual structure and shows com- paction in presence of Ca++. HYPK contains no intrinsic fluorophore other than a single tyrosine and displays an anomalous fluorescence peak at around 340 nm. The anomalous peak is re- duced to 303 nm by the addition of guanidine hydrochloride and at low pH, concomitant with the emission spectrum of L-tyrosine. At high pH the peak is shifted to ~350 nm with a reduction in intensity. In presence of sodium perchlorate there is no shift in HYPK fluorescence emission peak from ~340 nm suggesting localization of the lone tyrosine residue in helical regions. In CD experiments, however, a shift in local secondary structure is noticed upon perchlorate treatment. Acrylamide quenching experiments at different Ca++ concentrations demonstrate that Ca++ does not alter the accessibility of the tyro- sine to acrylamide. In the absence of any tryp- tophan contamination, these observations vali- date that, in vitro, HYPK possesses a loosely associated (pre-) molten globule like conforma- tion with the lone tyrosine being situated within an α-helix.

Effects of Side-Chain on Conformational Characteristics of Poly(3,5-Dimethyl-Phenyl Acrylate) in Toluene at 40℃

The intrinsic viscosity [η] of poly(3,5-dimethylphenylacrylate) (35PDMPA)solutions were evaluated throughout the measurements of the flow times of toluene and polymer solutions by classical Huggins, and Kraemer’s methods using a Cannon-Ubbelohde semi-micro-dilution capillary viscometer in a Cannon thermostated water bath at 40℃ ± 0.02℃. The values of Huggins’ constant estimated ranged from 0.2 to 0.4 which were within expectations. The intrinsic viscosities and molecular weight relationship was established with the two-parameter classical models of Staudinger-Mark-Houwink-Sakurada and Stockmayer-Fixman. Conformational parameter C∞ and σ indicated 35PDMPA be semi flexible. Also, the rigidity of 35PDMPA was confirmed by Yamakawa-Fuji wormlike theory modified by Bohdanecky. The molecular parameters were estimated and compared. The results showed that 35PDMPA behaves like a semi-rigid polymer in toluene at 40℃ rather than a random coil flexible macromolecule.

Small Molecule-Assisted PET: Approaches to Imaging of Conformational Diseases of the Brain

PET (positron emission tomography) in vivo imaging of cerebral conformational diseases is essentially based on non-peptide small molecule ligands used to detect early alterations in peptide secondary structures and subsequent accumulation of aberrant oligomers and protein deposits involved in progressive neurodegeneration, cognitive and movement disorders. In this article, an overview is given about tracers currently available and lead structures of potential PET probes for detection of?β-amyloid (Aβ), tau protein, α-synuclein, constitutive (PrPc) and infectious isoforms (PrPsc) of prions (proteinaceous infectious particles) as imaging targets. Whereas the styrylpyridine derivative florbetapir, approved for clinical applications, the stilbene derivative florbetaben and the benzoxazole derivative BF227 show high affinity binding to Aβ, preclinical investigations promise improved pharmacokinetics for benzoimidazothiazoles, aryloxazoles and benzofuran derivatives. Tau protein imaging based clinically, presently, on the pyridine-pyridoindole T807 has got new incentives following identification of a series of pyrrolopyridine quinolines and pharmacokinetic improvements of fluoropropoxy quinolines including for instance THK-5351. The pyridine isoquinoline MK6240 is involved now in clinical trials. Most forward-looking efforts apply to small molecule ligands of α-synuclein, which are expected to permit a breakthrough in differential diagnostics of Parkinson-related dementia and Lewy body diseases. However, at the moment the proposed lead structures are in affinity and blood brain barrier delivery properties below the possibilities of Aβ?and tau protein ligands. This is the case also for potential tracers of prion proteins.

Volume Change of the Random Coil to Folded Conformational Transition of <i>Thermomyces</i><i>lanuginosus</i>Xylanase at 24&#176C and pH = 7.0 via Application of the Clausius-Clapeyron Equation

A partial phase diagram characterizing the conformational change that occurs in Thermomyces lanuginosus xylanase as it is slowly heated in 150 mM sodium phosphate (pH = 7.0) has been con-structed from slow-scan-rate differential scanning calorimetry measurements. The Clausius-Clapeyron equation was applied to determine an associated volume change of -205 L·mol-1 at 24°C, the equilibrium transition temperature at 1.0 atm pressure. This value is in excellent agreement with that predicted using a previously published [1] empirical equation for calculating the hydro-dynamic radius if the transition is regarded as from a random coil to a functional, folded state and with the assumption that the hydrodynamic radius is a good approximation of the true random coil radius. The existence of a low-temperature random coil is confirmed by circular dichroism and dynamic light scattering measurements. Thus, at 24°C and 1.0 atm pressure the enzyme appears to fold from a random coil to a functional, folded form as it is slowly heated.

NMR STUDY ON THE CONFORMATION CHANGE IN THE AGGREGATION PROCESSES OF 1，3－DI（α－NAPHTHYL）PROPANE AND DI（α－NAPHTHYLMETHYL）ETHER

NMR study on the conformation change in the aggregation process of the titled compounds is reported in this letter.

In situ kinetics and flocs conformation studies of kaolinite flocculated by Chi-g-CPAM

This study presents a comparative study of the flocculation behavior of kaolinite induced by chitosan-graft-poly(acrylamide-dimethyl diallyl ammonium chloride)(Chi-g-CPAM) and a commercial cationic polyacrylamide(CPAM).The flocculation behaviour was characterised in terms of both flocculation kinetics and the corresponding morphology changes during flocculation.Both Chi-g-CPAM and CPAM were grafted from silica wafers by means of atom transfer radical polymerization(ATRP).The quartz crystal microbalance with dissipation(QCM-D) tests were conducted.The equilibrium time flocculated by Chi-g-CPAM was found to be 0.46 times as that of CPAM,together with a larger total mass of kaolinite layer.The flocculation behaviour by Chi-g-CPAM can be well captured by a pseudo-first-order model.In contrast,the presence of CPAM leads to a more complex kinetics.A relatively larger fitting slope(0.4663) was obtained at the initial stage but the fitting slope droped to 0.2026 after 800 min,indicating a densification process caused by CPAM.The flocculation kinetics of CPAM can be captured by the Elovich model for the inital stage but the combination of pseudo-first-order and pseudo-second-order models for the latter stages,which can be attributed to the long chain of CPAM.With a dosage of 75 g/t,the settling test with Chi-g-CPAM exhibits the same turbidity in the supernatant but a smaller layer thickness of the settlement compared to CPAM.The study enables a better understanding of the flocculation behavior and contributes to the development of efficient flocculants in mineral processing and tailings treatment.

Molecular dynamics simulations of a DNA photolyase protein: High-mobility and conformational changes of the FAD molecule at low temperatures

A molecular dynamics (MD) simulation is performed on a DNA photolyase to study the conformational behavior of the photoactive cofactor flavin adenine dinucleotide (FAD) inside the enzyme pocket. A DNA photolyase is a highly efficient light-driven enzyme that repairs the UV-induced cyclobutane pyrimidine dimer in damaged DNA. In this work, the FAD conformational and dynamic changes were studied within the total complex structure of a DNA photolyase protein (containing FADH–, MTHF, and DNA molecules) embedded in a water solvent. We aimed to compare the conformational changes of the FAD cofactor and other constituent fragments of the molecular system under consideration. The obtained results were discussed to gain insight into the light-driven mechanism of DNA repair by a DNA photolyase enzyme—based on the enzyme structure, the FAD mobility, and conformation shape.

GPCR A2AAR Agonist Binding and Induced Conformation Changes of Functional Switches

Agonist binding of A2A adenosine receptor （A2AAR） shows protective effects against inflammatory and immune. Efforts are exerted in understanding the general mechanism and developing A2AAR selectively binding agonists. Using molecular dynamics （MD） simula- tions, we have studied the interactions between A2AAR and its agonist （adenosine）, and analyzed the induced dynamic behaviors of the receptor. Key residues interacting with adenosine are identified： A63^2.61,I66^2.64,V84^3.32,L85^3.33,T88^3.36,F168^5.29,M177^5.38,L249^6.51,H250^6.52 and N253^6.55 interacting with adenosine with affinities larger than 0.5 kcal/mol. Moreover, no interaction between adenosine and L167^5.28 is observed, which supports our previous findings that L1675^5.28 is an antagonist specific binding reside. The dynamic be- haviors of agonist bound A2AAR are found to be different from apo-A2AAR in three typical functional switches： （i） tight ＂ionic lock＂ forms in adenosine-A2AAR, but it is in equilibrium between formation and breakage in apo-A2AAR; （ii） the ＂rotamer toggle switch＂, T88^3.36/F242^6.44/W246^6.48, adopted different rotameric conformations in adenosin-A2AAR and apo-A2AAR; （iii） adenosine-A2AAR has a flexible intracellular loop 2 （IC2） and s-helical IC3, while apo-A2AAR preferred s-helical IC2 and flexible IC3. Our results indicate that agonist binding induced different conformational rearrangements of these characteristic functional switches in adenosine-A2AAR and apo-A2AAR.

Spatial Conformation Analysis of Characteristic Urban Pedestrian Streets:A Case Study of Ancient Jinli Street (Phase-Ⅰ Project) in Chengdu City,Sichuan Province

By studying project background of Ancient Jinli Street (Phase-I Project) in Chengdu City, location environment and design concepts of the project were introduced. Spatial conformation of Ancient Jinli Street was analyzed from the perspectives of street type, spatial sequence, ratio scale and landscape node. Moreover, architectural image and spatial hierarchy of the street were interpreted through analyzing architectural characteristics and combination patterns of building and street. Finally, spatial conformation features of the Ancient Jinli Street were summarized to provide references for the protection and development of characteristic urban pedestrian streets.

Ca²⁺-Induced Conformational Change of Troponin C from the Japanese Pearl Oyster, <i>Pinctada fucata</i>

Troponin is a thin filament-associated regulator of vertebrate striated muscle contraction. Troponin changes its structure upon Ca2+ binding to troponin C, one of the subunits of troponin, allowing myosin to interact with actin. We recently elucidated the molecular characteristics of the Japanese pearl oyster Pinctada fucata troponin C (Pifuc-TnC), revealing the possibilities that Pifuc-TnC and vertebrate muscle TnC play dissimilar roles in muscle contraction. Pifuc-TnC has four EF-hand motifs, but, unlike vertebrate TnC, only one (site IV) was predicted to bind Ca2+. To confirm the number of Ca2+-binding sites in Pifuc-TnC and whether Ca2+ binding induces a conformational change, we purified the full-length protein and a variant, Pifuc-TnC-E142Q (that has a mutation in the predicted Ca2+-binding site of site IV), following their expression in laboratory E. coli. Isothermal titration calorimetry demonstrated Ca2+ binding to Pifuc-TnC, whereas Pifuc-TnC-E142Q was unable to bind Ca2+, confirming that site IV is the only Ca2+-binding site in Pifuc-TnC. Pifuc-TnC eluted in a later fraction from a gel filtration column in the presence of Ca2+ compared with the condition when Ca2+ was absent. In contrast, the elution profiles of Pifuc-TnC-E142Q were equivalent in both the presence and absence of Ca2+, suggesting that Ca2+ binding to Pifuc-TnC induces a conformational change that delays its elution from the column. UV-absorption spectral analysis revealed that binding of Ca2+ to Pifuc-TnC caused an increase in absorption at a wavelength of approximately 250 nm, possibly because phenylalanine residues had been exposed on the surface of the molecule as a result of a conformational change. Differential scanning calorimetric analyses of Pifuc-TnC showed aggregation in the presence of Ca2+ in accordance with an increase of temperature, but no aggregation was seen in the absence of Ca2+. In combination, these findings suggest that Ca2+ binding to site IV induces a conformational change in Pifuc-TnC.

Subunit Structure and Conformation of Bombyx Mori Silk Proteins

Molecular weights of the silk fibroin were determined by polyacrylamide gel electrophoresis in the presence of so-didium dodecyl sulfate (SDS - PAGE): The silk fibroin molecule consisted of subunits a, b and c with molecular weights of 280 kD, 230 kD and 25 kD respectively, of which the b subunit was composed of two subunits e and f with molecular weights of 130 kD and 125 kD, respec-tively, connected by disulfide bonds. The conformation of silk fibroin and subunits was determinated by Raman spectroscopy and Large angle X - ray diffraction) LAXS. The native silk fibroin only contained a - helix and random coil, but there were three conformation such as random - coil.a - helix and β - sheet in the silk fibroin dissolved in KSCN solution and frozen at - 20 °C. This suggested that KSCN solution and - 20°C freezing action could lead to the conformational transi-tion from random - coil and a - helix to P - sheet. The a subunit mainly existed in β - sheet conformation, in con-trast, the c subunit was

Conformational flexibility of the pharmacologically important insulin analogues

Understanding the conformational flexibility of the insulin drugs is of great importance for the treatment of diabetes mellitus. Once in the body, the drug must have a certain degree of mobility within a specified period of time for the manifestation of its pharmacological properties. This mobility ensures conformational states necessary for binding with the insulin receptor and activating specific biological processes. In this work we investigated conformational flexibility of the pharmacologically important insulin analogues—insulin lispro, insulin aspart, insulin glulisine, and insulin glargine, using the molecular dynamics simulation method. This study provides new insight into the nature of behaviour of A-and B-chains. It has been found out that B-chain substitutions result in rapid acting, while long-lasting action can be achieved by substitutions in both chains. The results of this study can be used for development of new insulin-based antidiabetic drugs.

Cyberspace Security Using Adversarial Learning and Conformal Prediction

This paper advances new directions for cyber security using adversarial learning and conformal prediction in order to enhance network and computing services defenses against adaptive, malicious, persistent, and tactical offensive threats. Conformal prediction is the principled and unified adaptive and learning framework used to design, develop, and deploy a multi-faceted?self-managing defensive shield to detect, disrupt, and deny intrusive attacks, hostile and malicious behavior, and subterfuge. Conformal prediction leverages apparent relationships between immunity and intrusion detection using non-conformity measures characteristic of affinity, a typicality, and surprise, to recognize patterns and messages as friend or foe and to respond to them accordingly. The solutions proffered throughout are built around active learning, meta-reasoning, randomness, distributed semantics and stratification, and most important and above all around adaptive Oracles. The motivation for using conformal prediction and its immediate off-spring, those of semi-supervised learning and transduction, comes from them first and foremost supporting discriminative and non-parametric methods characteristic of principled demarcation using cohorts and sensitivity analysis to hedge on the prediction outcomes including negative selection, on one side, and providing credibility and confidence indices that assist meta-reasoning and information fusion.