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 w...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.展开更多
Dynamic adaptability is a key feature in biological macromolecules,enabling selective binding and catalysis[1].From DNA supercoiling to enzyme conformational changes,biological systems have evolved intricate ways to d...Dynamic adaptability is a key feature in biological macromolecules,enabling selective binding and catalysis[1].From DNA supercoiling to enzyme conformational changes,biological systems have evolved intricate ways to dynamically adjust their structures to accommodate functional needs.Mimicking this adaptability in synthetic systems is an ongoing challenge in supramolecular chemistry.展开更多
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]metacy...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.展开更多
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 s...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.展开更多
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 c...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.展开更多
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 an...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.展开更多
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 me...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.展开更多
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 su...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.展开更多
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 d...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.展开更多
Using molecular dynamics modeling,the change in the shape and density of the macromolecular corona consisting of two oppositely charged polyelectrolytes,including those combined into one block copolymer,on the surface...Using molecular dynamics modeling,the change in the shape and density of the macromolecular corona consisting of two oppositely charged polyelectrolytes,including those combined into one block copolymer,on the surface of a polarized spherical metal nanoparticle was studied.A mathematical model of the structure of the block copolymer chain adsorbed on a polarized spherical nanoparticle is presented for the cases of polyelectrolyte blocks of large and small length.Based on the modeling results,radial and angular distributions of the density of atoms of polyelectrolyte polypeptides adsorbed on the surface of a spherical nanoparticle were calculated depending on its dipole moment.As the dipole moment of the nanoparticle increased,the dense macromolecular shell was destroyed,forming caps of polyelectrolyte macro molecules or fragments of block copolymer of different types on the poles of the polarized nanoparticle.In this case,the macromolecular corona in the region of the poles of the polarized nanoparticle swelled the more strongly,the greater the distance between the charged links in the polymer.展开更多
The assembly behaviors of two low-symmetric carboxylic acid molecules(50-(6-carboxynaphthalen-2-yl)-[1,10:30,100-triphenyl]-3,400,5-tricarboxylic acid(CTTA)and 30,50-bis(6-carboxynaphthalen-2-yl)-[1,10-biphenyl]-3,5-d...The assembly behaviors of two low-symmetric carboxylic acid molecules(50-(6-carboxynaphthalen-2-yl)-[1,10:30,100-triphenyl]-3,400,5-tricarboxylic acid(CTTA)and 30,50-bis(6-carboxynaphthalen-2-yl)-[1,10-biphenyl]-3,5-dicarboxylic acid(BCBDA))containing naphthalene rings on graphite surfaces have been investigated using scanning tunneling microscopy(STM).The transformation of nanostructures induced by the second components(EDA and PEBP-C4)have been also examined.Both CTTA and BCBDA molecules self-assemble at the 1-heptanoic acid(HA)/HOPG interface,forming porous network structures.The dimer represents the most elementary building unit due to the formation of double hydrogen bonds.Moreover,the flipping of naphthalene ring results in the isomerization of BCBDA molecule.The introduction of carboxylic acid derivative EDA disrupts the dimer,which subsequently undergoes a structural conformation to form a novel porous structure.Furthermore,upon the addition of pyridine derivative PEBP-C4,N–H⋯O hydrogen bonds are the dominant forces driving the three coassembled structures.We have also conducted density functional theory(DFT)calculations to determine the molecular conformation and analyze the mechanisms underlying the formation of nanostructures.展开更多
To regulate the sodium chloride content in Jinhua ham,the impact of NaCl on the activity and conformation of cathepsin B was investigated using spectroscopy and computational methods.The results showed that the activi...To regulate the sodium chloride content in Jinhua ham,the impact of NaCl on the activity and conformation of cathepsin B was investigated using spectroscopy and computational methods.The results showed that the activity of cathepsin B decreased with an increase in Na^(+)cation content and temperature.Additionally,decreasedα-helix content and increasedβ-sheet content were observed.The increase in sulfhydryl group content was attributed to the breaking of original disulfide bonds in the molecular structure or the release of embedded groups.Furthermore,the surface hydrophobicity gradually declined,which was consistent with the analysis of endogenous fluorescence spectroscopy.At the molecular level,the number of hydrogen bonds formed in NaCl-treated samples decreased,and the interactions between the hydrogen bonding were less powerful,which caused instability in the binding of the protein and substrate.The conformation of cathepsin B accurately characterized its activity,and the structural changes had a macroscopic effect on the decrease in protease activity.展开更多
The chain conformation of polymers in binary solvent mixtures is a key issue in the study of functional soft matter and lies at the heart of various applications such as smart soft materials.Based on a minimal lattice...The chain conformation of polymers in binary solvent mixtures is a key issue in the study of functional soft matter and lies at the heart of various applications such as smart soft materials.Based on a minimal lattice model,we employ Monte Carlo(MC)simulation to systematically investigate the effects of solvent qualities on the conformation of a single homopolymer chain in binary mixed solvents.We also perform calculations using a Flory-type mean-field theory.We focus on how the introduction of a second solvent B affects the dependence of chain conformation on the quality of solvent A.We mainly examine the effects of the composition of solvent B,denoted by x,and the interactions between the two solvents.First,when x is low,the mean-square chain radius of gyration exhibits qualitatively similar behaviors to those in an individual solvent A,with a slight chain contraction when solvent A is very good.Second,in equal-molar mixtures with x=0.5,a homopolymer chain collapses when solvent A is either poor or very good,while expands at intermediate qualities.Lastly,at large x,a chain undergoes a coil-to-globule transition with the increasing quality of solvent A when solvent B is good,but mainly adopts the collapsed conformation when solvent B is poor.Our findings not only improve our understanding on the chain conformation in binary solvent mixtures,but also provide valuable guidance on the rational design of stimuli-responsive polymeric materials.展开更多
Gaining insights into charge transport related to conformational changes and ion transport in valinomycin(VM)is crucial for understanding the underlying physiological processes and advancing ion carrier applications.O...Gaining insights into charge transport related to conformational changes and ion transport in valinomycin(VM)is crucial for understanding the underlying physiological processes and advancing ion carrier applications.Observing these processes in single molecules provides deeper insights and precision than those obtained through conventional ensemble measurements.Herein,we employed a single-molecule conductance measurement method based on the scanning tunneling microscopy break-junction(STM-BJ)to measure the charge transport of individual VM molecules in both non-polar and polar solvents,as well as when mediated by K^(+)ions.Single-molecule conductance measurements revealed that the bracelet and propeller-type conformations of VM in both non-polar and polar solvents significantly affect its conductance.In polar solvents,the propeller-type conformation of VM demonstrated a well-defined conductance signature,single-molecule rectification feature,and through-space transmission mechanism.Specifically,the introduction of K^(+)ions in polar solvents induced a conformational transition from the propeller-type to the bracelet-type form,facilitating K^(+)binding recognition.These observations were further supported by density functional theory combined with non-equilibrium Green’s function calculations.This study enhanced the fundamental understanding of the electronic transport mechanisms in VM and valinomycin-K^(+)molecular junctions,offering insights into VM ionophores and promoting supramolecular sensing applications.展开更多
Mechanically interlocked molecules (MIMs) have unique properties with broad applications, yet constructing both knotted and linked topologies from the same ligand remains challenging due to their distinct geometric de...Mechanically interlocked molecules (MIMs) have unique properties with broad applications, yet constructing both knotted and linked topologies from the same ligand remains challenging due to their distinct geometric demands. To address this, we design and synthesize a conformationally adaptive ligand 4,7-bis(3-(pyridin-4-yl) phenyl) benzo[c][1,2,5]thiadiazole (L1) with a tunable torsional angle θ of N1C1C2N2 ranging from 7.5° to 108.9°. Utilizing coordination-driven self-assembly at ambient temperature, L1 selectively assembles with binuclear half-sandwich units RhB1, RhB2, RhB3, and RhB4 featuring Cp*^(Rh^(Ⅲ)) (Cp* = η^(5)-pentam-ethylcyclopentadienyl) into distinct topologies: Solomon links Rh-1, trefoil knots Rh-2, molecular tweezers Rh 3, and Rh-4, respectively. Crucially, the self-adaptability of ligand L1 directs topology formation through pro-gramming different combination of noncovalent interactions (π-x stacking, CH..π interaction, and lone pair-π interaction), thus navigating divergent assembly pathways by conformational switching, as evidenced by X-ray crystallography analysis, independent gradient model (IGM) analysis, detailed nuclear magnetic resonance (NMR) spectroscopy and electrospray ionization time-of-flight/mass spectrometry (ESI-TOF/MS). This strategy can also be extended to construct Cp*^(Irl^(Ⅲ)) analogs (Solomon links Ir-1, trefoil knots Ir-2, molecular tweezers Ir-3 and Ir-4), demonstrating metal-independent control and achieving intricate topologies in a high yield.展开更多
Polymers often exhibit multi-state conformational transitions with multiple pathways as temperature varies.However,characterizing the inherent features of these pathways is hindered by the lack of physical characteriz...Polymers often exhibit multi-state conformational transitions with multiple pathways as temperature varies.However,characterizing the inherent features of these pathways is hindered by the lack of physical characterizations that can distinguish various transition pathways between complex and disordered states.In this work,we introduced a machine-learning framework based on spatiotemporal point-cloud neural networks to identify and analyze conformational transition pathways in polymer chains.As a case study,we applied this framework to the temperature-induced unfolding of a single semi-flexible polymer chain,simulated via coarse-grained molecular dynamics.We first combined spatiotemporal point cloud neural networks and contrastive learning to extract features of conformational evolution,and then we employed unsupervised learning methods to cluster distinct transition pathways and unfolding trajectories.Our results reveal that,with increasing temperature,semi-flexible polymer chains exhibit five distinct unfolding pathways:rigid rod→random coil;small toroid→large toroid→hairpin→random coil;rod bundle→hairpin→random coil;hairpin→random coil;and tailed structure→random coil.We further calculated the structural order parameters of those typical conformations with distinct transition pathways,we distincted five transition mechanisms,including the straightening of rigid rods,tightening of small rings,expansion of hairpin ends,symmetrization of rod bundles,and retraction of tailed structures.These findings demonstrate that our framework presents a promising data-driven approach for analyzing complex conformational transitions in disordered polymers,which might be potentially extendable to other heterogeneous systems like intrinsically disordered proteins.展开更多
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 mo...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展开更多
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 ...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.展开更多
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 agonist...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.展开更多
基金Supported by the the natural sciences plan projects of educationdepartment of Henan province(No:2010A310018)
文摘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.
基金the Natural Science Foundation of China(No.22301131)the Natural Science Foundation of Jiangsu Province(Nos.BK20220781,BK20240679)the National Key Research and Development Program of China(No.2024YFB3815700)are greatly acknowledged.
文摘Dynamic adaptability is a key feature in biological macromolecules,enabling selective binding and catalysis[1].From DNA supercoiling to enzyme conformational changes,biological systems have evolved intricate ways to dynamically adjust their structures to accommodate functional needs.Mimicking this adaptability in synthetic systems is an ongoing challenge in supramolecular chemistry.
文摘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.
文摘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.
文摘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.
文摘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.
文摘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.
文摘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.
文摘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.
基金the financial support of the Ministry of Science and Higher Education of the Russian Federation within the framework of a grant for conducting large scientific projects in priority areas of scientific and technological development 075-15-2024-550。
文摘Using molecular dynamics modeling,the change in the shape and density of the macromolecular corona consisting of two oppositely charged polyelectrolytes,including those combined into one block copolymer,on the surface of a polarized spherical metal nanoparticle was studied.A mathematical model of the structure of the block copolymer chain adsorbed on a polarized spherical nanoparticle is presented for the cases of polyelectrolyte blocks of large and small length.Based on the modeling results,radial and angular distributions of the density of atoms of polyelectrolyte polypeptides adsorbed on the surface of a spherical nanoparticle were calculated depending on its dipole moment.As the dipole moment of the nanoparticle increased,the dense macromolecular shell was destroyed,forming caps of polyelectrolyte macro molecules or fragments of block copolymer of different types on the poles of the polarized nanoparticle.In this case,the macromolecular corona in the region of the poles of the polarized nanoparticle swelled the more strongly,the greater the distance between the charged links in the polymer.
基金financially supported by the National Natural Science Foundation of China(No.22272039)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDB36000000)+1 种基金the Youth Program of the Liaoning Education Department(No.LJKQZ20222280)the Jilin Chinese Academy of Sciences-Yanshen Technology Co.,Ltd.
文摘The assembly behaviors of two low-symmetric carboxylic acid molecules(50-(6-carboxynaphthalen-2-yl)-[1,10:30,100-triphenyl]-3,400,5-tricarboxylic acid(CTTA)and 30,50-bis(6-carboxynaphthalen-2-yl)-[1,10-biphenyl]-3,5-dicarboxylic acid(BCBDA))containing naphthalene rings on graphite surfaces have been investigated using scanning tunneling microscopy(STM).The transformation of nanostructures induced by the second components(EDA and PEBP-C4)have been also examined.Both CTTA and BCBDA molecules self-assemble at the 1-heptanoic acid(HA)/HOPG interface,forming porous network structures.The dimer represents the most elementary building unit due to the formation of double hydrogen bonds.Moreover,the flipping of naphthalene ring results in the isomerization of BCBDA molecule.The introduction of carboxylic acid derivative EDA disrupts the dimer,which subsequently undergoes a structural conformation to form a novel porous structure.Furthermore,upon the addition of pyridine derivative PEBP-C4,N–H⋯O hydrogen bonds are the dominant forces driving the three coassembled structures.We have also conducted density functional theory(DFT)calculations to determine the molecular conformation and analyze the mechanisms underlying the formation of nanostructures.
基金supported by the National Natural Science Foundation of China(31972097)Jiangsu Key Research and Development Plan(Modern Agriculture)(BE2020302)+1 种基金the Natural Science Foundation of the Jiangsu Higher Education Institutions of China(24KJB550003)2024 Huaiyin Institute of Technology Talent Recruitment Research Startup Fund Project(Z301B24521)。
文摘To regulate the sodium chloride content in Jinhua ham,the impact of NaCl on the activity and conformation of cathepsin B was investigated using spectroscopy and computational methods.The results showed that the activity of cathepsin B decreased with an increase in Na^(+)cation content and temperature.Additionally,decreasedα-helix content and increasedβ-sheet content were observed.The increase in sulfhydryl group content was attributed to the breaking of original disulfide bonds in the molecular structure or the release of embedded groups.Furthermore,the surface hydrophobicity gradually declined,which was consistent with the analysis of endogenous fluorescence spectroscopy.At the molecular level,the number of hydrogen bonds formed in NaCl-treated samples decreased,and the interactions between the hydrogen bonding were less powerful,which caused instability in the binding of the protein and substrate.The conformation of cathepsin B accurately characterized its activity,and the structural changes had a macroscopic effect on the decrease in protease activity.
基金financially supported by the National Natural Science Foundation of China(Nos.22473024,22073016 and 21803011)the award of Shanghai Dongfang Scholar。
文摘The chain conformation of polymers in binary solvent mixtures is a key issue in the study of functional soft matter and lies at the heart of various applications such as smart soft materials.Based on a minimal lattice model,we employ Monte Carlo(MC)simulation to systematically investigate the effects of solvent qualities on the conformation of a single homopolymer chain in binary mixed solvents.We also perform calculations using a Flory-type mean-field theory.We focus on how the introduction of a second solvent B affects the dependence of chain conformation on the quality of solvent A.We mainly examine the effects of the composition of solvent B,denoted by x,and the interactions between the two solvents.First,when x is low,the mean-square chain radius of gyration exhibits qualitatively similar behaviors to those in an individual solvent A,with a slight chain contraction when solvent A is very good.Second,in equal-molar mixtures with x=0.5,a homopolymer chain collapses when solvent A is either poor or very good,while expands at intermediate qualities.Lastly,at large x,a chain undergoes a coil-to-globule transition with the increasing quality of solvent A when solvent B is good,but mainly adopts the collapsed conformation when solvent B is poor.Our findings not only improve our understanding on the chain conformation in binary solvent mixtures,but also provide valuable guidance on the rational design of stimuli-responsive polymeric materials.
基金supported by the National Key R&D Program of China(Nos.2022YFB3204402,2020YFA0714703 and 2022YFC2205003)the National Natural Science Foundation of China(No.22204135)+2 种基金Hunan Provincial Natural Science Foundation of China(No.2023JJ40619)the Education Department of Hunan Province(No.23A0114)the Science and Technology Innovation Program of Hunan Province(No.2022RC3027)。
文摘Gaining insights into charge transport related to conformational changes and ion transport in valinomycin(VM)is crucial for understanding the underlying physiological processes and advancing ion carrier applications.Observing these processes in single molecules provides deeper insights and precision than those obtained through conventional ensemble measurements.Herein,we employed a single-molecule conductance measurement method based on the scanning tunneling microscopy break-junction(STM-BJ)to measure the charge transport of individual VM molecules in both non-polar and polar solvents,as well as when mediated by K^(+)ions.Single-molecule conductance measurements revealed that the bracelet and propeller-type conformations of VM in both non-polar and polar solvents significantly affect its conductance.In polar solvents,the propeller-type conformation of VM demonstrated a well-defined conductance signature,single-molecule rectification feature,and through-space transmission mechanism.Specifically,the introduction of K^(+)ions in polar solvents induced a conformational transition from the propeller-type to the bracelet-type form,facilitating K^(+)binding recognition.These observations were further supported by density functional theory combined with non-equilibrium Green’s function calculations.This study enhanced the fundamental understanding of the electronic transport mechanisms in VM and valinomycin-K^(+)molecular junctions,offering insights into VM ionophores and promoting supramolecular sensing applications.
基金Department of Chemistry,Fudan Uni-versity,the National Natural Science Foundation of China(22031003,21720102004)the Shanghai Science Technology Committee(19DZ227010O)the Alexander von Humboldt Foundation for a Humboldt Research Award.
文摘Mechanically interlocked molecules (MIMs) have unique properties with broad applications, yet constructing both knotted and linked topologies from the same ligand remains challenging due to their distinct geometric demands. To address this, we design and synthesize a conformationally adaptive ligand 4,7-bis(3-(pyridin-4-yl) phenyl) benzo[c][1,2,5]thiadiazole (L1) with a tunable torsional angle θ of N1C1C2N2 ranging from 7.5° to 108.9°. Utilizing coordination-driven self-assembly at ambient temperature, L1 selectively assembles with binuclear half-sandwich units RhB1, RhB2, RhB3, and RhB4 featuring Cp*^(Rh^(Ⅲ)) (Cp* = η^(5)-pentam-ethylcyclopentadienyl) into distinct topologies: Solomon links Rh-1, trefoil knots Rh-2, molecular tweezers Rh 3, and Rh-4, respectively. Crucially, the self-adaptability of ligand L1 directs topology formation through pro-gramming different combination of noncovalent interactions (π-x stacking, CH..π interaction, and lone pair-π interaction), thus navigating divergent assembly pathways by conformational switching, as evidenced by X-ray crystallography analysis, independent gradient model (IGM) analysis, detailed nuclear magnetic resonance (NMR) spectroscopy and electrospray ionization time-of-flight/mass spectrometry (ESI-TOF/MS). This strategy can also be extended to construct Cp*^(Irl^(Ⅲ)) analogs (Solomon links Ir-1, trefoil knots Ir-2, molecular tweezers Ir-3 and Ir-4), demonstrating metal-independent control and achieving intricate topologies in a high yield.
基金financially supported by the National Key R&D Program of China(No.2022YFB3707303)the National Natural Science Foundation of China(No.52293471)。
文摘Polymers often exhibit multi-state conformational transitions with multiple pathways as temperature varies.However,characterizing the inherent features of these pathways is hindered by the lack of physical characterizations that can distinguish various transition pathways between complex and disordered states.In this work,we introduced a machine-learning framework based on spatiotemporal point-cloud neural networks to identify and analyze conformational transition pathways in polymer chains.As a case study,we applied this framework to the temperature-induced unfolding of a single semi-flexible polymer chain,simulated via coarse-grained molecular dynamics.We first combined spatiotemporal point cloud neural networks and contrastive learning to extract features of conformational evolution,and then we employed unsupervised learning methods to cluster distinct transition pathways and unfolding trajectories.Our results reveal that,with increasing temperature,semi-flexible polymer chains exhibit five distinct unfolding pathways:rigid rod→random coil;small toroid→large toroid→hairpin→random coil;rod bundle→hairpin→random coil;hairpin→random coil;and tailed structure→random coil.We further calculated the structural order parameters of those typical conformations with distinct transition pathways,we distincted five transition mechanisms,including the straightening of rigid rods,tightening of small rings,expansion of hairpin ends,symmetrization of rod bundles,and retraction of tailed structures.These findings demonstrate that our framework presents a promising data-driven approach for analyzing complex conformational transitions in disordered polymers,which might be potentially extendable to other heterogeneous systems like intrinsically disordered proteins.
基金the Foundation of Hao Yingdong Youth Teacher and Shanghai Youth Scientific
文摘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
文摘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.
文摘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.
