Conformational Studies Research Articles

Relevance of amphiphilicity and helicity on the antibacterial action of a histatin 5-derived peptide.

Peptide dhvar4, derived from the active domain of our salivary peptide histatin 5, bears a Phe residue in the middle of its hydrophilic face when folded into an α-helix. We then synthesized an analog with this Phe replaced by Lys and two analogs preserving Phe but bearing two and three α-aminoisobutyric acid (Aib) residues to stabilize the helical structure. The aim of this design was to verify which of the two features is more favorable to the biological activity. We performed a conformational study by means of circular dichroism and nuclear magnetic resonance, made antibacterial tests, and assessed the stability of the peptides in human serum. We observed that amphiphilicity is more important than helix stability, provided a peptide can adopt a helical conformation in a membrane-mimetic environment.

Milligram-scale assembly and NMR fingerprint of tau fibrils adopting the Alzheimer’s disease fold

In the Alzheimer’s disease (AD) brain, the microtubule-associated protein tau aggregates into paired helical filaments (PHFs) in which each protofilament has a C-shaped conformation. In vitro assembly of tau fibrils adopting this fold is highly valuable for both fundamental and applied studies of AD without requiring patient-brain extracted fibrils. To date, reported methods for forming AD-fold tau fibrils have been irreproducible and sensitive to subtle variations in fibrillization conditions. Here we describe a route to reproducibly assemble tau fibrils adopting the AD fold on the multi-milligram scale. We investigated the fibrilization conditions of two constructs, and found that a tau (297-407) construct that contains four AD phospho-mimetic glutamate mutations robustly formed the C-shaped conformation. Two- and three-dimensional correlation solid-state NMR spectra show a single predominant set of chemical shifts, indicating a single molecular conformation. Negative-stain electron microscopy and cryoelectron microscopy data confirm that the protofilament formed by 4E-tau (297-407) adopts the C-shaped conformation, which associates into paired, triple and quadruple helical filaments. In comparison, NMR spectra indicate that a previously reported construct, tau (297-391), forms a mixture of a four-layered dimer structure and the C-shaped structure, whose populations are highly sensitive to the environmental conditions. The determination of the NMR chemical shifts of the AD-fold tau opens the possibility for future studies of tau fibril conformations and ligand binding by NMR. The quantitative assembly of tau fibrils adopting the AD fold should facilitate the development of diagnostic and therapeutic compounds that target AD tau.

The forgotten adaptive social benefits of social learning in animals.

Theoretical and empirical scholars of cultural evolution have traditionally studied social learning strategies, such as conformity, as adaptive strategies to obtain accurate information about the environment, whereas within social psychology there has been a greater focus upon the social consequences of such strategies. Although these two approaches are often used in concert when studying human social learning, we believe the potential social benefits of conformity, and of social learning more broadly, have been overlooked in studies of non-humans. We review evidence from studies of homophily, imitation, and rapid facial mimicry that suggests that behaving like others affords social benefits to non-human animals and that behaviour matching may be deployed strategically to increase affiliation. Furthermore, we review studies of conformity in dispersers, and suggest that forgoing personal information or preferences in favour of those of the new group during immigration may be a strategy to facilitate social integration. We therefore propose that the informational and social functions of conformity apply to humans and animals alike. We use this perspective to generate several interesting research questions to inspire work in this field. For example, under what conditions do animals use informational or social conformity and what role does uncertainty play in social learning in immigrant individuals?

Design and support performance evaluation of medical multi-position auxiliary support exoskeleton mechanism

Aiming at the status of muscle and joint damage caused on surgeons keeping surgical posture for a long time, this paper designs a medical multi-position auxiliary support exoskeleton with multi-joint mechanism by analyzing the surgical postures and conducting conformational studies on different joints respectively. Then by establishing a human-machine static model, this study obtains the joint torque and joint force before and after the human body wears the exoskeleton, and calibrates the strength of the exoskeleton with finite element analysis software. The results show that the maximum stress of the exoskeleton is less than the material strength requirements, the overall deformation is small, and the structural strength of the exoskeleton meets the use requirements. Finally, in this study, subjects were selected to participate in the plantar pressure test and biomechanical simulation with the man-machine static model, and the results were analyzed in terms of plantar pressure, joint torque and joint force, muscle force and overall muscle metabolism to assess the exoskeleton support performance. The results show that the exoskeleton has better support for the whole body and can reduce the musculoskeletal burden. The exoskeleton mechanism in this study better matches the actual working needs of surgeons and provides a new paradigm for the design of medical support exoskeleton mechanism.

Conformational Stability of 3-aminopropionitrile: DFT and Ab initio Calculations.

Many conformers of 3-aminopropionitrile are known. Due to the biomedical importance of 3-aminopropionitrile a full investigation of structural, vibrational, and other associated properties of all possible conformers was performed. The geometrical structures, relative stability, and vibrational frequencies of the gauche and trans 3-aminopropionitrile conformers have been studied using ab initio (CCSD/6-311+G(d,p)) and DFT (B3LYP and M06 functionals at 6-311+G(d,p) and aug-cc-pVDZ basis set) calculations. The conformational and vibrational studies of 3-aminopropionitrile molecule were presented here are in very good interpretation of the calculated data compared with very poor interpretation in previous studies. The results showed that the gauche 2 conformer is more stable by 0.19 kcal/mol than gauche 1, outlined as enthalpy change ΔH between the conformers, at CCSD/6-311+G(d,p). Additionally, the population analysis shows that the gauche conformers are more prevalent than the trans conformers in the gas phase, present at 72.8%, with gauche 2 being the dominating gauche conformer at 40.1%. These results are in good agreement with earlier experimental and theoretical conclusions. All minima conformers' thermodynamic characteristics have also been studied. The relevant bond lengths, bond angles, and dihedral angles were calculated at a different level of theory for all possible conformers. The geometrical outcomes of the conformers agree very well with the previous experimental results. Electrostatic potential surface (ESP) has been used to interpret the structure-activity relationship. The atomic charges are examined, together with the energy difference between HOMO (Highest Occupied Molecular Orbital) and LUMO (Lowest Unoccupied Molecular Orbital). Additionally, the HOMO-LUMO energy gap and other relevant molecular properties are computed. The most stable conformers' stabilization energy has been determined by the Natural Bond Orbital (NBO) analysis.

Benzoylation of Iota Carrageenan: Development of a Stable, Conductive, and Hydrophobic Drug Carrier with Reduced Toxicity and Improved Gel‐Forming Ability

AbstractIota carrageenan is characterized as a hydrocolloid, with the limitations of hygroscopicity and hydrophilicity. Here, each of these factors is addressed to enhance the stability, and hydrophobicity through the protection of highly reactive primary alcohol and the formation of stable, improved hydrophobic, and conductive gel for the loading of lipophilic drugs. The functionalized polymer is evaluated through the microscopic and scanning electron microscopy (SEM) image of the compounds, which confirm the confined nature of the functionalized polymer. Moreover, the values changed from compound 1 (iota carrageenan) to compound 2 (benzoyl liked iota carrageenan) included Log P (partition coefficient) from −0.97 to 0.90, calculated partition coefficient (cLog P) from −2.50 to 0.12, and total polar surface area (TPSA) from 214.1 to 208.57, which strongly suggest the enhanced hydrophobic character of functionalized polymers. The enhancement is further concluded by the loading of the lipophilic drug inside the core of functionalized polymer‐based gel. The enhanced loading of the drug clearly shows the improved hydrophobicity (56–86%) of the gel core of the functionalized compounds. In summary, a polymer with enhanced stability, hydrophobicity, conductivity, and capacity to make a more stable gel, with enhanced drug‐loading capability of water‐insoluble drugs, will be the best way to resolve the low bioavailability issue of the water‐insoluble drug.

Ent-kaurane glycosides from Stevia rebaudiana and their α-glucosidase inhibition

Phytochemical investigation of the water soluble fraction of the plant Stevia rebaudiana led to isolation of 10 ent-kaurane glycosides, including two new derivatives namely stevibiosides A and B (1 and 2). Their structures were elucidated by extensive analysis of their 1D, 2D NMR, and HRQTOF mass spectra as well as quantum chemical calculations. Conformation studies and DFT-calculated chemical shifts combined with simple (R2, MAE) and DP4+ statistical analyses allow for the complete characterization of compounds 1 and 2. Among isolates, stevibioside A (1) exhibited potent α-glycosidase inhibitory effects with IC50 value of 8.9 ± 0.45 μM. Inhibitory kinetics analysis indicated that 1 had effect with an uncompetitive inhibition type and the Ki value of 2.18 ± 0.81 μM. In addition, docking studies were then used to analysis of the binding modes of the compounds 1 and 2 over the crystallographic structure of yeast α-glucosidase (pdb 3A4A) active site in comparison with acarbose as a standard inhibitor of this enzyme.

Evaluation of free radical‐induced structural changes and their effect on antioxidant and anti‐inflammatory activities of UV/H2O2‐degraded dextrans

AbstractAlthough ultraviolet (UV)/H2O2 treatment could effectively improve the bioactivities of polysaccharides, the relationship between free radical‐induced structural changes and the bioactivities of products remains unknown. Therefore, this work investigated the changes in the chemical characteristics and chain conformations of degraded dextrans by the UV/H2O2 system as well as their antioxidant and anti‐inflammatory activities. The apparent degradation efficiencies of dextrans under different UV/H2O2 parameters were first investigated. UV/H2O2 treatment effectively destroyed the pyranose rings and glycosidic bonds of dextrans and significantly improved their uronic acid and carboxy contents. Furthermore, conformational studies revealed that besides the rapid decrease in the molecular weight, the compact spherical conformation of dextrans was gradually depolymerized into the flexible random coil conformation. Moreover, the significant antioxidant and anti‐inflammatory activities of the degraded dextrans were mainly attributed to their more extended random coil chains, increased quantity of reducing groups, and lower molecular sizes. This study contributes to investigating the structure–activity relationship of polysaccharides prepared by free radicals‐mediated degradation.

Non-fluorescent transient states of tyrosine as a basis for label-free protein conformation and interaction studies

The amino acids tryptophan, tyrosine, and phenylalanine have been extensively used for different label-free protein studies, based on the intensity, lifetime, wavelength and/or polarization of their emitted fluorescence. Similar to most fluorescent organic molecules, these amino acids can undergo transitions into dark meta-stable states, such as triplet and photo-radical states. On the one hand, these transitions limit the fluorescence signal, but they are also highly environment-sensitive and can offer an additional set of parameters, reflecting interactions, folding states, and immediate environments around the proteins. In this work, by analyzing the average intensity of tyrosine emission under different excitation modulations with the transient state monitoring (TRAST) technique, we explored the photo physics of tyrosine as a basis for such environment-sensitive readouts. From how the dark state transitions of tyrosine varied with excitation intensity and solvent conditions we first established a photophysical model for tyrosine. Next, we studied Calmodulin (containing two tyrosines), and how its conformation is changed upon calcium binding. From these TRAST experiments, performed with 280 nm time-modulated excitation, we show that tyrosine dark state transitions clearly change with the calmodulin conformation, and may thus represent a useful source of information for (label-free) analyses of protein conformations and interactions.

Negatively Curved Octagon-Incorporated Aza-nanographene and its Assembly with Fullerenes.

A negatively curved aza-nanographene (NG) containing two octagons was synthesized by a regioselective and stepwise cyclodehydrogenation procedure, in which a double aza[7]helicene was simultaneously formed as an intermediate. Their saddle-shaped structures with negative curvature were unambiguously confirmed by X-ray crystallography, thereby enabling the exploration of the structure-property relationship by photophysical, electrochemical and conformational studies. Moreover, the assembly of the octagon-embedded aza-NG with fullerenes was probed by fluorescence spectral titration, with record-high binding constants (Ka=9.5×103 M-1 with C60, Ka=3.7×104 M-1 with C70) found among reported negatively curved polycyclic aromatic compounds. The tight association of aza-NG with C60 was further elucidated by X-ray diffraction analysis of their co-crystal, which showed the formation of a 1 : 1 complex with substantial concave-convex interactions.

Negatively Curved Octagon‐Incorporated Aza‐nanographene and its Assembly with Fullerenes

AbstractA negatively curved aza‐nanographene (NG) containing two octagons was synthesized by a regioselective and stepwise cyclodehydrogenation procedure, in which a double aza[7]helicene was simultaneously formed as an intermediate. Their saddle‐shaped structures with negative curvature were unambiguously confirmed by X‐ray crystallography, thereby enabling the exploration of the structure–property relationship by photophysical, electrochemical and conformational studies. Moreover, the assembly of the octagon‐embedded aza‐NG with fullerenes was probed by fluorescence spectral titration, with record‐high binding constants (Ka=9.5×103 M−1 with C60, Ka=3.7×104 M−1 with C70) found among reported negatively curved polycyclic aromatic compounds. The tight association of aza‐NG with C60 was further elucidated by X‐ray diffraction analysis of their co‐crystal, which showed the formation of a 1 : 1 complex with substantial concave‐convex interactions.

DFT modeling of new composite based on PANI/PVK functionalized With single-walled carbon nanotubes for optoelectronic applications

We present a comparative experimental and theoretical study of the vibrational, optical, and electronic properties of polyaniline at both emeraladine leuco-emeraldine forms and PVK. Our objective is first to select the appropriate form of PANI to be linked with PVK to form a hybrid polymer matrix. Then, on the basis of quantum chemical calculations, we present a theoretical study of a hybrid composite PANI/PVK functionalized with lower radius (5, 5) chiral single-walled carbon nanotubes (SWCNTs). The relationship structure-properties of the resulting nano-composite are proved based on the conformational and optical study made from Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) using B3LYP method with 6-31-G(d) basis set. First, it has been demonstrated that the resulting interaction between PANI and PVK leads to more advantageous properties, such as good optical absorption compatibility with the solar emission spectrum. It has also been found that after the incorporation of SWCNTs into the matrix of PANI/PVK hybrid polymer, a good organization of SWCNTs via π-staking interaction is imposed by polyaniline sequences. However, PVK moieties are grafted on the sidewalls of SWCNTs. Finally, the electronic structure of the resulting hybrid nano-composite PANI/PVK/SWCNTs was carried out with the use of different electrodes on both sides.

Uncertainty in Breast Cancer Risk Prediction: A Conformal Prediction Study of Race Stratification.

The use of Artificial Intelligence (AI) in medicine has attracted a great deal of attention in the medical literature, but less is known about how to assess the uncertainty of individual predictions in clinical applications. This paper demonstrates the use of Conformal Prediction (CP) to provide insight on racial stratification of uncertainty quantification for breast cancer risk prediction. The results presented here show that CP methods provide important information about the diminished quality of predictions for individuals of minority racial backgrounds.

Enhancement of Physicochemical and Pharmacokinetic Characteristics of Ranolazine drug substance using Cocrystalization Technique

Biopharmaceutical Classification System II drug, Ranolazine exhibits pH-dependent solubility and thus shows variable absorption along the gastrointestinal tract. Due to poor aqueous solubility particularly in basic pH, an attempt has been made to improve solubility through the cocrystallization technique. Cocrystals of Ranolazine with Nicotinamide have been synthesized at different molar ratios (1:1, 1:2, 1:3 2:1, and 3:1) through solvent-assisted grinding, slurry preparation, and solvent evaporation method and subsequently characterized by different analytical methodologies. Conformational characterization studies have been performed using techniques like melting point analysis, powder X-ray diffraction, and differential scanning calorimetry. Saturation solubility of Ranolazine alone along with cocrystals prepared in different molar ratios was conducted in water and buffers of different pH (1.2, 4.5, and 6.8) to establish enhancement in solubility. Ranolazine: Nicotinamide 1:2 cocrystals were found to be stable in accelerated and long-term stability conditions. In-vivo study performed in rats to demonstrate enhanced bioavailability. Ranolazine cocrystals with Nicotinamide were shown to have enhanced solubility in basic pH and improved peak plasma concentration, the area under the curve, and relative bioavailability by 2-folds.

Structural effects of inosine substitution in telomeric DNA quadruplex.

The telomeric DNA, a distal region of eukaryotic chromosome containing guanine-rich repetitive sequence of (TTAGGG)n, has been shown to adopt higher-order structures, specifically G-quadruplexes (G4s). Previous studies have demonstrated the implication of G4 in tumor inhibition through chromosome maintenance and manipulation of oncogene expression featuring their G-rich promoter regions. Besides higher order structures, several regulatory roles are attributed to DNA epigenetic markers. In this work, we investigated how the structural dynamics of a G-quadruplex, formed by the telomeric sequence, is affected by inosine, a prevalent modified nucleotide. We used the standard (TTAGGG)n telomere repeats with guanosine mutated to inosine at each G position. Sequences (GGG)4, (IGG)4, (GIG)4, (GGI)4, (IGI)4, (IIG)4, (GII)4, and (III)4, bridged by TTA linker, are studied using biophysical experiments and molecular modeling. The effects of metal cations in quadruplex folding were explored in both Na+ and K+ containing buffers using CD and UV-melting studies. Our results show that antiparallel quadruplex topology forms with the native sequence (GGG)4 and the terminal modified DNAs (IGG)4 and (GGI)4 in both Na+ and K+ containing buffers. Specifically, quadruplex hybrid was observed for (GGG)4 in K+ buffer. Among the other modified sequences, (GIG)4, (IGI)4 and (GII)4 show parallel features, while (IIG)4 and (III)4 show no detectable conformation in the presence of either Na+ or K+. Our studies indicate that terminal lesions (IGG)4 and (GGI)4 may induce certain unknown conformations. The folding dynamics become undetectable in the presence of more than one inosine substitution except (IGI)4 in both buffer ions. In addition, both UV melting and CD melting studies implied that in most cases the K+ cation confers more thermodynamic stability compared to Na+. Collectively, our conformational studies revealed the diverse structural polymorphisms of G4 with position dependent G-to-I mutations in different ion conditions.

Design, synthesis, and analysis of macrobicyclic peptides for targeting the Gαi protein.

Bicyclic peptides are important chemical tools that can function, for example, as bioactive ligands switching on/off signaling pathways mediated by guanine nucleotide-binding proteins as bicycles are more broadly applicable. Despite their relevance in medicinal chemistry, the synthesis of such peptides is challenging, and the final yield is highly dependent on the chemical composition and physicochemical properties of the scaffold. We recently discovered novel, state-specific peptide modulators targeting the Gαi protein, namely, GPM-2/GPM-3, by screening a one-bead-two-compound combinatorial library. A more detailed analysis, including sequence alignments and computer-assisted conformational studies based on the hit compounds, revealed the new peptide 10 as a potential macrobicyclic Gαi ligand sharing high sequence similarity to the known Gαi modulators. The Gαs protein was included in this study for comparison and to unravel the criteria for the specificity of modulator binding to Gαi versus Gαs. This work provides in-depth computer-assisted experimental studies for the analysis of novel macrobicyclic, library-derived Gαi protein ligands. The sequence and structural comparison of 10 with the lead compounds GPM-2 and GPM-3 reveals the importance of the size and amino acid composition of one ring of the bicyclic system and suggests features enhancing the binding affinity of the peptides to the Gαi protein.

Conformational Distribution of a Multidomain Protein Measured by Single-Pair Small-Angle X-ray Scattering.

The difficulty in evaluating the conformational distribution of proteins in solution often hinders mechanistic insights. One possible strategy for visualizing conformational distribution is distance distribution measurement by single-pair small-angle X-ray scattering (SAXS), in which the scattering interference from only a specific pair of atoms in the target molecule is extracted. Despite this promising concept, with few applications in synthetic small molecules and DNA, technical difficulties have prevented its application in protein conformational studies. This study used a synthetic tag to fix the lanthanide ion at desired sites on the protein and used single-pair SAXS with contrast matching to evaluate the conformational distribution of the multidomain protein enzyme MurD. These data highlighted the broad conformational and ligand-driven distribution shifts of MurD in solution. This study proposes an important strategy in solution structural biology that targets dynamic proteins, including multidomain and intrinsically disordered proteins.

Cytogenetics in the management of hematological malignancies: An overview of alternative technologies for cytogenetic characterization

Genomic characterization is an essential part of the clinical management of hematological malignancies for diagnostic, prognostic and therapeutic purposes. Although CBA and FISH are still the gold standard in hematology for the detection of CNA and SV, some alternative technologies are intended to complement their deficiencies or even replace them in the more or less near future. In this article, we provide a technological overview of these alternatives. CMA is the historical and well established technique for the high-resolution detection of CNA. For SV detection, there are emerging techniques based on the study of chromatin conformation and more established ones such as RTMLPA for the detection of fusion transcripts and RNA-seq to reveal the molecular consequences of SV. Comprehensive techniques that detect both CNA and SV are the most interesting because they provide all the information in a single examination. Among these, OGM is a promising emerging higher-solution technique that offers a complete solution at a contained cost, at the expense of a relatively low throughput per machine. WGS remains the most adaptable solution, with long-read approaches enabling very high-resolution detection of CAs, but requiring a heavy bioinformatics installation and at a still high cost. However, the development of high-resolution genome-wide detection techniques for CAs allows for a much better description of chromoanagenesis. Therefore, we have included in this review an update on the various existing mechanisms and their consequences and implications, especially prognostic, in hematological malignancies.

Analytical Study of Structural Conformation and Prestressing State of Drum-Shaped Honeycomb Quad-Strut Cable Dome Structure with Different Calculation Methods

Building upon the analytical study of the structural configuration and prestress state of the drum-shaped quad-strut cable dome, we conducted further investigation into its structural configuration. By employing the nodal equilibrium equations to solve the prestress state analysis of the cable dome, we compared the effects of two different cable laying methods on the prestress state of the cable dome structure. These methods include equal length of the radial horizontal projection of the upper chord ridge cables and equal radial chord length of the upper chord ridge cables. The analysis results show that the radial length of the top chord and its corresponding radial horizontal projection length of the cable dome structure can effectively reflect the trend of the prestress state of the structural configuration. Furthermore, by using a rise-to-span ratio of 0.11 as a threshold, the cable dome configuration is categorized into the flat spheroidal structural configuration and the small hemispheroidal structural configuration. When the structure is analyzed using a small rise-to-span ratio, the difference in prestress calculations between the two structural configurations is found to be less than 10%. Additionally, the structure exhibits a more uniform distribution of prestress, with the prestress gradually increasing from the inner circle to the outer circle. However, when the rise-to-span ratio increases, the difference between the prestress calculation results of the two configurations also increases, emphasizing the need to deploy upper chord ridge cables based on equal radial chord lengths (arc lengths). The research presented in this paper provides a novel insight into the structural topological form and prestress state calculation of cable domes with this configuration.

Beyond slow two-state protein conformational exchange using CEST: applications to three-state protein interconversion on the millisecond timescale.

Although NMR spectroscopy is routinely used to study the conformational dynamics of biomolecules, robust analyses of the data are challenged in cases where exchange is more complex than two-state, such as when a 'visible' major conformer exchanges with two 'invisible' minor states on the millisecond timescale. It is becoming increasingly clear that chemical exchange saturation transfer (CEST) NMR experiments that were initially developed to study systems undergoing slow interconversion are also sensitive to intermediate-fast timescale biomolecular conformational exchange. Here we investigate the utility of the amide 15N CEST experiment to characterise protein three-state exchange occurring on the millisecond timescale by studying the interconversion between the folded (F) state of the FF domain from human HYPA/FBP11 (WT FF) and two of its folding intermediates I1 and I2. Although 15N CPMG experiments are consistent with the F state interconverting with a single minor state on the millisecond timescale, 15N CEST data clearly establish an exchange process between F and a pair of minor states. A unique three-state exchange model cannot be obtained by analysis of 15N CEST data recorded at a single temperature. However, including the relative sign of the difference in the chemical shifts of the two minor states based on a simple two-state analysis of CEST data recorded at multiple temperatures, results in a robust three-state model in which the F, I1 and I2 states interconvert with each other on the millisecond timescale ( ~ 550s-1, ~ 1200s-1, ~ 5000s-1), with I1 and I2 sparsely populated at ~ 0.15% and ~ 0.35%, respectively, at 15°C. A computationally demanding grid-search of exchange parameter space is not required to extract the best-fit exchange parameters from the CEST data. The utility of the CEST experiment, thus, extends well beyond studies of conformers in slow exchange on the NMR chemical shift timescale, to include systems with interconversion rates on the order of thousands/second.