Conformational Studies Research Articles

Solubility and emulsifying properties of phosphorylated walnut protein isolate extracted by sodium trimetaphosphate

Low solubility and poor emulsifying properties of walnut protein isolate (WPI) greatly influences its applications in the food industry. In the current work, WPI was extracted and phosphorylated from defatted walnut flour by sodium trimetaphosphate (STMP) at various pH values (7.0, 9.0, and 11.0). The measured phosphorus content of STMP-extracted WPI was approximately 7-10-fold higher than that of the alkaline-extracted WPI (A-WPI). The results of X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR) further confirmed the successful phosphorylation of extracted WPI. Conformational studies using FTIR and circular dichroism (CD) indicated that phosphorylated WPI (P-WPI) contained higher α-helical and lower β-sheet contents than the A-WPI. Phosphorylation of WPIs altered the surface hydrophobicity and surface charges of the proteins, resulting in a significant improvement in the solubility of P-WPI. In addition, the emulsifying properties of P-WPI were significantly enhanced, which was exhibited by a 2.5-4-fold increase in the emulsifying activity index (EAI) and a maximum 6-fold increase in the emulsifying stability index (ESI). The emulsions stabilized by P-WPI manifested relatively smaller sizes and larger surface charges. This study demonstrated that phosphorylation modification can effectively modulate the surface hydrophobicity and charges of WPI to greatly improve its solubility and emulsifying ability.

Folding and Unfolding of Acetoxy Group-Terminated Alkyl Chains Inside a Size-Regulable Hemicarcerand.

A resorcinarene-based hemicarcerand, which consists of two cavitands covalently linked to each other by four alkyl chains, allows structural expansion and contraction by demetalation and metalation of Cu(I) cations with a size change of approximately 12 Å. This metal-mediated switching of the two states regulates the conformations of acetoxy group-terminated alkyl chains. A guest binding study reveals the encapsulation of heptyl to undecyl chains in metal-free and Cu(I)-coordinated capsules. The chemical shifts of the acetoxy groups of the bound guests are the same in the metal-free capsule, while those in the Cu(I)-coordinated one differ from each other. This indicates that the metal-free capsule regulates its size to the bound guests, while the bound guests adopt their conformations to the cavity of the Cu(I)-coordinated capsules. 1H NMR measurements and molecular mechanics calculations suggest that the bound guests have extended conformations in the metal-free capsule, while the Cu(I)-coordinated capsule forces the bound guests to adopt folded conformations. The presence of folded conformations is supported by the conformational study with structurally similar capsules and a nonsymmetric guest, allowing us to observe nuclear Overhauser effects stemming from the folded conformations of the guest in the cavity.

Synthesis and conformational studies on 1-aryl-cis-2,6-diphenylpiperidines

A facile and convenient synthesis of N-aryl-cis-2,6-diphenylpiperidines was achieved via reductive amination of 1,5-diphenyl-1,5-pentanedione with aryl ammonium formate under metal-free and microwave mediated Leuckrdt Wallach reaction conditions. The gas-phase (by Density Functional Theory studies), Liquid phase (by Nuclear Magnetic Resonance spectral analysis) and solid-phase (by X-ray crystallography along with Hirshfeld and Fingerprint plot analysis) structural studies on the title compound showed that the N-aryl, C(2) and C(6) phenyl rings were preferentially oriented equatorially and piperidine ring flattened-chair conformation. Besides, the DFT calculation showed a face-to-face arrangement of N-aryl ring with adjacent phenyl rings, and they were orthogonal to mean plane of the piperidine ring. The single-crystal structure (CCDC 1415313) analysis showed that the title compound crystallized in the monoclinic crystal system with P2(1)/C space group. The crystal packing was stabilized by intermolecular C-H…π interactions. Overall, the orientation of aryl rings looks like that of elephant ears flanking the snout.

Structural, conformational and therapeutic studies on new thiazole complexes: drug-likeness and MOE-simulation assessments

A series of new complexes derived from Pd(II), Cu(II) and Fe(III) ions reacted with thiazole derivative (HL, CPTP) was prepared. Structures of all new compounds were characterized and confirmed using analytical and spectroscopic (IR, UV–Vis and 13C&1H NMR) techniques. All complexes have non-electrolytic nature based on molar conductance measurements. TGA was executed to confirm the presence of water molecules inside or outside the coordination sphere as well as the mono-nuclear feature of isolated complexes. Accordingly, thermo kinetic parameters were calculated for all decomposition steps. The obtained analytical data regarding complexation in solution, molar ratio and continuous variation methods suggest 1 M:1 L molar ratio. The oriented structures using advanced program assert on best distribution for coordinating sites (NH& NH2). Moreover, electrostatic potential map as well as iso-surface with array plot of ligand reflects high nucleophilic feature with reduced outer contour on two coordinating sites. In vitro antimicrobial, anticancer and antioxidant activities of ligand and its complexes were checked. All complexes exhibited superiority on free ligand in successful treatment, specifically CPTPPd complex. Drug-likeness as well as MOE-docking simulation outcomes indicates promising inhibitory feature of CPTPPd and CPTPCu complexes, in agreement with in vitro results.

Enhanced capacitive behaviour of graphene nanoplatelets embedded epoxy nanocomposite

For the development of advanced polymer nanocomposite processability, high-quality and cost-efficiency plays a crucial role which combines mechanical robustness with functional electrochemical properties. In this study, we fabricated the epoxy/graphene nanocomposite (EGNC) with different wt% ratio of graphene nanoplatelets (GNPs). The EGNCs were fabricated through a solution mixing process and used it as an electrode to enhance electrochemical properties. The GNPs and EGNCs characterized using XRD, Raman spectroscopy, ATR FT-IR, and FE-SEM for the structural conformation and surface morphological study. The electrochemical analysis results show significant improvement in the specific capacitance in the EGNC samples as compared to the blank epoxy film. Specific capacitance 17.74 Fg−1 was recorded at 10 mVs−1 scan rate in 1.0 M KOH electrolyte solution for the 1.0 wt% EGNC film by cyclic voltammetry analysis. The Galvanostatic charge–discharge and Ragone plots also show mended results by the addition of GNPs.

Molecular dynamics study of structural properties of γ-aminobutyric acid (GABA)

The study of structural conformation of Gamma-aminobutyric acid (GABA) exhibits its biological and chemical activities. The GABA molecule is responsible in neurotransmission from one neuron to another neuron and activates the ion channels to pass the chlorine and sodium ions in nerve cells. Its conformation in solid state and gas state are extremely different and it also shows five different conformations in aqueous solution. The study of its structure in such environment can reveal its activity in cellular environment. We have performed the classical molecular dynamics study of this system of GABA in aqueous medium to deal its structure. Radial distribution function (RDF) has been used to study the structural properties of the system.
 BIBECHANA 18 (2021) 67-74

Biometric measurements of body and internal organ traits of indigenous chickens on free range in South-Eastern Nigeria

A biometric study of the body conformation and internal organs of the indigenous chickens on free range in rural areas of Imo State in South-Eastern Nigeria was conducted using 5 Local Government Areas. It was observed that the predominant plumage colours were black (51.25%) and brown (36.25%) for the hens while the cocks were predominantly black (30.36%) and red (25.01%). The dressed colour of the birds was majorly yellow and white comprising of (70.68%) and (29.32%) for the hens and (77.75%) and (22.25%) for the cocks, respectively. Shank colour was black (95.4%) and white (4.65%) for the hens, while the cocks were (54.24%) black and (46.76%) white respectively. The mean shank length, neck length and back length of 6.725±0.09 cm, 11.11±0.20 cm and 17.77±0.29 cm were estimated for the hens, while the cocks had mean shank length, neck length and back length of 7.79±0.13 cm, 11.35±0.30 cm and 18.29±0.44 cm, respectively. The mean body weights of the hens and cocks were 868.48±21.18 g, and 1032±57.84 g, respectively with cocks being significantly (P<0.05) higher in body weight and back length than hens. The mean biometric and internal organ measures of chickens per Local Government Area (LGA) were also investigated with no significant (P>0.05) differences among chickens in the five LGAs except for weight of proventriculus and full intestine. Regression equations for the prediction of body weight using the biometric and internal organ measurements were obtained under two functional forms (linear and semi-log) which showed a weak coefficient of determination (R2) ranging between 7.5 to 24.3% for biometric measurements, and a strong coefficient of determination (R2) ranging between 21.4 to 98.89% for internal organs. There was no significant correlation coefficient (r) between the biometric measurements taken, but strong and significant correlation (r) was shown between internal organs and body weight. Therefore, indigenous chickens of South-Eastern Nigeria exhibit wide variability among phenotypes in terms of physical appearance, biometric measurement and internal organ characteristics. More so, the internal organs can be predicted more effectively than biometric measurements by the body weight, using regression models of the two functional forms; and significant indirect selection can be made to improve internal organs like gizzard weight using the bodyweight, due to significant correlation coefficient established.

Characteristics of Gd(III) spin labels for the study of protein conformations.

Gd(III) complexes are currently established as spin labels for structural studies of biomolecules using pulse dipolar electron paramagnetic resonance (PD-EPR) techniques. This has been achieved by the availability of medium- and high-field spectrometers, understanding the spin physics underlying the spectroscopic properties of high spin Gd(III) (S=7/2) pairs and their dipolar interaction, the design of well-defined model compounds and optimization of measurement techniques. In addition, a variety of Gd(III) chelates and labeling schemes have allowed a broad scope of applications. In this review, we provide a brief background of the spectroscopic properties of Gd(III) pertinent for effective PD-EPR measurements and focus on the various labels available to date. We report on their use in PD-EPR applications and highlight their pros and cons for particular applications. We also devote a section to recent in-cell structural studies of proteins using Gd(III), which is an exciting new direction for Gd(III) spin labeling.

Geometric characteristics of a manifold with a symmetric-type quarter-symmetric projective conformal non-metric connection

We introduce a quarter-symmetric projective conformal non-metric connection family and study its geometrical properties. Further we investigate the geometries of a symmetric-type quarter-symmetric projective conformal non-metric connection satisfying the Schur?s theorem.

Development and in vivo evaluation of intranasal formulations of parathyroid hormone (1-34)

For efficient intranasal transport of parathyroid hormone (1-34) [PTH(1-34)], there is a great medical need to investigate permeation enhancers for intranasal formulations. In this study, the development of PTH(1-34) intranasal formulations was conducted. Based on conformation and chemical stability studies, the most preferable aqueous environment was determined to be 0.008 M acetate buffer solution (ABS). Subsequently, citric acid and Kolliphor® HS·15 were compared as permeation enhancers. The mechanisms of action of citric acid and Kolliphor® HS·15 were investigated using an in vitro model of nasal mucosa, and Kolliphor® HS·15 led to higher permeability of fluorescein isothiocyanate-labeled PTH(1-34) (FITC-PTH) by enhancing both the transcellular and paracellular routes. Moreover, citric acid showed severe mucosal toxicity resulting in cilia shedding, while Kolliphor® HS·15 did not cause obvious mucosa damage. Finally, Kolliphor® HS·15 was studied as a permeation enhancer using a liquid chromatography tandem mass spectrometry (LC-MS/MS) method. The results showed that 5% and 10% Kolliphor® HS·15 increased the bioavailability of PTH(1-34) to 14.76% and 30.87%, respectively. In conclusion, an effective and biosafe PTH(1-34) intranasal formulation was developed by using 10% Kolliphor® HS·15 as a permeation enhancer. Intranasal formulations with higher concentrations of Kolliphor® HS·15 for higher bioavailability of PTH(1-34) could be further researched.

Expression and Purification of Yeast-derived GPCR, Gα and Gβγ Subunits for Structural and Dynamic Studies.

In the last several years, as evidence of a surged number of GPCR-G complex structures, the expressions of GPCRs and G proteins for structural biology have achieved tremendous successes, mostly in insect and mammalian cell systems, resulting in more than 370 structures of over 70 GPCRs have been resolved. However, the challenge remains, particularly in the conformational transition and dynamics study area where a much higher quantity of the receptors and G proteins is required even in comparison to X-ray and cryo-EM (5 mg/ml, 3 μl/sample) when NMR spectroscopy (5 mg/ml, 250 μl /sample) is applied. As a result, the expression levels of the insect and mammalian systems are also difficult to meet this demand, not to mention the prohibitive cost of producing GPCRs and G proteins using these systems for a vast majority of laboratories. Therefore, exploration of an effective, affordable, and practical approach with broad applicability is demanded. Pichia pastoris expression system has shown its promise in the GPCR preparation with many merits that other eukaryotic expression systems can't compete with. GPCRs expressed in this system are inexpensive, easy-to-manipulate, and capable of isotopically labeling. Herein, we present related protocols recently developed and upgraded in our lab, including expressions and purifications of P. pastoris derived GPCR along with Gα and Gβγ proteins. We anticipate that these protocols will advance the conformational transition and dynamics studies of the GPCR and its complexes.

Conformational study of a strained DNA/RNA by dynamic 1H NMR biospectroscopy and computational methods for molecular modelling, simulation and biopectroscopic studies of DNA/RNA of gum cancer cells

Conformational study of a strained DNA/RNA by dynamic 1H NMR biospectroscopy and computational methods for molecular modelling, simulation and biopectroscopic studies of DNA/RNA of gum cancer cells

A comprehensive analysis in one run - in-depth conformation studies of protein-polymer chimeras by asymmetrical flow field-flow fractionation.

Polymer-based protein engineering has enabled the synthesis of a variety of protein–polymer conjugates that are widely applicable in therapeutic, diagnostic and biotechnological industries. Accurate characterizations of physical–chemical properties, in particular, molar masses, sizes, composition and their dispersities are critical parameters that determine the functionality and conformation of protein–polymer conjugates and are important for creating reproducible manufacturing processes. Most of the current characterization techniques suffer from fundamental limitations and do not provide an accurate understanding of a sample's true nature. In this paper, we demonstrate the advantage of asymmetrical flow field-flow fractionation (AF4) coupled with multiple detectors for the characterization of a library of complex, zwitterionic and neutral protein–polymer conjugates. This method allows for determination of intrinsic physical properties of protein–polymer chimeras from a single, rapid measurement.

Collective structural properties of embedded molecular motors in functionalized metal-organic frameworks.

Photo-responsive molecular motors incorporated in soft porous materials enable the amplification of the motion of individual motor units by employing their collective and cooperative behavior. Metal-organic frameworks (MOFs) provide in this regard, due to their structural diversity and modular assembly, a unique matrix to construct well-defined and systematically tunable molecular environments for the embedding of molecular motors. However, despite advances in the development of such photo-responsive functional materials, a thorough understanding of the governing interactions at the atomic scale has been missing so far, limiting the possibility of predicting and fully exploring the potential of these assembled machineries. Here, we present a conformational study to unravel the collective structural behavior and elucidate the impact of motor-motor interactions on the local and global properties of the scaffold. In particular, our work highlights the impact of full conversion of the embedded molecular motors on the overall network topology of the MotorMOF and thus acts as a benchmark for future studies to further explore the correlation of responsive building units with the resulting functionality of these hierarchical systems.

Water binding stabilizes stacked conformations of ferrocene containing sheet-like aromatic oligoamides.

While water clusters play an essential role in the stability of biological structures, their ability to stabilize synthetic oligomers is less understood. We have synthesized a heptameric sheet-like aromatic oligoamide foldamer with ferrocene as turn unit. It shows strong interactions with water in the solid state and in solution. The water binding limits the fluxional processes resulting from the flexible ferrocene unit, highlighting the importance of such interactions for conformational studies on this class of molecule.

Multidimensional Structure Conformation of Persulfurated Benzene for Highly Efficient Phosphorescence.

It is a challenge to acquire, realize, and comprehend highly emissive phosphorescent molecules. Herein, we report that, using persulfurated benzene compounds as models, phosphorescence can be strongly enhanced through the modification of molecular conformation and crystal growth conditions. By varying the peripheral groups in these compounds, we were able to control their molecular conformation and crystal growth mode, leading to one- (1D), two- (2D), and three-dimensional (3D) crystal morphologies. Two kinds of typical molecular conformations were separately obtained in these crystals through substituent group control or the solvent effect. Importantly, a symmetrical 3,3-conformer exhibits that a planar central benzene ring prefers a 3D-type crystal growth mode, demonstrating high phosphorescence efficiency. Such outcome is attributed to the strong crystal protection effect of the 3D crystal and the bright global minimum (GM) boat-like T1 state of the symmetrical 3,3-conformer. The conformation studies further reveal small deformation of the inner benzene ring in both singlet and triplet states. The GM boat-like T1 state is indicated by theoretical calculations, which is far away from the conical intersection (CI) point between the S0 and T1 potential energy surfaces. Meanwhile, the small energy gap between S1 and T1 states and the considerable spin-orbit coupling matrix elements allow an efficient population of the T1 state. Combined with the crystal protection and conformation effect, the 3,3-conformer crystal shows high phosphorescence efficiency. The unsymmetrical 2,4-conformer conformation with the twisted central benzene ring leads to 1D or 2D crystal growth mode, which has a weak crystal protection effect. In addition, the unsymmetrical conformation has a dark GM T1 state that is very close to the T1-S0 CI point, implying an efficient nonradiative T1-S0 quenching. Thus, weak phosphorescence was observed from the unsymmetrical conformation. This study provides an insight for the development of highly emissive phosphorescent materials.

Ligand based conformational space studies of the μ-opioid receptor

BackgroundG protein-coupled receptors (GPCRs) comprise a family of membrane proteins that can be activated by a variety of external factors. The μ-opioid receptor (MOR), a class A GPCR, is the main target of morphine. Recently, enhanced sampling molecular dynamics simulations of a constitutively active mutant of MOR in its apo form allowed us to capture the novel intermediate states of activation, as well as the active state. This prompted us to apply the same techniques to wild type MOR in complex with ligands, in order to explore their contributions to the receptor conformational changes in the activation process. MethodsMOR was modeled in complex with agonists (morphine, BU72), a partial agonist (naloxone benzoylhydrazone) and an antagonist (naloxone). Replica exchange with solute tempering (REST2) molecular dynamics simulations were carried out for all systems. Trajectory frames were clustered, and the activation state of each cluster was assessed by two different methods. ResultsCluster sizes and activation indices show that while agonists stabilized structures in a higher activation state, the antagonist behaved oppositely. Morphine tends to drive the receptor towards increasing R165-T279 distances, while naloxone tends to increase the NPxxYA motif conformational change. ConclusionsDespite not observing a full transition between inactive and active states, an important conformational change of transmembrane helix 5 was observed and associated with a ligand-driven step of the process. General significanceThe activation process of GPCRs is widely studied but still not fully understood. Here we carried out a step forward in the direction of gaining more details of this process.

Investigating the Mechanistic Inhibitory Discrepancies of Novel Halogen and Alkyl Di-Substituted Oxadiazole-Based Dibenzo-Azepine-Dione Derivatives on Poly (ADP-Ribose) Polymerase-1.

Numerous studies have established the involvement of Poly (ADP-ribose) Polymerase-1 (PARP-1) in cancer presenting it as an important therapeutic target over recent years. Although homology among the PARP protein family makes selective targeting difficult, two compounds [d11 (0.939 μM) and d21 (0.047 μM)] with disparate inhibitory potencies against PARP-1 were recently identified. In this study, free energy calculations and molecular simulations were used to decipher underlying mechanisms of differential PARP-1 inhibition exhibited by the two compounds. The thermodynamics calculation revealed that compound d21 had a relatively higher ΔGbind than d11. High involvement of van der Waal and electrostatic effects potentiated the affinity of d21 at PARP-1 active site. More so, incorporated methyl moiety in d11 accounted for steric hindrance which, in turn, prevented complementary interactions of key site residues such as TYR889, MET890, TYR896, TYR907. Conformational studies also revealed that d21 is more stabilized for interactions in the active site compared to d11. We believe that findings from this study would provide an important avenue for the development of selective PARP-1 inhibitors.

Quantitative measurements of forward head in college-aged students: A conformational study of intra-rater and inter-rater reliability of a novel Posture Measuring Device

IntroductionMedical professionals frequently encounter forward head postures (FHP) in the treatment of cervical spine pain. In the clinical setting, FHP measurements are often described subjectively using the phrase, “patient demonstrates forward head posture.” There are reliable tools that can objectively measure FHP, but they are not frequently used in the clinical setting on a regular basis because the tools are unavailable, inconvenient or overly time-consuming. The objective of this study was to confirm if FHP can be reliably measured using a novel posture-measuring device. The Posture Measuring Device (PMD) was designed to quickly obtain objective measurements of FHP in the outpatient clinical setting. A pilot study demonstrated good to excellent reliability in intra-rater (test-retest) measurements and good interrater reliability using two first-year Doctor of Physical Therapy Students as raters. This study is to confirm that the PMD is able to provide intra-rater and interrater reliability using two physical therapists and two second-year Doctor of Physical Therapy students to obtain FHP measurements. MethodsTwenty-three college-aged subjects were measured individually using a PMD by a panel of four raters consisting of two physical therapists and two second-year physical therapy students to develop interrater reliability. Each rater measured each subject twice on two separate occasions to obtain a measure of intra-rater (relative) reliability. ResultsPearson Correlations demonstrate high intra-rater correlation with inconsistent interrater correlation. The average measured Intraclass Correlation Coefficient (ICC) was .822 with a 95% confidence interval indicating a high degree of reliability between the eight measurements performed on each subject. Cronbach's alpha results confirm the ICC findings of strong correlation among the eight raters (α = 0.87). Discussion and conclusionObjective measurement of forward head posture is valuable to document and monitor patient response to treatment. This study identifies a convenient and time-efficient method for measuring forward head in the clinical setting. The PMD demonstrated a high degree of reliability in intra-rater measurements of FHP.

A Pilot Scale Study on the Extraction & Optimization of Keratin from Human Hair – An Adapted Strategy for the Control of Environmental Menace

Large aggregates of the keratin based pollutants are known to cause intense threat in contaminating the environment of contact region than in the discrete region. Diversifying the application of keratin could be a promising phenomenon for reducing the keratin pollution. Accordingly, the undertaken work was designed to optimize the parameters for the keratin extraction from human hair with a potential source of application in the environment. Sequence of the effective extraction dealt with pre-treatment of human hair with a surfactant (sodium dodecyl sulphate), followed by the digestion of hair with sodium sulfide (Na2S) at pH 12 - 14 and then stirred with magnetic stirrer at 50C. The aliquot was then centrifuged at pH of 3 - 4, following which the precipitated keratin was extracted, dried and pulverized. The conformational study of the extracted keratin was done by performing Ninhydrin test and Fourier transform infrared spectroscopy (FTIR) analysis. The extracted keratin can be exploited in several applications such as, active component in bone replacement, hydro-gel preparation, cosmetics, scaffold preparation, bio degradable films etc. Hence, this work highlighted on the optimal isolation of pure keratin from human hair, paving away the environmental pollutants and advent a healthy grid of societal benefit.