Conformational Differences Research Articles

Ethnic differences in meat consumption attitudes, norms and behaviors: A survey of White, South Asian and Black ethnic groups in the UK

A reduction in meat consumption is necessary to mitigate negative impacts of climate change and adverse health outcomes. The UK has an increasingly multi-ethnic population, yet there is little research on meat consumption habits and attitudes among ethnic groups in the UK. We ran a survey (N = 1014) with quota samples for ethnic groups and analyzed attitudes, behaviors and norm perceptions of White, South Asian and Black British respondents. Most respondents believe overconsumption of red and processed meat has negative impacts on health (73.3%) and the environment (64.3%).South Asian respondents were statistically significantly less likely to be meat eaters than White respondents (OR = 0.44, 95% CIs: 0.30-0.65, t = −4.15, p = 0.000), while there was no significant difference between White and Black respondents (OR = 1.06, 95% CIs: 0.63–1.76, t = 0.21, p = 0.834). Both South Asian (OR = 2.76, 95% CIs: 1.89–4.03 t = 5.25, p = 0.000) and Black respondents (OR = 2.09, 95% CIs: 0.1.30–3.35, t = 3.06, p = 0.002) were significantly more likely to express being influenced by friends and family in their food choices than White respondents. South Asian (OR = 3.24,95% CIs: 2.17–4.84, t = 5.74, p = 0.000) and Black (OR = 2.02,95% CIs: 1.21–3.39, t = 2.69, p = 0.007) respondents were also both significantly more likely to report they would want to eat similarly to their friends and family than White respondents. Statistical analyses suggested some gender and socioeconomic differences across and among ethnic groups, which are reported and discussed. The differences in meat consumption behaviors and norm conformity between ethnic groups raises the prospect that interventions that leverage social norms may be more effective in South Asian groups than Black and White groups in the UK.

Clinical Viability of an Active Spot Scanning Beam Delivery System With a Newly Developed Carbon-Ion Treatment Planning System

PurposeAlthough active spot scanning irradiation technique is theoretically superior to passive-scattered broad beam irradiation with respect to normal tissue sparing, corroborations of the clinical benefit of carbon-ion spot scanning have remained scarce. This study aims to investigate the feasibility and clinical implementation of an active spot scanning beam calculation algorithm in a homemade carbon-ion treatment planning system (TPS) by comparing it with a conventional passive uniform scanning technique. Materials and methodsCarbon-ion plans were initially formulated using spot/uniform scanning methods in 22 participants enrolled in a prospective observational clinical trial. Subsequently, two additional plans were designed, resulting in three carbon-ion plans for each participant: uniform and spot scanning with mini-ridge filters (MRFs) of 2mm and 4mm, respectively. ResultsThe findings revealed no significant differences in dose homogeneity; however, significant differences in dose conformity were found between the active and passive scanning plans. For dose drop-off outside the target volume, the average gradient index (GI) values were 1.94 (95% confidence interval (CI): 1.79%-2.09%), 1.87 (95% CI: 1.73%-2.01%), and 3.20 (95% CI: 2.80%-3.61%) for the MRF4, MRF2, and uniform scanning plans, respectively. The pre-treatment tumor volume was 124.7 cm3 (range, 54.2-234 cm3), and the average shrinkage observed was 38.4% (95% CI: 17.6%-59.4%). Seven participants experienced grade 1 acute toxicity, and four experienced grade 2 acute toxicity. However, none of the patients developed grade 3 acute toxicity. ConclusionsIncreasing evidence suggests that potential clinical advantages of spot scanning delivery underlie its technical characteristics. As one among the few institutions currently utilizing carbon-ion radiotherapy, the investigation also provides promising safety and efficacy outcomes from the initial groups of treated participants, thereby contributing to the established clinical evidence supporting the effectiveness and superiority of carbon-ion therapy.

Polymorphism Dependent Cytotoxicity, Cellular Uptake, and Live Cell Imaging Studies on Napthalimide-Vinyl-Phenothiazine Conjugate.

Polymorphism-dependent cytotoxicity and cellular uptake of drug molecules have been studied for the past two decades. However, the visualization of polymorph-dependent cellular uptake and cytotoxicity using microscopy imaging techniques has not yet been reported. The luminescent polymorph is an ideal candidate to validate the above hypothesis. Herein, we report the polymorph-dependent cellular uptake, cytotoxicity, and bio-imaging functions of polymorphs 1Y and 1R of a naphthalimide-phenothiazine dyad. These polymorphs show different luminescence colors in the solid state and exhibit aggregation-induced enhanced emission (AIEE) in the DMSO-Water mixture. Bioimaging, cytotoxicity assay, and fluorescence-activated cell sorting (FACS) studies revealed that these polymorphs show different levels of cytotoxicity, cellular uptake, localization, and imaging potential. Detailed photophysical, morphological, and biological studies revealed that the difference in molecular conformation in these polymorphs enables them to form aggregates of different sizes and morphology, which leads to the differential uptake of these into the cells and consequently shows different cytotoxicity and imaging potentials.

Abstract ND12: Discovery of PF-07220060, a potent and selective CDK4 inhibitor

Abstract PF-07220060 was developed based on the clinical need to improve efficacy and safety outcomes in patients treated with currently approved dual CDK4/6 inhibitors, including Palbociclib. Although all dual CDK4/6 inhibitors increase response rates and prolong disease control, they show common dose-limiting hematologic toxicities, foremost neutropenia. This poses challenges to provide these agents at doses necessary to extinguish cell cycling in tumors. Human ER+ breast cancer cells are highly dependent on CDK4 but not CDK6. By contrast, CDK4 is dispensable for human bone marrow derived cells, or cells enriched for neutrophil precursors or hematopoietic stem cells. This is primarily due to the compensatory role of CDK6 in these compartments. These observations prompted us to develop PF-07220060, an aminopyrimidine-based inhibitor, endowed with 20-fold and 4-fold increased selectivity for CDK4 over CDK6 when compared to Palbociclib and Abemaciclib/Ribociclib, respectively. CDK4-over-CDK6 selectivity is explained by G-loop conformational differences between the two kinases, with the G-loop of CDK4 being more flexible, assuming a more open conformation when bound to CDK4 selective versus non-selective inhibitors. PF-07220060 reduces dose-limiting neutropenia in beagle dogs by 15-fold when compared with Palbociclib, consistent with early clinical data obtained with PF-07220060. Higher tolerated plasma concentrations of PF-07220060 versus dual CDK4/6 inhibitors enable increased inhibition of CDK4 kinase activity in tumors. This translates to improved tumor growth inhibition across CDK4-driven models of human breast and prostate cancer at clinically relevant doses. Our work establishes proof-of-concept for CDK4 selective inhibition and introduces a best-in-class CDK4 inhibitor for treatment of HR+ HER2- breast cancer and other CDK4 dependent tumor types. Citation Format: Lars Anders, Gary Gallego. Discovery of PF-07220060, a potent and selective CDK4 inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr ND12.

Fabrication of soy protein microgels via two top-down methods and characterization of the foaming behavior

The aim of this study was to design and characterize soy protein microgels (SPM) using heat-induced (H-SPM) and enzyme cross-linking (E-SPM) methods, and then compared their conformational differences with soy protein isolate (SPI) and explored their foaming behavior. The results showed that transglutaminase-induced covalent cross-linking could fabricate SPM more effectively than that of simple heat treatment, resulting in larger particle sizes, higher surface charge and lower surface hydrophobicity, as well as more robust internal integrity and more ordered structure. Compared with SPI and H-SPM, the foamability of E-SPM decreased by 18.60% and 25.53%, respectively, while the short-term foam stability (60 min) increased by 20.50% and 5.81%, respectively. In terms of long-term foam stability, the foam volume of SPI and H-SPM eventually disappeared after standing for 300 min, while E-SPM still had a considerable foam volume (11.33 mL). Microstructure evaluation suggested that E-SPM stabilized foams via a Pickering-type mechanism. This study will facilitate the applications of SPM as a plant protein-based Pickering-type foam stabilizer in terms of generating aerated foods with long-term foam stability.

Collagen type I mimicking peptide additives to functionalize synthetic supramolecular hydrogels

Small bioactive peptide sequences derived from extracellular matrix proteins possess the ability to interact with cell receptors. As such, these peptide additives are excellent mimics to develop materials for 3D cell culture. Two types of supramolecular modified collagen type I mimicking peptide additives are presented; UPy-GFOGER (39 amino acids), with a novel superstructure, and the more simplistic UPy-DGEA (7 amino acids). Here, we studied the impact of the conformational differences between both peptide additives, on their biological performance. Various analyzing techniques demonstrated the ability of the supramolecular UPy-GFOGER to self-assemble into short nanofibers with brush-like outer features, suggesting trimerization into a triple helix. UPy-DGEA is a short additive without a complex structure. Since, collagen type I is a major component of the human corneal stroma, primary keratocytes (PKs) are encapsulated within the functionalized hydrogels to provide insights in the induced bioactivity of both additives. Incorporation of UPy-GFOGER supported an elongated morphology and (re-)differentiation of the encapsulated PKs, while tiny round-shaped cells were observed within the hydrogels functionalized with UPy-DGEA. This difference in biological success between UPy-GFOGER and UPy-DGEA indicates the difficulty of using short peptide additives without a complex structure to mimic the complex structure of natural collagen.

Studying the ssDNA loaded adeno-associated virus aggregation using coarse-grained molecular dynamics simulations

The aggregation of adeno-associated viral (AAV) capsids in an aqueous environment was investigated via coarse-grained molecular dynamics (CG-MD) simulations. The primary driving force and mechanism of the aggregation were investigated with or without single-strand DNA (ssDNA) loaded at various process temperatures. Capsid aggregation appeared to involve multiple residue interactions (i.e., hydrophobic, polar and charged residues) leading to complex protein aggregation. In addition, two aggregation mechanisms (i.e., the fivefold face-to-face contact and the edge-to-edge contact) were identified from this study. The ssDNA with its asymmetric structure could be the reason for destabilizing protein subunits and enhancing the interaction between the charged residues, and further result in the non-reversible face-to-face contact. At higher temperature, the capsid structure was found to be unstable with the significant size expansion of the loaded ssDNA which could be attributed to reduced number of intramolecular hydrogen bonds, the increased conformational deviations of protein subunits and the higher residue fluctuations. The CG-MD model was further validated with previous experimental and simulation data, including the full capsid size measurement and the capsid internal pressure. Thus, a good understanding of AAV capsid aggregation, instability and the role of ssDNA were revealed by applying the developed computational model.

Exploring Various Crystal and Molecular Structures of Gabapentin—A Review

Novel antiepileptic drugs have been developed at an unparalleled rate during the past 15 years. Gabapentin (GBP), which was approved for the treatment of refractory localization-related epilepsies in the U.K. and Europe in 1993, was one of the first drugs to come out of this era. Since then, GBP has become well-known across the world, not only for its antiepileptic qualities but also for its effectiveness in the treatment of chronic pain disorders, particularly neuropathic pain. In this review, the crystal structures of GBP and GBP-related compounds have been analyzed and compared. Particular attention has been paid to the polymorphism of GBP and its hydrates, their thermodynamic stability, and conformational differences. In addition, the puckering parameters for the cyclohexane ring of a total of 118 molecules of GBP found in the analyzed crystal structures have been calculated and analyzed. The results of recent high-pressure crystallization studies and quantum chemical calculations indicate that the entire landscape of GBP has not been revealed yet.

4-Fluoro-2-(phenyl-amino)-benzoic acid.

The title compound, C13H10FNO2, was obtained by the reaction of 2-bromo-4-fluoro-benzoic acid with aniline. There are two independent mol-ecules, A and B, in the asymmetric unit, with slight conformational differences: the dihedral angles between the aromatic rings are 55.63 (5) and 52.65 (5)°. Both mol-ecules feature an intra-molecular N-H⋯O hydrogen bond. In the crystal, the mol-ecules are linked by pairwise O-H⋯O hydrogen bonds to form A-B acid-acid dimers and weak C-H⋯F inter-actions further connect the dimers.

Biochemical and structural characterization of chlorhexidine as an ATP-assisted inhibitor against type 1 methionyl-tRNA synthetase from Gram-positive bacteria

Methionyl-tRNA synthetase (MetRS) catalyzes the attachment of l-methionine (l-Met) to tRNAMet to generate methionyl-tRNAMet, an essential substrate for protein translation within ribosome. Owing to its indispensable biological function and the structural discrepancies with human counterpart, bacterial MetRS is considered an ideal target for developing antibacterials. Herein, chlorhexidine (CHX) was identified as a potent binder of Staphylococcus aureus MetRS (SaMetRS) through an ATP-aided affinity screening. The co-crystal structure showed that CHX simultaneously occupies the enlarged l-Met pocket (EMP) and the auxiliary pocket (AP) of SaMetRS with its two chlorophenyl groups, while its central hexyl linker swings upwards to interact with some conserved hydrophobic residues. ATP adopts alternative conformations in the active site cavity, and forms ionic bonds and water-mediated hydrogen bonds with CHX. Consistent with this synergistic binding mode, ATP concentration-dependently enhanced the binding affinity of CHX to SaMetRS from 10.2 μM (no ATP) to 0.45 μM (1 mM ATP). While it selectively inhibited two representative type 1 MetRSs from S. aureus and Enterococcus faecalis, CHX did not show significant interactions with three tested type 2 MetRSs, including human cytoplasmic MetRS, in the enzyme inhibition and biophysical binding assays, probably due to the conformational differences between two types of MetRSs at their EMP and AP. Our findings on CHX may inspire the design of MetRS-directed antimicrobials in future.

Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation.

Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases-namely, the chromatin remodellers1. In plants, chromatin remodellers function in various biological processes and possess both conserved and plant-specific components2-5. DECREASE IN DNA METHYLATION 1 (DDM1) is a plant chromatin remodeller that plays a key role in the maintenance DNA methylation6-11. Here we determined the structures of Arabidopsis DDM1 in complex with nucleosome in ADP-BeFx-bound, ADP-bound and nucleotide-free conformations. We show that DDM1 specifically recognizes the H4 tail and nucleosomal DNA. The conformational differences between ADP-BeFx-bound, ADP-bound and nucleotide-free DDM1 suggest a chromatin remodelling cycle coupled to ATP binding, hydrolysis and ADP release. This, in turn, triggers conformational changes in the DDM1-bound nucleosomal DNA, which alters the nucleosome structure and promotes DNA sliding. Together, our data reveal the molecular basis of chromatin remodelling by DDM1.

Effect of pH on In-Electrospray Hydrogen/Deuterium Exchange of Carbohydrates and Peptides.

Carbohydrates are critical for cellular functions as well as an important class of metabolites. Characterizing carbohydrate structures is a difficult analytical challenge due to the presence of isomers. In-electrospray hydrogen/deuterium exchange mass spectrometry (in-ESI HDX-MS) is a method of HDX that samples the solvated structure of carbohydrates during the ESI process and requires little to no instrument modification. Traditionally, solution-phase HDX is utilized with proteins to sample conformational differences, and pH is a critical parameter to monitor and control due to the presence of both acid- and base-catalyzed mechanisms of exchange. For In-ESI HDX, the pH surrounding the analyte changes before and during labeling, which has the potential to affect the rate of labeling for analytes. Herein, we alter the pH of spray solutions containing model carbohydrates and peptides, perform in-ESI HDX-MS, and characterize the deuterium uptake trends. Varying pH results in altered D uptake, though the overall trends differ from the expected bulk-solution trends due to the electrospray process. These findings show the utility of varying pH prior to in-ESI HDX-MS for establishing different extents of HDX as well as distinguishing labile functional groups that are present in different analytes.

Allosteric modulation of subunit-specific conformational and functional differences in NMDA receptors

Allosteric modulation of subunit-specific conformational and functional differences in NMDA receptors

Nutritional management of aging pets

Nutritional management of aging pets Morgan A. Key from Hill’s Pet Nutrition outlines the changes associated with aging pets and how nutrition can help. Aging is a continuous, lifelong process. (1) The aging process can impact dogs’ health, behavior, and care requirements. Approximately 30% to 49% of dogs in the U.S. are ≥ 7 years old. (2, 3) Aging impacts individual animals differently due to differences in breed, frame size, conformation, genetics, and exposure to injuries and disease. One major contributor to aging is the excessive production of free radicals, also known as reactive oxygen species (ROS). Various studies demonstrate the positive role of antioxidants, including Vitamin C and E, in managing ROS and, thus, the aging process (Figure 1).

Conformity of Female College Students on Feminine Norms

Gender norms persist and continue to draw generalized expectations of the sexes. Consequently, women must fulfill these expectations to be regarded and valued. The current research was designed to examine the links between women and conformity to the present feminine norms and determine the magnitude of their conformity when grouped according to college department, religion, sexual orientation, and socioeconomic status. Female college student respondents (356) completed the CFNI-45 scale, which measures their conformity to the nine sub-facets of feminine norms. As hypothesized, women's conformity is influenced by their accorded groups. Z-scores and ANOVA were used to determine the conformity level of female colleges and the difference in conformity between groups. The study revealed that female college students are average in conformity to sub-facets of thinness, investment in appearance, modesty, relational, involvement with children, sweet and nice, and sexual fidelity. In between average and above average to domestic norms and above-average conformity to romantic relationship norms. Religion, sexual orientation, and socioeconomic status are linked to conformity to feminine norms. Results may contribute significant literature to understand women's conformity and the weight of gender norms.

Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells

Induced pluripotent stem cells (iPSCs) are the foundation of cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which could affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing, a process linked to both genome regulation and genome stability, is efficiently reprogrammed to the embryonic state. To answer this, we compare genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicate their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibits delayed replication at heterochromatic regions containing genes downregulated in iPSCs with incompletely reprogrammed DNA methylation. DNA replication delays are not the result of gene expression or DNA methylation aberrations and persist after cells differentiate to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and influence the quality of iPSCs.

Innovative tree-based method for sampling molecular conformations: exploring the ATP-binding cassette subfamily D member 1 (ABCD1) transporter as a case study.

We introduce a novel tree-based method for visualizing molecular conformation sampling. Our method offers enhanced precision in highlighting conformational differences and facilitates the observation of local minimas within proteins fold space. The projection of empirical laboratory data on the tree allows us to create a link between protein conformations and disease relevant data. To demonstrate the efficacy of our approach, we applied it to the ATP-binding cassette subfamily D member 1 (ABCD1) transporter responsible for very long-chain fatty acids (VLCFAs) import into peroxisomes. The genetic disorder called X-linked adrenoleukodystrophy (XALD) is characterized by the accumulation of VLCFA due to pathogenic variants in the ABCD1 gene. Using in silico molecular simulation, we examined the behavior of 16 prevalent mutations alongside the wild-type protein, exploring both inward and outward open forms of the transporter through molecular simulations. We evaluated from resulting trajectories the energy potential related to the ABCD1 interactions with ATP molecules. We categorized XALD patients based on the severity and progression of their disease, providing a unique clinical perspective. By integrating this data into our numerical framework, our study aimed to uncover the molecular underpinnings of XALD, offering new insights into disease progression. As we explored molecular trajectories and conformations resulting from our study, the tree-based method not only contributes valuable insights into XALD but also lays a solid foundation for forthcoming drug design studies. We advocate for the broader adoption of our innovative approach, proposing it as a valuable tool for researchers engaged in molecular simulation studies.

Identification and quantification of bipyridyl dicarboxylic acid isomers by ion mobility spectrometry

The identification of positional isomers is of interest because different isomers have different chemical or biological functions and applications. The analysis of positional isomers is sometimes challenging since they have similar chemical structures and properties. For example, the analysis of mass cannot identify different positional isomers because they have identical mass-to-charge ratios and show a single mass peak in mass spectrometry. In this study, an efficient and simple qualitative and quantitative analytical method for differentiating 2,2′-bipyridine-3,3′-dicarboxylic acid (3,3′-BDA), 2,2′-bipyridine-4,4′-dicarboxylic acid (4,4′-BDA), and 2,2′-bipyridine-5,5′-dicarboxylic acid (5,5′-BDA) was developed by using ion mobility spectrometry (IMS). The results revealed that the three BDA isomers formed non-covalent complexes with cyclodextrins (CDs) and Mg2+ ions in the gas phase: [β-CD+3,3′/4,4′/5,5′-BDA+Mg]2+ and [γ-CD+3,3′/4,4′/5,5′-BDA+Mg]2+, which were distinguished by measuring the mobility of the complexes because of their spatial conformational differences. The peak-to-peak resolution (Rp-p) values of the three isomers of [γ-CD+3,3′/4,4′/5,5′-BDA+Mg]2+ reached 2.983 and 2.892, respectively. The conformations of the ternary complexes simulated by the theoretical calculations revealed the different interactions and shapes of the stereoisomers, and the predicted results agreed with the experimental results. Simultaneously, further studies on the collisional dissociation of the ternary complexes revealed that the dissociation energies of the different complex ions varied were different owing to the diverse different conformations. Finally, the relative quantitative analysis of the different isomers in mixed samples was performed and satisfactory linearity results (R2 > 0.99) were obtained. Thus, an effective analytical method was proposed for the identification and quantification of BDA isomers without chemical derivatization, offering a promising approach for the identification of similar derivatives or positional isomers that could be applied in various fields including chemicals and pharmaceuticals.

Exploring ssDNA translocation through α-hemolysin using coarse-grained steered molecular dynamics.

Protein nanopores have proven to be effective for single-molecule studies, particularly for single-stranded DNA (ssDNA) translocation. Previous experiments demonstrated their ability to distinguish differences in purine and pyrimidine bases and in the orientation of the ssDNA molecule inside nanopores. Unfortunately, the microscopic details of ssDNA translocation over experimental time scales, which are not accessible through all-atom molecular dynamics (MD), have yet to be examined. However, coarse-grained (CG) MD simulations enable systems to be simulated over longer characteristic times closer to experiments than all-atom MD. This paper studies ssDNA translocation through α-hemolysin nanopores exploiting steered MD using the MARTINI CG force field. The impacts of the sequence length, orientation inside the nanopore and DNA charges on translocation dynamics as well as the conformational dynamics of ssDNA during the translocation are explored. Our results highlight the efficacy of CG molecular dynamics in capturing the experimental properties of ssDNA translocation, including a wide distribution in translocation times per base. In particular, the phosphate charges of the DNA molecule are crucial in the translocation dynamics and impact the translocation rate. Additionally, the influence of the ssDNA molecule orientation on the translocation rate is explained by the conformational differences of ssDNA inside the nanopore during its translocation. Our study emphasizes the significance of obtaining sufficient statistics via CG MD, which can elucidate the great variety of translocation processes.

Spin crossover of a Fe(II) mononuclear complex induced by intermolecular factors involving chloride and solvent ordering.

Two new salts of a mononuclear tripodal Fe(II) complex were prepared, using ClO4- and Cl-. The ClO4- sample (1) remained HS at low temperatures, similar to the previously reported BF4- analogue. Crystallising with the Cl- anion (2) led to a markedly different crystal packing arrangement, and engendered SCO activity. This has been correlated to the lower crystal packing density in 2 and the coordination complex conformational differences arising due to the packing motifs of 1 and 2. Further, solvent ordering effects have been proposed to facilitate spin transition behaviour in 2.