Tertiary Structure Research Articles

Multi-omics profiling and experimental verification of tertiary lymphoid structure-related genes: molecular subgroups, immune infiltration, and prognostic implications in lung adenocarcinoma.

Lung adenocarcinoma (LUAD), characterized by a low 5-year survival rate, is the most common and aggressive type of lung cancer. Recent studies have shown that tertiary lymphoid structures (TLS), which resemble lymphoid structures, are closely linked to the immune response and tumor prognosis. The functions of the tertiary lymphoid structure-related genes (TLS-RGs) in the tumor microenvironment (TME) are poorly understood. Based on publicly available data, we conducted a comprehensive study of the function of TLS-RGs in LUAD. Initially, we categorized LUAD patients into two TLS and two gene subtypes. Subsequently, risk scores were calculated, and prognostic models were constructed using seven genes (CIITA, FCRL2, GBP1, BIRC3, SCGB1A1, CLDN18, and S100P). To enhance the clinical application of TLS scores, we have developed a precise nomogram. Furthermore, drug sensitivity, tumor mutational burden (TMB), and the cancer stem cell (CSC) index were found to be substantially correlated with the TLS scores. Single-cell sequencing results reflected the distribution of TLS-RGs in cells. Finally, we took the intersection of overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) prognosis-related genes and then further validated the expression of these genes by qRT-PCR. Our in-depth investigation of TLS-RGs in LUAD revealed their possible contributions to the clinicopathological features, prognosis, and characteristics of TME. These findings underscore the potential of TLS-RGs as prognostic biomarkers and therapeutic targets for LUAD, thereby paving the way for personalized treatment strategies.

Effect of different precooling methods on the physicochemical changes, water migration and myofibrillar protein characteristics of pufferfish (Takifugu obscurus) during cold storage

SummaryThe objective of this study was to evaluate the effect of slurry ice (SI) in physicochemical changes, water migration, myofibrillar protein characterisation, and extended shelf life during cold storage of pufferfish (Takifugu obscurus). SI provided faster cooling rate, better structural stability of muscle tissue, and a significant reduction in total viable count (TVC). In addition, the use of SI treatment resulted in a considerable reduction in total volatile basic nitrogen (TVB‐N) and pH. The results of the texture profile analysis (TPA) demonstrated that SI had a significant inhibitory effect on the reduction of hardness, springiness, resilience, and chewiness. In addition, SI treatment better maintained a well‐structured myofibrillar protein stabilising the tertiary structure. Low‐field nuclear magnetic resonance (LF‐NMR) and magnetic resonance imaging (MRI) revealed that SI treatment could retard the water migration. Furthermore, the results of confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) indicated that SI treatment of pufferfish effectively slowed down the degradation of their myofibrillar protein fraction throughout the cold storage.

Mushroom polyphenol oxidase inactivation kinetics and structural changes during radiofrequency heating

The effects of radiofrequency (RF) heating on the activity, structure, and surface hydrophobicity of mushroom polyphenol oxidase (PPO) were examined and four kinetic models of inactivation (First-order model, Weibull model, Logistic model and Bi-phasic model) were fitted. The results demonstrated that RF heating could effectively inactivate PPO, logistic and Bi-phasic model attained the best fit. The circular dichroism (CD) and fluorescence spectroscopy spectra revealed that RF heating at 65 °C for 180 s caused changes in the secondary and tertiary structures of PPO, reducing the α-helix content from 38.5% to 30.3% and red-shifting the emission peak wavelength of the maximum fluorescence intensity from 318 nm to 321 nm. RF heating also caused a significant enhancement of the surface hydrophobicity of the PPO (P < 0.05). The color test results showed that RF heating could inhibit the browning of mushrooms (P < 0.05). Thus, RF heating is an effective technique for the inactivation of enzymes and further research should be performed on RF heating applications to inactivate enzymes in the food industry.

Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations.

Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. We present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.

Comprehensive bioinformatics assessments of the ROP34 of Toxoplasma gondii to approach vaccine candidates

IntroductionRhoptries proteins (ROPs) are crucial throughout different stages of the Toxoplasma gondii (T. gondii) lifecycle, playing key roles in both the invasion of host cells and their subsequent survival. ROP34 is particularly noteworthy as it significantly influences host gene expression and aids in the transition from the tachyzoite to the bradyzoite form.Materials and methodsThis research utilized various bioinformatics tools to assess physico-chemical properties, allergenic and antigenic characteristics, sites for post-translational modifications (PTMs) and protein's secondary and three-dimensional structures of the ROP34 protein. Furthermore, the study identified potential B-cell, MHC-binding, and cytotoxic T-lymphocyte (CTL) epitopes within the ROP34 sequence.ResultsThe ROP34 peptide comprised 553 amino acid residues, with a calculated average molecular weight (MW) of 61.60149 kDa, an aliphatic index of 73.98, and a GRAVY score of − 0.554. The antigenicity of the multi-epitope peptide was estimated to be 0.526563 and 0.6025 by the ANTIGENpro and VaxiJen servers, respectively, suggesting ROP34 as an immunogenic protein with no allergenic potential. Secondary structure analysis revealed a composition of 52.80% random coil, 36.17% alpha helix, and 11.03% extended strand. The Ramachandran plot for the refined model depicted that 97.46% of the residues were situated in the favored region.ConclusionThis in silico research serves as a foundation for designing effective immunization tactics to target toxoplasmosis. The present article lays the groundwork for future studies and offers perspectives for the advancement of an appropriate toxoplasmosis vaccine.Graphical

Tertiary lymphoid structure formation induced by LIGHT-engineered and photosensitive nanoparticles-decorated bacteria enhances immune response against colorectal cancer

Tertiary lymphoid structures (TLSs) are known to enhance the prognosis of patients with colorectal cancer (CRC) by fostering an immunologically active tumor microenvironment (TME). Inducing TLS formation therapeutically holds promise for treating immunologically cold CRC, though it poses technical challenges. Here, we design and fabricate a photosensitive bacterial system named E@L-P/ICG. This system is engineered bacteria internally loaded with the cytokine LIGHT and surface-modified with PLGA/ICG nanoparticles (P/ICG NPs). Once accumulated in orthotopic colonic tumors in mice, E@L-P/ICG generates a mild photothermal effect under laser irradiation due to the photosensitive P/ICG NPs. This photothermal effect triggers the self-rupture of E@L-P/ICG and the death of surrounding tumor cells to release adjuvants and antigens, respectively, which in turn synergistically activate the adaptive immune responses. Furthermore, the cytokine LIGHT released from ruptured E@L-P/ICG stimulates the generation of high endothelial vessels (HEVs), promoting lymphocyte recruitment within the TME. These mechanisms lead to the TLS formation in CRC, which further boosts adaptive immune responses through effective infiltration of T cells and B cells, resulting in effectively inhibited tumor growth and extended survival of mice. Our study shows the potential of the E@L-P/ICG system in photosensitively inducing the TLS formation to treat CRC in clinic.

Genome-Wide Identification and Expression Analysis of MYB Transcription Factor Family in Response to Various Abiotic Stresses in Coconut (Cocos nucifera L.).

Abiotic stresses such as nitrogen deficiency, drought, and salinity significantly impact coconut production, yet the molecular mechanisms underlying coconut's response to these stresses are poorly understood. MYB proteins, a large and diverse family of transcription factors (TF), play crucial roles in plant responses to various abiotic stresses, but their genome-wide characterization and functional roles in coconut have not been comprehensively explored. This study identified 214 CnMYB genes (39 1R-MYB, 171 R2R3-MYB, 2 3R-MYB, and 2 4R-MYB) in the coconut genome. Phylogenetic analysis revealed that these genes are unevenly distributed across the 16 chromosomes, with conserved consensus sequences, motifs, and gene structures within the same subgroups. Synteny analysis indicated that segmental duplication primarily drove CnMYB evolution in coconut, with low nonsynonymous/synonymous ratios suggesting strong purifying selection. The gene ontology (GO) annotation of protein sequences provided insights into the biological functions of the CnMYB gene family. CnMYB47/70/83/119/186 and CnMYB2/45/85/158/195 were identified as homologous genes linked to nitrogen deficiency, drought, and salinity stress through BLAST, highlighting the key role of CnMYB genes in abiotic stress tolerance. Quantitative analysis of PCR showed 10 CnMYB genes in leaves and petioles and found that the expression of CnMYB45/47/70/83/85/119/186 was higher in 3-month-old than one-year-old coconut, whereas CnMYB2/158/195 was higher in one-year-old coconut. Moreover, the expression of CnMYB70, CnMYB2, and CnMYB2/158 was high under nitrogen deficiency, drought, and salinity stress, respectively. The predicted secondary and tertiary structures of three key CnMYB proteins involved in abiotic stress revealed distinct inter-proteomic features. The predicted interaction between CnMYB2/158 and Hsp70 supports its role in coconut's drought and salinity stress responses. These results expand our understanding of the relationships between the evolution and function of MYB genes, and provide valuable insights into the MYB gene family's role in abiotic stress in coconut.

N-terminal domain of androgen receptor is a major therapeutic barrier and potential pharmacological target for treating castration resistant prostate cancer: a comprehensive review.

The incidence rate of prostate cancer (PCa) has risen by 3% per year from 2014 through 2019 in the United States. An estimated 34,700 people will die from PCa in 2023, corresponding to 95 deaths per day. Castration resistant prostate cancer (CRPC) is the leading cause of deaths among men with PCa. Androgen receptor (AR) plays a critical role in the development of CRPC. N-terminal domain (NTD) is the essential functional domain for AR transcriptional activation, in which modular activation function-1 (AF-1) is important for gene regulation and protein interactions. Over last 2decades drug discovery against NTD has attracted interest for CRPC treatment. However, NTD is an intrinsically disordered domain without stable three-dimensional structure, which has so far hampered the development of drugs targeting this highly dynamic structure. Employing high throughput cell-based assays, small-molecule NTD inhibitors exhibit a variety of unexpected properties, ranging from specific binding to NTD, blocking AR transactivation, and suppressing oncogenic proliferation, which prompts its evaluation in clinical trials. Furthermore, molecular dynamics simulations reveal that compounds can induce the formation of collapsed helical states. Nevertheless, our knowledge of NTD structure has been limited to the primary sequence of amino acid chain and a few secondary structure motif, acting as a barrier for computational and pharmaceutical analysis to decipher dynamic conformation and drug-target interaction. In this review, we provide an overview on the sequence-structure-function relationships of NTD, including the polymorphism of mono-amino acid repeats, functional elements for transcription regulation, and modeled tertiary structure of NTD. Moreover, we summarize the activities and therapeutic potential of current NTD-targeting inhibitors and outline different experimental methods contributing to screening novel compounds. Finally, we discuss current directions for structure-based drug design and potential breakthroughs for exploring pharmacological motifs and pockets in NTD, which could contribute to the discovery of new NTD inhibitors.

Podoplanin expressing macrophages and their involvement in tertiary lymphoid structures in mouse models of Sjögren's disease.

Tertiary lymphoid structures (TLSs) are formed in tissues targeted by chronic inflammation processes, such as infection and autoimmunity. In Sjögren's disease, the organization of immune cells into TLS is an important part of disease progression. Here, we investigated the dynamics of tissue resident macrophages in the induction and expansion of salivary gland TLS. We induced Sjögren's disease by cannulation of the submandibular glands of C57BL/6J mice with LucAdV5. In salivary gland tissues from these mice, we analyzed the different macrophage populations prior to cannulation on day 0 and on day 2, 5, 8, 16 and 23 post-infection using multicolored flow cytometry, mRNA gene analysis, and histological evaluation of tissue specific macrophages. The histological localization of macrophages in the LucAdV5 induced inflamed salivary glands was compared to salivary glands of NZBW/F1 lupus prone mice, a spontaneous mouse model of Sjögren's disease. The evaluation of the dynamics and changes in macrophage phenotype revealed that the podoplanin (PDPN) expressing CX3CR1+ macrophage population was increased in the salivary gland tissue during LucAdV5 induced inflammation. This PDPN+ CX3CR1+ macrophage population was, together with PDPN+CD206+ macrophages, observed to be localized in the parenchyma during the acute inflammation phase as well as surrounding the TLS structure in the later stages of inflammation. This suggests a dual role of tissue resident macrophages, contributing to both proinflammatory and anti-inflammatory processes, as well as their possible interactions with other immune cells within the inflamed tissue. These macrophages may be involved with lymphoid neogenesis, which is associated with disease severity and progression. In conclusion, our study substantiates the involvement of proinflammatory and regulatory macrophages in autoimmune pathology and underlines the possible multifaceted functions of macrophages in lymphoid cell organization.

Protein Structure Inspired Discovery of a Novel Inducer of Anoikis in Human Melanoma.

Drug discovery historically starts with an established function, either that of compounds or proteins. This can hamper discovery of novel therapeutics. As structure determines function, we hypothesized that unique 3D protein structures constitute primary data that can inform novel discovery. Using a computationally intensive physics-based analytical platform operating at supercomputing speeds, we probed a high-resolution protein X-ray crystallographic library developed by us. For each of the eight identified novel 3D structures, we analyzed binding of sixty million compounds. Top-ranking compounds were acquired and screened for efficacy against breast, prostate, colon, or lung cancer, and for toxicity on normal human bone marrow stem cells, both using eight-day colony formation assays. Effective and non-toxic compounds segregated to two pockets. One compound, Dxr2-017, exhibited selective anti-melanoma activity in the NCI-60 cell line screen. In eight-day assays, Dxr2-017 had an IC50 of 12 nM against melanoma cells, while concentrations over 2100-fold higher had minimal stem cell toxicity. Dxr2-017 induced anoikis, a unique form of programmed cell death in need of targeted therapeutics. Our findings demonstrate proof-of-concept that protein structures represent high-value primary data to support the discovery of novel acting therapeutics. This approach is widely applicable.

SSR-DTA: Substructure-aware multi-layer graph neural networks for drug–target binding affinity prediction

Accurate prediction of drug–target binding affinity (DTA) is essential in the field of drug discovery. Recently, scientists have been attempting to utilize artificial intelligence prediction to screen out a significant number of ineffective compounds, thereby mitigating labor and financial losses. While graph neural networks (GNNs) have been applied to DTA, existing GNNs have limitations in effectively extracting substructural features across various sizes. Functional groups play a crucial role in modulating molecular properties, but existing GNNs struggle with feature extraction from certain motifs due to scale mismatches. Additionally, sequence-based models for target proteins lack the integration of structural information. To address these limitations, we present SSR-DTA, a multi-layer graph network capable of adapting to diverse structural sizes, which can extract richer biological features, thereby improving the robustness and accuracy of predictions. Multi-layer GNNs enable the capture of molecular motifs across different scales, ranging from atomic to macrocyclic motifs. Furthermore, we introduce BiGNN to simultaneously learn sequence and structural information. Sequence information corresponds to the primary structure of proteins, while graph information represents the tertiary structure. BiGNN assimilates richer information compared to sequence-based methods while mitigating the impact of errors from predicted structures, resulting in more accurate predictions. Through rigorous experimental evaluations conducted on four benchmark datasets, we demonstrate the superiority of SSR-DTA over state-of-the-art models. Particularly, in comparison to state-of-the-art models, SSR-DTA demonstrates an impressive 20% reduction in mean squared error on the Davis dataset and a 5% reduction on the KIBA dataset, underscoring its potential as a valuable tool for advancing DTA prediction.

The Y44 residue point mutation in CXCL14 reveals the significance of CXCL14 protein stability in anti-tumor activity

Abstract Objectives CXCL14, a member of the CXC chemokine family, plays a significant role in tumor development, progression, and metastasis, making it a potential target for cancer diagnosis and treatment. This study aims to investigate the impact of a point mutation in the (41VSRYR45) motif of CXCL14 on its anti-tumor activity. Methods Phylogenetic analysis, tertiary structure prediction, homology modeling, and cell culture experiments were employed to assess the effects of CXCL14 mutations on protein stability and anti-tumor activity. Phylogenetic analysis identified conserved regions critical for function, while computational tools predicted structural changes due to mutations. Homology modeling provided structural insights, and cell culture experiments involved transfecting HeLa cells with wild-type or mutant CXCL14 plasmids, assessing stability and anti-tumor effects. Additionally, in vivo, xenograft experiments using nude mice were conducted to evaluate the anti-tumor efficacy of CXCL14 variants. Results The conserved Y44 site within the (41VSRYR45) motif was identified as a key ubiquitination site. Mutations Y44V and Y44F enhanced CXCL14 stability, reducing HeLa cell proliferation and migration while increasing apoptosis. In vivo, tumor xenograft experiments confirmed the stronger inhibitory effect of these CXCL14 variants on tumor growth compared to the wild-type protein. Conclusion The Y44 site in CXCL14 is crucial for its stability and anti-tumor activity. Mutations Y44V and Y44F enhance CXCL14 stability and anti-tumor effects, suggesting that targeting this site could be a promising therapeutic strategy for cervical cancer.

Evaluating AlphaFold for Clinical Pharmacology and Pharmacogenetics: A Case-Study of Huntingtin Variants Linked to Huntington's Disease.

To evaluate the artificial intelligence (AI)-guided AlphaFold algorithm for studying the binding interactions of human huntingtin and the aggregation of huntingtin peptides. Variants of huntingtin protein implicated in Huntington's disease were used as a model system to evaluate AlphaFold. Variants of huntingtin and huntingtin peptides with polyglutamine tracts (PQT) containing 21, 31, 51, or 78 glutamines were studied. The 3-dimensional structures of huntingtin variants and their interactions with huntingtin-associated protein-40 (HAP40) were obtained. Aggregation experiments were conducted with peptide sequences corresponding to variants of PQT, amino terminal sequence (NTS) plus PQT, NTS plus PQT plus proline rich region (PRR), and the 300 amino acid sequence from the NTS through HEAT3 of huntingtin. Oligomerization experiments with 1, 3, 6, or 12 peptide sequences were used to assess the quaternary structures of aggregates. The PQT and PQT plus NTS peptides formed a helical secondary structure that formed a central core in the quaternary structure of the aggregates The PRR formed an extended type II polyproline helix that did not participate in central core the aggregates. The distance between the amino and carboxyl termini of disease-linked 31Q, 51Q, and 78Q variants of full-length huntingtin was prominently decreased compared to the 21Q huntingtin. The interaction of HAP40 with the 78Q variant increased the distance between the amino and carboxyl termini. AlphaFold identified key tertiary structure changes in human huntingtin that have been independently corroborated in experimental models. The results highlight the utility of AlphaFold for hypothesis generation in pharmaceutical research.

Solvation free energy in governing equations for DNA hybridization, protein-ligand binding, and protein folding.

This work examines the thermodynamics of model biomolecular interactions using a governing equation that accounts for the participation of bulk water in the equilibria. In the first example, the binding affinities of two DNA duplexes, one of nine and one of 10 base pairs in length, are measured and characterized by isothermal titration calorimetry (ITC) as a function of concentration. The results indicate that the change in solvation free energy that accompanies duplex formation (ΔGS) is large and unfavorable. The duplex with the larger number of G:C pairings yields the largest change in solvation free energy, ΔGS = +460 kcal·mol-1per base pair at 25 °C. A van't Hoff analysis of the data is complicated by the varying degree of intramolecular base stacking within each DNA strand as a function of temperature. A modeling study reveals how the solvation free energy alters the output of a typical ITC experiment and leads to a good, though misleading, fit to the classical equilibrium equation. The same thermodynamic framework is applied to a model protein-ligand interaction, the binding of ribonuclease A with the nucleotide inhibitor 3'-UMP, and to a conformational equilibrium, the change in tertiary structure of α-lactalbumin in molar guanidinium chloride solutions. The ribonuclease study yields a value of ΔGS = +160 kcal·mol-1, whereas the folding equilibrium yields ΔGS ≈ 0, an apparent characteristic of hydrophobic interactions. These examples provide insight on the role of solvation energy in binding equilibria and suggest a pivot in the fundamental application of thermodynamics to solution chemistry.

Thermal-induced interactions between soy protein isolate and malondialdehyde: Effects on protein digestibility, structure, and formation of advanced lipoxidation end products

Thermally processed lipid- and protein-rich foods have sparked widespread concern since they may degrade food nutrition and even risk food safety. This study investigated soy protein isolate (SPI) alterations of digestibility and structure, as well as the formation of potentially hazardous chemicals, i.e., advanced lipoxidation end products (ALEs), after interacting with malondialdehyde (MDA, a lipid oxidation product) under high-temperature cooking conditions (100–180 °C, up to 60 min). In-vitro protein digestion of the SPI-MDA mixtures suggested that their room-temperature interactions damaged SPI digestibility, and increasing the temperature and the duration of the thermal treatment exacerbated the adverse effects. Protein oxidation, covalent aggregation of subunits, and changes in secondary and tertiary structures were revealed using thiol quantification, gel electrophoresis, fluorescence spectroscopy, and circular dichroism (CD) spectra, which could explain reduced protein digestibility. High-resolution mass spectrometry (HRMS) identified seven non-crosslinked ALEs and two crosslinked ALEs. Increased MDA concentrations promoted the generation of ALEs. Moreover, the acrolein-derived ALEs with reactive carbonyl groups were prone to further reacting into crosslinked ALEs, potentially responsible for the subunit aggregation.

Backbone assignment of CcdB_G100T toxin from E.coli in complex with the toxin binding C-terminal domain of its cognate antitoxin CcdA.

The CcdAB system expressed in the E.coli cells is a prototypical example of the bacterial toxin-antitoxin (TA) systems that ensure the survival of the bacterial population under adverse environmental conditions. The solution and crystal structures of CcdA, CcdB and of CcdB in complex with the toxin-binding C-terminal domain of CcdA have been reported. Our interest lies in the dynamics of CcdB-CcdA complex formation. Solution NMR studies have shown that CcdB_G100T, in presence of saturating concentrations of CcdA-c, a truncated C-terminal fragment of CcdA exists in equilibrium between two major populations. Sequence specific backbone resonance assignments of both equilibrium forms of the ~ 27kDa complex, have been obtained from a suite of triple resonance NMR experiments acquired on 2H, 13C, 15N enriched samples of CcdB_G100T. Analysis of 1H, 13Cα, 13Cβ secondary chemical shifts, shows that both equilibrium forms of CcdB_G100T have five beta-strands and one alpha-helix as the major secondary structural elements in the tertiary structure. The results of these studies are presented below.

Covalent interaction of ovalbumin with proanthocyanidins improves its thermal stability and antioxidant and emulsifying activity.

The structure of proanthocyanidins (PC) contains a large number of active phenolic hydroxyl groups, which makes it have strong antioxidant capacity. This study investigated the structural and functional properties of ovalbumin (OVA) modified by its interaction with PC. It was found that on increasing the concentration ratio of PC to OVA from 10:1 to 40:1, the free amino and total sulfhydryl contents of OVA decreased from 470.59 ± 38.77 and 29.81 ± 0.31 nmol mg-1 to 96.61 ± 4.55 and 21.22 ± 0.78 nmol mg-1, respectively, and the free sulfhydryl content increased from 7.65 ± 0.41 to 9.48 ± 0.58 nmol mg-1. These results indicated that CN and CS bonds were formed and PC was covalently linked with OVA. The PC content in the OVA-PC conjugates increased from 281.93 ± 12.92 to 828.81 ± 46.09 nmol mg-1 on increasing the concentration ratio of PC to OVA from 10:1 to 40:1. The contents of α-helix and β-turn of OVA decreased, and the contents of β-sheet and random coil increased, confirmed by circular dichroism. The tertiary structure of OVA was also altered according to the results of fluorescence and ultraviolet absorption spectra. The surface hydrophobicity of OVA-PC conjugates decreased with increasing bound polyphenol content. The conjugation of OVA to PC significantly improved its emulsification and antioxidant activity and denaturation temperature. This study may provide valuable information for improving OVA's functional properties and its PC conjugates for applications in the food industry. © 2024 Society of Chemical Industry.

Evaluation of the water state and protein characteristics of Tibetan pork under the storage conditions of modified atmosphere packaging: Effect of oxygen concentration

To explore the changes in water status and protein characteristics of Tibetan pork (TP) under modified atmosphere packaging (MAP) with different oxygen concentrations compared to Duroc×Landrace×Yorkshire pork (DLY), the water holding capacity (WHC), water distribution, protein oxidation, and conformation of both types were determined. Results indicate that under MAP, TP pork and DLY pork exhibited higher water retention and lower protein oxidation compared to air packaging. However, with increased oxygen concentration in the MAP, protein oxidation intensified, leading to reduced WHC in the pork. Compared to DLY pork, TP pork in different packaging conditions maintained the integrity of protein secondary and tertiary structures, reducing protein cross-linking aggregation. The lower content of P3 in the two-dimensional relaxation spectra, shorter T1 and T2 relaxation times, and higher proton density suggest better water retention properties in Tibetan pork. These findings support the development of long-distance preservation and transportation technologies for TP pork.

Experimental characterization and prediction of Escherichia coli host cell proteome retention during preparative chromatography.

Purification of recombinantly produced biopharmaceuticals involves removal of host cell material, such as host cell proteins (HCPs). For lysates of the common expression host Escherichia coli (E. coli) over 1500 unique proteins can be identified. Currently, understanding the behavior of individual HCPs for purification operations, such as preparative chromatography, is limited. Therefore, we aim to elucidate the elution behavior of individual HCPs from E. coli strain BLR(DE3) during chromatography. Understanding this complex mixture and knowing the chromatographic behavior of each individual HCP improves the ability for rational purification process design. Specifically, linear gradient experiments were performed using ion exchange (IEX) and hydrophobic interaction chromatography, coupled with mass spectrometry-based proteomics to map the retention of individual HCPs. We combined knowledge of protein location, function, and interaction available in literature to identify trends in elution behavior. Additionally, quantitative structure-property relationship models were trained relating the protein 3D structure to elution behavior during IEX. For the complete data set a model with a cross-validated R2 of 0.55 was constructed, that could be improved to a R2 of 0.70 by considering only monomeric proteins. Ultimately this study is a significant step toward greater process understanding.

Isolation and characterization of lycopene β cyclase from Capsicum frutescens

Lycopene β cyclase (LCY-B) catalyzes the conversion of linear lycopene to cyclic β carotene, a crucial component of the photosynthetic machinery and a source of vitamin A for humans and animals. The gene was amplified in fragments using primers designed from conserved sequences of available nucleotide sequences from NCBI and a sequence of 1494 bp was observed upon amplification of the complete gene. The deduced amino acid sequence had a significant overall similarity with sequences of other Capsicum plants. It was observed that C. frutescens occurred in the same cluster as C. annuum and C. baccatum, while LCYB from all the other plants of the Solanaceae family were placed in one cluster signifying the conserved nature of the protein. The tertiary structure obtained from the protein was validated using the Ramachandran plot and ERRANT scores were determined. The protein function analysis gives insight into important parameters of the protein such as the number of cysteine residues, glycosylation sites, phosphorylation sites, etc.