Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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Item Biopolymer-polyphenol conjugates: Novel multifunctional materials for active packaging(Elsevier B V, 2024-11) Sahraeian S; Abdollahi B; Rashidinejad AThe development of natural active packaging materials and coatings presents a promising alternative to petroleum-based packaging solutions. These materials are engineered by incorporating functional ingredients with preservative capabilities. Concurrently, research has highlighted the diverse physicochemical, functional, and health-promoting properties of protein-polyphenol, polysaccharide-polyphenol, and protein-polysaccharide-polyphenol conjugates within various food formulations. However, a critical gap exists regarding the exploration of these biopolymers as active packaging materials. In contrast to conventional approaches for developing active packaging materials, this review presents a novel perspective by focusing on biopolymer-polyphenol conjugates. In this work, we delve into the realm of active packaging materials and coatings constructed from these conjugates, highlighting their potential as multifunctional active components in food packaging and preservation. This review comprehensively investigates the physicochemical properties, functionalities, and health-promoting activities associated with biopolymer-polyphenol conjugates. Their emulsification, antioxidant, and antimicrobial activities, coupled with enhancements in mechanical strength and permeability properties, contribute to their multifunctional nature. Furthermore, we explore the potential advantages and limitations of utilizing these conjugates in active packaging applications. Finally, the review concludes by proposing crucial research avenues for further exploration of biopolymer-polyphenol conjugates within the domain of active food packaging.Item Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A.(Springer Nature Limited, 2023-10-11) Harjes S; Kurup HM; Rieffer AE; Bayarjargal M; Filitcheva J; Su Y; Hale TK; Filichev VV; Harjes E; Harris RS; Jameson GBThe normally antiviral enzyme APOBEC3A is an endogenous mutagen in human cancer. Its single-stranded DNA C-to-U editing activity results in multiple mutagenic outcomes including signature single-base substitution mutations (isolated and clustered), DNA breakage, and larger-scale chromosomal aberrations. APOBEC3A inhibitors may therefore comprise a unique class of anti-cancer agents that work by blocking mutagenesis, slowing tumor evolvability, and preventing detrimental outcomes such as drug resistance and metastasis. Here we reveal the structural basis of competitive inhibition of wildtype APOBEC3A by hairpin DNA bearing 2'-deoxy-5-fluorozebularine in place of the cytidine in the TC substrate motif that is part of a 3-nucleotide loop. In addition, the structural basis of APOBEC3A's preference for YTCD motifs (Y = T, C; D = A, G, T) is explained. The nuclease-resistant phosphorothioated derivatives of these inhibitors have nanomolar potency in vitro and block APOBEC3A activity in human cells. These inhibitors may be useful probes for studying APOBEC3A activity in cellular systems and leading toward, potentially as conjuvants, next-generation, combinatorial anti-mutator and anti-cancer therapies.Item Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A.(Royal Society of Chemistry, 2023-06-21) Kurup HM; Kvach MV; Harjes S; Jameson GB; Harjes E; Filichev VVThe APOBEC3 (APOBEC3A-H) enzyme family as a part of the human innate immune system deaminates cytosine to uracil in single-stranded DNA (ssDNA) and thereby prevents the spread of pathogenic genetic information. However, APOBEC3-induced mutagenesis promotes viral and cancer evolution, thus enabling the progression of diseases and development of drug resistance. Therefore, APOBEC3 inhibition offers a possibility to complement existing antiviral and anticancer therapies and prevent the emergence of drug resistance, thus making such therapies effective for longer periods of time. Here, we synthesised nucleosides containing seven-membered nucleobases based on azepinone and compared their inhibitory potential against human cytidine deaminase (hCDA) and APOBEC3A with previously described 2'-deoxyzebularine (dZ) and 5-fluoro-2'-deoxyzebularine (FdZ). The nanomolar inhibitor of wild-type APOBEC3A was obtained by the incorporation of 1,3,4,7-tetrahydro-2H-1,3-diazepin-2-one in the TTC loop of a DNA hairpin instead of the target 2'-deoxycytidine providing a Ki of 290 ± 40 nM, which is only slightly weaker than the Ki of the FdZ-containing inhibitor (117 ± 15 nM). A less potent but notably different inhibition of human cytidine deaminase (CDA) and engineered C-terminal domain of APOBEC3B was observed for 2'-deoxyribosides of the S and R isomers of hexahydro-5-hydroxy-azepin-2-one: the S-isomer was more active than the R-isomer. The S-isomer shows resemblance in the position of the OH-group observed recently for the hydrated dZ and FdZ in the crystal structures with APOBEC3G and APOBEC3A, respectively. This shows that 7-membered ring analogues of pyrimidine nucleosides can serve as a platform for further development of modified ssDNAs as powerful A3 inhibitors.Item DL-PPI: a method on prediction of sequenced protein-protein interaction based on deep learning(BioMed Central Ltd, 2023-12) Wu J; Liu B; Zhang J; Wang Z; Li JPURPOSE: Sequenced Protein-Protein Interaction (PPI) prediction represents a pivotal area of study in biology, playing a crucial role in elucidating the mechanistic underpinnings of diseases and facilitating the design of novel therapeutic interventions. Conventional methods for extracting features through experimental processes have proven to be both costly and exceedingly complex. In light of these challenges, the scientific community has turned to computational approaches, particularly those grounded in deep learning methodologies. Despite the progress achieved by current deep learning technologies, their effectiveness diminishes when applied to larger, unfamiliar datasets. RESULTS: In this study, the paper introduces a novel deep learning framework, termed DL-PPI, for predicting PPIs based on sequence data. The proposed framework comprises two key components aimed at improving the accuracy of feature extraction from individual protein sequences and capturing relationships between proteins in unfamiliar datasets. 1. Protein Node Feature Extraction Module: To enhance the accuracy of feature extraction from individual protein sequences and facilitate the understanding of relationships between proteins in unknown datasets, the paper devised a novel protein node feature extraction module utilizing the Inception method. This module efficiently captures relevant patterns and representations within protein sequences, enabling more informative feature extraction. 2. Feature-Relational Reasoning Network (FRN): In the Global Feature Extraction module of our model, the paper developed a novel FRN that leveraged Graph Neural Networks to determine interactions between pairs of input proteins. The FRN effectively captures the underlying relational information between proteins, contributing to improved PPI predictions. DL-PPI framework demonstrates state-of-the-art performance in the realm of sequence-based PPI prediction.Item Enhanced properties of non-starch polysaccharide and protein hydrocolloids through plasma treatment: A review(Elsevier B V, 2023-09-30) Sahraeian S; Rashidinejad A; Niakousari MHydrocolloids are important ingredients in food formulations and their modification can lead to novel ingredients with unique functionalities beyond their nutritional value. Cold plasma is a promising technology for the modification of food biopolymers due to its non-toxic and eco-friendly nature. This review discusses the recent published studies on the effects of cold plasma treatment on non-starch hydrocolloids and their derivatives. It covers the common phenomena that occur during plasma treatment, including ionization, etching effect, surface modification, and ashing effect, and how they contribute to various changes in food biopolymers. The effects of plasma treatment on important properties such as color, crystallinity, chemical structure, rheological behavior, and thermal properties of non-starch hydrocolloids and their derivatives are also discussed. In addition, this review highlights the potential of cold plasma treatment to enhance the functionality of food biopolymers and improve the quality of food products. The mechanisms underlying the effects of plasma treatment on food biopolymers, which can be useful for future research in this area, are also discussed. Overall, this review paper presents a comprehensive overview of the current knowledge in the field of cold plasma treatment of non-starch hydrocolloids and their derivatives and highlights the areas that require further investigation.Item Small-Angle X-ray Scattering (SAXS) Measurements of APOBEC3G Provide Structural Basis for Binding of Single-Stranded DNA and Processivity(MDPI (Basel, Switzerland), 2022-09-06) Barzak FM; Ryan TM; Mohammadzadeh N; Harjes S; Kvach MV; Kurup HM; Krause KL; Chelico L; Filichev VV; Harjes E; Jameson GB; De la Torre JC; Andrei GAPOBEC3 enzymes are polynucleotide deaminases, converting cytosine to uracil on single-stranded DNA (ssDNA) and RNA as part of the innate immune response against viruses and retrotransposons. APOBEC3G is a two-domain protein that restricts HIV. Although X-ray single-crystal structures of individual catalytic domains of APOBEC3G with ssDNA as well as full-length APOBEC3G have been solved recently, there is little structural information available about ssDNA interaction with the full-length APOBEC3G or any other two-domain APOBEC3. Here, we investigated the solution-state structures of full-length APOBEC3G with and without a 40-mer modified ssDNA by small-angle X-ray scattering (SAXS), using size-exclusion chromatography (SEC) immediately prior to irradiation to effect partial separation of multi-component mixtures. To prevent cytosine deamination, the target 2'-deoxycytidine embedded in 40-mer ssDNA was replaced by 2'-deoxyzebularine, which is known to inhibit APOBEC3A, APOBEC3B and APOBEC3G when incorporated into short ssDNA oligomers. Full-length APOBEC3G without ssDNA comprised multiple multimeric species, of which tetramer was the most scattering species. The structure of the tetramer was elucidated. Dimeric interfaces significantly occlude the DNA-binding interface, whereas the tetrameric interface does not. This explains why dimers completely disappeared, and monomeric protein species became dominant, when ssDNA was added. Data analysis of the monomeric species revealed a full-length APOBEC3G-ssDNA complex that gives insight into the observed "jumping" behavior revealed in studies of enzyme processivity. This solution-state SAXS study provides the first structural model of ssDNA binding both domains of APOBEC3G and provides data to guide further structural and enzymatic work on APOBEC3-ssDNA complexes.Item β-Lactoglobulin nanofibrils: Effect of temperature on fibril formation kinetics, fibril morphology and the rheological properties of fibril dispersions(Elsevier Ltd, 2012-05) Loveday SM; Wang XL; Rao MA; Anema SG; Singh HAlmost all published studies of heat-induced b-lactoglobulin self-assembly into amyloid-like fibrils at low pH and low ionic strength have involved heating at 80 C, and the effect of heating temperature on self-assembly has received little attention. Here we heated b-lactoglobulin at pH 2 and 75 C, 80 C, 90 C, 100 C, 110 C or 120 C and investigated the kinetics of self-assembly (using Thioflavin T fluorescence), the morphology of fibrils, and the rheological properties of fibril dispersions. Self-assembly occurred at all temperatures tested. Thioflavin T fluorescence increased sigmoidally at all temperatures, however it decreased sharply with >3.3 h heating at 110 C and with >5 h heating at 120 C. The sharp decreases were attributed partly to local gelation, but destruction of fibrils may have occurred at 120 C. Thioflavin T fluorescence results indicated that maximal rates of fibril formation increased with increasing temperature, especially above 100 C, but fibril yield (maximum Thioflavin T fluorescence) was not affected by temperature. At 100 C and 110 C, fibrils were slightly shorter than at 80 C, but otherwise they looked very similar. Fibrils made by heating at 120 C for 1 h were also similar, but heating at 120 C for 8 h gave predominantly short fibrils, apparently the products of larger fibrils fragmenting. Heating at 100 C gave consistently higher viscosity than at 80 C, and heating for >2 h at 120 C decreased viscosity, which may have been linked with fibril fragmentation seen in micrographs.Item Phase and Rheological Behavior of High-Concentration Colloidal Hard-Sphere and Protein Dispersions(Wiley-Blackwell, 2007) Loveday, SM; Creamer, Lawrence K.; Singh, Harjinder; Rao, M. A.Colloidal hard-sphere particles of narrow-size distribution exhibit crystalline and glassy states beginning at the particle volume fractions φ=0.494 and φG=0.58, respectively. Dynamic rheological data on the dispersions was strongly modified to solid-like behavior as φ approached φG. In addition, cooperative motion in structural relaxation has been observed microscopically in the colloidal dispersions near the glassy state. Very high viscosities and glassy states were also found in high-concentration dispersions of sodium caseinate, and the globular proteins: bovine serum albumin and β-lactoglobulin. Viscosity models developed for hard-sphere dispersions provided reasonable predictions of relative viscosities of colloidal protein dispersions. Dispersions of food colloidal particles may be employed in studies, in which volume fraction is the thermodynamic variable, for understanding the relaxation and transport processes related to first-order and colloidal glass transitions