Copper-induced conformational change in a marsupial prion protein repeat peptide probed using FTIR spectroscopy

AbstractWe report the first Fourier transform infrared analysis of prion protein (PrP) repeats and the first study of PrP repeats of marsupial origin. Large changes in the secondary structure and an increase in hydrogen bonding within the peptide groups were evident from a red shift of the amide I band by >7 cm−1 and an approximately five-fold reduction in amide hydrogen–deuterium exchange for peptide interacting with Cu2+ ions. Changes in the tertiary structure upon copper binding were also evident from the appearance of a new band at 1564 cm−1, which arises from the ring vibration of histidine. The copper-induced conformational change is pH dependent, and occurs at pH >7

The Potential Selective Oncolytic Effects of Newcastle Disease Virus (NDV) on Cervical and Colon Cancer Cell Lines

The mesogenic and velogenic strains of the avian Newcastle Disease Viruses (NDV) have been investigated for use in cancer virotherapy. However, despite its promising results, these strains have the potential to cause outbreaks leading to morbidity and mortality in large numbers of avians that can devastate the poultry industry. Therefore, there is a growing interest towards the use of lentogenic strains such as NDV LaSota vaccine strain for virotherapy. This study investigated the oncolytic potential of the NDV LaSota strain on colorectal cancer (HT29) and cervical cancer (HeLa) cell lines. The NDV LaSota stain was propagated in pathogen free embryonated chicken eggs and quantified using a hemagglutination assay. The oncolytic activity was evaluated by comparison of HT29 and HeLa cell lines to the non-cancerous human embryonic kidney (HEK293) cell line using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) viability assay. The highest NDV concentration of 16 HAU was found to reduce the viability of HT29, HeLa, and HEK293 cell lines to 42±3% (p = 0.0001), 49±12% (p = 0.0009), and 77±5% (p = 0.007), respectively, indicating its potential selective cytotoxicity, as supported by the disturbed cell morphology.  The NDV LaSota strain exhibits a potential selective oncolytic activity towards cancer cell lines, thus may serve as an interesting candidate for virotherapy against colorectal and cervical cancer

Conformation of Prion Protein Repeat Peptides Probed by FRET Measurements and Molecular Dynamics Simulations

We report the combined use of steady-state fluorescence resonance energy transfer (FRET) experiments and molecular dynamics (MD) simulations to investigate conformational distributions of the prion protein (PrP) repeat system. FRET was used for the firs

Copper-induced conformational change in a marsupial prion protein repeat peptide probed using FTIR spectroscopy

We report the first Fourier transform infrared analysis of prion protein (PrP) repeats and the first study of PrP repeats of marsupial origin. Large changes in the secondary structure and an increase in hydrogen bonding within the peptide groups were evident from a red shift of the amide I band by >7 cm-1 and an approximately five-fold reduction in amide hydrogen-deuterium exchange for peptide interacting with Cu2+ ions. Changes in the tertiary structure upon copper binding were also evident from the appearance of a new band at 1564 cm-1, which arises from the ring vibration of histidine. The copper-induced conformational change is pH dependent, and occurs at pH >7

Immunoinformatics Analysis of SARS-CoV-2 ORF1ab Polyproteins to Identify Promiscuous and Highly Conserved T-Cell Epitopes to Formulate Vaccine for Indonesia and the World Population

SARS-CoV-2 and its variants caused the COVID-19 pandemic. Vaccines that target conserved regions of SARS-CoV-2 and stimulate protective T-cell responses are important for reducing symptoms and limiting the infection. Seven cytotoxic (CTL) and five helper T-cells (HTL) epitopes from ORF1ab were identified using NetCTLpan and NetMHCIIpan algorithms, respectively. These epitopes were generated from ORF1ab regions that are evolutionary stable as reflected by zero Shannon’s entropy and are presented by 56 human leukocyte antigen (HLA) Class I and 22 HLA Class II, ensuring good coverage for the Indonesian and world population. Having fulfilled other criteria such as immunogenicity, IFNγ inducing ability, and non-homology to human and microbiome peptides, the epitopes were assembled into a vaccine construct (VC) together with β-defensin as adjuvant and appropriate linkers. The VC was shown to have good physicochemical characteristics and capability of inducing CTL as well as HTL responses, which stem from the engagement of the vaccine with toll-like receptor 4 (TLR4) as revealed by docking simulations. The most promiscuous peptide 899WSMATYYLF907 was shown via docking simulation to interact well with HLA-A*24:07, the most predominant allele in Indonesia. The data presented here will contribute to the in vitro study of T-cell epitope mapping and vaccine design in Indonesia

Conformation of Prion Protein Repeat Peptides Probed by FRET Measurements and Molecular Dynamics Simulations

We report the combined use of steady-state fluorescence resonance energy transfer (FRET) experiments and molecular dynamics (MD) simulations to investigate conformational distributions of the prion protein (PrP) repeat system. FRET was used for the first time to probe the distance, as a function of temperature and pH, between a donor Trp residue and an acceptor dansyl group attached to the N-terminus in seven model peptides containing one to three repeats of the second decarepeat of PrP from marsupial possum (PHPGGSNWGQ)(n)G, and one and two human PrP consensus octarepeats (PHGGGWGQ)(n)G. In multirepeat peptides, single-Trp mutants were made by replacing other Trp(s) with Phe. As previous work has shown PrP repeats do not adopt a single preferred stable conformation, the FRET values are averages reflecting heterogeneity in the donor-acceptor distances. The T-dependence of the conformational distributions, and derived average dansyl-Trp distances, were obtained directly from MD simulation of the marsupial dansyl-PHPGGSNWGQG peptide. The results show excellent agreement between the FRET and MD T-dependent distances, and demonstrate the remarkable sensitivity and reproducibility of the FRET method in this first-time use for a set of disordered peptides. Based on the results, we propose a model involving cation-π or π-π His-Trp interactions to explain the T- (5–85°C) and pH- (6.0, 7.2) dependencies on distance, with HW i, i + 4 or WH i, i + 4 separations in sequence being more stable than HW i, i + 6 or WH i, i + 6 separations. The model has peptides adopting loosely folded conformations, with dansyl-Trp distances very much less than estimates for fully extended conformations, for example, ∼16 vs. 33, ∼21 vs. 69, and ∼22 vs. 106 Å for 1–3 decarepeats, and ∼14 vs. 25 and ∼19 vs. 54 Å for 1–2 octarepeats, respectively. The study demonstrates the usefulness of combining FRET with MD, a combination reported only once previously. Initial “mapping” of the conformational distribution of flexible peptides by simulation can assist in designing and interpreting experiments using steady-state intensity methods, and indicating how time-resolved or anisotropy methods might be used