The present report regards a computational study aimed at assessing the conformational profile of the four stereoisomers of the peptide Ace-Pro-c3Phe-NMe, previously reported to exhibit beta-turn structures in dichloromethane with different type I/type II beta-turn profiles. Molecular systems were represented at the molecular mechanics level using the parm96 parameterization of the AMBER force field. Calculations were carried out in dichloromethane using an implicit solvent approach. Characterization of the conformational features of the peptide analogs was carried out using simulated annealing (SA), molecular dynamics (MD) and replica exchange molecular dynamics (REMD). Present results show that MD calculations do not provide a reasonable sampling after 300 ns. In contrast, both SA and REMD provide similar results and agree well with experimental observations.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1002/bip.21293 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Sensitive detection and propagation of brain-derived tau assemblies in HEK293 based wild-type tau seeding assays.
J Biol Chem
January 2025
UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge, CB2 0AH, United Kingdom. Electronic address:
The assembly of tau into filaments defines tauopathies, a group of neurodegenerative diseases including Alzheimer's disease (AD), Pick's disease (PiD), corticobasal degeneration (CBD) and progressive supranuclear palsy (PSP). The seeded aggregation of tau has been modelled in cell culture using pro-aggregant modifications such as truncation of N- and C-termini and point-mutations within the microtubule-binding repeat domain. This limits the applicability of research findings to sporadic disease, where aggregates contain wild-type, full-length tau.
View Article and Find Full Text PDFEstimated breeding values of dairy sires for cow colostrum and transfer of passive immunity traits.
JDS Commun
January 2025
Laboratory of Animal Husbandry, Faculty of Veterinary Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Greece PC 54124.
The objective of this study was to derive the estimated breeding values (EBVs) of Holstein sires for colostrum and passive transfer of immunity traits to (1) estimate the genetic association between these new traits and established production, conformation, and function, and (2) explore whether sires can be classified in specific profiles regarding the new traits. For cow colostrum traits, the study included 699 daughters of 67 sires from 6 commercial dairy herds. The number of daughters per sire ranged from 5 to 49.
View Article and Find Full Text PDFMetabolic profiles and potential antioxidant mechanisms of hawk tea.
Sci Rep
January 2025
Department of Food Science and Engineering, Moutai Institute, Renhuai, 564502, People's Republic of China.
Hawk tea has received increasing attention for its unique flavor and potential health benefits, with antioxidant function being one of its significant bioactivities. However, the metabolic profiles, potential antioxidant components, and action mechanisms of different types of hawk tea are still unclear. In this study, the chemical components of five hawk teas were determined using untargeted metabolomics.
View Article and Find Full Text PDFCarboxy-Amidated AamAP1-Lys has Superior Conformational Flexibility and Accelerated Killing of Gram-Negative Bacteria.
Biochemistry
January 2025
Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa.
C-terminal amidation of antimicrobial peptides (AMPs) is a frequent minor modification used to improve antibacterial potency, commonly ascribed to increased positive charge, protection from proteases, and a stabilized secondary structure. Although the activity of AMPs is primarily associated with the ability to penetrate bacterial membranes, hitherto the effect of amidation on this interaction has not been understood in detail. Here, we show that amidation of the scorpion-derived membranolytic peptide AamAP1-Lys produces a potent analog with faster bactericidal activity, increased membrane permeabilization, and greater Gram-negative membrane penetration associated with greater conformational flexibility.
View Article and Find Full Text PDFscHiGex: predicting single-cell gene expression based on single-cell Hi-C data.
NAR Genom Bioinform
March 2025
Department of Computer Science, University of Miami, Coral Gables, FL 33146, United States.
A novel biochemistry experiment named HiRES has been developed to capture both the chromosomal conformations and gene expression levels of individual single cells simultaneously. Nevertheless, when compared to the extensive volume of single-cell Hi-C data generated from individual cells, the number of datasets produced from this experiment remains limited in the scientific community. Hence, there is a requirement for a computational tool that can forecast the levels of gene expression in individual cells using single-cell Hi-C data from the same cells.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!