Computational methods and tools in antimicrobial peptide research

PGA Aronica, LM Reid, N Desai, J Li… - Journal of Chemical …, 2021 - ACS Publications
The evolution of antibiotic-resistant bacteria is an ongoing and troubling development that
has increased the number of diseases and infections that risk going untreated. There is an …

Constant ph molecular dynamics simulations: Current status and recent applications

VM de Oliveira, R Liu, J Shen - Current opinion in structural biology, 2022 - Elsevier
Many important protein functions are carried out through proton-coupled conformational
dynamics. Thus, the ability to accurately model protonation states dynamically has wide …

Biomedical applications of peptide-gold nanoarchitectonics

S Maghsoudian, E Sajjadi, N Hadavi, M Soltani… - International Journal of …, 2024 - Elsevier
Gold nanoparticles (AuNPs) have become a focus of interest in biomedicine due to their
unique properties. By attaching peptides to these nanoparticles (NPs), they can be utilized …

Molecular mechanisms of the influenza fusion peptide: insights from experimental and simulation studies

D Lousa, CM Soares - FEBS Open Bio, 2021 - Wiley Online Library
A key step in infections by enveloped viruses, such as influenza, is the fusion between the
viral envelope and the host cell membrane, which allows the virus to insert its genetic …

Parainfluenza fusion peptide promotes membrane fusion by assembling into oligomeric porelike structures

M Valério, DA Mendonça, J Morais, CC Buga… - ACS Chemical …, 2022 - ACS Publications
Paramyxoviruses are enveloped viruses harboring a negative-sense RNA genome that must
enter the host's cells to replicate. In the case of the parainfluenza virus, the cell entry process …

PKAD-2: new entries and expansion of functionalities of the database of experimentally measured pKa's of proteins

N Ancona, A Bastola, E Alexov - Journal of computational biophysics …, 2023 - World Scientific
Almost all biological reactions are pH-dependent and understanding the origin of pH
dependence requires knowledge of the pKa's of ionizable groups. Here, we report a new …

[HTML][HTML] Effect of microstructure and chemical proximate composition on mechanical properties of Procambarus clarkii shell

C Wang, G Shi, F Que, Y Xia, X Li, H Yang, L Shi, W Wu… - Lwt, 2022 - Elsevier
Procambarus clarkii was harvested in different months (April, May, and June) and classified
to different groups based on weight (small, 10–20 g; medium, 20–30 g; and large, 30–40 g) …

What Is the Protonation State of Proteins in Crystals? Insights from Constant pH Molecular Dynamics Simulations

N Aho, G Groenhof, P Buslaev - The Journal of Physical Chemistry …, 2024 - ACS Publications
X-ray crystallography is an important technique to determine the positions of atoms in a
protein crystal. However, because the native environment in which proteins function, is not a …

Two modes of fusogenic action for influenza virus fusion peptide

M Michalski, P Setny - PLOS Computational Biology, 2023 - journals.plos.org
The entry of influenza virus into the host cell requires fusion of its lipid envelope with the host
membrane. It is catalysed by viral hemagglutinin protein, whose fragments called fusion …

Molecular dynamics investigation of the influenza hemagglutinin conformational changes in acidic pH

SA Badiee, V Govind Kumar… - The Journal of Physical …, 2024 - ACS Publications
The surface protein hemagglutinin (HA) of the influenza virus plays a pivotal role in
facilitating viral infection by binding to sialic acid receptors on host cells. Its conformational …