Keyword search (4,163 papers available)

"Molecular dynamics" Keyword-tagged Publications:

Title Authors PubMed ID
1 In silico molecular targets, docking, dynamics simulation and physiologically based pharmacokinetics modeling of oritavancin Fatoki TH; Balogun TC; Ojewuyi AE; Omole AC; Olukayode OV; Adewumi AP; Umesi AJ; Ijeoma NP; Apooyin AE; Chinedu CP; Idowu IE; Isah MJ; 39439008
CHEMBIOCHEM
2 In Silico Study of the Early Stages of Aggregation of β-Sheet Forming Antimicrobial Peptide GL13K Hamidabad MN; Watson NA; Wright LN; Mansbach RA; 38572930
PHYSICS
3 Interrogation of Bacillus anthracis SrtA active site loop forming open/close lid conformations through extensive MD simulations for understanding binding selectivity of SrtA inhibitors Selvaraj C; Selvaraj G; Mohamed Ismail R; Vijayakumar R; Baazeem A; Wei DQ; Singh SK; 34220215
BIOLOGY
4 Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation. Lindsay RJ, Mansbach RA, Gnanakaran S, Shen T 33581430
PHYSICS
5 Virtual screening, docking, and dynamics of potential new inhibitors of dihydrofolate reductase from Yersinia pestis. Bastos Lda C, de Souza FR, Guimarães AP, Sirouspour M, Cuya Guizado TR, Forgione P, Ramalho TC, França TC 26494420
CHEMISTRY

 

Title:In Silico Study of the Early Stages of Aggregation of β-Sheet Forming Antimicrobial Peptide GL13K
Authors:Hamidabad MNWatson NAWright LNMansbach RA
Link:https://pubmed.ncbi.nlm.nih.gov/38572930/
DOI:10.1002/cbic.202400088
Publication:Chembiochem : a European journal of chemical biology
Keywords:antimicrobial peptidesbiophysicsmolecular dynamics simulation
PMID:38572930 Category: Date Added:2024-04-04
Dept Affiliation: PHYSICS
1 Physics Department, Concordia University, Montréal, QC, H4B 1R6, Canada.

Description:

Antimicrobial peptides (AMPs) are of growing interest as potential candidates that may offer more resilience against antimicrobial resistance than traditional antibiotic agents. In this article, we perform the first in silico study of the synthetic ß sheet-forming AMP GL13K. Through atomistic simulations of single and multi-peptide systems under different conditions, we are able to shine a light on the short timescales of early aggregation. We find that isolated peptide conformations are primarily dictated by sequence rather than charge, whereas changing charge has a significant impact on the conformational free energy landscape of multi-peptide systems. We demonstrate that the loss of charge-charge repulsion is a sufficient minimal model for experimentally observed aggregation. Overall, our work explores the molecular biophysical underpinnings of the first stages of aggregation of a unique AMP, laying necessary groundwork for its further development as an antibiotic candidate.





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