Protein folding simulation with solvent-induced force field: Folding pathway ensemble of three-helix-bundle proteins

Author(s):  
Shoji Takada
Author(s):  
Nur Shima Fadhilah Mazlan ◽  
Nurul Bahiyah Ahmad Khairudin

The structure and trajectories of the mutant peptide of ubiquitin (PDB ID: 1E0Q) has been studied using Molecular Dynamics (MD) simulation. The simulation was performed using AMBER 11 utilizing force field 99 for 50 ns at constant temperature 325 K. The purpose of this study is to investigate the protein folding pathway of protein 1E0Q. In this simulation, the protein 1E0Q has folded into its near native β-hairpin structure within 5 ns. The RMSD value as compared to the NMR structure from the first residue to 17 residues is 2.17 Å. It has been observed that Gly 10 had been responsible to promote β-turn which caused the structure to turn into β-hairpin. In secondary structure analysis, it is shown that the residue from Thr 6 to Lys 11 has formed a bend in the structure. Two beta strands has also been found comprising residues Glu 2 to Lys 5 and Ile 13 to Glu 16.


2012 ◽  
Vol 2 (1) ◽  
pp. 4-11
Author(s):  
Amedeo Caflisch ◽  
Peter Hamm

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Mélanie Roch ◽  
Emmanuelle Lelong ◽  
Olesya O. Panasenko ◽  
Roberto Sierra ◽  
Adriana Renzoni ◽  
...  

AbstractStaphylococcus aureus is a major human pathogen and represents a clinical challenge because of widespread antibiotic resistance. Methicillin resistant Staphylococcus aureus (MRSA) is particularly problematic and originates by the horizontal acquisition of mecA encoding PBP2a, an extracellular membrane anchored transpeptidase, which confers resistance to β-lactam antibiotics by allosteric gating of its active site channel. Herein, we show that dual disruption of PrsA, a lipoprotein chaperone displaying anti-aggregation activity, together with HtrA1, a membrane anchored chaperone/serine protease, resulted in severe and synergistic attenuation of PBP2a folding that restores sensitivity to β-lactams such as oxacillin. Purified PBP2a has a pronounced unfolding transition initiating at physiological temperatures that leads to irreversible precipitation and complete loss of activity. The concordance of genetic and biochemical data highlights the necessity for extracellular protein folding factors governing MRSA β-lactam resistance. Targeting the PBP2a folding pathway represents a particularly attractive adjuvant strategy to combat antibiotic resistance.


2011 ◽  
Vol 100 (9) ◽  
pp. L47-L49 ◽  
Author(s):  
Stefano Piana ◽  
Kresten Lindorff-Larsen ◽  
David E. Shaw

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