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LpxA: A natural nanotube
Author(s) -
Das Atanu,
Mukhopadhyay Chaitali
Publication year - 2010
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.21475
Subject(s) - chemistry , molecular dynamics , energy landscape , chemical physics , stability (learning theory) , crystallography , computational chemistry , biochemistry , computer science , machine learning
UDP‐N‐acetylglucosamine 3‐O‐acyltransferase is a protein with a left‐handed parallel β‐helix, which is a natural nanotube. They are associated with unusual high stability. To identify the reason behind the structural stability of β‐helical nanotubular structure, we have performed a total of 4 μs molecular dynamics simulations of the protein in implicit solvent at four different temperatures and monitored the unfolding pathway. The correlation in movement between different regions of the nanotubular structure has been identified from the dynamical cross‐correlation map and contribution of some specific residues towards unfolding transition has been identified by principal component analysis. Difference in stability of the three loop regions has also been characterized. Construction of the unfolding conformational energy landscape identifies the probable intermediates that can appear in the unfolding pathway of the protein. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 845–853, 2010.