2002
DOI: 10.1273/cbij.2.32
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Flexibility of a loop in a pheromone binding protein from <I>Bombyx mori</I>: a molecular dynamics simulation

Abstract: The three dimensional structure of a pheromone binding protein from Bombyx mori complexed with its substrate was determined recently [Sandler et al., Chem. Biol. 7, 143-151 (2000)]. The structure suggested that a loop formed by amino acid residues 60-69 could serve as a flexible lid into the pheromone binding pocket. To examine the above hypothesis, a molecular dynamics simulation was performed for a substrate free form of the protein starting from the crystal structure. In the simulation loop 60-69 took a con… Show more

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Cited by 9 publications
(6 citation statements)
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“…and Met55Leu) were found in MvitPBP1. A loop formed by amino acid residues 60-69 is the most flexible region of the protein, and it serves as the lid into the pheromone-binding pocket (Nemoto, Uebayasi, & Komeiji, 2002). Thus, the identified MvitPBPs are similar to the structure of already reported lepidopteran PBPs or GOBPs.…”
Section: Discussionsupporting
confidence: 68%
See 1 more Smart Citation
“…and Met55Leu) were found in MvitPBP1. A loop formed by amino acid residues 60-69 is the most flexible region of the protein, and it serves as the lid into the pheromone-binding pocket (Nemoto, Uebayasi, & Komeiji, 2002). Thus, the identified MvitPBPs are similar to the structure of already reported lepidopteran PBPs or GOBPs.…”
Section: Discussionsupporting
confidence: 68%
“…A loop formed by amino acid residues 60-69 is the most flexible region of the protein, and it serves as the lid into the pheromone-binding pocket (Nemoto, Uebayasi, & Komeiji, 2002). A loop formed by amino acid residues 60-69 is the most flexible region of the protein, and it serves as the lid into the pheromone-binding pocket (Nemoto, Uebayasi, & Komeiji, 2002).…”
Section: Discussionmentioning
confidence: 99%
“…Analysis of RMSF shows that the maximum fluctuation is found to be associated with the residues forming the loop regions (L1 and L2). The result is in good agreement with the experimental observation showing that loops are more flexible than helix and strands [29]. The results of simulations performed at different temperatures indicate that the native structure PhD1 is stable (except at 490 K) and all the secondary structures are intact at all temperatures used in the calculation.…”
Section: Discussionsupporting
confidence: 87%
“…The simulation box was neutralized by adding 9 and 10 Cl − ions to βPTH and αHTH, respectively. MD simulations were performed using the Peach 5.8 software package [36], in periodic boundary conditions and the canonical ensemble. The long-range Coulomb forces were calculated using the particle mesh Ewald method [37].…”
Section: Methodsmentioning
confidence: 99%