title: Thermal stability and unfolding pathways of hyperthermophilic and mesophilic periplasmic binding proteins studied by molecular dynamics simulation.
abstract: The ribose binding protein (RBP), a sugar-binding periplasmic protein, is involved in the transport and signaling processes in both prokaryotes and eukaryotes. Although several cellular and structural studies have been reported, a description of the thermostability of RBP at the molecular level remains elusive. Focused on the hyperthermophilic Thermoytoga maritima RBP (tmRBP) and mesophilic Escherichia coli homolog (ecRBP), we applied molecular dynamics simulations at four different temperatures (300, 380, 450, and 500 K) to obtain a deeper insight into the structural features responsible for the reduced thermostability of the ecRBP. The simulations results indicate that there are distinct structural differences in the unfolding pathway between the two homologs and the ecRBP unfolds faster than the hyperthermophilic homologs at certain temperatures in accordance with the lower thermal stability found experimentally. Essential dynamics analysis uncovers that the essential subspaces of ecRBP and tmRBP are non-overlapping and these two proteins show different directions of motion within the simulations trajectories. Such an understanding is required for designing efficient proteins with characteristics for a particular application.
authors: a College of Chemistry and Chemical Engineering , Qiqihar University , Qiqihar 161006 , P.R. China.
authors: Lin
authors: L
authors: Chen
authors: b College of Chemistry and Biology , Beihua Uuniversity , Jilin 132000 , P.R. China.
authors: Xue
authors: X
authors: Li
authors: a College of Chemistry and Chemical Engineering , Qiqihar University , Qiqihar 161006 , P.R. China.
authors: Ruige
authors: R
authors: Wang
authors: a College of Chemistry and Chemical Engineering , Qiqihar University , Qiqihar 161006 , P.R. China.
authors: Fengqin
authors: F
authors: Fang
authors: a College of Chemistry and Chemical Engineering , Qiqihar University , Qiqihar 161006 , P.R. China.
authors: Wanli
authors: W
authors: Yang
authors: a College of Chemistry and Chemical Engineering , Qiqihar University , Qiqihar 161006 , P.R. China.
authors: Wei
authors: W
authors: Kan
mesh_terms: D000595:Amino Acid Sequence; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D033902:Periplasmic Binding Proteins / Q000737:chemistry*; D011487:Protein Conformation; D055550:Protein Stability; D058767:Protein Unfolding; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D033902:Periplasmic Binding Proteins
keywords: essential dynamics analysis; hyperthermophilic; mesophilic; molecular dynamics simulations; unfolding pathway