title: Temperature dependent dynamics of DegP-trimer: A molecular dynamics study.
abstract: DegP is a heat shock protein from high temperature requirement protease A family, which reacts to the environmental stress conditions in an ATP independent way. The objective of the present analysis emerged from the temperature dependent functional diversity of DegP between chaperonic and protease activities at temperatures below and above 28 °C, respectively. DegP is a multimeric protein and the minimal functional unit, DegP-trimer, is of great importance in understanding the DegP pathway. The structural aspects of DegP-trimer with respect to temperature variation have been studied using molecular dynamics simulations (for 100 ns) and principal component analysis to highlight the temperature dependent dynamics facilitating its functional diversity. The DegP-trimer revealed a pronounced dynamics at both 280 and 320 K, when compared to the dynamics observed at 300 K. The LA loop is identified as the highly flexible region during dynamics and at extreme temperatures, the residues 46-80 of LA loop express a flip towards right (at 280) and left ( at 320 K) with respect to the fixed β-sheet connecting the LA loop of protease for which Phe46 acts as one of the key residues. Such dynamics of LA loop facilitates inter-monomeric interaction with the PDZ1 domain of the neighbouring monomer and explains its active participation when DegP exists as trimer. Hence, the LA loop mediated dynamics of DegP-trimer is expected to provide further insight into the temperature dependent dynamics of DegP towards the understanding of its assembly and functional diversity in the presence of substrate.
authors.affiliation: Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India.
authors.forename: Nivedita
authors.initials: N
authors.lastname: Rai
authors.affiliation: Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India.
authors.forename: Amutha
authors.initials: A
authors.lastname: Ramaswamy
keywords: DegP-trimer; LA loop; Molecular dynamics simulation; PDZ1; PDZ2; Principal component analysis