Premium
Insight into the early stages of thermal unfolding of peanut agglutinin by molecular dynamics simulations
Author(s) -
Hansia Priti,
Dev Sagarika,
Surolia Avadhesha,
Vishveshwara Saraswathi
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21512
Subject(s) - tetramer , protein quaternary structure , molecular dynamics , chemistry , monomer , crystallography , structural stability , thermal stability , chemical physics , protein tertiary structure , protein structure , molten globule , protein folding , agglutinin , peanut agglutinin , biophysics , computational chemistry , biochemistry , circular dichroism , biology , organic chemistry , lectin , protein subunit , structural engineering , engineering , gene , enzyme , polymer
Abstract Peanut agglutinin is a homotetrameric nonglycosylated protein. The protein has a unique open quaternary structure. Molecular dynamics simulations have been employed to follow the atomistic details of its unfolding at different temperatures. The early events of the deoligomerization of the protein have been elucidated in the present study. Simulation trajectories of the monomer as well as those of the tetramer have been compared and the tetramer is found to be substantially more stable than its monomeric counterpart. The tetramer shows retention of most of its secondary structure but considerable loss of the tertiary structure at high temperature. This observation implies the generation of a molten globule‐like intermediate in the later stages of deoligomerization. The quaternary structure of the protein has weakened to a large extent, but none of the subunits are separated. In addition, the importance of the metal‐binding to the stability of the protein structure has also been investigated. Binding of the metal ions not only enhances the local stability of the metal‐ion binding loop, but also imparts a global stability to the overall structure. The dynamics of different interfaces vary significantly as probed through interface clusters. The differences are substantially enhanced at higher temperatures. The dynamics and the stability of the interfaces have been captured mainly by cluster analysis, which has provided detailed information on the thermal deoligomerization of the protein. Proteins 2007. © 2007 Wiley‐Liss, Inc.