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Assessing the effect of D59P mutation in the DE loop region in amyloid aggregation propensity of β2‐microglobulin: A molecular dynamics simulation study
Author(s) -
Narang Simranjeet S.,
Shuaib Suniba,
Goyal Deepti,
Goyal Bhupesh
Publication year - 2018
Publication title -
journal of cellular biochemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.028
H-Index - 165
eISSN - 1097-4644
pISSN - 0730-2312
DOI - 10.1002/jcb.26241
Subject(s) - molecular dynamics , mutation , amyloid (mycology) , chemistry , amyloidosis , hydrogen bond , energy landscape , loop (graph theory) , biophysics , amyloid fibril , fibril , crystallography , biology , computational chemistry , biochemistry , molecule , mathematics , amyloid β , medicine , inorganic chemistry , organic chemistry , pathology , combinatorics , gene , disease
Dialysis‐related amyloidosis (DRA) is a severe condition characterized by the accumulation of amyloidogenic β2‐microglobulin (β2m) protein around skeletal joints and bones. The recent studies highlighted a critical role of the DE loop region for β2m stability and amyloid aggregation propensity. Despite significant efforts, the molecular mechanism of enhanced aggregation due to D59P mutation in the DE loop region remain elusive. In the present study, explicit‐solvent molecular dynamics (MD) simulations were performed to examine the key changes in the structural and dynamic properties of wild type (wt) β2m upon D59P mutation. MD simulations reveal a decrease in the average number of hydrogen bonds in the loop regions on D59P mutation that enhances conformational flexibility, which lead to higher aggregation propensity of D59P as compare to wt β2m. The principal component analysis (PCA) highlight that D59P covers a larger region of phase space and display a higher trace value than wt β2m, which suggest an overall enhancement in the conformational flexibility. D59P display two minimum energy basins in the free energy landscape (FEL) that are associated with thermodynamically less stable conformational states as compare to single minimum energy basin in wt β2m. The present study provides theoretical insights into the molecular mechanism behind the higher aggregation propensity of D59P as compare to wt β2m.