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NMR characterizations of an amyloidogenic conformational ensemble of the PI3K SH3 domain
Author(s) -
Ahn HeeChul,
Le Yen T.H.,
Nagchowdhuri Partha S.,
DeRose Eugene F.,
PutnamEvans Cindy,
London Robert E.,
Markley John L.,
Lim Kwang Hun
Publication year - 2006
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.062154306
Subject(s) - sh3 domain , chemistry , monomer , protein folding , native state , amyloid (mycology) , crystallography , biophysics , peptide , relaxation (psychology) , molecular dynamics , proto oncogene tyrosine protein kinase src , kinase , biochemistry , computational chemistry , biology , inorganic chemistry , organic chemistry , polymer , neuroscience
Amyloid formation is associated with structural changes of native polypeptides to monomeric intermediate states and their self‐assembly into insoluble aggregates. Characterizations of the amyloidogenic intermediate state are, therefore, of great importance in understanding the early stage of amyloidogenesis. Here, we present NMR investigations of the structural and dynamic properties of the acid‐unfolded amyloidogenic intermediate state of the phosphatidylinositol 3‐kinase (PI3K) SH3 domain—a model peptide. The monomeric amyloidogenic state of the SH3 domain studied at pH 2.0 (35°C) was shown to be substantially disordered with no secondary structural preferences. 15 N NMR relaxation experiments indicated that the unfolded polypeptide is highly flexible on a subnanosecond timescale when observed under the amyloidogenic condition (pH 2.0, 35°C). However, more restricted motions were detected in residues located primarily in the β‐strands as well as in a loop in the native fold. In addition, nonnative long‐range interactions were observed between the residues with the reduced flexibility by paramagnetic relaxation enhancement (PRE) experiments. These indicate that the acid‐unfolded state of the SH3 domain adopts a partly folded conformation through nonnative long‐range contacts between the dynamically restricted residues at the amyloid‐forming condition.