Preventing fibril formation of a protein by selective mutation.
The origins of formation of an intermediate state involved in amyloid formation and ways to prevent it are illustrated with the example of the Formin binding protein 28 (FBP28) WW domain, which folds with biphasic kinetics. Molecular dynamics of protein folding trajectories are used to examine local and global motions and the time dependence of formation of contacts between C(α)s and C(β)s of selected pairs of residues. Focus is placed on the WT FBP28 WW domain and its six mutants (L26D, L26E, L26W, E27Y, T29D, and T29Y), which have structures that are determined by high-resolution NMR spectroscopy. The origins of formation of an intermediate state are elucidated, viz. as formation of hairpin 1 by a hydrophobic collapse mechanism causing significant delay of formation of both hairpins, especially hairpin 2, which facilitates the emergence of an intermediate state. It seems that three-state folding is a major folding scenario for all six mutants and WT. Additionally, two-state and downhill folding scenarios were identified in ∼ 15% of the folding trajectories for L26D and L26W, in which both hairpins are formed by the Matheson-Scheraga mechanism much faster than in three-state folding. These results indicate that formation of hairpins connecting two antiparallel β-strands determines overall folding. The correlations between the local and global motions identified for all folding trajectories lead to the identification of the residues making the main contributions in the formation of the intermediate state. The presented findings may provide an understanding of protein folding intermediates in general and lead to a procedure for their prevention.
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; gm56@cornell.edu maria.macias@irbbarcelona.org has5@cornell.edu.
Gia G
GG
Maisuradze
Structural Characterization of Macromolecular Assemblies, Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain;
Jordi
J
Medina
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301;
Khatuna
K
Kachlishvili
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland;
Pawel
P
Krupa
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland;
Magdalena A
MA
Mozolewska
Structural Characterization of Macromolecular Assemblies, Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain;
Pau
P
Martin-Malpartida
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301;
Luka
L
Maisuradze
Structural Characterization of Macromolecular Assemblies, Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain; Catalan Institution for Research and Advanced Studies, Barcelona, 08010, Spain gm56@cornell.edu maria.macias@irbbarcelona.org has5@cornell.edu.
Maria J
MJ
Macias
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301; gm56@cornell.edu maria.macias@irbbarcelona.org has5@cornell.edu.
Harold A
HA
Scheraga
D000465:Algorithms; D000682:Amyloid / Q000737:chemistry*; D002352:Carrier Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018360:Crystallography, X-Ray; D006801:Humans; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009154:Mutation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D013816:Thermodynamics
D000682:Amyloid; D002352:Carrier Proteins; D011506:Proteins; C473939:formin binding protein 28, human
FBP28 WW domain; fibril formation; high-resolution NMR spectroscopy; millisecond-timescale MD simulations; selective mutation