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Determination of the structural ensemble of the molten globule state of a protein by computer simulations
Author(s) -
Shimizu Masahiro,
Kajikawa Yukihito,
Kuwajima Kunihiro,
Dobson Christopher M.,
Okamoto Yuko
Publication year - 2019
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.25688
Subject(s) - radius of gyration , molten globule , maxima and minima , state (computer science) , molecular dynamics , histogram , gyration , chemistry , replica , statistical physics , crystallography , physics , computational chemistry , computer science , mathematics , algorithm , mathematical analysis , geometry , artificial intelligence , circular dichroism , art , visual arts , organic chemistry , image (mathematics) , polymer
We have used computer simulations to investigate the structural nature of the molten globule (MG) state of canine milk lysozyme. To sample the conformational space efficiently, we performed replica‐exchange umbrella sampling simulations with the radius of gyration as a reaction coordinate. We applied the Weighted Histogram Analysis Method to the trajectory of the simulations to obtain the potential of mean force, from which we identified representative structures corresponding to local minima in the free energy surface. The representative structures obtained in this way are in accord with the characteristics of the MG state reported previously by experimental studies. We conjecture that the MG state comprises a series of partially structured states undergoing relatively fast conformational interchange.