Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins.
We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.
Institute for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, Parc Científic de Barcelona , Josep Samitier 1-5, Barcelona 08028, Spain.
Agustí
http://orcid.org/0000-0002-8441-1821
A
Emperador
Institute for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, Parc Científic de Barcelona , Josep Samitier 1-5, Barcelona 08028, Spain.|Joint IRB-BSC Program on Computational Biology , Barcelona 08028, Spain.|Departament de Bioquímica i Biomedicina, Facultat de Biología, Universitat de Barcelona , Avgda Diagonal 647, Barcelona 08028, Spain.
Modesto
http://orcid.org/0000-0002-8608-3278
M
Orozco
D064267:Intrinsically Disordered Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D066329:Protein Aggregates; D011487:Protein Conformation; D055503:Protein Multimerization
D064267:Intrinsically Disordered Proteins; D066329:Protein Aggregates