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Relation between free energy landscapes of proteins and dynamics.

ABSTRACT: By examining the molecular dynamics (MD) of protein folding trajectories, generated with the coarse-grained UNRES force field, for the B-domain of staphylococcal protein A and the triple ?-strand WW domain from the Formin binding protein 28 (FBP), by principal component analysis (PCA), it is demonstrated how different free energy landscapes (FELs) and folding pathways of trajectories can be, even though they appear to be very similar by visual inspection of the time-dependence of the root-mean-square deviation (rmsd). Approaches to determine the minimal dimensionality of FELs for a correct description of protein folding dynamics are discussed. The correlation between the amplitude of the fluctuations of proteins and the dimensionality of the FELs is shown. The advantage of internal coordinate PCA over Cartesian PCA for small proteins is also illustrated.

SUBMITTER: Maisuradze GG

PROVIDER: S-EPMC3633568 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature

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Relation between free energy landscapes of proteins and dynamics.

Maisuradze Gia G GG Liwo Adam A Scheraga Harold A HA

Journal of chemical theory and computation 20100201 2

By examining the molecular dynamics (MD) of protein folding trajectories, generated with the coarse-grained UNRES force field, for the B-domain of staphylococcal protein A and the triple β-strand WW domain from the Formin binding protein 28 (FBP), by principal component analysis (PCA), it is demonstrated how different free energy landscapes (FELs) and folding pathways of trajectories can be, even though they appear to be very similar by visual inspection of the time-dependence of the root-mean-s ...[more]

PMID: 23620713

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Project description:The genetic missense A30P mutation of the wild-type ?-synuclein protein results in the replacement of the 30th amino acid residue from alanine (Ala) to proline (Pro) and was initially found in the members of a German family who developed Parkinson's disease. Even though the structures of these proteins have been measured before, detailed understanding about the structures and their relationships with free energy landscapes is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson's disease. We report the secondary and tertiary structures and conformational free energy landscapes of the wild-type and A30P mutant-type ?-synuclein proteins in an aqueous solution environment via extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations. In addition, we present the residual secondary structure component transition stabilities at the atomic level with dynamics in terms of free energy change calculations using a new strategy that we reported most recently. Our studies yield new interesting results; for instance, we find that the A30P mutation has local as well as long-range effects on the structural properties of the wild-type ?-synuclein protein. The helical content at Ala18-Gly31 is less prominent in comparison to the wild-type ?-synuclein protein. The ?-sheet structure abundance decreases in the N-terminal region upon A30P mutation of the wild-type ?-synuclein, whereas the NAC and C-terminal regions possess larger tendencies for ?-sheet structure formation. Long-range intramolecular protein interactions are less abundant upon A30P mutation, especially between the NAC and C-terminal regions, which is linked to the less compact and less stable structures of the A30P mutant-type rather than the wild-type ?-synuclein protein. Results including the usage of our new strategy for secondary structure transition stabilities show that the A30P mutant-type ?-synuclein tendency toward aggregation is higher than the wild-type ?-synuclein but we also find that the C-terminal and NAC regions of the A30P mutant-type ?-synuclein are reactive toward fibrillzation and aggregation based on atomic level studies with dynamics in an aqueous solution environment. Therefore, we propose that small molecules or drugs blocking the specific residues, which we report herein, located in the NAC- and C-terminal regions of the A30P mutant-type ?-synuclein protein might help to reduce the toxicity of the A30P mutant-type ?-synuclein protein.

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Relation between free energy landscapes of proteins and dynamics.

Publications

Relation between free energy landscapes of proteins and dynamics.

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