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1.
J Phys Chem B ; 121(15): 3636-3643, 2017 04 20.
Article in English | MEDLINE | ID: mdl-28059510

ABSTRACT

Extensive molecular dynamics (MD) simulations have been used to characterize the multiple roles of water in solvating different types of proteins under different environmental conditions. We analyzed a small set of proteins, representative of the most prevalent meta-folds under native conditions, in the presence of crowding agents, and at high temperature with or without high concentration of urea. We considered also a protein in the unfolded state as characterized by NMR and atomistic MD simulations. Our results outline the main characteristics of the hydration environment of proteins and illustrate the dramatic plasticity of water, and its chameleonic ability to stabilize proteins under a variety of conditions.


Subject(s)
Molecular Dynamics Simulation , Proteins/chemistry , Water/chemistry , Magnetic Resonance Spectroscopy , Protein Stability , Solubility , Temperature , Urea/chemistry
2.
PLoS Comput Biol ; 12(7): e1005040, 2016 07.
Article in English | MEDLINE | ID: mdl-27471851

ABSTRACT

The habitat in which proteins exert their function contains up to 400 g/L of macromolecules, most of which are proteins. The repercussions of this dense environment on protein behavior are often overlooked or addressed using synthetic agents such as poly(ethylene glycol), whose ability to mimic protein crowders has not been demonstrated. Here we performed a comprehensive atomistic molecular dynamic analysis of the effect of protein crowders on the structure and dynamics of three proteins, namely an intrinsically disordered protein (ACTR), a molten globule conformation (NCBD), and a one-fold structure (IRF-3) protein. We found that crowding does not stabilize the native compact structure, and, in fact, often prevents structural collapse. Poly(ethylene glycol) PEG500 failed to reproduce many aspects of the physiologically-relevant protein crowders, thus indicating its unsuitability to mimic the cell interior. Instead, the impact of protein crowding on the structure and dynamics of a protein depends on its degree of disorder and results from two competing effects: the excluded volume, which favors compact states, and quinary interactions, which favor extended conformers. Such a viscous environment slows down protein flexibility and restricts the conformational landscape, often biasing it towards bioactive conformations but hindering biologically relevant protein-protein contacts. Overall, the protein crowders used here act as unspecific chaperons that modulate the protein conformational space, thus having relevant consequences for disordered proteins.


Subject(s)
Models, Molecular , Protein Conformation , Protein Folding , Proteins/chemistry , Proteins/metabolism , Computational Biology , Macromolecular Substances , Polyethylene Glycols/chemistry , Water/chemistry
3.
PLoS Comput Biol ; 9(12): e1003393, 2013.
Article in English | MEDLINE | ID: mdl-24348236

ABSTRACT

After decades of using urea as denaturant, the kinetic role of this molecule in the unfolding process is still undefined: does urea actively induce protein unfolding or passively stabilize the unfolded state? By analyzing a set of 30 proteins (representative of all native folds) through extensive molecular dynamics simulations in denaturant (using a range of force-fields), we derived robust rules for urea unfolding that are valid at the proteome level. Irrespective of the protein fold, presence or absence of disulphide bridges, and secondary structure composition, urea concentrates in the first solvation shell of quasi-native proteins, but with a density lower than that of the fully unfolded state. The presence of urea does not alter the spontaneous vibration pattern of proteins. In fact, it reduces the magnitude of such vibrations, leading to a counterintuitive slow down of the atomic-motions that opposes unfolding. Urea stickiness and slow diffusion is, however, crucial for unfolding. Long residence urea molecules placed around the hydrophobic core are crucial to stabilize partially open structures generated by thermal fluctuations. Our simulations indicate that although urea does not favor the formation of partially open microstates, it is not a mere spectator of unfolding that simply displaces to the right of the folded ←→ unfolded equilibrium. On the contrary, urea actively favors unfolding: it selects and stabilizes partially unfolded microstates, slowly driving the protein conformational ensemble far from the native one and also from the conformations sampled during thermal unfolding.


Subject(s)
Protein Unfolding , Proteome
4.
Proc Natl Acad Sci U S A ; 110(15): 5933-8, 2013 Apr 09.
Article in English | MEDLINE | ID: mdl-23536295

ABSTRACT

We present here the characterization of the structural, dynamics, and energetics of properties of the urea-denatured state of ubiquitin, a small prototypical soluble protein. By combining state-of-the-art molecular dynamics simulations with NMR and small-angle X-ray scattering data, we were able to: (i) define the unfolded state ensemble, (ii) understand the energetics stabilizing unfolded structures in urea, (iii) describe the dedifferential nature of the interactions of the fully unfolded proteins with urea and water, and (iv) characterize the early stages of protein refolding when chemically denatured proteins are transferred to native conditions. The results presented herein are unique in providing a complete picture of the chemically unfolded state of proteins and contribute to deciphering the mechanisms that stabilize the native state of proteins, as well as those that maintain them unfolded in the presence of urea.


Subject(s)
Protein Denaturation , Ubiquitin/chemistry , Urea/chemistry , Computer Simulation , Hydrogen Bonding , Hydrogen-Ion Concentration , Magnetic Resonance Spectroscopy , Molecular Dynamics Simulation , Protein Folding , Protein Structure, Secondary , Scattering, Radiation , Solvents/chemistry , Time Factors , Water/chemistry , X-Rays
5.
PLoS One ; 5(2): e9234, 2010 Feb 16.
Article in English | MEDLINE | ID: mdl-20169066

ABSTRACT

The action of dopamine on the aggregation of the unstructured alpha-synuclein (alpha-syn) protein may be linked to the pathogenesis of Parkinson's disease. Dopamine and its oxidation derivatives may inhibit alpha-syn aggregation by non-covalent binding. Exploiting this fact, we applied an integrated computational and experimental approach to find alternative ligands that might modulate the fibrillization of alpha-syn. Ligands structurally and electrostatically similar to dopamine were screened from an established library. Five analogs were selected for in vitro experimentation from the similarity ranked list of analogs. Molecular dynamics simulations showed they were, like dopamine, binding non-covalently to alpha-syn and, although much weaker than dopamine, they shared some of its binding properties. In vitro fibrillization assays were performed on these five dopamine analogs. Consistent with our predictions, analyses by atomic force and transmission electron microscopy revealed that all of the selected ligands affected the aggregation process, albeit to a varying and lesser extent than dopamine, used as the control ligand. The in silico/in vitro approach presented here emerges as a possible strategy for identifying ligands interfering with such a complex process as the fibrillization of an unstructured protein.


Subject(s)
Dopamine/analogs & derivatives , Dopamine/chemistry , alpha-Synuclein/chemistry , Circular Dichroism , Dopamine/metabolism , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Indoles/chemistry , Indoles/metabolism , Ligands , Microscopy, Atomic Force , Microscopy, Electron, Transmission , Molecular Dynamics Simulation , Molecular Structure , Oxidation-Reduction , Protein Binding , Protein Conformation , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Recombinant Proteins/ultrastructure , Static Electricity , Tyramine/chemistry , Tyramine/metabolism , Water/chemistry , alpha-Synuclein/genetics , alpha-Synuclein/metabolism
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