Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective
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Keywords:
Energy landscape
Association (psychology)
Basis (linear algebra)
Metastability
Electrostatics
We show that the interplay between excluded volume effects, hydrophobicity, and hydrogen bonding in a tubelike representation of a polypeptide chain gives rise to free energy landscapes that, in addition to a clear global minimum, are characterized by the general presence of a small number of metastable minima, which correspond to common structural motifs observed in proteins. The complexity of the landscape increases only moderately with the length of the chain. Analysis of the temperature dependence of these landscapes reveals that the stability of specific metastable states is maximal at a temperature close to the midpoint of folding. These mestastable states are therefore likely to be of particular significance in determining the generic tendency of proteins to aggregate into potentially pathogenic agents.
Metastability
Energy landscape
Maxima and minima
Folding (DSP implementation)
Chain (unit)
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We report a systematic study of low energy metastable states in van der Waals semimetals TiS2, TiSe2 and TiTe2 within the DFT theory by means the evolutionary search algorithm. We find a big difference between TiSe2, TiS2 and TiTe2 in low energy metastable states. While several metastable states exist in TiSe2 and TiS2, no low energy metastable states were found in TiTe2. We show that some of the obtained metastable states can be identified as charge density wave (CDW). We argue that existence of the low energy metastable phases indicates that emergence CDW as a ground state in these compounds.
Metastability
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We report a systematic study of low energy metastable states in van der Waals semimetals TiS2, TiSe2 and TiTe2 within the DFT theory by means the evolutionary search algorithm. We find a big difference between TiSe2, TiS2 and TiTe2 in low energy metastable states. While several metastable states exist in TiSe2 and TiS2, no low energy metastable states were found in TiTe2. We show that some of the obtained metastable states can be identified as charge density wave (CDW). We argue that existence of the low energy metastable phases indicates that emergence CDW as a ground state in these compounds.
Metastability
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We have performed molecular dynamics (MD) simulations of NaCl solution separated by two charged plates. In order to establish its applicability to future simulations of the transmembrane electrochemical gradient, we have employed the EW3DC technique for calculations of long range electrostatics. EW3DC allows for different salt concentrations on the two sides of the plates. Hence, the system mimics a transmembrane concentration gradient, a phenomena not previously simulated via MD. Molecular-level ordering of oxygens, hydrogens and salt ions produced oscillations in the electrostatic potential profile.
Electrostatics
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Computer simulations of a model glass-forming system are presented, which study the correlation between the dynamics in real space and the topography of the potential energy landscape. This analysis clearly reveals that in the supercooled regime the dynamics is strongly influenced by the presence of deep valleys in the energy landscape, corresponding to long-lived metastable amorphous states. We explicitly relate nonexponential relaxation effects and dynamic heterogeneities to these metastable states and thus to the specific topography of the energy landscape.
Supercooling
Metastability
Energy landscape
Dynamics
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Metastability
Stretched exponential function
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We study a theoretical possibility of conversion from stable crystals to metastable ones under grinding, by means of a generalized Becker–Döring model. When acceleration of crystal growth via clusters is effective, the metastable phase dominates and the stable phase vanishes if the relative excess of the metastable crystals to the stable ones is large enough in the initial state.
Metastability
Crystal (programming language)
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Significance Quantitative understanding of how individual interactions contribute to the kinetics and thermodynamics of protein folding is critical for deciphering the underlying molecular mechanisms that define the energy folding landscape. We applied a structure-based model that explicitly accounts for the interactions between charges, to folding–unfolding of four different protein pairs: rationally stabilized, via optimization of surface charge–charge interactions, variants, and respective wild types. First, we established that the models predict both thermodynamic and kinetic differences observed experimentally for all four studied protein pairs. Second, we used the results of the computational modeling to provide a molecular level explanation of how optimization of charge–charge interactions leads to an increase in the folding rates of designed variants, without changes in the unfolding rates.
Energy landscape
Electrostatics
Folding (DSP implementation)
Static electricity
Surface charge
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Metastability
Solid-state physics
Carbon fibers
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We report a systematic study of low energy metastable states in van der Waals semimetals TiS2, TiSe2 and TiTe2 within the DFT theory by means the evolutionary search algorithm. We find a big difference between TiSe2, TiS2 and TiTe2 in low energy metastable states. While several metastable states exist in TiSe2 and TiS2, no low energy metastable states were found in TiTe2. We show that some of the obtained metastable states can be identified as charge density wave (CDW). We argue that existence of the low energy metastable phases indicates that emergence CDW as a ground state in these compounds.
Metastability
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