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Register a new userMultiscale models and approximation algorithms for protein electrostatics
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Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model have been surprisingly successful for simple biological questions, but fail for important problems such as understanding the effects of protein mutations. In this paper we highlight the advantages of boundary-integral methods for these problems, and our use of boundary integrals to design and test more accurate theories. Examples include a multiscale model based on nonlocal continuum theory, and a nonlinear boundary condition that captures atomic-scale effects at biomolecular surfaces.
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In this paper we extend the familiar continuum electrostatic model with a perturbation to the usual macroscopic boundary condition. The perturbation is based on the mean spherical approximation (MSA), to derive a multiscale hydration-shell boundary condition (HSBC). We show that the HSBC/MSA model reproduces MSA predictions for Born ions in a variety of polar solvents, including both protic and aprotic solvents. Importantly, the HSBC/MSA model predicts not only solvation free energies accurately but also solvation entropies, which standard continuum electrostatic models fail to predict. The HSBC/MSA model depends only on the normal electric field at the dielectric boundary, similar to our recent development of an HSBC model for charge-sign hydration asymmetry, and the reformulation of the MSA as a boundary condition enables its straightforward application to complex molecules such as proteins.
Sucralose is a commonly employed artificial sweetener that appears to destabilize protein native structures. This is in direct contrast to the bio-preservative nature of its natural counterpart, sucrose, which enhances the stability of biomolecules against environmental stress. We have further explored the molecular interactions of sucralose as compared to sucrose to illuminate the origin of the differences in their bio-preservative efficacy. We show that the mode of interactions of sucralose and sucrose in bulk solution differ subtly using hydration dynamics measurement and computational simulation. Sucralose does not appear to disturb the native state of proteins for moderate concentrations (<0.2 M) at room temperature. However, as the concentration increases, or in the thermally stressed state, sucralose appears to differ in its interactions with protein leading to the reduction of native state stability. This difference in interaction appears weak. We explored the difference in the preferential exclusion model using time-resolved spectroscopic techniques and observed that both molecules appear to be effective reducers of bulk hydration dynamics. However, the chlorination of sucralose appears to slightly enhance the hydrophobicity of the molecule, which reduces the preferential exclusion of sucralose from the protein-water interface. The weak interaction of sucralose with hydrophobic pockets on the protein surface differs from the behavior of sucrose. We experimentally followed up upon the extent of this weak interaction using isothermal titration calorimetry (ITC) measurements. We propose this as a possible origin for the difference in their bio-preservative properties.
Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be determined from the same set of X-ray data. We demonstrate here how barriers of activation can be determined solely from five-dimensional crystallography [5]. Directly linking molecular structures with barriers of activation between them allows for gaining insight into the structural nature of the barrier. We analyze comprehensive time series of crystal-lographic data at 14 different temperature settings and determine entropy and enthalpy contributions to the barriers of activation. 100 years after the discovery of X-ray scattering, we advance X-ray structure determination to a new frontier, the determination of energy landscapes.
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic contributions of the hydrophobic effect explicitly in an implicit solvent model. This allows us to capture two important effects: a length-scale dependence and a temperature dependence for the solvation of a hydrophobic particle. This consistent treatment of the hydrophobic effect explains cold denaturation and heat capacity measurements of solvated proteins.
Realistic 3D-conformations of protein structures can be embedded in a cubic lattice using exclusively integer numbers, additions, subtractions and boolean operations.
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