Protein 3D Hydration: A Case of Bovine Pancreatic Trypsin Inhibitor

Characterization of the hydrated state of a protein is crucial for understanding its structural stability and function. In the present study, we have investigated the 3D hydration structure of the protein BPTI (bovine pancreatic trypsin inhibitor) by molecular dynamics (MD) and the integral equation method in the three-dimensional reference interaction site model (3D-RISM) approach. Both methods have found a well-defined hydration layer around the protein and revealed the localization of BPTI buried water molecules corresponding to the X-ray crystallography data. Moreover, under 3D-RISM calculations, the obtained positions of waters bound firmly to the BPTI sites are in reasonable agreement with the experimental results mentioned above for the BPTI crystal form. The analysis of the 3D hydration structure (thickness of hydration shell and hydration numbers) was performed for the entire protein and its polar and non-polar parts using various cut-off distances taken from the literature as well as by a straightforward procedure proposed here for determining the thickness of the hydration layer. Using the thickness of the hydration shell from this procedure allows for calculating the total hydration number of biomolecules properly under both methods. Following this approach, we have obtained the thickness of the BPTI hydration layer of 3.6 Å with 369 water molecules in the case of MD simulation and 3.9 Å with 333 water molecules in the case of the 3D-RISM approach. The above procedure was also applied for a more detailed description of the BPTI hydration structure near the polar charged and uncharged radicals as well as non-polar radicals. The results presented for the BPTI as an example bring new knowledge to the understanding of protein hydration.

Investigating the mechanisms of photosynthetic proteins using continuum electrostatics

Computational methods based on continuum electrostatics are widely used in theoretical biochemistry to analyze the function of proteins. Continuum electrostatic methods in combination with quantum chemical and molecular mechanical methods can help to analyze even very complex biochemical systems. In this article, applications of these methods to proteins involved in photosynthesis are reviewed. After giving a short introduction to the basic concepts of the continuum electrostatic model based on the Poisson-Boltzmann equation, we describe the application of this approach to the docking of electron transfer proteins, to the comparison of isofunctional proteins, to the tuning of absorption spectra, to the analysis of the coupling of electron and proton transfer, to the analysis of the effect of membrane potentials on the energetics of membrane proteins, and to the kinetics of charge transfer reactions. Simulations as those reviewed in this article help to analyze molecular mechanisms on the basis of the structure of the protein, guide new experiments, and provide a better and deeper understanding of protein functions.

Protein Dynamics Tightly Connected to the Dynamics of Surrounding and Internal Water Molecules

Proteins are key components of biological cells. For example, enzymes catalyze biochemical reactions, membrane transporters are responsible for uptake and release of critical and superfluous components from the cell environment, and structural proteins are responsible for the stability of the cell wall and cytoskeleton. Many of the diverse protein functions involve dynamic transitions ranging from small local atomic displacements up to large allosteric conformational changes. In any conformation, proteins are in contact with the universal solvent medium of cells, water. Water not only surrounds proteins but is often an integral part of proteins and also is involved in key mechanistic steps. This Minireview discusses recent experimental and theoretical results on the role of water for protein dynamics and function.

Determination of the interfacial water content in protein-protein complexes from free energy simulations

The question as to how many tightly or weakly bound water molecules are located in interfaces between protein-protein complex constituents is addressed from a phase equilibrium point of view by developing a theory in the canonical ensemble. A fast method based on free energy simulations is described for computing the number of water molecules in the interface regions. Results are given for 211 interfacial cavities of 26 antigen-antibody complexes for which experimentally determined structures are found in the Protein Data Bank. The accuracy of the method is assessed and the computational water content is compared with experimental data, revealing the amount of water molecules not resolved by experimental approaches.

Monte Carlo simulation of an inhomogeneous dielectric continuum model for B-DNA

Thermodynamic and structural properties of the counterion atmosphere surrounding B-DNA are calculated by Monte Carlo simulation in a spatially inhomogeneous, but piecewise uniform, dielectric continuum cell model - the "barbarous" model. A boundary element formulation is implemented to study the sensitivity of these properties with respect to perturbations in the location of discontinuous dielectric boundaries relative to fixed and mobile charges. High concentrations are considered corresponding to the liquid crystalline hexagonally ordered phase of DNA. Primitive model results are verified against other simulation reports and a comparison of barbarous model predictions with experimental data is discussed. The internal energy, osmotic coefficient, radial distributions and the population ratio of counterions in the geometrically resolved major and minor grooves are all found to strongly depend on the dielectric boundary position. This suggests that a self-consistent development of the model should consider a free surface problem where the boundary is not specified a priori.