Protein-water system dynamics

In order to understand the effect of temperature on the water dynamics and how it leads to the glass transition of the protein, we have performed a study of a model protein-water system. The model is quite similar to the DEM, which deals with the collective dynamics within and outside the hydration layer. However, since we want to calculate the mean square displacement and diffusion coefficients, we are primarily interested in the single particle properties. The single particle dynamics is essentially the motion of a particle in an effective potential described by its neighbors and thus coupled to the collective dynamics. A schematic representation of the d)mamics of a water molecule within the hydration layer can be given by ... 

The hydration of proteins at subzero temperatures is reviewed. The thermodynamics of the protein-water system and the water molecule dynamics are discussed. The hydration layer around a protein at low temperature is best thought of as being in a glass-like state with the water molecules selectively oriented near ionic and polar groups at the protein surface. Water motions in the nanosecond and microsecond range have been detected. 

One solution to this problem is that implemented in the dynamical equations (6) and (7), which couple the classical Langevin equation for the atoms in the protein-water system to the stationary Schrodinger equation for the quantum excitations (thus ensuring that only quantum eigenstates are considered). One limitation of this solution is that it is only valid when the quantum excitation responds very fast to any changes in the classical conformation, something which is assumed to be true here. 

In another recent study of dielectric properties of a protein-water system, Loeffler et al. ° presented a rigorous derivation of a theory for the calculation of the frequency-dependent dielectric properties of each component of a system which, in their example, consisted of the HIV-1 zinc finger peptide, water, and one zinc and two chloride ions. A 13.1 ns molecular dynamics simulation was performed, and, from it, dielectric constants for the various components of the system were extracted. It was discovered that the first hydration layer had a much lower dielectric response (47) than that of ordinary bulk water (80). The... 

A detailed examination of LN behavior is available [88] for the blocked alanine model, the proteins BPTI and lysozyme, and a large water system, compared to reference Langevin trajectories, in terms of energetic, geometric, and dynamic behavior. The middle timestep in LN can be considered an adjustable quantity (when force splitting is used), whose value does not significantly affect performance but does affect accuracy with respect to the reference trajectories. For example, we have used Atm = 3 fs for the proteins in vacuum, but 1 fs for the water system, where librational motions are rapid. 

Edsall, J. T., and McKenzie, H. A. (1983). Water and proteins IE The location and dynamics of water in protein systems and its relation to their stability and properties. Adv. Biophys. 16, 53-184. 

The complex of protein, crystallographic water and the counter ions are treated as a fully solvated system. Two key developments were made to treat the system in a more realistic manner during molecular dynamics (i) water molecules were placed as a spherical shell with a radius 34 A from the center of the protein. The outer boundary of the spherical shell was defined by means of an artificial wall with a potential of the type W defined as ... 

Ice cream serves as a wonderful (and tasty) example of a complex, dynamically heterogeneous food system. A typical ice cream mix contains milk or cream (water, lactose, casein and whey proteins, lipids, vitamins, and minerals), sucrose, stabilizers and emulsifiers, and some type of flavor (e.g., vanilla). After the ingredients are combined, the mix is pasteurized and homogenized. Homogenization creates an oil-in-water emulsion, consisting of millions of tiny droplets of milk fat dispersed in the water phase, each surrounded by a layer of proteins and emulsifiers. The sucrose is dissolved in... 

Dynamics of water at surface of complex systems Study of aqueous micelles and proteins... 

We recently developed a systematic method that uses the intrinsic tryptophan residue (Trp or W) as a local optical probe [49, 50]. Using site-directed mutagenesis, tryptophan can be mutated into different positions one at a time to scan protein surfaces. With femtosecond temporal and single-residue spatial resolution, the fluorescence Stokes shift of the local excited Trp can be followed in real time, and thus, the location, dynamics, and functional roles of protein-water interactions can be studied directly. With MD simulations, the solvation by water and protein (residues) is differentiated carefully to determine the hydration dynamics. Here, we focus our own work and review our recent systematic studies on hydration dynamics and protein-water fluctuations in a series of biological systems using the powerful intrinsic tryptophan as a local optical probe, and thus reveal the dynamic role of hydrating water molecules around proteins, which is a longstanding unresolved problem and a topic central to protein science. 

In this section, we review our first examinations of tryptophan probing sensitivity and water dynamics in a series of important model systems from simple to complex, which range from a tripeptide [70], to a prototype membrane protein melittin [70], to a common drug transporter human serum albumin [71], and to lipid interface of a nanochannel [86]. At the end, we also give a special case that using indole moiety of tryptophan probes supramolecule crown ether solvation, and we observed solvent-induced supramolecule folding [87]. The obtained solvation dynamics in these systems are linked to properties or functions of these biological-relevant macromolecules. 

Using fs resolution, two residence times of water at the surface of two proteins have been reported (Fig. 7.6) [21]. The natural probe tryptophan amino acid was used to follow the dynamics of water at the protein surface. For comparison, the behavior in bulk water was also studied. The experimental result together with the theoretical simulation-dynamical equilibrium in the hydration shell, show the direct relationship between the residence time of water molecules at the surface of proteins and the observed slow component in solvation dynamics. For the two biological systems studied, a bimodal decay for the hydration correlation function, with two primary relaxation times was observed an ultrafast time, typically 1 ps or less, and a longer one typically 15-40 ps (Fig. 7.7) [21]. Both times are related to the residence period of water at the protein surface, and their values depend on the binding energy. Measurement of the OH librational band corresponding to intermolecular motion in nanoscopic pools of water and methanol... 

Interest in water at protein surfaces and other surfaces arises from a desire to understand structural, functional, and dynamic factors as well as their interrelationships. Nuclear magnetic resonance (NMR) spectroscopy provides both structural and dynamic information. This presentation will focus on dynamical aspects of the water-protein Interaction. In particular, the phenomenon of cross relaxation between the water and protein proton systems will be discussed and new evidence will be reported. Failure to recognize the importance of cross relaxation effects leads to incorrect conclusions about the dynamics of water at protein surfaces. 

Application to the BPTI Crystal. The system to be simulated consisted of the protein atoms of one BPTI molecule (5) and 140 water molecules. The required number of water molecules could be calculated both from the volume of the crystal for which protein-water energy is zero or negative (solvent space) (9) and from unit cell volume and density of protein and water. Protein-water interactions were calculated as in the first part of this article, protein-protein interactions as described elsewhere ( ). Interactions between water molecules were calculated using the ST2 model, introduced by Rahman and Stillinger in a molecular dynamics simulation of liquid water (11). 

Recently, the competitive adsorption dynamics of phospholipid/protein mixed system at the chloroform/water interface was investigated by using the drop volume technique. The three proteins P-Lactoglobulin, P-Casein, and Human Serum Albumin were used in this study. To investigate the influence of the phospholipid structure at concentrations close to the CAC (critic aggregation concentration) the four lipids dipalmitoyl phosphatidyl choline (DPPC), dimyristoyl phosphatidyl choline (DMPC), dimyristoyl phosphatidyl ethanolamine (DMPE)... 

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