Protein dynamics exploring techniques

Serum albumin circulates in the blood stream transporting essential nutrients such as fatty acids to peripheral tissue. Transported molecules, called ligands, often have a special affinity for selected binding sites on proteins and nucleic acids. In this experiment, the dynamics of ligand-protein interactions will be explored with the binding of the dye phenol red to bovine serum albumin. The technique of gel filtration will be used to separate the dye-protein complex. Data will be analyzed in order to construct binding curves. 

In proteins, all these different motions are localized within one macromolecule or a few molecules bound to each other. Thus, the space of motions is limited compared to the car race picture, just as if we were to explore the motions of selected parts of the engine and the cockpit during the race. Clearly, movements of the pistons and the crankshaft occur on a different time scale than that of the wheels or the full car, not to mention the driver-controlled steering wheel and transmission. In summary, molecular motions cover a wide range of time scales, occur in a spatially limited manner and, unlike cars and racing events, are not even directly observable. That is why we need sophisticated experimental techniques to characterize dynamics in biomacromolecules. 

EXPLORING PROTEIN STRUCTURE AND DYNAMICS A BRIEF OVERVIEW OF TECHNIQUES... 

For an understanding of protein-solvent interactions it is necessary to explore the modifications of the dynamics and structure of the surrounding water induced by the presence of the biopolymer. The theoretical methods best suited for this purpose are conventional molecular dynamics with periodic boundary conditions and stochastic boundary molecular dynamics techniques, both of which treat the solvent explicitly (Chapt. IV.B and C). We focus on the results of simulations concerned with the dynamics and structure of water in the vicinity of a protein both on a global level (i.e., averages over all solvation sites) and on a local level (i.e., the solvent dynamics and structure in the neighborhood of specific protein atoms). The methods of analysis are analogous to those commonly employed in the determination of the structure and dynamics of water around small solute molecules.163 In particular, we make use of the conditional protein solute -water radial distribution function,... 

Exploration of the conformational space of protein models could be done using different computational techniques. These include MD [21], Brownian dynamics [22,23], Monte Carlo methods [24-27], and other simulation or optimization techniques such as genetic algorithms [25,28-31]. 

We have recently started to explore a type of calculations in which DFT treatment of the quantum mechanical (QM) site is combined with either continuum electrostatics treatment of the protein, or with microscopic molecular mechanics/dynamics treatment of the protein, or with a combined molecular mechanics and continuum electrostatics treatment of the protein in a truly multiscale type of calculations. All these calculations have a spirit of QM/MM (quantum mechanics combined with molecular mechanics) method, which is currently in wide use in protein calculations. The DFT and the solvation energy calculations are performed in a self-consistent way. The work aims at both improving the QM part of p/ calculations and the MM or electrostatic part, in which of the protein dielectric properties are involved. In these studies, an efficient procedure has been developed for incorporating inhomogeneous dielectric models of the proteins into self-consistent DFT calculations, in which the polarization field of the protein is efficiently represented in the region of the QM system by using spherical harmonics and singular value decomposition techniques [41,42]. 

Formation of a stable protein-DNA complex involves the rearrangement of water molecules and release of counter ions and water molecules to the bulk. Zewail and co-workers have used the time-resolved fluorescence up-conversion technique to explore the dynamics of the histone-DNA complex formation and the participation of hydration water in the stability and specificity of the recognition process [9]. This important study established the contribution from the entropic gain due to the release of hydration water (often termed dynamically ordered water) to the bulk. 

Samouillan et al. (2011) studied the dielectric properties of elastin at different degrees of hydration and specifically at the limit of freezable water apparition. The quantification of freezable water was performed by DSC. Two dielectric techniques were used to explore the dipolar relaxations of hydrated elastin dynamic dielectric spectroscopy (DDS), performed isothermally with the frequency varying from 10 to 3 x 10 Hz, and the TSDC technique, an isochronal spectrometry running at variable temperature, analogous to a low-frequency spectroscopy (10 to 10 Hz). A complex relaxation map was evidenced by the two techniques. Assignments for the different processes can be proposed by the combination of DDS and TSDC experiments and the determination of the activation parameters of the relaxation times. As already observed for globular proteins, the concept of solvent-slaved protein motions was checked for the fibrillar hydrated elastin (Samouillan et al. 2011). 

Over the past 10-15 years computational methods have been developed which permit the study of protein and nucleic acid motions and structure, as well as some aspects of their reactivity. These techniques, known as biopolymer dynamics and mechanics [1,2], evolved from pioneering work by Alder and Wainwright [3] and Rahman [4] on the classical simulation of condensed phase systems. They were solidified by the first application of classical molecular dynamics to proteins by McCammon, Gelin and Karplus in 1977 [5]. Today a broad range of biophysical processes are explored using molecular simulation methods [1, 2]. 

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