Dynamics biomacromolecules

T Ichiye, RB Yelle, JB Koerner, PD Swartz, BW Beck. Molecular dynamics simulation studies of electron transfer properties of Ee-S proteins. Biomacromolecules Erom 3-D Structure to Applications. Hanford Symposium on Health and the Environment 34, Pasco, WA, 1995, pp 203-213. 

Equation (4-5) can be directly utilized in statistical mechanical Monte Carlo and molecular dynamics simulations by choosing an appropriate QM model, balancing computational efficiency and accuracy, and MM force fields for biomacromolecules and the solvent water. Our group has extensively explored various QM/MM methods using different quantum models, ranging from semiempirical methods to ab initio molecular orbital and valence bond theories to density functional theory, applied to a wide range of applications in chemistry and biology. Some of these studies have been discussed before and they are not emphasized in this article. We focus on developments that have not been often discussed. 

Hossain, K. S., Ochi, A., Ooyama, E., Magoshi,J., and Nemoto, N. (2003). Dynamic light scattering of native silk fibroin solution extracted from different parts of the middle division of the silk gland of the Bombyx mori silkworm. Biomacromolecules 4, 350-359. 

Various applications of NMR in biochemistry include structural identification of biomolecules, chemistry of individual groups in macromolecules, structural and dynamic information of biomacromolecules, metabolic studies, and kinetic and association constants of ligand bindings to macromolecules (Wiithrich, 1986). 

Yang, J., Wu, K., Konak, C., and Kopecek, J. "Dynamic light scattering study of self-assembly of HPMA hybrid graft copolymers". Biomacromolecules 9(2), 510-517 (2008). 

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. 

Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful method to determine the structure of biomacromolecules and their complexes in solution. It allows determination of the dynamics of proteins, RNA, DNA, and their complexes at atomic resolution. Therefore, NMR spectroscopy can monitor the often transient weak interactions in the interactome of proteins and the interaction between proteins and small-molecule ligands. In addition, intrinsically unstructured proteins can be investigated, and first reports of structure determination of membrane proteins in the immobilized state (solid state) are developing. This review will introduce the fundamental NMR observables as well as the methods to investigate structure and dynamics, and it will discuss several examples where NMR spectroscopy has provided valuable information in the context of Chemical Biology. 

Quantum mechanical calculations of the potential energy surfaces of smaller molecules or solids are widely used by physicists and chemists. In principle, they would also provide a more accurate basis for calculating the potential energy surfaces of proteins and DNAs. For these large biomacromolecules, however, such calculations are prohibitive because of the required amount of CPU time, especially during dynamics simulations, where energy calculations are extensive. Empirical energy functions are much faster to calculate and they have been... 

The combination of analytical pyrolysis, molecular modeling, and computational chemistry has also been stressed in investigating the structure of HS. It was reported that computational chemistry which allows to draw, construct and optimize in 3D space biomacromolecules, e.g., aquatic and terrestrial humic substances, with precise bond distances, bond angles, torsion angles, nonbonded distances, hydrogen bonds, charges, and chirality is a powerful tool, and molecular visualization and simulation can also be used to further understand the structure and dynamics of humic and dissolved organic matter. 

SDSL EPR as pioneered by W. L. Hubbel and co-workers has become a powerful tool for studying structure and dynamics of macromolecules, in particular biological macromolecules as proteins, which do not necessarily contain endogenous paramagnetic centers [1 ]. While SDSL EPR is applied to many biomacromolecules, this chapter provides a rather selective insight into the field of SDSL EPR of proteins and is organized as follows. 

Molecules are dynamic, undergoing vibrations and rotations continually. Therefore the static picture of molecular structure provided by MM is not realistic. Flexibility and motion are clearly important to the biological functioning of biomacromolecules. These molecules are not static structures, but exhibit a variety of complex motions both in solution and in the crystalline state. Energy minimization concerns only the potential energy term of the total energy and so it treats the biomacromolecule as a static entity. The dynamic properties of the atoms in a macromolecule or the momentum of the atoms in space requires the description of the kinetic term. The momentum (p) is related to the force exerted on the atom (Ft) and the potential energy (V) by... 

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