Molecular motion, biological functioning

As the current correlation function in the time integral has sums over all charge velocities z, effects of cross terms between ionic and molecular motions appear which cannot be identified or separated by electromagnetic measurements. In addition to static solvation and saturation effects on permittivity often considered in biological contexts, Hubbard and Onsager have pointed out "kinetic depolarization" effects which need to be considered. In II, we discuss experimental evidence and implications of the theoretical predictions of such effects. 

All of the simulation approaches, other than harmonic dynamics, include the basic elements that we have outlined. They differ in the equations of motion that are solved (Newton s equations, Langevin equations, etc.), the specific treatment of the solvent, and/or the procedures used to take account of the time scale associated with a particular process of interest (molecular dynamics, activated dynamics, etc.). For example, the first application of molecular dynamics to proteins considered the molecule in vacuum.15 These calculations, while ignoring solvent effects, provided key insights into the important role of flexibility in biological function. Many of the results described in Chapts. VI-VIII were obtained from such vacuum simulations. Because of the importance of the solvent to the structure and other properties of biomolecules, much effort is now concentrated on systems in which the macromolecule is surrounded by solvent or other many-body environments, such as a crystal. 

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... 

DNA Is Involved In several biological functions requiring substantial changes In conformation. For example, the Intrinsically stiff DNA molecule Is wrapped fairly tightly about histones In nucleosomes, and this entire complex must be partially unraveled during replication and transcription. The ability of DNA to assume several different conformational forms In response to Its solid and solution environments has been evident for some time. Recent applications of spectroscopic methods sensitive to molecular dynamics have Indicated that double stranded DNA can also undergo rapid local motions of significant amplitude. 

NMR relaxation and its field dependence are a very important source of experimental information on dynamics of molecular motions. This information is conveyed through spectral density functions, which in turn are related to time-correlation functions (TCFs), fundamental quantities in the theory of liquid state. In most cases, characterizing the molecular dynamics through NMR relaxation studies requires the identification of the relaxation mechanism (for example the dipole-dipole interaction between a pair of spins) and models for the spectral densities/correlation functions." During the period covered by this review, such model development was concerned with both small molecules and large molecules of biological interest, mainly proteins. 

Measurements of spin-lattice relaxation rate as a function of the magnetic field/resonance frequency are commonly referred to as nuclear magnetic relaxation dispersion, NMRD. Measurements of this kind, when performed over a broad range, are an invaluable source of information on frequency-resolved molecular motions in complex biological or colloidal systems. Several years ago, Halle proposed a theory for relaxation of quadrupolar spins in dynamically heterogeneous systems... 

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