Molecular dynamics, NMR

NMR is a ubiquitous and indispensable tool for elucidating molecular structures, determining impurities, and studying molecular dynamics. NMR is also used to analyze simple mixtures without physical separation, and to measure molecular properties and bulk properties of the medium. The nondestructive nature of NMR permits the sample to be used for further investigation. As a noninvasive technique, NMR is often used to study molecular binding and to screen potential drug candidates. Therefore, despite its low sensitivity, NMR has become an essential analytical tool in academic and industrial environments. However, the inherent insensitivity causes detection limits of NMR to be a few orders below that of other standard analytical techniques [14], At present, the limit of detection achieved by NMR in concentration terms is in the millimolar range. 

Determination of pharmacophoric geometry for collagenase inhibitors using a novel computational method and its veriflcation using molecular dynamics, NMR, and X-ray crystallography. J. Am. Chem. Soc., 117, 4671-4682. 

NMR is a spectroscopic technique and as such it is very suited for investigations of molecule aspects such as molecular arrangements and molecular dynamics. NMR has gone through a dramatic devel opment over the last decades. For this reason there are numerous monographs treating many different aspects of the method (2-4). Here, we will attempt to introduce the technique from the point of view of emulsion science. 

J. Graf P.H. Nguyen, G. Stock, H. Schwalbe, Structure and dynamics of the homologous series of alanine peptides a joint molecular dynamics/NMR study, J. Am. Chem. Soc. 129 (2007) 1179-1189. 

Due to the high selectivity to details of chanical structure and molecular dynamics, NMR spectroscopy is a powerful method to provide relevant information about morphological and dynamic properties of the polymer [172,181-183]. 

The input to a minimisation program consists of a set of initial coordinates for the system. The initial coordinates may come from a variety of sources. They may be obtained from an experimental technique, such as X-ray crystallography or NMR. In other cases a theoretical method is employed, such as a conformational search algorithm. A combination of experimenfal and theoretical approaches may also be used. For example, to study the behaviour of a protein in water one may take an X-ray structure of the protein and immerse it in a solvent bath, where the coordinates of the solvent molecules have been obtained from a Monte Carlo or molecular dynamics simulation. 

A particularly important application of molecular dynamics, often in conjunction with the simulated annealing method, is in the refinement of X-ray and NMR data to determine the three-dimensional structures of large biological molecules such as proteins. The aim of such refinement is to determine the conformation (or conformations) that best explain the experimental data. A modified form of molecular dynamics called restrained moleculai dynarrdcs is usually used in which additional terms, called penalty functions, are added tc the potential energy function. These extra terms have the effect of penalising conformations... 

The greatest value of molecular dynamic simulations is that they complement and help to explain existing data for designing new experiments. The simulations are increasingly useful for structural refinement of models generated from NMR, distance geometry, and X-ray data. 

You can often use experimental data, such as Nuclear Overhauser Effect (NOE) signals from 2D NMR studies, as restraints. NOE signals give distances between pairs of hydrogens in a molecule. Use these distances to limit distances during a molecular mechanics geometry optimization or molecular dynamics calculation. Information on dihedral angles, deduced from NMR, can also limit a conformational search. 

You can add restraints to any molecular mechanics calculation (single point, optimization or dynamics). These might be NMR restraints, for example, or any situation where a length, angle, or torsion is known or pre-defined. Restraints with large force constants result in high frequency components in a molecular dynamics calculation and can result in instability under some circumstances. 

A molecular dynamics force field is a convenient compilation of these data (see Chapter 2). The data may be used in a much simplified fonn (e.g., in the case of metric matrix distance geometry, all data are converted into lower and upper bounds on interatomic distances, which all have the same weight). Similar to the use of energy parameters in X-ray crystallography, the parameters need not reflect the dynamic behavior of the molecule. The force constants are chosen to avoid distortions of the molecule when experimental restraints are applied. Thus, the force constants on bond angle and planarity are a factor of 10-100 higher than in standard molecular dynamics force fields. Likewise, a detailed description of electrostatic and van der Waals interactions is not necessary and may not even be beneficial in calculating NMR strucmres. 

Modeling in NMR Structure Determination B. Molecular Dynamics Simulated Annealing... 

Another principal difficulty is that the precise effect of local dynamics on the NOE intensity cannot be determined from the data. The dynamic correction factor [85] describes the ratio of the effects of distance and angular fluctuations. Theoretical studies based on NOE intensities extracted from molecular dynamics trajectories [86,87] are helpful to understand the detailed relationship between NMR parameters and local dynamics and may lead to structure-dependent corrections. In an implicit way, an estimate of the dynamic correction factor has been used in an ensemble relaxation matrix refinement by including order parameters for proton-proton vectors derived from molecular dynamics calculations [72]. One remaining challenge is to incorporate data describing the local dynamics of the molecule directly into the refinement, in such a way that an order parameter calculated from the calculated ensemble is similar to the measured order parameter. 

Molecular modeling is an indispensable tool in the determination of macromolecular structures from NMR data and in the interpretation of the data. Thus, state-of-the-art molecular dynamics simulations can reproduce relaxation data well [9,96] and supply a model of the motion in atomic detail. Qualitative aspects of correlated backbone motions can be understood from NMR structure ensembles [63]. Additional data, in particular residual dipolar couplings, improve the precision and accuracy of NMR structures qualitatively [12]. 

MI Sutcliffe, CM Dobson, RE Oswald. Solution structure of neuronal bungarotoxm determined by two-dimensional NMR spectroscopy Calculation of tertiary structure using systematic homologous model building, dynamical simulated annealing, and restrained molecular dynamics. Biochemistry 31 2962-2970, 1992. 

If the amount of the sample is sufficient, then the carbon skeleton is best traced out from the two-dimensional INADEQUATE experiment. If the absolute configuration of particular C atoms is needed, the empirical applications of diastereotopism and chiral shift reagents are useful (Section 2.4). Anisotropic and ring current effects supply information about conformation and aromaticity (Section 2.5), and pH effects can indicate the site of protonation (problem 24). Temperature-dependent NMR spectra and C spin-lattice relaxation times (Section 2.6) provide insight into molecular dynamics (problems 13 and 14). 

FIQ. 3 Diffusion coefficient of benzene molecules in benzene-polystyrene mixtures normalized by the diffusion coefficient of neat benzene molecular dynamics results, NMR measurements and prediction by the Mackie-Meares model [26]. 

More detailed aspects of protein function can be obtained also by force-field based approaches. Whereas protein function requires protein dynamics, no experimental technique can observe it directly on an atomic scale, and motions have to be simulated by molecular dynamics (MD) simulations. Also free energy differences (e.g. between binding energies of different protein ligands) can be characterised by MD simulations. Molecular mechanics or molecular dynamics based approaches are also necessary for homology modelling and for structure refinement in X-ray crystallography and NMR structure determination. 

It was demonstrated in Chapter 6 that impact theory is able to describe qualitatively the main features of the drastic transformations of gas-phase spectra into liquid ones for the case of a linear molecule. The corresponding NMR projection of spectral collapse is also reproduced qualitatively. Does this reflect any pronounced physical mechanism of molecular dynamics In particular, can molecular rotation in dense media be thought of as free during short time intervals, interrupted by much shorter collisions ... 

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