Derivation from molecular dynamics

Wlodek, S. T., Antosiewicz, J., McCammon, J. A. Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories. Protein Sci. 6 (1997) 373-382. 

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. 

Further progress in understanding membrane instability and nonlocality requires development of microscopic theory and modeling. Analysis of membrane thickness fluctuations derived from molecular dynamics simulations can serve such a purpose. A possible difficulty with such analysis must be mentioned. In a natural environment isolated membranes assume a stressless state. However, MD modeling requires imposition of special boundary conditions corresponding to a stressed state of the membrane (see Refs. 84,87,112). This stress can interfere with the fluctuations of membrane shape and thickness, an effect that must be accounted for in analyzing data extracted from computer experiments. 

D. Chesnut and B. Rusiloski, A study of NMR chemical shielding in water clusters derived from molecular dynamics simulations, J. Molec. Struct. (THEOCHEM), 314 (1994), 19-30. 

The combination of Metastable Impact Electron Spectroscopy (MIES) and Ultraviolet Photoelectron Spectroscopy, UPS(Hel) has been applied to the study of the interaction between halides (Csl, CsF, and Nal) with solid water and methanol around their respective Tg values [11,12]. Surface segregation of iodide, but not of fluoride or Cs ions, took place from ASW, exposed to Csl or CsF vapour, during annealing [11]. The same behaviour was also derived from molecular dynamics (MD) simulations of the corresponding aqueous salt solutions. In contrast, no appreciable surface segregation of ions was observed in methanol under similar conditions, neither in the experiment nor in the simulation of the corresponding liquid solution. It was pointed out that, as far as solvation phenomena are concerned, water and methanol ices, when heated above their respective Tg values, behave remarkably similar to the corresponding liquid solutions. The surface propensity of iodide is also seen when Cs is replaced by Na [12]. 

Genheden S, Diehl C, Akke M, Ryde U (2010) Starting-condition dependence of order parameters derived from molecular dynamics simulations. J Chem Theory Comput 6 2176-2190... 

Figure 13. Swelling behavior for a smectite clay derived from molecular dynamics simulations of montmorillonite. The equilibrium d-spacing is presented as a function of water content of the clay. The plateaus in the experimental and simulation results at 12 A and 15 A represe nt the stabiUzation of, respectively, the one-layer (insert stracture) and two-layer hydrates. No further expansion of the smectite is observed in nature beyond the two-layer hydrate. The simulations suggest that further swelling of the clay is possible although not thermodynamically favored.

L. Murawski, R.J. Barczynski, A. Rybicka, V2O5-P5O5 glass and its polaron transport properties derived from molecular dynamic simulations of structure. In dielectric and related phenomena materials physico-chemistry, spectrometric investigations, and apphcations (1997), pp. 136-141... 

The first computations of ionization constants of residues in proteins for structures derived from molecular dynamics trajectories were described by Wendoloski and Matthew for tuna cytochrome c. In that study, conformers were generated using molecular dynamics simulations with a range of solvents, simulating macroscopic dielectric formalisms, and one solvent model that explicitly included solvent water molecules. The authors calculated individual pR values, overall titration curves, and electrostatic potential surfaces for average structures and structures along each simulation trajectory. However, the computational scheme for predicting electrostatic interactions in proteins used by Wendoloski and Matthew was not based on a FDPB model but on the modified Tanford-Kirkwood approach, which is not discussed in this chapter. 

S. T. Wlodek, J. Antosiewicz, and J. A. McCammoi Protein Set., 6,373 (1997). Prediction of Titration Properties of Structures of a Protein Derived from Molecular Dynamics Trajectories. 

This observation is in accordance with expectation, that is, enhanced ion-ion interactions in concentrated solutions. Furthermore, Hr(LiPF6-PC) > Hr(LiBF4-PC) is valid for the whole concentration range, indicating that the contact ion pair formation ability of PFg" is weaker than that of Bp4. This conclusion is in accordance with results from conductivity measurements for dilute solutions, see Table 17.7. Hr ratios were also derived from molecular dynamics (MD) trajectories and qualitatively agree with experimental values. 

Table 1. Average surface accessibilities (x) and the differences of the surface accessibility areas of CIDNP-sensitive residues derived from molecular dynamics calculations between the wild-type of EcorL (x) and the three single-site mutants [7]. All area values are given in A. Dot density 1 test sphere radius 1.5 A. denotes the site of mutation substituting the respective tyrosine residue with CIDNP-inert alanine.

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