NOE-restrained molecular dynamics

Study of the ascidian L. patella (order Enterogona, family Didemnidae) yielded two new closely related cyclic peptide alkaloids namely lissoclinamide 9 389 and lissoclinamide 10 390 <2000T8345>. Their structures were determined by a combination of 2-D NMR, selective 1-D TOCSY, MS, and series-wound electrospray ionization (ESI)-MS (MSn) techniques, and the assignment of absolute stereochemistry was achieved by the hydrolysis of lissoclinamides followed by chiral thin layer chromatography. In the case of lissoclinamide 9, 389, NOE-restrained molecular dynamics studies were also performed confirming the proposed stereochemistry. 

K. Perturbations to NMR DNA chemical shifts and 24 intermolecular NOEs identified the 5 -ApG and 5 -GpT steps as the principle intercalation sites and allowed a structural model to be refined using NOE-restrained molecular dynamics (Figure 6a and b). 

Cachau RE, Gussio R, Beutler JA, Chmurny GN, Hilton BD, Muschik GM, Erickson JW (1994) Solution Structure of Taxol Determined Using a Novel Feedback-Scaling Procedure for Noe-Restrained Molecular Dynamics. Supercomput Appl High Perform Comput 8 24... 

Morris, LA., Kettenes van den Bosch, Vershris, K., Thompson, G.S., and (aspars, M. (2000) Structure determination and MS" analysis of two new lissodinamides isolated from the Indo-Padfrc ascidian lissocUnum patella NOE restrained molecular dynamics confirms the absolute stereochemistry derived by d radative mefliods. Tetrahedron, 56, 8345-8353. 

If all nuclei are assigned and the spectral parameters for the conformational analysis are extracted, a conformation is calculated - usually by distance geometry (DG) or restrained molecular dynamics calculations (rMD). A test for the quality of the conformation, obtained using the experimental restraints, is its stability in a free MD run, i.e. an MD without experimental restraints. In this case, explicit solvents have to be used in the MD calculation. An indication of more than one conformation in fast equilibrium can be found if only parts of the final structure are in agreement with experimental data [3]. Relaxation data and heteronuclear NOEs can also be used to elucidate internal dynamics, but this is beyond the scope of this article. 

Fig. 6.8 Correlation of experimental and theoretical residual dipolar couplings calculated using the structural data obtained from restrained molecular dynamics with NOEs, dihedral angle and RDCs-...

Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data A lac Repressor Headpiece Structure Based on Information on /-Coupling and from Presence and Absence of NOEs. 

In another application, 19F NMR studies have provided critical information on the bioactive conformation of taxoids. Fluorine-containing taxoids have been used as probes for NMR analysis of the conformational dynamics of paclitaxel in conjunction with molecular modeling [166], The dependence of the 19F chemical shifts and the Jm--ny values of these fluorinated analogues is examined through 19F and H variable-temperature (VT) NMR measurements. The experiments clearly indicate highly dynamic behavior of these molecules and the existence of equilibrium between conformers. The analysis of the VT NMR data in combination with molecular modeling, including restrained molecular dynamics (RMD), has identified three key conformers, which were further confirmed by the 19F- H heteronuclear NOE measurements. 

Pardaxin P-2 is a 33 amino acid peptide isolated from the mucc al secretion of the Pacific sole, Pardachirus pavoninus, that exhibits surfactant properties. Pardaxin has been shown to interfere with ion transport in both epithelium and nerve cells. At concentration below 10 mmol T, pardaxin forms voltage-dependent, ion-permeable channels in artificial liposomes. The structure of pardaxin P2 in aqueous trifluoroethanol solution has been determined using the NOE distance restrained/molecular dynamics method. This study showed that the peptide adopts an amphiphilic helix over residues 7-11, a bend at residues 12-13 and another helix over residues 14-26. 

J. De Vlieg, R. Boelens, R. M. Scheek, R. Kaptein, and W. F. van Gunsteren, hr. J. Chem., 27, 181 (1986). Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data A lac Repressor Headpiece Structure Based on Information on J-Coupling and from Presence and Absence of NOE s. 

Figure 7 Three-dimensional structure of DNA hairpin d(GCGAAGC) determined using NMR data obtained on a C- and N-labeled molecule. NOE, dihedral, and RDC restrains were applied to refine the structure using molecular dynamics simulations using AMBER 7.0 software package.

Recent developments in molecular dynamics techniques allow consideration of values and NOE restraints as an ensemble property (Lindorff-Larsen et al. 2005 Richter et al. 2007). The obtained ensembles represent a more realistic view of these flexible molecules in solution than those calculated with conventional NMR structure refinement methods. The dynamically restrained ensembles occupy a considerably larger conformational space than the conventionally calculated ones, and reproduce independent NMR parameters (e.g., chemical shifts) much better. 

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