Molecular dynamics restrained

Solving Protein Structures Using Restrained Molecular Dynamics and Simulated Annealing... 

In a related way, ensemble molecular dynamics derives a pharmacophore using restrained molecular dynamics for a collection of molecules. A force field model is set up so that none of the atoms in each molecule sees the atoms in ainy other molecule. This enables the molecules to be overlaid in space. A restraint term is included in the potential, which forces the appropriate atoms or functional groups to be overlaid in space. 

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. 

Fig. 2.47 The (P)-2.5-helical structure of N.N -linked oligoureas as determined by NMR meaurements in pyridine-c/5. (A) Stereo-view along the helix axis of a low energy conformer of nonamer 178 generated by restrained molecular dynamics calculations. (Adapted from [274]). The helix is characterized by (i) a rigid +)-SYnclinal arrangement around the C(a)-...

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. 

Ragg, E., Tagliavini, F., Malesani, P., Monticelli, L., Bugiani, O., Forloni, G., and Salmona, M. (1999). Determination of solution conformations of PrP106-126, a neurotoxic fragment of prion protein, by 1H NMR and restrained molecular dynamics. Eur.J. Biochem. 266, 1192-1201. 

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-...

The most definitive proof of p-sheet structure requires the determination of the three-dimensional solution structure of the peptide. For the calculation of such structures one requires the accurate determination of coupling constants by DQF-COSY experiments which give backbone dihedral restraints and through-space connectivities (ROESY or NOESY experiments) which give rise to distance restraints. A combination of these restraints allows the calculation of the three-dimensional structure of the peptide using restrained molecular dynamics simulations. Utilizing this methodology, the three-dimensional structures of a number of cyclic peptides have been solved.[411... 

P R E CONTENTS Preface. Stable-Isotope Assisted Protein NMR Spectroscopy in Solution, Brian J. Stockman and John L. Mar-kley. 31P and 1H Two-Dimensional NMR and NOESY-Dis-tance Restrained Molecular Dynamics Methodologies for Defining Sequence-Specific Variations in Duplex Oligonucleotides, David G. Gorenstein, Robert P. Meadows, James T. Metz, Edward Nikonowcz and Carol Beth Post. NMR Study of B- and Z-DNA Hairpins of d[(CG) 3T4(CG)3] in Solution, Sa-toshi Ikuta and Yu-Sen Wang. Molecular Dynamics Simulations of Carbohydrate Molecules, J.W. Brady. Diversity in the Structure of Hemes, Russell Timkovich and Laureano L. Bon-doc. Index. Volume 2,1991, 180 pp. 112.50/E72.50 ISBN 1-55938-396-8... 

W. F. van Gunsteren, R. Boelens, R. Kaptein, R. M. Scheek, and E. R. P. Zuiderweg, in Molecular Dynamics and Protein Structure, J. Hermans, Ed., Polycrystal Book Service, Western Springs, Illinois, 1985, pp. 92-99. An Improved Restrained Molecular Dynamics Technique to Obtain Protein Tertiary Structure from Nuclear Magnetic Resonance Data. 

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. 

G. M. Clore, M. Nilges, D. K. Sukumaran, A. T. Briinger, M. Karplus, and A. M. Gronen-born, EMBO J., 5, 2729 (1986). The Three-Dimensional Structure of a-Purothionin in Solution Combined Use of Nuclear Magnetic Resonance, Distance Geometry, and Restrained Molecular Dynamics. 

Solution Conformation of a Heptadecapeptide Comprising the DNA Binding Helix F of the Cyclic AMP Receptor Protein of Escherichia coli. Combined Use of H Nuclear Magnetic Resonance and Restrained Molecular Dynamics. 

J. de Vlieg, R. M. Scheek, W. F. van Gunsteren, H. J. C. Berendsen, R. Kaptein, and J. Thomason, Proteins, 3, 209 (1988). Combined Procedure of Distance Geometry and Restrained Molecular Dynamics Techniques for Protein Structure Determination from Nuclear Magnetic Resonance Data Application to the DNA Binding Domain of lac Repressor from Escherichia coli. 

---