Structures Determined using NMR Data

Conformational Sampling Conformational Search Proteins Distance Geometry Theory, Algorithms, and Chemical Applications Macromolecular Structures Determined using NMR Data NMR Refinement Simulated Anneeding. 

Yet, distance constraints or restraints are the most commonly used for the determination of nucleic acid structures from NMR experiments. However, this topic is much too large to be reviewed here and we will refer the reader to reviews (see also Macromolecular Structures Determined using NMR Data and NMR Refinement). 

The other exciting use of simulations is in helping to refine experimental structures. Unlike small molecule X-ray studies, macromolecular crystallography and NMR lead to structures which are underdetermined and, thus, simulations can be useful in conjunction with the experimental data to refine/determine such structures. Structural refinement and analysis is covered by articles by Billeter Macromolecular Structures Determined using NMR Data), Brunger Macromolecular Structure Calculation and Refinement by Simulated Annealing Methods and Applications), Case NMR Refinement), and Miller Molecular Superposition). 

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.

We will discuss in this article first some general problems which arise in the NMR spectroscopy of peptides. Then, NMR techniques for signal assignment and extraction of conformational parameters will be described, followed by a short excursion into structure determination using NMR parameters. The final part will include the analysis of peptide dynamics based on NMR data. 

Conformationally heterogeneous states of proteins can be determined using NMR-derived structural data and suitable molecular dynamics techniques.100 Residual dipolar couplings have been shown to represent motions in ubiquitin slower than its correlation time.101 Using an extensive set of residual dipolar couplings, namely, 36 sets of amide NH, 6 sets of HNC and NC as well as 11... 

The overall approach to determining the structure of a protein is to use computational power to take into account concurrently (1) the known sequence of the amino acids in the protein (2) the known molecular structure of each of those amino acid residues, including bond distances and angles (3) the known planar structure of the peptide group (4) internuclear distances and interresidue bond angles, as determined from NMR data (5) correlations of chemical shifts and structural features and (6) minimization of energy and avoidance of unreasonable atomic contacts. There are a number of ways to handle the computations and to derive the molecular structure, but all of them depend critically on the data supplied by NMR. 

NMR has become an important tool for determination of high-resolution three-dimensional structures of biomolecules. As of the end of 2006, over 14% of all structures deposited in the protein data bank (PDB) were determined using NMR, a trend showing tremendous growth since the first NMR structure of a protein was reported in... 

Chart 1) have particular preferences for the formation of a 14-helix and a 12-helix, respectively. The crystal structure of oligomers 6 (based on the former monomer) indeed revealed a perfect 14-helix, but although strong indications for the presence of a similar structure in solution were obtained, no definitive solution data have been presented yet.29 For a hexamer (7a) and an octamer (7b) of the cyclopen-tane-derived /1-peptide, the solution structure was determined using NMR. This supported the existence of the 12-helix structure which was also found in the solid state.30 More recently also X-ray data on the packing of these helices in the solid state have become available, which may help to design tertiary structures based on these foldamers.31... 

The accuracy of a procedure for structure determination can also be assessed using NMR data simulated for model structures 238-240,326 Using this approach, a possible bias in refined structures due to a particular choice of computational procedure, force field, number and type of experimental restraints, and so on can be investigated. However, the source of the bias may also be due to experimental data, such as mis-assignments, incorrectly estimated experimental errors, or conformational averaging. 

The upper size limitation for complete structure determination is not well defined. Structures of proteins that are less than 30 kDa should be obtainable by NMR methods. However, it is certainly possible to obtain some degree of structural information on much larger proteins (e.g., 30-80 kDa). The five different types of constraints that are commonly used in structure determination by NMR spectroscopy are listed below. The first two are the most common forms of constraints for the generation of structures from the NMR data. 

In the PDB, it is strongly encouraged that the depositors also submit files containing experimental data that were used in the structure calculation. These hies include the distance and torsion angle constraints used in the structure calculations. These data are essential to judge the quality of a structure determined by NMR, and will be useful to reproduce the coordinates in other laboratories as structure calculation methods advance. Because of the different approaches for structure determinations by different depositors, it is, usually, difficult to compare and assess the quality of coordinates in the PDB. 

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