Interresidue distance

Haas E, McWherter C, Scheraga H. Conformational unfolding in the N-terminal region of ribonuclease A detected by nonradiative energy transfer Distribution of interresidue distances in the native, denatured, and reduced-denatured states. Biopolymers 1988 27 1-21. 

Jeschke G, Wegener C, Nietschke M, Jung H, Steinhoff HJ (2004) Interresidual distance determination by four-pulse double electron-electron resonance in an integral membrane protein the NaVproline transporter PutP of Escherichia coli. Biophys J 86(4) 2551-2557... 

Another DFT calculations of the interresidual coupling constants in DNA have been reported in the paper by Barfield et al . Here the model has been extended to the DNA triplets T-A-T and C" Gr-C, but the calculations have been restricted to the FC terms obtained by means of the finite field method. The DFT calculations for several different base pairs separated by various interresidual distances have led to a good correlation between J(NN ) coupling and confirmed by the experimental data... 

Table II. Interresidue distances (in A) in neurotoxin II (pH 5-6) as evaluated by (a) EPR on di-spin labeled derivatives (31-33) and by (b) fluorescence study on spin- and dansyl-labeled derivatives(44).

D = one-dimensional ID. structure = one-dimensional (e.g., sequence or string of secondary structure) 2D = two-dimensional 2D structure = two-dimensional (e.g., interresidue distances) 3D = three-dimensional 3D structure = three-dimensional (coordinates of protein structure) PDB = Protein Data Bank of experimentally determined 3D structures... 

RMS deviations (in A) for nine distance constraints corresponding to observed interresidue connectivities in NOESY data set on globoside... 

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. 

The relationship between NOEs and proton-proton distances is well established and can be worked out, at least semiquantitavely and also quantitatively, when a full matrix relaxation analysis is considered. The detailed study of the conformation and dynamics of a tetrasaccharide related to the LeX antigen provides a good example of this approach.215 NOE intensities are sensitive to the respective conformer populations, and that therefore, an indication of the population distribution when these molecules are free in solution and even in the protein-bound state may be obtained by focusing on key interresidual NOEs.216... 

Under all circumstances, and due to the (r-6) or (r-3) dependence of the NOE, minor populations of conformers can be detected, provided that they show exclusive interresidue proton-proton distances 223... 

As mentioned earlier, in the event that interresidue NOEs arise from averaging of conformations, the use of ISPA distances as constraints may lead to virtual conformations. Moreover, the ISPA assumption that no spin diffusion is occurring is generally true only when the NOE mixing times are extremely short. In... 

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