Protein long-range

Because of the intrinsic flexibility and poor resonance dispersion of unfolded and partly folded proteins, long-range NOEs are generally very difficult to observe and assign. While observation of a long-range NOE between two protons provides a definitive indication that they are in close proximity in at least some structures in the conformational ensemble, determination of the nature of the folded structures is difficult unless an extensive network of NOEs can be observed. This has so far been achieved in only one case (Mok et al., 1999). 

All the long-range forces discussed in this chapter play a role in biological processes. Interactions between membranes, proteins, ligands, antibodies... 

Loncharich, R.J., Brooks, B.R. The effects of truncating long-range forces on protein dynamics. Proteins 6 (1989) 32 5. 

Volkov, S.N. Conformational transitions and the mechanism of transmission of long-range effects in DNA. Preprint ITP-88-12E, Kiev (1988) 22 Krumhansl, J.A., Alexander, D.M. Nonlinear dynamics and conformational exitations in biomolecular materials. In Structure and dynamics nucleic acids and proteins. (Clementi, E., Sarma, R.H., eds) Adenine Press, New York (1983) 61-80... 

The development of efficient algorithms and the sophisticated description of long-range electrostatic effects allow calculations on systems with 100 000 atoms and more, which address biochemical problems like membrane-bound protein complexes or the action of molecular machines . 

Eor a macromolecule such as a large protein, the steps in characterization involve, first, identification of the spin systems present, using correlated spectroscopy, and identification of neighboring amino acids. The long range noes are then assigned, and three bond coupling constants ate deterrnined. 

N Go, H Taketomi. Respective roles of short- and long-range interactions m protein folding. Proc Natl Acad Sci USA 75 559-563, 1978. 

Membrane proteins in many cases are randomly distributed through the plane of the membrane. This was one of the corollaries of the fluid mosaic model of Singer and Nicholson and has been experimentally verified using electron microscopy. Electron micrographs show that integral membrane proteins are often randomly distributed in the membrane, with no apparent long-range order. 

Long range electron transfer in peptides and proteins. S. S. Isied, Prog. Inorg. Chem., 1984, 32, 443 (187). 

Hoffman BM, Natan MJ, Nocek JM, Wallin SA (1991) Long-Range Electron Transfer Within Metal-Substituted Protein Complexes. 75 85-108 Hoffmann BM, see Ibers JA (1982) 50 1-55... 

X-ray structures of mitochondrial 6ci complexes from three different sources (113, 124, 125) have found the b- and c-type hemes at roughly identical positions, whereas the Rieske protein was seen in different places as a function of crystal space group and presence or absence of inhibitors of the enzyme. This fact was interpreted to suggest a long-range conformational movement of the Rieske protein during turnover of the complex. The range of observed positions of the Rieske protein indicated that the soluble domain can move like a... 

The Effects of Long Range Cutoffs on Protein Dynamics... 

Methods. To explore the effects of long range truncation on molecular dynamics simulations of proteins, a series of simulations have been performed. The two main questions which have been addressed are ... 

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