Backbone conformations

Fig. 10. Conformational flooding accelerates conformational transitions and makes them accessible for MD simulations. Top left snapshots of the protein backbone of BPTI during a 500 ps-MD simulation. Bottom left a projection of the conformational coordinates contributing most to the atomic motions shows that, on that MD time scale, the system remains in its initial configuration (CS 1). Top right Conformational flooding forces the system into new conformations after crossing high energy barriers (CS 2, CS 3,. . . ). Bottom right The projection visualizes the new conformations they remain stable, even when the applied flooding potentials (dashed contour lines) is switched off.

M.J. Sippl, M. Hendlich and P. Lackner, Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments. Protein Sci. 1 (1992), 625-640. 

Backbone generation is the first step in building a three-dimensional model of the protein. First, it is necessary to find structurally conserved regions (SCR) in the backbone. Next, place them in space with an orientation and conformation best matching those of the template. Single amino acid exchanges are assumed not to affect the tertiary structure. This often results in having sections of the model compound that are unconnected. 

Perform a conformation search of the protein backbone using the meso-scale side-chain representation. 

Changes in the conformation of polymer chain backbone occur much more slowly in the vicinity of Tg than most of the molecular processes that serve as examples of simpler equilibria. 

The birefringence for phenyl-substituted PC (4) (T = 176 C) is reduced to about 50%, for benzyl substituted PC (5) (T = 138 C) to about 25%, and for four-ring bisphenol PC (6) to 8% of the value for BPA-PC (183,190,195,197,198) on condition of an optimum conformation of the phenyls in the side groups perpendicular to the aromatic rings in the backbone. In reaUty, however, these low birefringence values are not achieved, because the optimum conformation of the phenyl rings cannot be achieved in injection-stamped disks. 

Fig. 2. Protein secondary stmcture (a) the right-handed a-helix, stabilized by intrasegmental hydrogen-bonding between the backbone CO of residue i and the NH of residue t + 4 along the polypeptide chain. Each turn of the helix requires 3.6 residues. Translation along the hehcal axis is 0.15 nm per residue, or 0.54 nm per turn and (b) the -pleated sheet where the polypeptide is in an extended conformation and backbone hydrogen-bonding occurs between residues on adjacent strands. Here, the backbone CO and NH atoms are in the plane of the page and the amino acid side chains extend from C ...

To understand the function of a protein at the molecular level, it is important to know its three-dimensional stmcture. The diversity in protein stmcture, as in many other macromolecules, results from the flexibiUty of rotation about single bonds between atoms. Each peptide unit is planar, ie, oJ = 180°, and has two rotational degrees of freedom, specified by the torsion angles ( ) and /, along the polypeptide backbone. The number of torsion angles associated with the side chains, R, varies from residue to residue. The allowed conformations of a protein are those that avoid atomic coUisions between nonbonded atoms. 

The unusual properties of xanthan undoubtedly result from its stmctural rigidity, which in turn is a consequence of its Linear, ceUulosic backbone that is stiffened and shielded by the trisaccharide side chains. The conformation of xanthan in solution is a matter of debate. It does appear that the conformation changes with conditions. 

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