Loop segments

Fig. 4. Schematic of the protein threading problem, where I L represent particular core segments and (-) corresponds to variable loop segments ...

The distribution of loop segments is a simple exponential function of the distance from the surface while that of tail segments is the difference of two exponential functions and has a maximum at an intermediate distance. 

The thickness of the adsorbed region B which consists of a number of layers, each with Ms sites, is assumed to be <5 Pf where 6 and P are constants. Silberberg47) assumes that <5 = 1/2 and P = 1. Beyond this region is there a homogeneous bulk solution of polymer volume fraction < > from which adsorption has taken place. Except for solvent, all that is found in the region B are loop segments of the adsorbed polymer chains. Thus, the fraction of adsorbed polymer segments is expressed by... 

Kallikreins can be roughly divided into two categories, the classical kallikreins (hKl, hK2, and hK3) and the new kallikreins. The new kallikreins appear to be unique in their three-dimensional structure and share some features with trypsins and other features with the classical kallikreins. Comparative protein models show that the pattern of hydrophobic side-chain packing in the protein core is nearly identical in all human kallikreins, and the observed differences occur within the solvent-exposed loop segments. 

Hobartner, C., and Micura, R. (2004). Chemical synthesis of selenium-modified oligo-ribonucleotides and their enzymatic ligation leading to an U6 SnRNA stem-loop segment. J. Am. Chem. Soc. 126, 1141—1149. 

How general are such conclusions Do they apply to more complex proteins Are there more elusive features that influence turn preferences Selection for catalytic activity, an extremely sensitive probe of structural integrity, has the potential to reveal more subtle sequence preferences than simple screening protocols. We tested this premise using the EcCM enzyme (Fig. 3.4B) as a template [85]. The two identical polypeptides that make up this helical bundle protein consist of three helices joined by two loop segments (Fig. 3.12A) [33], The L2 loop connecting the H2 and H3 helices lies farthest from the active site and was targeted for analysis. 

Out of the six amino acid residues in the loop segment, which undergo conformation upon reduction, the only residue whose solvent accessibility to the intermembrane space changes is Asp 51. In the fully oxidized state. 

To mimic a prominent loop of the immunomodulatory cytokine interleukin la (IL-la), formed by residues 41-48, researchers s at Hoffmann-La Roche replaced the side chains of Leu-41 and Val-48 with a nonpeptide spacer. The purpose of this modification was to constrain the remainder of the loop segment so that it would maintain the proper distance and torsional angles. The 7-(2-aminoethyl)naphthalene-2-propionic acid (89) fragment was selected... 

As I have shown, the origin for the finite amorphous fraction formed by the (prevaiUng) loops is due to the balance between the entropic spring force created by the finite separation of the anchoring segments on the one hand side and the effort to remove the loop segments from the thermodynamically preferred crystalline phase on the other side. 

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