Polypeptide fold

Waddle, J. J., Johnston, T. C., and Baldwin, T. O. (1987). Polypeptide folding and dimerization in bacterial luciferase occur by a concerted mechanism in vivo. Biochemistry 26 4917-4921. 

As it is the case in polypeptide folding, nonspecific or promiscuous RNA-binding proteins can prevent RNA mis-folding and resolve mis-foldedRNAs, thereby ensuring that RNA is accessible for its biological function [ 1 ]. Certain DEAD-box proteins as well as some proteins that are involved in the assembly of ribonuleoparticles were shown to act as RNA chaperones. 

Matthews DA, Smith WW, Ferre RA, Condon B, Budahazi G, Sisson W, Villafranca JE, Janson CA, McElroy HE, Gribskov CL et al (1994) Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein. CeU 77 761-771... 

Figure 3 shows the three-dimensional structure of the MoFe protein from Klebsiella pneumoniae, Kpl, obtained at 1.65-A resolution (7). The overall structure of the polypeptides is frilly consistent with that reported earlier for Avl (3). The a and /8 subunits exhibit similar polypeptide folds with three domains of parallel /3 sheet/a helical type. At the interface between the three domains in the a subunit is a wide shallow cleft with the FeMoco at the bottom of the cleft about 10 A from the solvent. FeMoco is enclosed within the a subunit. The P cluster, however, is buried within the protein at the interface between the a and /8 subunits, being bound by cysteine residues from each subunit. A pseudo-twofold rotation axis passes between the two halves of the P cluster and relates the a and (3 subunits. Each af3 pair of subunits contains one FeMoco and one P cluster and thus appears... 

Investigation of the polypeptide folding properties of iron-sulfur via NMR spectroscopy began in 1997 (122). All studies performed to date have focused on the effect of the addition of guanidinium chloride (GdmCl hereafter) to protein solutions. Under these conditions, re-... 

How do the results reported in this chapter integrate in the so-called landscape perspective of polypeptide folding The essence of this... 

A particular goal of chemical theory is to predict protein structure from the amino acid sequence—to calculate how polypeptides fold into the compact geometries of proteins. One strategy is to develop methods (often based on bioinformatics) for predicting structures approximately and then refining the structures... 

Upon biosynthesis, a polypeptide folds into its native conformation, which is structurally stable and functionally active. The conformation adopted ultimately depends upon the polypeptide s amino acid sequence, explaining why different polypeptide types have different characteristic conformations. We have previously noted that stretches of secondary structure are stabilized by short-range interactions between adjacent amino acid residues. Tertiary structure, on the other hand, is stabilized by interactions between amino acid residues that may be far apart from each other in terms of amino acid sequence, but which are brought into close proximity by protein folding. The major stabilizing forces of a polypeptide s overall conformation are ... 

D. Hoffmann and E. W. Knapp, Polypeptide folding with off-lattice Monte Carlo... 

Figure 13.16 (a) Polypeptide fold and (b) electron transfer distances in E. coli quinol-fumarate reductase, (c) intercofactor distances in the Wolinella succinogenes enzyme. (From Iverson et al., 2002. Reproduced by permission of the Journal of Biological Chemistry.)... 

Ulmschneider, J.P., Ulmschneider, M.B., Di Nola, A. Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations. J. Phys. Chem. B 2006, 110, 16733 12. 

NiFe hydrogenase, see NiFe hydrogenase nitrate reductase, 47 3, 5,13-14, 396,403-406, 472, 475 NMR studies, 4na5 -Tll electron relaxation times, 47 252-257 polypeptide folding, 47 271-276 reduction potential, 47 265-266 solution structure, 47 266-271 valence delocalization, XJOSl, 259, 261-265... 

Polyoxygen fluoride radicals, 16 115 Polypeptide chain, transferrins, 41 397-398 folding, 41 400-402, 417-418 Polypeptide folding, iron-sulfur proteins, 47 271-276... 

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