Folding of the firefly luciferase polypeptide chain with immobilized C-terminus

Refolding of Photinus pyralis firefly luciferase from a denatured state is a slow process; its rate and productivity depend on molecular chaperones of the Hsp70 family. In contrast, cotranslational folding of the enzyme is fast and productive in the absence of chaperones [Svetlov et al., 2006. Protein Sci. 15, 242-247]. During cotranslational folding, the C-termini of polypeptides are bound to massive particles - ribosomes. The question arises whether the immobilization of the polypeptide C-terminus on a massive particle promotes the folding. To test this experimentally, the luciferase with oligohistidine tag at its C-terminus was prepared. This allowed us to immobilize the protein C-terminal segment on chelating Sepharose beads. Here we show that both immobilized and free chains of urea-denatured enzyme refold with the same rate. At the same time, the immobilization of luciferase results in higher refolding yield due to prevention of inter-molecular aggregation. Chaperones of the Hsp70 family promote refolding of both immobilized and free luciferase polypeptides. The results presented here suggest that the high rate of cotranslational folding is not caused by the immobilization of polypeptide C-termini by itself, but is rather due to a favorable start conformation of the growing polypeptide in the peptidyl-transferase center of the ribosome and/or the strongly vectorial character of the folding from N- to C-terminus during polypeptide synthesis.     

Folding of the firefly luciferase polypeptide chain with the immobilized C terminus

Refolding of firefly Photinus pyralis luciferase from a denatured state is a slow process; its rate and productivity depend on molecular chaperones of the Hsp70 family. In contrast, cotranslational folding of luciferase is fast and productive in the absence of chaperones. During cotranslational folding, the C termini of polypeptides are associated with ribosomes, massive particles. The question arises as to whether C-terminal immobilization on a massive particle promotes folding. To study this problem experimentally, luciferase was C-tagged with hexahistidine to allow its C-terminal immobilization of chelating Sepharose. Both immobilized and free chains of the urea-denatured enzyme refolded at the same rate. At the same time, immobilization led to a higher refolding yield owing to the prevention of intermolecular aggregation. Chaperones of the Hsp70 family promoted folding of both immobilized and free luciferase polypeptides. It was assumed that the high rate of cotranslational folding is not ensured by mere immobilization of the C terminus of the polypeptide, but is rather due to a favorable start conformation of the growing peptide in the peptidyltransferase center of the ribosome and/or the vectorial character of the folding, proceeding from the N to the C end during polypeptide synthesis.     

Folding of polypeptide chains induced by the amino acid side-chains

Conformational calculations with the use of semi-empirical potential functions have been applied to the analysis of the folding of peptide chains. In particular, the part played by the amino acid side-chains in the adoption of folded conformations has been investigated.The results show that the preferred conformations of short peptides are mostly extended ones. However, from a given peptide chain-length, the side-chain to backbone and side-chain to side-chain interactions become strong enough so that definite sequences of amino acids can induce a transition from extended to folded conformations. We propose to call these folded structures “conformational nuclei”. The type of “nucleus” formed is dependent on both the amino acid composition and the sequence.Our results strongly support the hypothesis that folding of polypeptide chains can occur through a nucleation process that could be induced by the side-chains.     

Folding of the polypeptide chain(s), conformational flexibility and reactivity of the metal active site of hemocyanin and tyrosinase

Summary The comparative accessibility of the active sites of hemocyanin and tyrosinase, two proteins containing a binuclear type-3 copper site, has been investigated. The approaches were: (a) the kinetic study of the reaction of hemocyanin with cyanide in the presence of conformation perturbants; (b) the comparison between the kinetic parameters of the cyanide reaction on hemocyanin and tyrosinase; (c) the study of the efficiency and reaction mechanism of hemocyanin interaction with a typical tyrosinase substrate like catechol. The results indicate that the active site of tyrosinase is much more exposed than that of hemocyanin.     

Stability of polypeptide conformational states. II. Folding of a polypeptide chain by the scanning simulation method, and calculation of the free energy of the statistical coil

The scanning simulation method suggested by Meirovitch is extended to a study of the stability of decaglycine at 100 and 300 K. The model is based on the potential energy function ECEPP (Empirical Conformational Energy Program for Peptides) with rigid geometry and without solvent. The free energy of the statistical coil, which is defined over the whole phase space excluding the region of the right-handed α-helix, is calculated. At 100 K, the molecule is found to be unstable in the statistical coil region, and the method generates (i.e., “folds”) conformations that are left-handed or right-handed α-helices with very high preference. Their free energy is found to be comparable with that obtained by another method developed in our previous paper (paper I) [H. Meirovitch, M. Vásquez, and H. A. Scheraga, (1987) Biopolymers 26 , 651–671]. At 300 K the statistical coil becomes the most stable state; sample conformations of the coil are generated efficiently with the scanning method and the free energy is calculated. It appears that both the scanning method and the method of paper I can be used to carry out a complete analysis of the stability of a polypeptide based on free energy considerations.     

Hydrogen-tritium exchange of the random chain polypeptide

The Hydrogen–tritium exchange character of poly-D ,L -alanine was studied in detail as a model for the hydrogen exchange behavior of the unhindered, polymeric peptide group. The random chain nature of poly-D ,L -alanine was evident in the uniformity of exchange rate of all its hydrogens and in the similarity between this rate and that of random chain poly-D ,L -lysine and other known, unhindered secondary amide groups. An equilibrium isotope effect favoring the binding of tritium over protium to the extent of 21% was measured. Specific acid and base catalysis of the exchange and the absence of detectable general catalysis were demonstrated. Apparent energy of activation is 17 kcal/mole for deprotonation, largely due to dependence of K_w on temperature, and 15 kcal/mole for protonation, which correlates with the extreme apparent pK. The hydrogen –tritium exchange half-time rate; of poly-D ,L -alamine at any pH and temperature (T: °C) is given by the equation:      

Change in entropy of the free polypeptide chain during formation of hydrogen bonds]

Formation probabilities of different hydrogen bonds between carbonyl oxygen and amide hydrogen were determined by Monte Carlo simulations using a computer model in the space of sterically allowable conformations of alanine and glycine oligopeptides, and the corresponding entropy losses for the peptide backbone, T delta S, were calculated. The model was studied at different criteria of steric interactions. Comparison with the data of other authors showed the values of T delta S to be mainly determined by overall extent and type of the state space and to be only slightly dependent on its energy profile. Both short-range and long-range steric interactions were shown to prevent hydrogen bonding, especially in alanine peptides. In the model studied, the initiation of alpha(R)-helices is associated with T delta S = 8-10 kT, and prior formation of a 3/10-turn or one three-center H-bond does not appreciably decrease this entropy barrier. Elongation of the alpha(R)-helix by one residue leads to T delta S = 3.0-3.7 kT, the helices begin to stabilize after at least three sequential H-bonds are formed. The difference in the probability of insertion of Ala and Gly into the helix is lower than it follows from comparison of their mobility. The results could be explained assuming that factors different from helical H-bonds take part in the stabilization of the helices. One may suppose upon modeling of folding that even three sequential H-bonds are unable to fix the structure of a flexible peptide loop, while the elongation of alpha(R)-helices in the supersecondary helix-loop-helix structure is favorable as long as the loop conformation remains nearly optimal.     

Folding versus aggregation: polypeptide conformations on competing pathways

Protein aggregation has now become recognised as an important and generic aspect of protein energy landscapes. Since the discovery that numerous human diseases are caused by protein aggregation, the biophysical characterisation of misfolded states and their aggregation mechanisms has received increased attention. Utilising experimental techniques and computational approaches established for the analysis of protein folding reactions has ensured rapid advances in the study of pathways leading to amyloid fibrils and amyloid-related aggregates. Here we describe recent experimental and theoretical advances in the elucidation of the conformational properties of dynamic, heterogeneous and/or insoluble protein ensembles populated on complex, multidimensional protein energy landscapes. We discuss current understanding of aggregation mechanisms in this context and describe how the synergy between biochemical, biophysical and cell-biological experiments are beginning to provide detailed insights into the partitioning of non-native species between protein folding and aggregation pathways.     

Polymerization mechanism of polypeptide chain aggregation

The misfolding of polypeptide chains and aggregation into the insoluble inclusion body state is a serious problem for biotechnology and biomedical research. Developing a rational strategy to control aggregation requires understanding the mechanism of polymerization. We investigated the in vitro aggregation of P22 tailspike polypeptide chains by classical light scattering, nondenaturing gel electrophoresis, two-dimensional polyacrylamide gel electrophoresis (PAGE), and computer simulations. The aggregation of polypeptide chains during refolding occurred by multimeric polymerization, in which two multimers of any size could associate to form a larger aggregate and did not require a sequential addition of monomeric subunits. The cluster-cluster polymerization mechanism of aggregation is an important determinant in the kinetic competition between productive folding and inclusion body formation. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 333-343, 1997.     

A sugar chain at a specific position in the nascent polypeptide chain induces forward movement during translocation through the translocon

Nascent polypeptide chains synthesized by membrane bound ribosomes are cotranslationally translocated through and integrated into the endoplasmic reticulum translocon. Hydrophobic segments and positive charges on the chain are critical to halt the ongoing translocation. A marginally hydrophobic segment, which cannot be inserted into the membrane by itself, can be a transmembrane segment depending on its downstream positive charges. In certain conditions, positive charges even 60 residues downstream cause the marginally hydrophobic segment to span the membrane by inducing the segment to slide back from the lumen. Here we systematically examined the effect of a core sugar chain on the fate of a marginally hydrophobic segment using a cell-free translation and translocation system. A sugar chain added within 12 residues upstream of the marginally hydrophobic segment prevents the sliding back and promotes forward movement of the polypeptide chain. The sugar chain apparently functions as a ratchet to keep the polypeptide chain in the lumen. We propose that the sugar chain is a third topology determinant of membrane proteins, in addition to a hydrophobic segment and positive charges of the nascent chain.     

Folding of the nascent peptide chain into a biologically active protein

The refolding of denatured proteins with complete sequences may not be fast enough to account for the in vivo folding of growing peptide chains during biosynthesis. As some peptide fragments have secondary structures not unlike those of the corresponding segments in the intact molecules and native disulfide bonds of some proteins can form cotranslationally, it is suggested that the folding of the nascent chain begins early during synthesis. However, further adjustments may be necessary during chain elongation and after posttranslational modifications of the completed peptide chain to generate the native conformation of a biologically active protein.