Additives and Enzyme Stability

The polypeptide chain of an enzyme is folded so that the necessary functional groups are brought together in the active site. Conformational changes may disrupt this arrangement and cause loss of enzymic activity. The effect of soluble additives on the unfolding process is discussed. Additives may be classified as substrates and similar ligands, small uncharged organic molecules, specific and non-specific ionic species, and polymers.     

Microsecond Dynamics During the Binding-induced Folding of an Intrinsically Disordered Protein

Tau is an intrinsically disordered protein implicated in many neurodegenerative diseases. The repeat domain fragment of tau, tau-K18, is known to undergo a disorder to order transition in the presence of lipid micelles and vesicles, in which helices form in each of the repeat domains. Here, the mechanism of helical structure formation, induced by a phospholipid mimetic, sodium dodecyl sulfate (SDS) at sub-micellar concentrations, has been studied using multiple biophysical probes. A study of the conformational dynamics of the disordered state, using photoinduced electron transfer coupled to fluorescence correlation spectroscopy (PET-FCS) has indicated the presence of an intermediate state, I, in equilibrium with the unfolded state, U. The cooperative binding of the ligand (L), SDS, to I has been shown to induce the formation of a compact, helical intermediate (IL₅) within the dead time (∼37 µs) of a continuous flow mixer. Quantitative analysis of the PET-FCS data and the ensemble microsecond kinetic data, suggests that the mechanism of induction of helical structure can be described by a U ↔ I ↔ IL₅ ↔ FL₅ mechanism, in which the final helical state, FL₅, forms from IL₅ with a time constant of 50–200 µs. Finally, it has been shown that the helical conformation is an aggregation-competent state that can directly form amyloid fibrils.     

Spatial organization and conformational peculiarities of the callatostatin family of neuropeptides.

The structures and conformational peculiarities of five members of the callatostatin family of neuropeptides, i.e. Leu- and Met-callatostatins, ranging in size from 8 to 16 amino acid residues have been investigated by a theoretical conformational analysis method. A comparative analysis of the conformational flexibilities of Met-callatostatin with those of the hydroxylated analogues, [Hyp2]- and [Hyp3]-Met-callatostatin has been carried out. Helically packed C-terminal pentapeptide in the structure of all investigated Leu-callatostatins are shown to be possible. The reason for the great number low-energy conformers for the callatostatin N-terminus is discussed.     

Egg-laying strategy under natural conditions of Leptopilina boulardi, a hymenopteran parasitoid of Drosophila spp

The hypothesis of optimal host species selection predicts that when a parasitoid has the choice between two host species, it will choose the species thay gives the best survival chances for its progeny. We confirmed this hypothesis by laboratory experiments with Leptopilina boulardi Barb. et al., a cynipid parasitoid which prefers Drosophila melanogaster Meigen (the host species most suitable for parasitoid survival) above D. simulans Sturt. As far as fitness parameters are concerned, the fertility of L. boulardi is higher with D. melanogaster; the egg laying can be spread out over a long period when this host is relatively scarce. This does not occur with D. simulans in which parasitic oviposition stops soon when this host is not abundant.Investigations of this foraging strategy were done under more complex natural conditions. We found that L. boulardi has a type III functional response with D. melanogaster only; furthermore, it seems that a switching effect may exist with this host. Parasitoid females appear to distribute their eggs more regularly on D. melanogaster, thus avoiding superparasitism. This seems to be independent of the relative frequency of this host. However, superparasitism of D. simulans did occur more frequently when this host was scarce.

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Stratégie de ponte de Leptopilina boulardi (hyménoptère parasite de drosophiles) dans les conditions naturelles

Résumé Le concept de réponse optimale d'un parasite vis-à-vis de l'hôte le plus favorable pour son développement demeure surtout théorique et n'a pu être vérifié que dans les conditions de laboratoire. Nous avons montré que Drosophila melanogaster s'avère être, par rapport à D. simulans, l'hôte le plus favorable pour le développement du cynipide parasite Leptopilina boulardi. Une étude sur le terrain a démontré que ce parasite présente une réponse fonctionnelle densité dépendante vis-à-vis de D. melanogaster et non vis-à-vis de D. simulans, avec un effet de bascule. D'autre part, il s'avère que ce parasite exploite beaucoup mieux son hôte, en évitant le superparasitisme, ceci étant démontré au laboratoire et dans la nature. Enfin, il apparaît qu'il est capable d'allonger sa période de ponte lorsque cet hôte est rare, ce qui ne se produit pas avec D. simulans.

     

Export of proteins across membranes: The helix reversion hypothesis

A model is presented which explains the biological role of the leader peptide in protein export. Along the lines of this model, the conformational changes of a protein with environment serves as a general mechanism for translocation. The leader peptide in the cytoplasm takes a hairpin like conformation which reverts to an extended helix upon integration into the membrane. The essential features of this model are in accord with recent results of protein export.     

Periodic electric field as a biopolymer conformation switch: a possible mechanism

A theoretical model is proposed to describe the influence of a periodic electric field (PEF) upon a biopolymer. The biopolymer is treated as a classical mechanical system consisting of subsystems (molecular groups) which interact with each other through potential forces. The PEF is treated as a periodic driving force applied to a molecular group. The energy dissipation is considered using the model of fluid (viscous) friction. Arguments for the non-linear character of the friction-velocity dependence caused by the non-Newtonian rheology of a viscous medium are formulated.A forced molecular-group motion is investigated for the situation of a small driving-force period, with oscillations overdamped and a driving force consisting of more than one harmonic. As a result, it is established that the motion always gets to a terminal stage when only a small-scale vibration about some point, X ^*, takes place. The terminal motion is preceded by a transient characterized by the presence of a directional velocity component and so by a drift along a potential profile. the drift goes on until a barrier is met which has a sufficiently large steepness (the barrier height is not important). As a result, the point X ^* may happen to be remote from the conformation potential local minimum (conformational state). The physical reasons for the drift are described.If we consider the small-scale vibration about X ^* in the framework of the hierarchy of scales for intramolecular mobility, it can be regarded as an equilibrium mobility, whereas the drift can be regarded as a functionally important motion, and X ^* as a new conformational state which is realizable only in the presence of the PEF. It may be concluded, as the result of a consistent treatment and neglecting the small-scale vibration, that the conformational potential is modified by adding a linear term (in the one-dimensional case). In this connection, the set of conformational states can both deform (deviation of the positions of minima and their relative depth) and rearrange qualitatively (some minima can vanish and/or new minima can appear). In particular, the transition from one conformation to another one may happen due to rearrangement.     

Comparison of the predicted structure for the activated form of the P21 protein with the X-ray crystal structure

The predicted conformation and position of the central transforming region (residues 55–67) of the p21 protein are compared with the conformation and position of this segment in a recently determined X-ray crystal structure of residues 1–166 of this protein in the activated state bound to a nonhydrolyzable GTP derivative. We previously predicted that this segment of the protein would adopt a roughly extended conformation from Ile 55-Thr 58, a reverse turn at Ala 59-Gln 61, followed by an -helix from Glu 62-Met 67. We further predicted that this region of the activated protein occupies a position that is virtually identical to corresponding regions in the homologous purine nucleotide-binding proteins, bacterial elongation factor (EF-tu), and adenylate kinase (ADK). We find that there is a close correspondence between the conformation and position of our predicted structure and those found in the X-ray crystal structure. A mechanism for activation of the protein is proposed and is corroborated by X-ray crystallographic data.     

Prediction of the secondary structures of bovine blood coagulation factor IX, factor X, and prothrombin

The secondary structures of bovine blood coagulation factors IX and X, as well as that of bovine prothrombin, were predicted on the basis of a computerized combination of the Chou-Fasman and Burgess algorithms. Refinements in the predictions were made after consideration of the content of various secondary structures, as determined by circular dichroism studies of these same proteins. The final turn assignments were in good agreement with those assigned with use of an algorithm involving pattern matching of -turns in proteins of known structure.     

Prediction of the packing arrangement of strands in β-sheets of globular proteins

A method is proposed for predicting the adjacency order in which strands pack in a -sheet in a protein, on the basis of its amino acid sequence alone. The method is based on the construction of a predicted contact map for the protein, in which the probability that various residue pairs are close to each other is computed from statistically determined average distances of residue pairs in globular proteins of known structure. Compact regions, i.e., portions of the sequence with many interresidue contacts, are determined on the map by using an objective search procedure. The proximity of strands in a -sheet is predicted from the density of contacts in compact regions associated with each pair of strands. The most probable -sheet structures are those with the highest density of contacts. The method has been tested by computing the probable strand arrangements in a five-strand -sheet in five proteins or protein domains, containing 62–138 residues. Of the theoretically possible 60 strand arrangements, the method selects two to eight arrangements as most probable; i.e., it leads to a large reduction in the number of possibilities. The native strand arrangement is among those predicted for three of the five proteins. For the other two, it would be included in the prediction by a slight relaxation of the cutoff criteria used to analyze the density of contacts.     

Structure and function of ferredoxin-NADP+-oxidoreductase

The redox-enzyme ferredoxin-NADP-oxidoreductase has been shown to be activated by light and inactivated in the dark. This review will summarize recent data concerning the biochemical characterization of the enzyme compared to its in-vivo activation. Further-more the mechanism of this activation process is discussed as a conformational change caused by the light-driven proton gradient.Abbreviations cyt cytochrome - fd ferredoxin - FNR1 large form of ferredoxin-NADP-oxidoreductase - FNRox oxidized FNR - FNRred reduced FNR - FNRs small form of FNR - FNRsq FNR-semiquinone