Spurious conformational transitions in proteins?

A link between hinge-bending domain motions and the temperature dependence of catalysis in 3-isopropylmalate dehydrogenase

Enzyme function depends on specific conformational motions. We show that the temperature dependence of enzyme kinetic parameters can provide insight into these functionally relevant motions. While investigating the catalytic properties of IPMDH from Escherichia coli, we found that its catalytic efficiency (k(cat)/K(M,IPM)) for the substrate IPM has an unusual temperature dependence, showing a local minimum at approximately 35 degrees C. In search of an explanation, we measured the individual constants k(cat) and K(M,IPM) as a function of temperature, and found that the van 't Hoff plot of K(M,IPM) shows sigmoid-like transition in the 20-40 degrees C temperature range. By means of various measurements including hydrogen-deuterium exchange and fluorescence resonance energy transfer, we showed that the conformational fluctuations, including hinge-bending domain motions increase more steeply with temperatures >30 degrees C. The thermodynamic parameters of ligand binding determined by isothermal titration calorimetry as a function of temperature were found to be strongly correlated to the conformational fluctuations of the enzyme. Because the binding of IPM is associated with a hinge-bending domain closure, the more intense hinge-bending fluctuations at higher temperatures increasingly interfere with IPM binding, thereby abruptly increasing its dissociation constant and leading to the observed unusual temperature dependence of the catalytic efficiency.

Protein dynamics and fluorescence quenching

There are both theoretical and experimental data which strongly suggest that the intramolecular dynamics of the protein matrix play an important role in protein functions. The interrelationship between theory and experiments is rather weak mainly because of the lack of relevant experimental methods and (model-dependent) misinterpretation of experimental data. We give a short account of a few fluorescence-quenching techniques that can provide adequate information concerning protein dynamics provided that the experimental data sets are correctly processed.

A study of the hinge-bending mechanism of yeast 3-phosphoglycerate kinase

The hinge-bending mechanism proposed as part of the catalytic mechanism for phosphoglycerate kinase (PGK) has been investigated using yeast PGK and the site-directed mutant [H388Q]PGK, where His388 is replaced by Gln. The emission and quenching of fluorescence, supported by the aromatic CD band, show that the mutation in the waist region affects the tryptophan environment in the C-terminal domain. The mutant is also less stable to guanidine denaturation and less cooperative in its unfolding. The effect of substrates on the conformation of PGK was studied using 8-anilino-1-naphthalenesulphonic acid (ANS), a competitive inhibitor of ATP binding to the C-terminal domain, and 8-(2-[(iodoacetyl)ethyl]amino)naphthalene (I-AEDANS), attached to Cys197 on the N-terminal domain. Under the influence of substrates the novel anisotropy decay curves for ANS indicate a 1-5 degrees change in the orientation of the probe, interpreted as a small reorientation of the domains about the waist region. The experimental data are interpreted as a small swivelling of the domains about the waist region under the influence of substrate. The results with AEDANS anisotropy decay are consistent with those for ANS. The enzyme activity of PGK shows a break in the Arrhenius plot at 20 degrees C mirrored by a break in the temperature dependence of tryptophan ellipticity. This is interpreted as a change in protein dynamics associated with destabilisation of the waist region. This destabilisation is shown to have already taken place in the mutant enzyme and in the wild type at pH 5.6, both of which exhibit linear Arrhenius plots. NMR titration curves show that the pH effect must be due to a group other than histidine. The results give further support to the permissive model of hinge bending previously proposed by one of the authors, in which binding of substrate destabilises the waist region. This loosens the hinge which can then swing slightly to bring the domains closer together to make favourable interactions between the domains and the substrates, with the exclusion of water.

Quenching by acrylamide and temperature of a fluorescent probe attached to the active site of ribonuclease

The fluorescence properties of ribonuclease labelled at its active site with N-(iodoacetylamino)-ethyl-5-naphthylamine-1-sulfonic acid have been studied at different temperatures and in the presence of acrylamide. The rate constant for the quenching of the fluorescence of labelled ribonuclease by acrylamide is apparently not limited by the "accessibility" of the probe: similar values are obtained for the native and denatured states of the protein. Instead, acrylamide seems to be a rather inefficient quencher of this fluorescent group [acetamidoamino)ethyl-5-naphthylamine-1-sulfonic acid), as shown by non-linear Stern-Volmer representations, biphasic decay kinetics, and a low value of the rate constant. The fluorescence intensity of the native state of the labelled protein is highly sensitive to temperature and exhibits a 20% decrease for an increase of temperature of from 10 degrees C to 30 degrees C, independent of solvent viscosity. This thermal quenching is specific for the native conformation and disappears when the protein is unfolded. When the fluorescence lifetime of the label is shortened by addition of acrylamide, the effect of temperature becomes identical for native and unfolded structures. This suggests that the cause of the thermal quenching is the presence of conformational fluctuations within the native protein which apparently take place in the time range from 35 to 200 ns.

Proteins related to the mouse L-cell major heat shock protein are synthesized in the absence of heat shock gene expression

Heat shock of mouse L cells induces the synthesis of two polypeptides of Mrs 68,000 and 89,000. Using a fragment of a cloned gene encoding the Drosophila melanogaster Mr 70,000 heat shock protein (hsp70), we have shown that this protein has been highly conserved during eukaryotic evolution. We extended this observation by probing at low stringency for the expression in mouse L cells of RNA homologous to the Drosophila hsp70 gene. In addition to the RNA encoding the inducible Mr 68,000 heat shock protein (hsp68), there are mouse mRNAs encoding proteins of Mrs 70,000 and 74,000 that are homologous to the Drosophila hsp70 gene. The Mrs 70,000 and 74,000 proteins and their mRNAs are abundant components of unstressed mouse L cells. These constituitively expressed proteins are unique polypeptides in contrast to the several isoelectric point variants of the inducible hsp68. We do not detect hsp68 or its mRNA in unstressed L cells. In addition to the mRNAs corresponding to hsp68 and the Mrs 74,000 and 70,000 proteins, we detect a fourth RNA homologous to the Drosophila hsp70 gene but whose protein product has not been identified. Our results suggest that the hsp68 gene of mouse L cells is a member of a multigene family and that the individual family members are distinguishable by their degree of similarity but show differences in the regulation of their expression.