Isomerization of proline-93 during the unfolding and refolding of ribonuclease A

Using the method of isomer-specific proteolysis, the isomerization of proline-93 has been monitored directly during the time course of the unfolding and refolding reactions of RNase A. It has been found that proline-93 is 100% cis in the native protein and 70% cis in the reversibly unfolded protein. During the unfolding reaction, the change from 100% to 70% cis occurs as a first-order process with a relaxation time of 140 s in 8.5 M urea, 10 degrees C. For refolding, the change from 70% to 100% cis also occurs as a first-order process, with a relaxation time (10 degrees C) of 90 s in 0.3 M urea, 130 s in 1.0 M urea, and 310 s in 2.0 M urea. Parallel experiments which measured the recovery of enzyme activity during refolding were also conducted. These show that 30% of the activity recovers in a slow phase with a first-order relaxation time (10 degrees C) of 100 s in 0.3 M urea. Because of the excellent agreement of both the amplitude and relaxation time for trans-to-cis isomerization and for activity recovery, it is concluded that the slowest phase in the recovery of enzyme activity is rate limited by the isomerization of proline-93. These results demonstrate that proline-93 must be cis before refolding to the active form can take place, in contrast to previous suggestions, and argue against the existence of a nativelike intermediate form on the refolding pathway which contains proline-93 in the incorrect trans configuration.

Structural domains of vesicular stomatitis virus. A study by differential scanning calorimetry, thermal gel analysis, and thermal electron microscopy

Differential scanning calorimetry has been used in combination with thermal gel analysis and electron microscopy to identify and study the structural domains of the membrane-enclosed vesicular stomatitis virus and its isolated internal components. Three major endothermic transitions centered at approximately 52, 76, and 80 degrees C and at least two minor transitions are observed at pH 7.0 for the intact virion. Thermal gel analysis suggests the possibility that specific proteins of vesicular stomatitis virus are involved in two or more of the calorimetric transitions. The effect of heating to defined temperatures on the morphology of the virion was studied by negative stain electron microscopy. The results of these "thermal EM" studies show discrete irreversible morphological changes in the virion which seem to coincide with the three major calorimetric transitions.

Protein involvement in structural transition of erythrocyte ghosts. Use of thermal gel analysis to detect protein aggregation

In this study, it is shown that systematic temperature-induced protein aggregation occurs on the erythrocyte membrane by intermolecular disulfide bond formation. Specific protein bands disappear from acrylamide gel profiles over rather narrow temperature regions. The aggregation appears to be the result of irreversible structural transitions of the membrane, which can be seen in a sensitive scanning calorimeter. When this method of thermal gel analysis is used, the results suggest that spectrin is a participant in the A transition, that bands 2.1, 4.1, and 4.2 and the cytoplasma portion of 3 are involved in the B transition, and that the transmembrane portion of band 3 may undergo changes in the C transition, previously shown to occur in the anion transport domain of the membrane. The aggregation of specific proteins in the narrow temperature region of these transitions persists as the transitions are moved around on the temperature axis by varying solution conditions. The assignment of particular proteins to specific transitions is reinforced by selective extraction of membrane proteins. Large variations in both the calorimetry and the aggregation pattern occur as salt concentration is increased from 77 mosm to 310 mosm, which is manifested in the splitting of the B transition into two separate transitions, B1 and B2. It is speculated that this occurs as the result of a structural change which may involve components of the cytoskeletal network.

A relationship between anion transport and a structural transition of the human erythrocyte membrane

Scanning microcalorimetry was employed as an aid in examining some structural features of the anion transport system in red blood cell vesicles. Two structural transitions were previously shown to be sensitive to several covalent and non-covalent inhibitors of anion transport in red cells. In this study, these transitions were selectively removed, either thermally or enzymatically, and the subsequent effect on 35SO2- 4 efflux in red cell vesicles was determined. It is shown that removal of one of these transitions (B2) has a negligible inhibitory effect on anion transport. Cytoplasmic, intermolecular disulfide linkages between band 3 dimers are known to form during the B2 transition. The integrity of the 4,4-diisothiocyanostilbene-2,2-disulfonate-sensitive C transition, on the other hand, is shown to be a requirement for anion transport. The localized region of the membrane giving rise to this transition contains the transmembrane segment of band 3, as well as membrane phospholipids. The calorimetric results suggest a structure of band 3 which involves independent structural domains, and are consistent with the transmembrane segment playing a direct role in the transport process.

Evidence suggesting that some proteolytic enzymes may cleave only the trans form of the peptide bond

The rates of hydrolysis of glycy-L-proline and L-phenylalanyl-L-proline, catalyzed by prolidase, have been measured at several temperatures under conditions where a high ratio of prolidase activity to substrate concentration existed. Two well-separated kinetic phases, which can be adequately treated as two first-order reactions, were observed for the hydrolysis. The relative amplitudes of the two phases are nearly independent of temperature, but strongly dependent on the initial state of protonation of the dipeptides. It was found that the amplitude of the slow phase is strictly proportional to the known amount of cis isomer, while the amplitude of the fast phase correlates with the amount of the trans isomer. Furthermore, the relaxation time and activation energy of the slow phase of hydrolysis are in good agreement with the same parameters determined for cis-trans isomerization of the dipeptides, as measured by a pH-jump method for samples not being hydrolyzed. These results lead us to the conclusion that the slow phase seen for hydrolysis is rate limited by cis-trans isomerization of the X-pro peptide bond. Thus, this proline-specific protease appears to have an absolute requirement for the trans form of the peptide bond and appears not to cleave the cis form or to cleave it extremely slowly.

The effects of anion transport inhibitors on structural transitions in erythrocyte membranes

Red blood cell membranes have been labeled with several covalent and noncovalent inhibitors of anion transport and their heat capacity profiles determined as a function of temperature. Covalent inhibitors include the amino reactive agents 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid, 4-acetamido-4'-isothiocyanostilbene-2,2'-disulfonic acid, pyridoxal phosphate and 1-fluoro-2,4-dinitro benzene. The non-covalent inhibitors include several well known local anesthetics. The study was underataken in order to identify regions of the membrane involved in anion transport. Covalent modification in all case resulted in a large upward shift of the C transition, which is beleived to involve a localized phospholipid region. Evidence is presented which indicates that Band III protein and this phospholipid region are in close physical proximity on the membrane. Addition of non-covalent inhibitors affects the membrane in either or both of two ways. In some cases, a lowering and broadening of the C transition occurs; in others the B1 and B2 transitions are altered. These latter transitions are beleived to involve both phospholipid and protein, including Band III. These results may indicate that the non-covalent inhibitors produce their inhibitory effect on anion transport at least in part by interacting with membrane phospholipid.

Calorimetric studies of the structural transitions of the human erythrocyte membrane. Studies of the B and C transitions

Differential scanning calorimetry has been used to study several structural transitions of the human erythrocyte membrane. Earlier studies have shown that one of these transitions (the A transition) is due to the thermal unfolding of spectrin on the membrane. In this paper, it is shown that two of the other transitions (B and C) exhibit a high sensitivity to a local anesthetic, benzyl alcohol. Increasing the ionic strength of the suspending medium results in a splitting of the B transition into two indepent transitions (B1 and B2). It is found that one of these (B2) is associated with titrating groups, since the midpoint for the transitions shifts by about 20 degrees C, with an apparent pK near 7.5 Extensive bilateral proteolysis by papain causes a drastic decrease in the size of all transitions except the C transition, which remains unaltered. On the other hand, treatment with phospholipase by A2 largely affects the C transition, causing its disappearance. Because of the lack of sensitivity to proteolysis and the high sensitivity to phospholipase, it appears that the C transition has a large extent of 'lipid involvement'. It might result from the melting of a small fraction of phospholipid which exists in a crystalline state under physiological conditions. Alternatively, the C transition could arise from changes in protein-lipid interactions or from lipid-dependent changes in protein-protein interactions, providing one assumes that only protease-resistant portions of membrane proteins are participating.

Unfolding and refolding occur much faster for a proline-free proteins than for most proline-containing proteins

The kinetics for unfolding and refolding of a parvalbumin (band 5) have been examined as a function of pH near the transition region, using stopped-flow techniques. This protein is rather unusual in that it has no proline residues, and therefore serves as a good example to test the hypothesis that the rate-limiting step seen in denaturation reactions is due to the cis-trans isomerization of proline peptide bonds in the denatured state. The kinetics for parvalbumin unfolding and refolding are complex, with the data being resolvable into two fast phases at 25 degrees. The slower of the two phases seen for the parvalbumin is about 100 to 500 times faster than the slow phase seen for proline-containing proteins under the same conditions! These results argue strongly in support of the proline isomerization hypothesis. It is also suggested that the slower phase seen for parvalbumin and the second-slowest phase seen for proline-containing proteins might be due to the cis-trans isomerization of peptide bonds of non-proline residues.

Consideration of the Possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues

A model is proposed to account for the observation that the denaturation of small proteins apparently occurs in two kinetic phases. It is suggested that only one of these phases--the fast one--is actually an unfolding process. The slow phase is assumed to arise from the cis-trans isomerism of proline residues in the denaturated protein. From model compound data, it is shown that the expected rate for isomerism is in satisfactory agreement with the rates actually observed for protein folding. It is also shown that a simple model of protein unfolding based on the isomerism concept is very successful in accounting for many known experimental characteristics of the kinetics and thermodynamic of protein denaturation. Thus, the model is able to predict that two kinetic phases will be seen in the transition region while none are seen in the base-line regions, that both the fast and slow refolding phases lead to the native protein as the product, that the fast phase becomes the only observable phase for jumps ending far in the denatured base-line region, that most or all small proteins show a limiting low-temperature activation energy of ca. 20,000 cal, and that the relaxtion time for the slow phase seen in cytochrome c denaturation is much shorter than for all other small proteins. By utilizing "double-jump" experiments, it is shown directly that the slow phase is not part of the unfolding process but that it corresponds to a transition among two or more denatured forms which have identical spectroscopic (286.5 nm) properties. Thus, the slow relaxation is "invisible" except in the transition region where it couples to the fast unfolding equilibrium. Finally, since the present model assumes that only one of the major kinetic phases seen in denaturation reactions is concerned with the denaturation process per se, it is in agreement with numerous thermodynamic studies which show consistency with the two-state model for unfolding.