Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria.

Adenylate kinases (AK) from Gram-negative bacteria are generally devoid of metal ions in their LID domain. However, three metal ions, zinc, cobalt, and iron, have been found in AK from Gram-negative bacteria. Crystal structures of substrate-free AK from Desulfovibrio gigas with three different metal ions (Zn(2+), Zn-AK; Co(2+), Co-AK; and Fe(2+), Fe-AK) bound in its LID domain have been determined by X-ray crystallography to resolutions 1.8, 2.0, and 3.0 Å, respectively. The zinc and iron forms of the enzyme were crystallized in space group I222, whereas the cobalt-form crystals were C2. The presence of the metals was confirmed by calculation of anomalous difference maps and by X-ray fluorescence scans. The work presented here is the first report of a structure of a metal-containing AK from a Gram-negative bacterium. The native enzyme was crystallized, and only zinc was detected in the LID domain. Co-AK and Fe-AK were obtained by overexpressing the protein in Escherichia coli. Zn-AK and Fe-AK crystallized as monomers in the asymmetric unit, whereas Co-AK crystallized as a dimer. Nevertheless, all three crystal structures are very similar to each other, with the same LID domain topology, the only change being the presence of the different metal atoms. In the absence of any substrate, the LID domain of all holoforms of AK was present in a fully open conformational state. Normal mode analysis was performed to predict fluctuations of the LID domain along the catalytic pathway.

Cobalt-, zinc- and iron-bound forms of adenylate kinase (AK) from the sulfate-reducing bacterium Desulfovibrio gigas: purification, crystallization and preliminary X-ray diffraction analysis.

Adenylate kinase (AK; ATP:AMP phosphotransferase; EC 2.7.4.3) is involved in the reversible transfer of the terminal phosphate group from ATP to AMP. AKs contribute to the maintenance of a constant level of cellular adenine nucleotides, which is necessary for the energetic metabolism of the cell. Three metal ions, cobalt, zinc and iron(II), have been reported to be present in AKs from some Gram-negative bacteria. Native zinc-containing AK from Desulfovibrio gigas was purified to homogeneity and crystallized. The crystals diffracted to beyond 1.8 A resolution. Furthermore, cobalt- and iron-containing crystal forms of recombinant AK were also obtained and diffracted to 2.0 and 3.0 A resolution, respectively. Zn(2+)-AK and Fe(2+)-AK crystallized in space group I222 with similar unit-cell parameters, whereas Co(2+)-AK crystallized in space group C2; a monomer was present in the asymmetric unit for both the Zn(2+)-AK and Fe(2+)-AK forms and a dimer was present for the Co(2+)-AK form. The structures of the three metal-bound forms of AK will provide new insights into the role and selectivity of the metal in these enzymes.

Study of pH- and temperature-induced transitions in F-protein (phosphofructokinase) by spectroscopy and microcalorimetry methods.

The temperature- and pH-induced transitions in F-protein (phosphofructokinase (ATP:D-fructose-6-phosphate 1-phosphotransferase, EC 2.7.1.11] have been studied by means of microcalorimetry and fluorescence and CD spectroscopy. An increase in pH from approx. 6.0 to approx. 8.0 causes a change in the protein state which seems to correspond to a shift of the dimer-tetramer equilibrium in favour of the tetramers. In the absence of phosphate, stability of the protein to temperature- and urea-induced denaturation at pH 6.0 is higher than that at pH 8.0. An addition of 150 mM phosphate results in a pronounced increase in the protein's stability in such a way that the protein becomes more stable at pH 8.0 than at pH 6.0. The shift of the denaturational heat capacity peak induced by the phosphate binding exceeds 25 degrees C at pH 8.0 and 9 degrees C at pH 6.0.

Effects of cation binding on the thermal transitions in calmodulin.

The thermal transitions in different forms of bovine brain calmodulin (0, 1, 2, 3 and 4 bound Ca2+ ions per molecule) have been studied by means of microcalorimetry, intrinsic tyrosine fluorescence, circular dichroism and infrared spectroscopy. The heating of the apoprotein from 5 to 110 degrees C induces at least three unfolding transitions. The heating of Ca2+-loaded calmodulin causes at least two structural transitions, one of which occurs at relatively low temperatures, from approx. 30 to approx 50 degrees C. The binding of the biologically significant Ca2+, Mg2+, Na+ and K+ ions has been measured at 12, 20, 28, 37 and 50 degrees C by means of the fluorescence method. The values of the binding parameters for these cations do not depend on temperature within the range 12 to 50 degrees C. It has been proposed that the temperature independence of the metal-ion-binding properties of calmodulin is achieved due to the temperature-induced structural changes, which adjust the protein conformation in such a way that the protein-binding parameters remain constant.

Interactions of parvalbumins with model phospholipid vesicles.

Interactions of Ca2+-binding proteins, parvalbumins, with model vesicles formed with both synthetic (dipalmitoylphosphatidylcholine) and natural (phosphatidylcholine and phosphatidylethanolamine) phospholipids have been revealed and studied by means of gel-chromatography, electron microscopy, intrinsic fluorescence and microcalorimetry methods. There are at least two populations of liposome-bound parvalbumin one of which has higher affinity to the liposomes (effective binding constant about 10(6) M-1) than the other one. The interaction is modulated by Ca2+ and Mg2+ ions and induces changes in properties of both parvalbumin and liposomes.

Two partially unfolded states of Torpedo californica acetylcholinesterase.

Chemical modification with sulfhydryl reagents of the single, nonconserved cysteine residue Cys231 in each subunit of a disulfide-linked dimer of Torpedo californica acetylcholinesterase produces a partially unfolded inactive state. Another partially unfolded state can be obtained by exposure of the enzyme to 1-2 M guanidine hydrochloride. Both these states display several important features of a molten globule, but differ in their spectroscopic (CD, intrinsic fluorescence) and hydrodynamic (Stokes radii) characteristics. With reversal of chemical modification of the former state or removal of denaturant from the latter, both states retain their physiochemical characteristics. Thus, acetylcholinesterase can exist in two molten globule states, both of which are long-lived under physiologic conditions without aggregating, and without either intraconverting or reverting to the native state. Both states undergo spontaneous intramolecular thioldisulfide exchange, implying that they are flexible. As revealed by differential scanning calorimetry, the state produced by chemical modification lacks any heat capacity peak, presumably due to aggregation during scanning, whereas the state produced by guanidine hydrochloride unfolds as a single cooperative unit, thermal transition being completely reversible. Sucrose gradient centrifugation reveals that reduction of the interchain disulfide of the native acetylcholinesterase dimer converts it to monomers, whereas, after such reduction, the two subunits remain completely associated in the partially unfolded state generated by guanidine hydrochloride, and partially associated in that produced by chemical modification. It is suggested that a novel hydrophobic core, generated across the subunit interfaces, is responsible for this noncovalent association. Transition from the unfolded state generated by chemical modification to that produced by guanidine hydrochloride is observed only in the presence of the denaturant, yielding, on extrapolation to zero guanidine hydrochloride, a high free energy barrier (ca. 23.8 kcal/mol) separating these two flexible, partially unfolded states.

Irreversible thermal denaturation of Torpedo californica acetylcholinesterase.

Thermal denaturation of Torpedo californica acetylcholinesterase, a disulfide-linked homodimer with 537 amino acids in each subunit, was studied by differential scanning calorimetry. It displays a single calorimetric peak that is completely irreversible, the shape and temperature maximum depending on the scan rate. Thus, thermal denaturation of acetylcholinesterase is an irreversible process, under kinetic control, which is described well by the two-state kinetic scheme N-->D, with activation energy 131 +/- 8 kcal/mol. Analysis of the kinetics of denaturation in the thermal transition temperature range, by monitoring loss of enzymic activity, yields activation energy of 121 +/- 20 kcal/mol, similar to the value obtained by differential scanning calorimetry. Thermally denatured acetylcholinesterase displays spectroscopic characteristics typical of a molten globule state, similar to those of partially unfolded enzyme obtained by modification with thiol-specific reagents. Evidence is presented that the partially unfolded states produced by the two different treatments are thermodynamically favored relative to the native state.

Thermal transitions in the purple membrane from Halobacterium halobium.

The application of a successive annealing procedure to the scanning calorimetric endotherm of the purple membrane from Halobacterium halobium in phosphate buffer, pH 7.5, leads to five thermal transitions beneath the overall endotherm. Circular dichroism and fluorescence experiments have also been carried out with the native membrane heated at the same scan rate as in calorimetric runs (1 degrees C/min) as well as with previously heated membrane samples. These results, together with others from the literature, have been used to suggest a preliminary explanation of the five thermal transitions.

Thermal denaturation of the alkali light chain-20 kDa fragment complex obtained from myosin subfragment 1.

The thermal denaturation of the myosin subfragment 1 (S1) from rabbit skeletal muscle and of its derivatives obtained by tryptic digestion has been studied by means of differential scanning calorimetry. Two distinct thermal transitions were revealed in the isolated complex of the C-terminal 20 kDa fragment of the S1 heavy chain with the alkali light chain. These transitions were identified by means of a thermal gel analysis method. It has been shown that the thermal denaturation of the 20 kDa fragment of the S1 heavy chain correlates with the melting of the most thermostable domain in the S1 molecule. It is concluded that this domain is located in the C-terminal 20 kDa segment of the S1 heavy chain.

pH-dependent thermal transitions of lentil lectin.

The thermal stability of lentil lectin in the 5.0-10.0 pH range was studied by high-sensitivity differential scanning calorimetry and infrared spectroscopy. The thermally induced transitions for protein were irreversible and strongly dependent upon the scan rate at all pH values, suggesting that the denaturation is under kinetic control. It is shown that process of lentil lectin denaturation can be interpreted with sufficient accuracy in terms of the simple kinetic scheme, N-->D, where k is a first-order kinetic constant that changes with temperature, as given by the Arrhenius equation, N is the native state, and D is the denatured state. On the basis of this model, the parameters of the Arrhenius equation were calculated.

Domain structure of myosin subfragment-1. Selective denaturation of the 50 kDa segment.

The structure of the myosin subfragment-1 (S1) from rabbit skeletal muscle was studied using differential scanning microcalorimetry. Three independently melting regions (domains) were revealed in S1. Selective denaturation of the middle 50 kDa segment of the S1 heavy chain resulted in the disappearance of the heat sorption peak corresponding to the melting of the first, the most thermolabile domain without any effect on the thermally induced blue shift of the intrinsic tryptophan fluorescence spectrum which occurs within the temperature region of melting of the second domain. It is concluded that the most thermolabile domain seems to correspond to the N-terminal part of the 50 kDa segment devoid of tryptophan residues.

Microcalorimetry and electrophoresis of the erythrocyte membrane of spontaneously hypertensive rats.

Abnormalities of both structure and function have been described in the erythrocyte membrane of spontaneously hypertensive rats (SHR). In order to elucidate the molecular basis of these abnormalities we have carried out differential scanning microcalorimetry of the erythrocyte membrane and gel electrophoresis of membrane polypeptides. The partial enthalpy of so-called 'C-transition' (at 63 degrees C) was found to be increased. This may be explained by increased content of band 3 protein in SHR erythrocyte membrane.

Dynamic properties of bacteriorhodopsin in purple membranes upon heat treatment.

Reversible temperature-dependent conformational changes in bacteriorhodopsin of the purple membranes from Halobacterium halobium have been studied by the method of deuterium exchange. A noticeable increase in the mobility of structured peptide groups in bacteriorhodopsin was revealed upon reorganization of the supermolecular structure at about 60 degrees C. In the supermolecular structure formed, bacteriorhodopsin molecules have no contacts with external medium at 75-80 degrees C. Membrane destruction results in a drastic increase in molecular mobility within the narrow temperature range 100-110 degrees C. The effects observed are induced by predenaturation changes in the bacteriorhodopsin structure and rearrangements in the structure of a protein-lipid complex. The temperature dependence of the number of peptide groups involved in reversible conformational rearrangements is in good agreement with the microcalorimetry data.

A spectrofluorometric study of the environment of tryptophans in bacteriorhodopsin.

The emission spectrum of intact purple membranes of Halobacterium halobium has a very short wavelength position (the main maximum at 314 nm) and can be fitted by two spectral components, one of which (component A) corresponds to the fluorescence of buried tryptophan residues located in a highly hydrophobic rigid environment (like the single tryptophan residue in azurin), the other (component I) being due to the emission of buried tryptophan residues located in a rather polar environment. Treatment of bacteriorhodopsin by NaBH4, fragmentation of the membranes and thermal formation of vesicles result in a decrease in the contribution of component A, an increase in that of component I and the appearance of spectral components corresponding to the emission of surface tryptophan residues. Temperature induces at least two distinct changes of the fluorescence parameters of the protein: one change occurs from 45 to 65 degrees C. the other from 65 to 90 degrees C. The spectral changes correlate with the peaks of heat sorption caused by thermal transitions in the purple membrane structure and conformational changes in the protein structure. Alkaline denaturation of bacteriorhodopsin registered by tryptophan fluorescence begins at pH > 11.0.

Analysis of differential scanning calorimetry data for proteins. Criteria of validity of one-step mechanism of irreversible protein denaturation.

We consider in this work the analysis of the excess heat capacity C(p)(ex) versus temperature profiles in terms of a model of thermal protein denaturation involving one irreversible step. It is shown that the dependences of ln C(p)(ex) on 1 T (T is the absolute temperature) obtained at various temperature scanning rates have the same form. Several new methods for estimation of parameters of the Arrhenius equation are explored. These new methods are based on the fitting of theoretical equations to the experimental heat capacity data, as well as on the analysis of the dependence d(ln C (p)(ex)) d ( 1 T ) on 1 T . We have applied the proposed methods to calorimetric data corresponding to the irreversible thermal denaturation of Torpedo californica acetylcholinesterase, cellulase from Streptomyces halstedii JM8, and lentil lectin. Criteria of validity for the one-step irreversible denaturation model are discussed.

Comparative calorimetric study of non-amyloidogenic and amyloidogenic variants of the homotetrameric protein transthyretin.

Familial amyloidotic polyneuropathy (FAP) is an autosomal dominant hereditary type of amyloidosis involving amino acid substitutions in transthyretin (TTR). V30M-TTR is the most frequent variant, and L55P-TTR is the variant associated with the most aggressive form of FAP. The thermal stability of the wild-type, V30M-TTR, L55P-TTR and a non-amyloidogenic variant, T119M-TTR, was studied by high-sensitivity differential scanning calorimetry (DSC). The thermal unfolding of TTR is a spontaneous reversible process involving a highly co-operative transition between folded tetramers and unfolded monomers. All variants of transthyretin are very stable to the thermal unfolding that occurs at very high temperatures, most probably because of their oligomeric structure. The data presented in this work indicated that for the homotetrameric form of the wild-type TTR and its variants, the order of stability is as follows: wild-type TTR approximately > T119M-TTR > L55P-TTR > V30M-TTR, which does not correlate with their known amyloidogenic potential.

Thermodynamical characteristics and volume compressibility of dipalmitoylphosphatidylcholine liposomes containing bacteriorhodopsin.

The effects of bacteriorhodopsin (BR) interaction with large dipalmitoylphosphatidylcholine (DPPC) liposomes (approx. 100 nm in diameter) were examined at various BR/DPPC ratios, using differential scanning calorimetry (DSC) and ultrasonic velocimetry (USV). On DSC, the lipid phase transition temperature, Tc, and the half-width of the phase transition peak, delta T1/2, showed significant non-monotonic changes with the increasing BR concentration. Two exponential segments could be distinguished in the dependence of the transition enthalpy change per mol of lipid (delta H/nL) on the BR/DPPC ratio: one corresponding to ratios between 0:1 and 1:64, and another corresponding to ratios between 1:44 and 1:16. A maximal value of delta H/nL was observed for BR/DPPC ratio 1:44, probably corresponding to maximal BR-lipid ordering with each BR molecule being surrounded by two layers of lipid molecules. The nonmonotonic changes of thermodynamical parameters suggest long-distance interactions between regions of altered bilayer structure which form around each BR molecule. The results obtained with USV provided support for the above conclusions. The dependence of ultrasound velocity increment A on BR concentration supplies information on relative changes of membrane volume compressibility. Decreasing volume compressibility is reflected in increasing values of parameter A. Within T less than Tc, the values of A increased with the increasing BR concentration; saturation was observed at BR/DPPC ratio 1:500 (A = A(BR/DPPC]. No significant BR-concentration dependent changes of A were observed at T greater than Tc. From these values the average diameter of the distorted region of lipid bilayer was estimated to be approximately 20 nm.

Interactions of calcium binding proteins, parvalbumin and alpha-lactalbumin, with dipalmitoylphosphatidylcholine vesicles.

Interactions of Ca2+ binding proteins, pike (Esox lucius) parvalbumins pI 4.2 and 5.0, and bovine and human alpha-lactalbumins, with dipalmitoylphosphatidylcholine vesicles were studied by means of scanning microcalorimetry and intrinsic tyrosine and tryptophan fluorescence methods. The interactions of pike parvalbumins are modulated by Ca2+ and Mg2+ binding to the protein and induce some changes in the physical properties of both the proteins and liposomes. Liposomes increased thermal stability of Ca2+-loaded parvalbumin and decreased thermal stability of both Mg2+-loaded and metal-free protein. The interaction of parvalbumin with liposomes affects the phase transition from gel to liquid-crystalline state in liposomes. Ca2+-loaded alpha-lactalbumin interacts with liposomes in its native state while the metal-free protein binds to the liposomes mainly in its thermally denatured state. The results of the microcalorimetric and spectrofluorometric studies are supported by data obtained by means of gel-chromatography on Sepharose 4B. It may be suggested that these metal-modulated interactions of Ca2+-binding proteins with membranes have some functional significance.

Conformational changes in the muscle proteins of cured beef during heating.

Structural changes caused by heating in the proteins of cured beef longissimus dorsi muscle were examined by fluorescence and differential scanning calorimetry. Denaturation occurred in four temperature ranges-40-55°C, 55-61°C, 62-70°C and above 70°C, in contrast to the three endothermic transitions reported for non-cured meats.

[Modification of the retina photoreceptor membranes and temperature stability of rhodopsin]. / Modifikatsiia fotoretseptornykh membran setchatki i temperaturnaia stabil'nost' rodopsina.

The effect of modification of photoreceptor membranes of the bovine retina on the termodynamical parameters that characterize heat denaturation of rodopsin was studied. The highest increase of the rate constant and the corresponding maximal drop of the free energy change of heat denaturation of the pigment were obtained by using 7 M urea or 25% Triton X-100 in the presence of 5.10(-4) M EDTA. After chipping off one third of the protein from the rodopsin molecule by papain treatment a significant decrease of the slope of the Arrenius curve and a maximal decrease of entropy change compared to the parameters known for heat denaturation of the pigment in native photoreceptor membranes were found. Modification of the lipid components of the photoreceptor membranes (treatment with Triton X-100 and phospholipase C) reduced the thermostability of rodopsin. Maximal changes were obtained at Triton X-100 concentrations 0.1--1%, further concentration increas (1--25%) did not lead to significant changes. Phospholipase C treatment resulted in a decrease of free energy change and an increase of entropy change without affecting entalpy changes, accompaning the heat denaturation of rodopsin. Bivalent cations (Ca2+, Mg2+) increased the termostability of rodopsin both in photoreceptor membranes and in solutions to 25% Triton X-100.