Cold Adaptation: Structural and Functional Characterizations of Psychrophilic and Mesophilic Acetate Kinase

Acetate kinase catalyzes the reversible magnesium-dependent phosphoryl transfer from ATP to acetate to form acetyl phosphate and ADP. Here, we report functional and some structural properties of cold-adapted psychrotrophic enzyme; acetate kinase with those from mesophilic counterpart in Escherichia coli K-12. Recombinant acetate kinase from Shewanella sp. AS-11 (SAK) and E. coli K-12 (EAK) were purified to homogeneity following affinity chromatography and followed by Super Q column chromatography as reported before [44]. Both purified enzymes are shared some of the common properties such as (similar molecular mass, amino acid sequence and similar optimum pH), but characterized shift in the apparent optimum temperature of specific activity to lower temperature as well as by a lower thermal stability compared with EAK. The functional comparisons reveal that SAK is a cold adapted enzyme, having a higher affinity to acetate than EAK. In the acetyl phosphate and ADP-forming direction, the catalytic efficiency (k _cat/K _m) for acetate was 8.0 times higher for SAK than EAK at 10 °C. The activity ratio of SAK to EAK was increased with decreasing temperature in both of the forward and backward reactions. Furthermore, the activation energy, enthalpy and entropy in both reaction directions that catalyzed by SAK were lower than those catalyzed by EAK. The model structure of SAK showed the significantly reduced numbers of salt bridges and cation-pi interactions as compared with EAK. These results suggest that weakening of intramolecular electrostatic interactions of SAK is involved in a more flexible structure which is likely to be responsible for its cold adaptation.     

Interaction of branched chain polymeric polypeptides with phospholipid model membranes

The surface properties at the air/water interface and the interaction of branched chain polymeric polypeptides with a general formula poly[Lys-(DL -Ala_m-X₁)], where X = Π (AK), Ser (SAK), or Glu (EAK), with phospholipids were investigated. Polylysine derivatives with polycationic (SAK, AK) or amphoteric (EAK) were capable to spread and form stable monomolecular layers. The stability of monolayers at the air/water interface was dependent on the side-chain terminal amino acid residue of polymers and can be described by SAK < AK < EAK order. The area per amino acid residue values calculated from compression isotherms were in the same range as compared to those of linear poly-α-amino acids and proteins. Moreover, these polymers interact with phospholipid monomolecular layers composed of dipalmitoyl phosphatidyl choline (DPPC) or DPPC/PG (PG: phosphatidyl glycerol; 95/5, mol/mol). Data obtained from compression isotherms of phospholipids spread on aqueous polymer solutions at different initial surface pressure indicated that insertion into lipid monolayers for SAK or AK is more pronounced than for EAK. The interaction between branched polypeptides and phospholipid membranes was further investigated using lipid bilayers with DPPC/PG and fluorescent probes located either at the polar surface [1-(4-trimethylammonium-phenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH) sodium anilino naphthalene sulfonate (ANS)] or within the hydrophobic core (DPH) of the liposome. Changes in fluorescence intensity and in polarization were observed when TMA-DPH or ANS, but not DPH were used. Comparative data also indicate that all three polymers interact only with the outer surface of the bilayer, but even the most marked penetration of polycationic polypeptide (SAK) did not result in alteration of the ordered state of the alkyl chains in the bilayer. Taken together, data obtained from mono- or bilayer experiments suggest that the interaction between branched polymers and phospholipids are highly dependent on the charge properties (Ser vs Glu) and on the identity (Ser vs Ala) of side-chain terminating amino acids. The binding of polymers to the model membranes could be mainly driven by electrostatic forces, but the significant role of hydrophilic properties in case of SAK cannot be excluded. © 1998 John Wiley & Sons, Inc. Biopoly 46: 169–179, 1998     

Effect of phospholipid bilayers on solution conformation of branched polymeric polypeptides and peptide-polymer conjugates

This report provides a detailed analysis on the influence of phosholipid bilayers on the conformation of poly[Lys(X(i)-DL-Ala(m))] (XAK, where X = Ser, Orn, Glu, or AcGlu) type branched polypeptides and their peptide conjugates. CD spectra of polycationic (SAK, OAK), amphoteric (EAK), or polyanionic (Ac-EAK) polylysine derivatives were recorded in 0.25M acetate buffer at pH 7.4 as well as in the presence of DPPC or DPPC/PG (95/5, 80/20 mol/mol) liposomes. Based on these data, two groups of polypeptides are described. Group one contains polypeptides with significantly ordered conformation even in buffer solution (SAK, AcEAK), which is essentially not altered by phospholipids. Group two, branched polypeptides (OAK, EAK), with only partially ordered conformation in aqueous solution in the presence of phospholipid bilayers with high PG content, could adopt more (EAK) or less (OAK) ordered alpha-helical structure depending on their charge properties. In addition, we report on the synthesis of two new sets of oligopeptide-branched polypeptide conjugates. Studies with selected conjugates suggest that these compounds are highly ordered in buffer solution almost regardless from the helix-forming ability of the carrier (AK, SAK, EAK) and from the hydrophilic/hydrophobic character of peptides attached (AVKDEL vs FWRGDLVFDFQV). Addition of phospholipid bilayers with different composition essentially had no modifying effect on conformation of conjugates. From this we can conclude that the covalently coupled oligopeptides has a predominant effect of the conformational properties of conjugates.     

Optimization of staphylokinase production inBacillus subtilis using inducible and constitutive promoters

Staphylokinase (SAK) was produced inB. subtillis using two different promoter systems,i.e. the P43 andsacB promoters. To maximize SAK expression inB. subtilis, fermentation control strategies for each promoter were examined. SAK, under P43, a vegetative promoter transcribed mainly by σ^B containing RNA polymerase, was overexpressed at low dissolved oxygen (D.O.) levels, suggesting that thesigB operon is somewhat affected by the energy charge of the cells. The expression of SAK at the 10% D.O. level was three times higher than that at the 50% D.O. level. In the case ofsacB, a sucrose-inducible promoter, sucrose feeding was used to control the induction period and induction strength. Since sucrose is hydrolyzed by two sucrose hydrolyzing enzymes in the cell and culture broth, the control strategy was based on replenishing the loss of sucrose in the culture. With continuous feeding of sucrose, WB700 (pSAKBQ), which contains the SAK gene undersacB promoter, yieldedca. 35% more SAK than the batch culture. These results present efficient promoter-dependent control strategies inB. subtilis host system for foreign protein expression.     

Fluorometric studies of ligand-induced conformational changes of CD38

The lymphoid surface antigen CD38 is a NAD⁺-glycohydrolase that also catalyzes the transformation of NAD⁺ into cyclic ADP-ribose, a calcium mobilizing second messenger. In addition, ligation of CD38 by antibodies triggers signaling in lymphoid cells. Since the cytoplasmic tail of CD38 is dispensable for this latter property, we have previously proposed that CD38-mediated receptor signal transduction might be regulated by its conformational state. We have now examined the molecular changes of this protein during its interaction with NAD⁺ by measuring the intrinsic fluorescence of CD38. We have shown that addition of the substrate produced a dramatic decrease in the fluorescence of the catalytically active recombinant soluble ectodomain of murine CD38. Analysis of this event revealed that the catalytic cycle involves a state of the enzyme that is characterized by a low fluorescence which, upon substrate turnover, reverts to the initial high intrinsic fluorescence level. In contrast, non-hydrolyzable substrates trap CD38 in its altered low fluorescence state. Studies with the hydrophilic quencher potassium iodide revealed that the tryptophan residues that are mainly involved in the observed changes in fluorescence, are remote from the active site. Similar data were also obtained with human CD38, indicating that studies of intrinsic fluorescence will be useful in monitoring the transconformation of CD38 from different species. Together, these data demonstrate that CD38 undergoes a reversible conformational change after substrate binding, and suggest a mechanism by which this change could alter interactions with different cell-surface partners.     

Photoinhibition of photosynthesis in intact kiwifruit (Actinidia deliciosa) leaves: effect of growth temperature on photoinhibition and recovery

Intact leaves of kiwifruit (Actinidia deliciosa (A. Chev.) C.F. Liang et A.R. Ferguson) from plants grown in a range of controlled temperatures from 15/10 to 30/25°C were exposed to a photon flux density (PFD) of 1500 μmol·m⁻²·s⁻¹ at leaf temperatures between 10 and 25°C. Photoinhibition and recovery were followed at the same temperatures and at a PFD of 20 μmol·m⁻²·s⁻¹, by measuring chlorophyll fluorescence at 77 K and 692 nm, by measuring the photon yield of photosynthetic O₂ evolution and light-saturated net photosynthetic CO₂ uptake. The growth of plants at low temperatures resulted in chronic photoinhibition as evident from reduced fluorescence and photon yields. However, low-temperature-grown plants apparently had a higher capacity to dissipate excess excitation energy than leaves from plants grown at high temperatures. Induced photoinhibition, from exposure to a PFD above that during growth, was less severe in low-temperature-grown plants, particularly at high exposure temperatures. Net changes in the instantaneous fluorescence,F ₀, indicated that little or no photoinhibition occurred when low-temperature-grown plants were exposed to high-light at high temperatures. In contrast, high-temperature-grown plants were highly susceptible to photoinhibitory damage at all exposure temperatures. These data indicate acclimation in photosynthesis and changes in the capacity to dissipate excess excitation energy occurred in kiwifruit leaves with changes in growth temperature. Both processes contributed to changes in susceptibility to photoinhibition at the different growth temperatures. However, growth temperature also affected the capacity for recovery, with leaves from plants grown at low temperatures having moderate rates of recovery at low temperatures compared with leaves from plants grown at high temperatures which had negligible recovery. This also contributed to the reduced susceptibility to photoinhibition in low-temperature-grown plants. However, extreme photoinhibition resulted in severe reductions in the efficiency and capacity for photosynthesis.     

Synthesis and photophysical properties of zinc myoglobin appending an ethidium ion as a DNA intercalator

In order to elucidate the intramolecular photoinduced electron-transfer or energy-transfer mechanisms of the zinc myoglobin (ZnMb) dyad and to construct a photoreaction system within a Mb–DNA complex, we newly prepared ZnMb appending an ethidium ion (Et⁺). The steady-state fluorescence of ZnMb–Et⁺ at 600 nm and its lifetime (2.2 ns) indicate that the excited singlet state of ¹(ZnMb)* is not quenched by the Et⁺ moiety, whereas the lifetime of the excited triplet state of ³(ZnMb)*–Et⁺ was shorter (τ = 4.3 ms) than those of ZnMb and the intermolecular (ZnMb + ethidium) system. Upon photoirradiation of Et⁺, fluorescence studies indicated the intramolecular quenching reactions from the excited singlet state, ¹(Et⁺)*, to ZnMb, the process of which is likely the photoinduced energy-transfer reaction via a through-space mechanism. We also demonstrate the photophysical and spectroscopic properties of ZnMb–Et⁺ in the presence of calf thymus (CT) DNA. The changes in the absorption and fluorescence spectra of ZnMb–Et⁺ on the addition of CT-DNA up to 15 equiv were very small, indicating that there are no major changes in the heme pocket. However, we observed a longer lifetime of ³(ZnMb)*–Et⁺ in the presence of CT-DNA (τ = 5.3 ms) by single flash photolysis. This was induced by noncovalent interactions between Et⁺ and CT-DNA, followed by a conformational change of Et⁺ at the surface of ZnMb, where the donor–acceptor distance was probably elongated by CT-DNA. The synthetic manipulation at the Mb surface, by using a DNA intercalator coupled with photoinduced reaction, may provide a sensitive transient signal for DNA and valuable information to construct new Mb–DNA complex. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Fluorescence and FTIR study of pressure-induced structural modifications of horse liver alcohol dehydrogenase (HLADH).

The process of pressure-induced modification of horse liver alcohol dehydrogenase (HLADH) was followed by measuring in situ catalytic activity (up to 250 MPa), intrinsic fluorescence (0.1-600 MPa) and modifications of FTIR spectra (up to 1000 MPa). The tryptophan fluorescence measurements and the kinetic data indicated that the pressure-induced denaturation of HLADH was a process involving several transitions and that the observed transient states have characteristic properties of molten globules. Low pressure (< 100 MPa) induced no important modification in the catalytic efficiency of the enzyme and slight conformational changes, characterized by a small decrease in the centre of spectral mass of the enzyme's intrinsic fluorescence: a native-like state was assumed. Higher pressures (100-400 MPa) induced a strong decrease of HLADH catalytic efficiency and further conformational changes. At 400 MPa, a dimeric molten globule-like state was proposed. Further increase of pressure (400-600 MPa) seemed to induce the dissociation of the dimer leading to a transition from the first dimeric molten globule state to a second monomeric molten globule. The existence of two independent structural domains in HLADH was assumed to explain this transition: these domains were supposed to have different stabilities against high pressure-induced denaturation. FTIR spectroscopy was used to follow the changes in HLADH secondary structures. This technique confirmed that the intermediate states have a low degree of unfolding and that no completely denatured form seemed to be reached, even up to 1000 MPa.     

Molecular interactions of thymol with bovine serum albumin: Spectroscopic and molecular docking studies

Thymol is the main monoterpene phenol present in the essential oils which is used in the food industry as flavoring and preservative agent. In this study, the interaction of thymol with the concentration range of 1 to 6 μM and bovine serum albumin (BSA) at fixed concentration of 1 μM was investigated by fluorescence, UV‐vis, and molecular docking methods under physiological‐like condition. Fluorescence experiments were performed at 5 different temperatures, and the results showed that the fluorescence quenching of BSA by thymol was because of a static quenching mechanism. The obtained binding parameters, K, were in the order of 10⁴ M^?1, and the binding number, n, was approximately equal to unity indicating that there is 1 binding site for thymol on BSA. Calculated thermodynamic parameters for enthalpy (ΔH), entropy (ΔS), and Gibb's free energy (ΔG) showed that the reaction was spontaneous and hydrophobic interactions were the main forces in the binding of thymol to BSA. The results of UV‐vis spectroscopy and Arrhenius' theory showed the complex formation in the interaction of thymol and BSA. Negligible conformational changes in BSA by thymol were observed in fluorescence experiments, and the same results were also obtained from UV‐vis studies. Results of molecular docking indicated that the subdomain IA of BSA was the binding site for thymol.     

An FT-IR Study of DNA and RNA Conformational Transitions at Low Temperatures

Abstract

Fourier Transform Infrared (FT-IR) spectra of solid samples of DNA and RNA obtained from freeze-drying at solid CO₂ and liquid nitrogen temperatures, have been recorded and correlation between the conformational transitions and spectral changes is proposed. It is concluded that an equilibrium exists between A, B and Z conformations at low temperatures for the DNA molecule, which is temperature dependent, whereas the RNA molecule exhibits only the A conformation. The results have been compared with the metal-adducts of DNA and RNA, where one of the conformations is predominant.

Marker infrared bands for the B conformer have been found to be the strong band at 825 cm^?1 (sugar conformer mode) and a band with medium intensity at 690 cm^?1 (guanine breathing mode). The A conformation showed characteristic bands at 810 and 675 cm^?1. The B to Z conformational transition was characterized by the strong absorption bands near 820-810 cm^?1 and at 665-600 cm^?1.     

A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics

The process of large RNA folding is believed to proceed from many collapsed structures to a unique functional structure requiring precise organization of nucleotides. The diversity of possible structures and stabilities of large RNAs could result in non-exponential folding kinetics (e.g. stretched exponential) under conditions where the molecules have not achieved their native state. We describe a single-molecule fluorescence resonance energy transfer (FRET) study of the collapsed-state region of the free energy landscape of the catalytic domain of RNase P RNA from Bacillus stearothermophilus (C_thermo). Ensemble measurements have shown that this 260 residue RNA folds cooperatively to its native state at ≥1 mM Mg²⁺, but little is known about the conformational dynamics at lower ionic strength. Our measurements of equilibrium conformational fluctuations reveal simple exponential kinetics that reflect a small number of discrete states instead of the expected inhomogeneous dynamics. The distribution of discrete dwell times, collected from an “ensemble” of 300 single molecules at each of a series of Mg²⁺ concentrations, fit well to a double exponential, which indicates that the RNA conformational changes can be described as a four-state system. This finding is somewhat unexpected under [Mg²⁺] conditions in which this RNA does not achieve its native state. Observation of discrete well-defined conformations in this large RNA that are stable on the seconds timescale at low [Mg²⁺] (<0.1 mM) suggests that even at low ionic strength, with a tremendous number of possible (weak) interactions, a few critical interactions may produce deep energy wells that allow for rapid averaging of motions within each well, and yield kinetics that are relatively simple.     

Tet repressor-tetracycline interaction

Previous studies [Wasylewskiet al. (1996),J. Protein Chem. 15, 45–58] have shown that the W43 residue localized within the helix-turn-helix structure domain of Tet repressor can exist in the ground state in two conformational states. In this paper we investigate the fluorescence properties of W43 of TetR upon binding of tetracycline inducer and its chemical analogs such as anhydro- and epitetracycline. Binding of the drug inducer to the protein indicates that the W43 residue still exists in two conformational states; however, its environment changes drastically, as can be judged by the changes in fluorescence parameters. The FQRS (fluorescence-quenching-resolved spectra) method was used to decompose the total emission spectrum. The resolved spectra exhibit maxima of fluorescence at 346 and 332 nm and the component quenchable by KI (346 nm) is shifted 9 nm toward the blue side of the spectrum upon inducer binding. The observed shift does not result from the changes in the exposure of W43, since the bimolecular quenching rate constant remains the same and is equal to about 2.7×10⁹M^–1sec^–1. The binding of tetracycline leads to drastic decrease of the W43 fluorescence intensity and increase of the tetracycline intensity as well as the decrease of fluorescence lifetime, especially of the W43 component characterized by the emission at 332 nm. The observed energy transfer from W43 to tetracycline is more efficient for the state characterized by the fluorescence emission at 332 nm (88%) than for the component quenchable by iodide (53%) Tetracycline and several of its derivatives were also used to observe how chemical modifications of the hydrophilic groups in tetracycline influence the mechanism of binding of the antibiotic to Tet repressor. By use of pulsed-laser photoacoustic spectroscopy it is shown that the binding of tetracyclines to Tet repressor leads to significant increase of tetracycline fluorescence quantum yields. Steady-state fluorescence quenching of tetracycline analogs in complexes with Tet repressor using potassium iodide as a quencher allowed us to determine the dependence of the exposure of bound antibiotic on the modifications of hydrophilic substituents of tetracycline. Circular dichroism studies of the TetR-[Mg · tc]⁺ complex do not indicate dramatic changes in the secondary structure of the protein; however, the observed small decrease in the TetR helicity may occur due to partial unfolding of the DNA recognition helix of the protein. The observed changes may play an important role in the process of induction in which tetracycline binding results in the loss of specific DNA binding.Abbreviations FQRS fluorescence-quenching-resolved spectra - HTH helix-turn-helix motif - tc tetracycline - TetR tetracycline repressor from Escherichia coli - TetR WT wild-type TetR - TetR W43 single point mutant with phenylalanine substituted for tryptophan at position 75 in both subunits     

The X-ray crystallographic structure and specificity profile of HAD superfamily phosphohydrolase BT1666: comparison of paralogous functions in B. thetaiotaomicron

Analysis of the haloalkanoate dehalogenase superfamily (HADSF) has uncovered homologues occurring within the same organism that are found to possess broad, overlapping substrate specificities, and low catalytic efficiencies. Here we compare the HADSF phosphatase BT1666 from Bacteroides thetaiotaomicron VPI‐5482 to a homologue with high sequence identity (40%) from the same organism BT4131, a known hexose‐phosphate phosphatase. The goal is to find whether these enzymes represent duplicated versus paralogous activities. The X‐ray crystal structure of BT1666 was determined to 1.82 Å resolution. Superposition of the BT1666 and BT4131 structures revealed a conserved fold and identical active sites suggestive of a common physiological substrate. The steady‐state kinetic constants for BT1666 were determined for a diverse panel of phosphorylated metabolites to define its substrate specificity profile and overall level of catalytic efficiency. Whereas BT1666 and BT4131 are both promiscuous, their substrate specificity profiles are distinct. The catalytic efficiency of BT1666 (k_cat/K_m = 4.4 × 10²M^?1 s^?1 for the best substrate fructose 1,6‐(bis)phosphate) is an order of magnitude less than that of BT4131 (k_cat/K_m = 6.7 × 10³M^?1 s^?1 for 2‐deoxyglucose 6‐phosphate). The seemingly identical active‐site structures point to sequence variation outside the active site causing differences in conformational dynamics or subtle catalytic positioning effects that drive the divergence in catalytic efficiency and selectivity. The overlapping substrate profiles may be understood in terms of differential regulation of expression of the two enzymes or a conferred advantage in metabolic housekeeping functions by having a larger range of possible metabolites as substrates. Proteins 2011;. © 2011 Wiley‐Liss, Inc.     

Spectroscopic and molecular modeling approaches to investigate the binding of proton pump inhibitors to human serum albumin

The interaction between two proton pump inhibitors viz., omeprazole (OME) and esomeprazole (EPZ) with human serum albumin (HSA) was studied by fluorescence, absorption, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR), voltammetry, and molecular modeling approaches. The Stern–Volmer quenching constants (K_sv) for OME-HSA and EPZ-HSA systems obtained at different temperatures revealed that both OME and EPZ quenched the intensity of HSA through dynamic mode of quenching mechanism. The binding constants of OME-HSA and EPZ-HSA increased with temperature, indicating the increased stability of these systems at higher temperatures. Thermodynamic parameters viz., ?H^°, ?S^°, and ?G^° were determined for both systems. These values revealed that both systems were stabilized by hydrophobic forces. The competitive displacement and molecular docking studies suggested that OME/EPZ was bound to Sudlow’s site I in subdomain IIA in HSA. The extent of energy transfer from HSA to OME/EPZ and the distance of separation in tryptophan (Trp214) Trp214-OME and Trp214-EPZ was determined based on the theory of fluorescence resonance energy transfer. UV absorption, 3D fluorescence, and CD studies indicated that the binding of OME/EPZ to HSA has induced micro environmental changes around the protein which resulted changes in its secondary structure.     

Acid-induced Molten Globule State of a Prion Protein: CRUCIAL ROLE OF STRAND 1-HELIX 1-STRAND 2 SEGMENT*

The conversion of a cellular prion protein (PrP^C) to its pathogenic isoform (PrP^Sc) is a critical event in the pathogenesis of prion diseases. Pathogenic conversion is usually associated with the oligomerization process; therefore, the conformational characteristics of the pre-oligomer state may provide insights into the conversion process. Previous studies indicate that PrP^C is prone to oligomer formation at low pH, but the conformation of the pre-oligomer state remains unknown. In this study, we systematically analyzed the acid-induced conformational changes of PrP^C and discovered a unique acid-induced molten globule state at pH 2.0 termed the “A-state.” We characterized the structure of the A-state using far/near-UV CD, 1-anilino-8-naphthalene sulfonate fluorescence, size exclusion chromatography, and NMR. Deuterium exchange experiments with NMR detection revealed its first unique structure ever reported thus far; i.e. the Strand 1-Helix 1-Strand 2 segment at the N terminus was preferentially unfolded, whereas the Helix 2-Helix 3 segment at the C terminus remained marginally stable. This conformational change could be triggered by the protonation of Asp¹⁴⁴, Asp¹⁴⁷, and Glu¹⁹⁶, followed by disruption of key salt bridges in PrP^C. Moreover, the initial population of the A-state at low pH (pH 2.0–5.0) was well correlated with the rate of the β-rich oligomer formation, suggesting that the A-state is the pre-oligomer state. Thus, the specific conformation of the A-state would provide crucial insights into the mechanisms of oligomerization and further pathogenic conversion as well as facilitating the design of novel medical chaperones for treating prion diseases.     

Electrogenic Partial Reactions of the SR-Ca-ATPase Investigated by a Fluorescence Method

A fluorescence method was adapted to investigate active ion transport in membrane preparations of the SR-Ca-ATPase. The styryl dye RH421 previously used to investigate the Na,K-ATPase was replaced by an analogue, 2BITC, to obtain optimized fluorescence changes upon substrate-induced partial reactions. Assuming changes of the local electric field to be the source of fluorescence changes that are produced by uptake/release or by movement of ions inside the protein, 2BITC allowed the determination of electrogenic partial reactions in the pump cycle. It was found that Ca²⁺ binding on the cytoplasmic and on the lumenal side of the pump is electrogenic while phosphorylation and conformational transition showed only minor electrogenicity. Ca²⁺ equilibrium titration experiments at pH 7.2 in the two major conformations of the protein indicated cooperative binding of two Ca²⁺ ions in state E₁ with an apparent half-saturation concentration, K _M of 600 nm. In state P-E₂ two K _M values, 5 μm and 2.2 mM, were determined and are in fair agreement with published data. From Ca²⁺ titrations in buffers with various pH and from pH titrations in P-E₂, it could be demonstrated that H⁺ binding is electrogenic and that Ca²⁺ and H⁺ compete for the same binding site(s). Tharpsigargin-induced inhibition of the Ca-ATPase led to a state with a specific fluorescence level comparable to that of state E₁ with unoccupied ion sites, independent of the buffer composition. Received: 21 September 1998/Revised: 18 December 1998     

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 ∼35°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°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°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.     

Photosystem II reaction centres stay intact during low temperature photoinhibition

Photoinhibition of photosynthesis was studied in intact barley leaves at 5 and 20°C, to reveal if Photosystem II becomes predisposed to photoinhibition at low temperature by 1) creation of excessive excitation of Photosystem II or, 2) inhibition of the repair process of Photosystem II. The light and temperature dependence of the reduction state of Q_A was measured by modulated fluorescence. Photon flux densities giving 60% of Q_A in a reduced state at steady-state photosynthesis (300 mol m^–2s^–1 at 5°C and 1200 mol m^–2s^–1 at 20°C) resulted in a depression of the photochemical efficiency of Photosystem II (F_v/F_m) at both 5 and 20°C. Inhibition of F_v/F_m occurred with initially similar kinetics at the two temperatures. After 6h, F_v/F_m was inhibited by 30% and had reached steady-state at 20°C. However, at 5°C, F_v/F_m continued to decrease and after 10h, F_v/F_m was depressed to 55% of control. The light response of the reduction state of Q_A did not change during photoinhibition at 20°C, whereas after photoinhibition at 5°C, the proportion of closed reaction centres at a given photon flux density was 10–20% lower than before photoinhibition.Changes in the D1-content were measured by immunoblotting and by the atrazine binding capacity during photoinhibition at high and low temperatures, with and without the addition of chloramphenicol to block chloroplast encoded protein synthesis. At 20°C, there was a close correlation between the amount of D1-protein and the photochemical efficiency of photosystem II, both in the presence or in the absence of an active repair cycle. At 5°C, an accumulation of inactive reaction centres occurred, since the photochemical efficiency of Photosystem II was much more depressed than the loss of D1-protein. Furthermore, at 5°C the repair cycle was largely inhibited as concluded from the finding that blockage of chloroplast encoded protein synthesis did not enhance the susceptibility to photoinhibition at 5°C.It is concluded that, the kinetics of the initial decrease of F_v/F_m was determined by the reduction state of the primary electron acceptor Q_A, at both temperatures. However, the further suppression of F_v/F_m at 5°C after several hours of photoinhibition implies that the inhibited repair cycle started to have an effect in determining the photochemical efficiency of Photosystem II.Abbreviations CAP D-threochloramphenicol - F₀ and F ₀ fluorescence when all Photosystem II reaction centres are open in dark- and light-acclimated leaves, respectively - F_m and F _m fluorescence when all Photosystem II reaction centres are closed in dark- and light-acclimated leaves, respectively - F_s fluorescence at steady state - Q_A the primary, stable quinone acceptor of Photosystem II - q_N non-photochemical quenching of fluorescence - q_P photochemical quenching of fluorescence     

Effect of Mg2+ during reactivation and refolding of guanidine hydrochloride-denatured creatine kinase

Creatine kinase (ATP: creatine N-phosphotransferase, EC 2.7.3.2) was completely denatured using 3 M guanidine hydrochloride for 2 h as in previous studies [Yao et al. (1982), Sci. Sin. 25B, 1296–1302; Yao et al. (1984), Biochemistry 23, 2740–2744; Yao et al. (1982), Sci. Sin. 25B, 1186–1193]. Under suitable conditions, about 60–70% of the activity can be recovered in the presence of different Mg²⁺ concentrations. Both the reactivation and the refolding processes follow two-phase courses after dilution in the proper solutions. A comparison of the rate constants for the refolding of unfolded creatine kinase with those for the recovery of its catalytic activity at various Mg²⁺ concentrations shows that these are not synchronized. The reactivity of guanidine hydrochloride-denatured creatine kinase can be inhibited by Mg²⁺; however, the rates of reactivation are independent of the Mg²⁺ concentration. In addition, Mg²⁺ affects the fluorescence intensity, but the rate constants of refolding are independent of Mg²⁺ concentration. Although the reactivation of GdHCl-denatured creatine kinase is complete about 3 h after dilution with reactivation solutions, the conformational changes during refolding occur in a much slower reaction. Mg²⁺ can induce complex changes in the relative fluorescence intensity during refolding over a broad range of concentrations.     

Kinetic Analysis of Conformational Changes of GroEL Based on the Fluorescence of Tyrosine 506

The conformational changes of GroEL during the ATPase cycle in the presence of GroES were studied by measuring the fluorescence intensity time course of intrinsic tyrosine Y506, which is located near the nucleotide-binding site. A GroEL solution containing GroES was mixed with an ATP solution to initiate the reaction cycle. The tyrosine fluorescence intensity relative to that without the nucleotide reached 112% within the dead time of the apparatus (>15 s^?1) and further increased to 123% at 0.57 s^?1 followed by a decrease to 102% at 0.32 s^?1. An initial conformational change and a second intermediate state were expected to occur in ATP-bound GroEL because similar changes were observed for the ATPase-deficient D398A mutant. The conformational change to the third intermediate state corresponded to a process during or after ATP hydrolysis because D398A had no decreasing phase. The second intermediate state before ATP hydrolysis was characterized for the first time.