ADP Complex Research Articles

The tethered motor domain of a kinesin-microtubule complex catalyzes reversible synthesis of bound ATP.

Although the steps for the forward reaction of ATP hydrolysis by the motor protein kinesin have been studied extensively, the rates for the reverse reactions and thus the energy changes at each step are not as well defined. Oxygen isotopic exchange between water and P(i) was used to evaluate the reverse rates. The fraction of the kinesin x ADP x P(i) complex that reverts to ATP before release of P(i) during net hydrolysis was approximately 0 and approximately 2.6% in the absence and presence of microtubules (MTs), respectively. The rate of synthesis of bound ATP from free P(i) and the MT x kinesin x ADP complex was approximately 1.7 M(-1) x s(-1) (K0.5 ADP = 70 microM) with monomeric kinesin in the absence of net hydrolysis. Synthesis of bound ATP from the ADP of the tethered head of a dimer-MT complex was 20-fold faster than for the monomer-MT complex. This MT-activated ATP synthesis at the tethered head is in marked contrast to the lack of MT stimulation of ADP release from the same site. The more rapid ATP synthesis with dimers suggests that the tethered head binds behind the strongly attached head, because this positions the neck linker of the tethered head toward the plus end of the MT and would thus facilitate its docking on synthesis of ATP. The observed rate of ATP synthesis also puts limits on the overall energetics that suggest that a significant fraction of the free energy of ATP hydrolysis is available to drive the docking of the neck linker on binding of ATP.

Nucleotide specificity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase : Kinetics, fluorescence spectroscopy, and molecular simulation studies

Phosphoenolpyruvate carboxykinases, depending on the enzyme origin, preferentially use adenine or guanine nucleotides as substrates. In this work, analyses of the substrate specificity of the Saccharomyces cerevisiae ATP-dependent enzyme have been carried out. Kinetics studies gave relative values of k cat/ K m for the nucleoside triphosphate complexes in the order ATP ≫ GTP > ITP > UTP > CTP. For the nucleoside diphosphate complexes the order is ADP ≫ GDP > IDP ≅ UDP > CDP. This shows that the enzyme has a strong preference for ADP (or ATP) over other nucleotides, being this preference about an order of magnitude higher for the diphosphorylated than for the triphosphorylated nucleosides. The calculated binding free energies (kcal mol −1) at 25 °C are 7.39 and 6.51 for ATP and ADP, respectively. These values decrease with the nucleotide structure in the same order than the kinetic specificity. The binding energy for any triphosphorylated nucleoside is more favourable than for the corresponding diphosphorylated compound, showing the relevance of the P γ for nucleotide binding. Homology models of the adenine and guanine nucleotides in complex with the enzyme show that the base adopts a similar conformation in the diphosphorylated nucleosides while in the triphosphorylated nucleosides the sugar-base torsion angle is 61° for ATP and −53° for GTP. Differences are also noted in the distance between P β and Mn 2+ at site 1. This distance is almost the same in the ATP, GTP, and UTP complexes, however in the ADP, GDP and UDP complexes it is 2.9, 5.1, and 7 Å, respectively. Experimental data obtained with a Thr463Ala mutant enzyme agree with molecular simulation predictions. The results here presented are discussed in terms of the proposed interactions of the nucleotides with the protein.

A Family Portrait of the RIO Kinases

The RIO family of atypical serine protein kinases has been first characterized only recently. It consists of enzymes that contain a unique domain with a characteristic kinase sequence motif and usually some additional domains. At least two RIO proteins, Rio1 and Rio2, are present in organisms varying from Archaea to humans, with a third Rio3 subfamily present only in multicellular eukaryotes. Yeast Rio1 and Rio2 proteins have been implicated in the processing of 20 S pre-rRNA and are necessary for survival of the cells. Crystal structures of Archaeoglobus fulgidus Rio1 and Rio2 have shown that whereas the overall fold of these enzymes resembles typical protein kinases, some of the structural domains, particularly those involved in peptide substrate binding, are not present. The mode of binding of nucleotides also differs from that found in typical protein kinases. Although it has been shown that both Rio1 and Rio2 have the enzymatic activity of kinases and are capable of autophosphorylation, the biological substrates of RIO proteins and their full biological role still remain to be discovered.

Autophosphorylation of Archaeoglobus fulgidus Rio2 and crystal structures of its nucleotide–metal ion complexes

The highly conserved, atypical RIO serine protein kinases are found in all organisms, from archaea to man. In yeast, the kinase activity of Rio2 is necessary for the final processing step of maturing the 18S ribosomal rRNA. We have previously shown that the Rio2 protein from Archaeoglobus fulgidus contains both a small kinase domain and an N-terminal winged helix domain. Previously solved structures using crystals soaked in nucleotides and Mg2+ or Mn2+ showed bound nucleotide but no ordered metal ions, leading us to the conclusion that they did not represent an active conformation of the enzyme. To determine the functional form of Rio2, we crystallized it after incubation with ATP or ADP and Mn2+. Co-crystal structures of Rio2-ATP-Mn and Rio2-ADP-Mn were solved at 1.84 and 1.75 angstroms resolution, respectively. The gamma-phosphate of ATP is firmly positioned in a manner clearly distinct from its location in canonical serine kinases. Comparison of the Rio2-ATP-Mn complex with the Rio2 structure with no added nucleotides and with the ADP complex indicates that a flexible portion of the Rio2 molecule becomes ordered through direct interaction between His126 and the gamma-phosphate oxygen of ATP. Phosphopeptide mapping of the autophosphorylation site of Rio2 identified Ser128, within the flexible loop and directly adjacent to the part that becomes ordered in response to ATP, as the target. These results give us further information about the nature of the active site of Rio2 kinase and suggest a mechanism of regulation of its enzymatic activity.

The Nucleotide-Binding Site of the <I>Escherichia coli</I> DnaC Protein: Molecular Topography of DnaC Protein–Nucleotide Cofactor Complexes

The structure of the nucleotide-binding site of the Escherichia coli replication factor DnaC protein and the effect of the nucleotide cofactor on the protein structure have been examined using ultraviolet, steady-state, and time-dependent fluorescence spectroscopy. Emission spectra and quenching studies of the fluorescent nucleotide analogs, 3'-O-(N-methylantraniloyl)-5'-triphosphate (MANT-ATP) and 3'-O-(N-methylantraniloyl)-5'-diphosphate (MANT-ADP), bound to the DnaC protein indicate that the nucleotide-binding site forms a hydrophobic cleft on the surface of the protein. Fluorescence decays of free and bound MANT-ATP and MANT-ADP indicate that cofactors exist in two different conformations both, free and bound to the protein. However, the two conformations of the bound nucleotides differ in their solvent accessibilities. Moreover, there are significant differences in the solvent accessibility between ATP and ADP complexes. Specific binding of magnesium to the protein controls the structure of the binding site, particularly, in the case of the ATP complex, leading to additional opening of the binding site cleft. Both tyrosine and tryptophan residues are located on the surface of the protein. The tryptophans are clustered at a large distance from the nucleotide-binding site. However, in spite of a large spatial separation, binding of both cofactors induces significant and different changes in the structure of the environment of tryptophans, indicating long-range structural effects through the DnaC molecule. Moreover, only ATP induces changes in the distribution of the tyrosine residues on the surface of the protein. The data reveal that the nucleotide-DnaC protein complex is a sophisticated allosteric system, responding differently to the ATP and ADP binding.

Regulation of the HscA ATPase Reaction Cycle by the Co-chaperone HscB and the Iron-Sulfur Cluster Assembly Protein IscU

The ATPase activity of HscA, a specialized hsp70 molecular chaperone from Escherichia coli, is regulated by the iron-sulfur cluster assembly protein IscU and the J-type co-chaperone HscB. IscU behaves as a substrate for HscA, and HscB enhances the binding of IscU to HscA. To better understand the mechanism by which HscB and IscU regulate HscA, we examined binding of HscB to the different conformational states of HscA and the effects of HscB and IscU on the kinetics of the individual steps of the HscA ATPase reaction cycle. Affinity sensor studies revealed that whereas IscU binds both ADP (R-state) and ATP (T-state) HscA complexes, HscB interacts only with an ATP-bound state. Studies of ATPase activity under single-turnover and rapid mixing conditions showed that both IscU and HscB interact with the low peptide affinity T-state of HscA (HscA++.ATP) and that both modestly accelerate (3-10-fold) the rate-determining steps in the HscA reaction cycle, k(hyd) and k(T-->R). When present together, IscU and HscB synergistically stimulate both k(hyd) (approximately = 500-fold) and k(T-->R) (approximately = 60-fold), leading to enhanced formation of the HscA.ADP-IscU complex (substrate capture). Following ADP/ATP exchange, IscU also stimulates k(R-->T) (approximately = 50-fold) and thereby accelerates the rate at which the low peptide affinity HscA++.ATP T-state is regenerated. Because HscA nucleotide exchange is fast, the overall rate of the chaperone cycle in vivo will be determined by the availability of the IscU-HscB substrate-co-chaperone complex.

Normal platelets possess the soluble form of IL-6 receptor

Interleukin 6 is a multifunctional cytokine that exerts its biological activity through binding to an 80 Kd specific receptor (IL-6Rα) and a 130 Kd signal-transducing unit (gp130). A 55 Kd soluble IL-6R (IL-6sR) has also been described which, after binding to IL-6 is also able to activate gp130. The presence of IL-6Rα was described in some megakaryoblastic cell lines but is still controversial in normal megakaryocytes. In this study we demonstrate the presence of intraplatelet IL-6sR by Western blot through the appearance of a 55 Kd protein and the finding of detectable amounts of IL-6sR in the platelet content by ELISA technique. Besides, we showed IL-6sR release during platelet activation induced by thrombin and a complex of ADP and epinephrine. IL-6Rα on platelet membrane could not be found neither by Western blot nor by flow cytometry. The IL-6sR released during platelet activation and complexed to IL-6 could act on cell types such as endothelial cells that do not possess IL-6Rα through binding to gp130.Besides, since we could not find IL-6R on platelet membrane, the potentiating effect of IL-6 on platelet function could be explained through binding of IL-6sR/IL-6 complex to platelet membrane gp130.

Conformational Changes Induced by Nucleotide Binding in Cdc6/ORC From Aeropyrum pernix

Archaea contain one or more proteins with homology to eukaryotic ORC/Cdc6 proteins. Sequence analysis suggests the existence of at least two subfamilies of these proteins, for which we propose the nomenclature ORC1 and ORC2. We have determined crystal structures of the ORC2 protein from the archaeon Aeropyrum pernix in complexes with ADP or a non-hydrolysable ATP analogue, ADPNP. Between two crystal forms, there are three crystallographically independent views of the ADP complex and two of the ADPNP complex. The protein molecules in the three complexes with ADP adopt very different conformations, while the two complexes with ADPNP are the same. These structures indicate that there is considerable conformational flexibility in ORC2 but that ATP binding stabilises a single conformation. We show that the ORC2 protein can bind DNA, and that this activity is associated with the C-terminal domain of the protein. We present a model for the interaction of the winged helix (WH) domain of ORC2 with DNA that differs from that proposed previously for Pyrobaculum aerophilum ORC/Cdc6.

Beryllium(II) binding to ATP and ADP: potentiometric determination of the thermodynamic constants and implications for in vivo toxicity.

Highly toxic beryllium(II) is divalent metal ion with a high charge density, making it a potential target for binding to bio-molecules rich in O donor groups. In aqueous solution Be2+ binds to ATP and ADP to form 1:1 Be2+:ATP and Be2+:ADP complexes in relatively acidic media. At neutral pH the complex formed undergoes hydrolysis. Be2+ binding to ATP and ADP is much stronger than Ca2+ and Mg2+ binding. The high affinity of Be2+ toward ATP and ADP binding suggests a mechanism relevant to understanding the in vivo chemical toxicity of this metal.

Two-headed binding of the unphosphorylated nonmuscle heavy meromyosin.ADP complex to actin.

The enzymatic and motor function of smooth muscle and nonmuscle myosin II is activated by phosphorylation of the regulatory light chains located in the head portion of myosin. Dimerization of the heads, which is brought about by the coiled-coil tail region, is essential for regulation since single-headed fragments are active regardless of the state of phosphorylation. Utilizing the fluorescence signal on binding of myosin to pyrene-labeled actin filaments, we investigated the interplay of actin and nucleotide binding to thiophosphorylated and unphosphorylated recombinant nonmuscle IIA heavy meromyosin constructs. We show that both heads of either thiophosphorylated or unphosphorylated heavy meromyosin bind very strongly to actin (K(d) < 10 nM) in the presence or absence of ADP. The heads have high and indistinguishable affinities for ADP (K(d) around 1 microM) when bound to actin. These findings are in line with the previously observed unusually loose coupling between nucleotide and actin binding to nonmuscle myosin IIA subfragment-1 (Kovács et al. (2003) J. Biol. Chem. 278, 38132.). Furthermore, they imply that the structure of the two heads in the ternary actomyosin-ADP complex is symmetrical and that the asymmetrical structure observed in the presence of ATP and the absence of actin in previous investigations (Wendt et al. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 4361) is likely to represent an ATPase intermediate that precedes the actomyosin-ADP state.

Reduction of Fe(III) Ions Complexed to Physiological Ligands by Lipoyl Dehydrogenase and Other Flavoenzymes in Vitro: IMPLICATIONS FOR AN ENZYMATIC REDUCTION OF Fe(III) IONS OF THE LABILE IRON POOL

Enzymatic reduction of physiological Fe(III) complexes of the "labile iron pool" has not been studied so far. By use of spectrophotometric assays based on the oxidation of NAD(P)H and formation of [Fe(II) (1,10-phenanthroline)3]2+ as well as by utilizing electron paramagnetic resonance spectrometry, it was demonstrated that the NAD(P)H-dependent flavoenzyme lipoyl dehydrogenase (diaphorase, EC 1.8.1.4) effectively catalyzes the one-electron reduction of Fe(III) complexes of citrate, ATP, and ADP at the expense of the co-enzymes NAD(P)H. Deactivated or inhibited lipoyl dehydrogenase did not reduce the Fe(III) complexes. Likewise, in the absence of NAD(P)H or in the presence of NAD(P)+, Fe(III) reduction could not be detected. The fact that reduction also occurred in the absence of molecular oxygen as well as in the presence of superoxide dismutase proved that the Fe(III) reduction was directly linked to the enzymatic activity of lipoyl dehydrogenase and not mediated by O2. Kinetic studies revealed different affinities of lipoyl dehydrogenase for the reduction of the low molecular weight Fe(III) complexes in the relative order Fe(III)-citrate > Fe(III)-ATP > Fe(III)-ADP (half-maximal velocities at 346-485 microm). These Fe(III) complexes were enzymatically reduced also by other flavoenzymes, namely glutathione reductase (EC 1.6.4.2), cytochrome c reductase (EC 1.6.99.3), and cytochrome P450 reductase (EC 1.6.2.4) with somewhat lower efficacy. The present data suggest a (patho)physiological role for lipoyl dehydrogenase and other flavoenzymes in intracellular iron metabolism.

Role of the gamma-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics.

Productive cis folding by the chaperonin GroEL is triggered by the binding of ATP but not ADP, along with cochaperonin GroES, to the same ring as non-native polypeptide, ejecting polypeptide into an encapsulated hydrophilic chamber. We examined the specific contribution of the gamma-phosphate of ATP to this activation process using complexes of ADP and aluminium or beryllium fluoride. These ATP analogues supported productive cis folding of the substrate protein, rhodanese, even when added to already-formed, folding-inactive cis ADP ternary complexes, essentially introducing the gamma-phosphate of ATP in an independent step. Aluminium fluoride was observed to stabilize the association of GroES with GroEL, with a substantial release of free energy (-46 kcal/mol). To understand the basis of such activation and stabilization, a crystal structure of GroEL-GroES-ADP.AlF3 was determined at 2.8 A. A trigonal AlF3 metal complex was observed in the gamma-phosphate position of the nucleotide pocket of the cis ring. Surprisingly, when this structure was compared with that of the previously determined GroEL-GroES-ADP complex, no other differences were observed. We discuss the likely basis of the ability of gamma-phosphate binding to convert preformed GroEL-GroES-ADP-polypeptide complexes into the folding-active state.

ATP Binding Modulates the Nucleic Acid Affinity of Hepatitis C Virus Helicase

The helicase of hepatitis C virus (HCV) unwinds nucleic acid using the energy of ATP hydrolysis. The ATPase cycle is believed to induce protein conformational changes to drive helicase translocation along the length of the nucleic acid. We have investigated the energetics of nucleic acid binding by HCV helicase to understand how the nucleotide ligation state of the helicase dictates the conformation of its nucleic acid binding site. Because most of the nucleotide ligation states of the helicase are transient due to rapid ATP hydrolysis, several compounds were analyzed to find an efficient unhydrolyzable ATP analog. We found that the beta-gamma methylene/amine analogs of ATP, ATPgammaS, or [AlF4]ADP were not effective in inhibiting the ATPase activity of HCV helicase. On the other hand, [BeF3]ADP was found to be a potent inhibitor of the ATPase activity, and it binds tightly to HCV helicase with a 1:1 stoichiometry. Equilibrium binding studies showed that HCV helicase binds single-stranded nucleic acid with a high affinity in the absence of ATP or in the presence of ADP. Upon binding to the ATP analog, a 100-fold reduction in affinity for ssDNA was observed. The reduction in affinity was also observed in duplex DNA with 3' single-stranded tail and in RNA but not in duplex DNA. The results of this study indicate that the nucleic acid binding site of HCV helicase is allosterically modulated by the ATPase reaction. The binding energy of ATP is used to bring HCV helicase out of a tightly bound state to facilitate translocation, whereas ATP hydrolysis and product release steps promote tight rebinding of the helicase to the nucleic acid. On the basis of these results we propose a Brownian motor model for unidirectional translocation of HCV helicase along the nucleic acid length.

The Allosteric Transition of GroEL Induced by Metal Fluoride–ADP Complexes

To understand the mechanism of a functionally important ATP-induced allosteric transition of GroEL, we have studied the effect of a series of metal fluoride–ADP complexes and vanadate–ADP on GroEL by kinetic fluorescence measurement of pyrene-labeled GroEL and by small-angle X-ray scattering measurement of wild-type GroEL. The metal fluorides and vanadate, complexed with ADP, are known to mimic the γ-phosphate group of ATP, but they differ in geometry and size; it is expected that these compounds will be useful for investigating the strikingly high specificity of GroEL for ATP that enables the induction of the allosteric transition. The kinetic fluorescence measurement revealed that aluminium, beryllium, and gallium ions, when complexed with the fluoride ion and ADP, induced a biphasic fluorescence change of pyrenyl GroEL, while scandium and vanadate ions did not induce any kinetically observed change in fluorescence. The burst phase and the first phase of the fluorescence kinetics were reversible, while the second phase and subsequent changes were irreversible. The dependence of the burst-phase and the first-phase fluorescence changes on the ADP concentration indicated that the burst phase represents non-cooperative nucleotide binding to GroEL, and that the first phase represents the allosteric transition of GroEL. Both the amplitude and the rate constant of the first phase of the fluorescence kinetics were well understood in terms of a kinetic allosteric model, which is a combination of transition state theory and the Monod–Wyman–Changeux allosteric model. From the kinetic allosteric model analysis, the relative free energy of the transition state in the metal fluoride–ADP-induced allosteric transition of GroEL was found to be larger than the corresponding free energy of the ATP-induced allosteric transition by more than 5.5 kcal/mol. However, the X-ray scattering measurements indicated that the allosteric state induced by these metal fluoride–ADP complexes is structurally equivalent to the allosteric state induced by ATP. These results suggested that both the size and coordination geometry of γ-phosphate (and its analogs) are related to the allosteric transition of GroEL. It was therefore concluded that the tetrahedral geometry of γ-phosphate (or its analogs) and the inter-atomic distance (∼1.6 Å) between phosphorus (vanadium, or metal atom) and oxygen (or fluorine) are both important for inducing the allosteric transition of GroEL, leading to the high selectivity of GroEL for ATP about ligand adenine nucleotides, which function as the preferred allosteric ligand.

Conserved positions for ribose recognition: importance of water bridging interactions among ATP, ADP and FAD-protein complexes.

Analysis of the spatial arrangement of protein and water atoms that form polar interactions with ribose has been performed for a structurally non-redundant dataset of ATP, ADP and FAD-protein complexes. The 26 ligand-protein structures were separated into two groups corresponding to the most populated furanose ring conformations (N and S-domains). Four conserved positions were found for S-domain protein-ligand complexes and five for N-domain complexes. Multiple protein folds and secondary structural elements were represented at a single conserved position. The following novel points were revealed: (i) Two complementary positions sometimes combine to describe a putative atomic spatial location for a specific conserved binding spot. (ii) More than one third of the interactions scored were water-mediated. Thus, conserved spatial positions rich in water atoms are a significant feature of ribose-protein complexes.

Low stability for monomeric human chaperonin protein 10: interprotein interactions contribute majority of oligomer stability

Co-chaperonin protein 10 (cpn10, GroES in Escherichia coli) is a ring-shaped heptameric protein that facilitates substrate folding when in complex with cpn60 (GroEL in E. coli). The cpn10 from the hyperthermophilic, ancient bacterium Aquifex aeolicus (Aacpn10) has a 25-residue C-terminal extension in each monomer not found in any other cpn10 protein. Earlier in vitro work has shown that this tail is not needed for heptamer assembly or protein function. Without the tail, however, the heptamers (Aacpn10del-25) readily aggregate into fibrillar stacked rings. To explain this phenomenon, we performed binding experiments with a peptide construct of the tail to establish its specificity for Aacpn10del-25 and used cryo-electron microscopy to determine the three-dimensional (3D) structure of the GroEL–Aacpn10–ADP complex at an 8-Å resolution. We found that the GroEL–Aacpn10 structure is similar to the GroEL–GroES structure at this resolution, suggesting that Aacpn10 has molecular interactions with cpn60 similar to other cpn10s. The cryo-electron microscopy density map does not directly reveal the density of the Aacpn10 25-residue tail. However, the 3D statistical variance coefficient map computed from multiple 3D reconstructions with randomly selected particle images suggests that the tail is located at the Aacpn10 monomer–monomer interface and extends toward the cis-ring apical domain of GroEL. The tail at this location does not block the formation of a functional co-chaperonin/chaperonin complex but limits self-aggregation into linear fibrils at high temperatures. In addition, the 3D variance coefficient map identifies several regions inside the GroEL–Aacpn10 complex that have flexible conformations. This observation is in full agreement with the structural properties of an effective chaperonin.

Crystallographic and thiol-reactivity studies on the complex of pig muscle phosphoglycerate kinase with ATP analogues: correlation between nucleotide binding mode and helix flexibility.

Crystal structure of the ternary complex of pig muscle phosphoglycerate kinase (PGK) with the substrate 3-phosphoglycerate (3-PG) and the Mg(2+) complex of beta,gamma-methylene-adenosine-5'-triphosphate (AMP-PCP), a nonreactive analogue of the nucleotide substrate, MgATP, has been determined by X-ray diffraction at 2.5 A resolution. The overall structure of the protein exhibits an open conformation, similar to that of the previously determined ternary complex of the pig muscle enzyme with beta,gamma-imido-adenosine-5'-triphosphate (AMP-PNP) in place of AMP-PCP (May, Vas, Harlos, and Blake (1996) Proteins 24, 292-303). The orientation and details of interactions of the nucleotide phosphates, however, show marked differences. The beta-phosphate is linked to the conserved Asp 218, i.e., to the N-terminus of helix 8, through the Mg(2+) ion; the previously observed interactions of the metal complex of AMP-PNP or ADP with the conserved Asn 336 and the N-terminus of helix 13 are completely absent. These structural differences are maintained themselves in solution studies. Inhibition and binding experiments show a slightly weaker interaction of PGK with MgAMP-PCP than with MgAMP-PNP: at pH 7.5, the K(d) values are 1.07 +/- 0.18 and 0.41 +/- 0.08 mM, respectively. The difference is further enhanced by 3-PG: the K(d) values are 2.80 +/- 0.66 and 0.68 +/- 0.11 mM, respectively. Thus, the previously observed weakening effect of 3-PG on nucleotide binding (Merli, Szilágyi, Flachner, Rossi, and Vas (2002) Biochemistry 41, 111-119) is more pronounced with MgAMP-PCP. The discordance between substrate analogues also shows up in thiol reactivity studies. In their binary complexes, both ATP analogues protect the fast-reacting thiols of PGK in helix 13 against modification to similar extent. In their ternary complexes, however, which also contain bound 3-PG, the protective effect of MgAMP-PCP, but not of MgAMP-PNP, is largely abolished. This indicates a much smaller effect of MgAMP-PCP on the conformation of helix 13, which is in good correlation with its altered mode of phosphate binding and the ensuing increase in the flexibility of helix 13, as shown by elevated crystallographic B-factors. The possible existence of alternative site(s) for binding of the nucleotide phosphates may have functional relevance.

Myosin II from rabbit skeletal muscle and Dictyostelium discoideum and its interaction with F-actin studied by 1H NMR spectroscopy

Mg-F-actin occurs in two conformational states, I and M, where the N-terminal amino acids are either immobile or highly mobile. In the rigor or ADP complex of rabbit myosin S1 with Mg-F-actin the N-terminal acetyl group of actin stays in its highly mobile state. The same is true for the complexes with the myosin motor domain from Dictyostelium discoideum. This excludes a direct strong interaction of the N-terminal amino acids with myosin in the rigor state as suggested. An interaction of the N-terminus of F-actin with myosin is also not promoted by occupying its low-affinity binding site(s) with divalent ions. The N-terminal high-mobility region may be part of a structural system which has evolved for releasing inadequate stress applied to the actin filaments

Molecular physiology of phosphoryl group transfer from carbamoyl phosphate by a hyperthermophilic enzyme at low temperature.

Enzymes from thermophilic organisms often exhibit low activity at reduced temperature. To obtain a better understanding of this sluggishness, we have studied the reaction at 24 degrees C of the carbamate kinase (CK) from the hyperthermophile Pyrococcus furiosus. This enzyme is much slower at low temperature than is the CK from the mesophile Enterococcus faecalis. X-ray structures demonstrated bound ADP (even when no nucleotide was added) with the hyperthermophilic but not with the mesophilic CK. We use centrifugal gel filtration, rate of dialysis and pulse-chase experiments to demonstrate that the pyrococcal enzyme, at 24 degrees C, binds ADP avidly (K(D) = 34 nM), that ADP dissociates from this complex with a t1/2 value of 2.4 s, and that ADP binding is very fast (kappa = 8.4 x 10(6) M(-1) x s(-1)). The high affinity, rather than restrictions to dissociation, explains the isolation of the pyrococcal enzyme as an ADP complex. Carbamoyl phosphate adds quickly to this complex, and ADP cannot dissociate from the resulting ternary complex, being that it is converted very slowly (t1/2 = 10.3 s) to ATP, which dissociates quickly (t1/2 < 2.4 s). The slow conversion is a part of the normal enzyme reaction and limits the rate of the reaction at 24 degrees C. Thus, the sluggishness of the enzyme at low temperature is not due to slow substrate binding or product release but to the very slow rate of isomerization between enzyme-bound substrates and products. Probably the catalysis of the phosphoryl group transfer is less efficient at low temperature, as suggested by structural data showing that Lys131 is improperly positioned to assist the transfer.

Determining the differences in actin binding by human ADF and cofilin

The actin-depolymerizing factor (ADF)/cofilin family of proteins play an essential role in actin dynamics and cytoskeletal re-organization. Human tissues express two isoforms in the same cells, ADF and cofilin, and these two proteins are more than 70 % identical in amino acid sequence. We show that ADF is a much more potent actin-depolymerizing agent than cofilin: the maximum level of depolymerization at pH 8 by ADF is about 20 μM compared to 5 μM for cofilin, but little depolymerization occurs at pH 6.5 with either protein. However, we find little difference between the two proteins in their binding to filaments, their severing activities or their activation of subunit release from the pointed ends of filaments. Likewise, they show no significant differences in their affinities for monomeric actin: both bind 15-fold more tightly to actin.ADP than to actin.ATP. Complexes between actin.ADP and ADF or cofilin associate with both barbed and pointed ends of filaments at similar rates (close to those of actin.ATP and much higher than those of actin.ADP). This explains why high concentrations of both proteins reverse the activation of subunit release at pointed ends. The major difference between the two proteins is that the nucleating activity of cofilin-actin.ADP complexes is twice that of ADF-actin.ADP complexes and this, in turn, is twice that of actin.ATP alone. It is this weaker nucleating potential of ADF-actin.ADP that accounts for the much higher steady-state depolymerizing activity. The pH-sensitivity is due to the nucleating activity of complexes being greater at pH 6.5 than at pH 8. Sequence analysis of mammalian and avian isoforms shows a consistent pattern of charge differences in regions of the protein associated with F-actin-binding that may account for the differences in activity between ADF and cofilin.