X-ray crystal structure determination and molecular dynamics simulation of prophospholipase A2 inhibited by amide-type substrate analogues.

X-ray crystal structures of bovine pancreas prophospholipase A2 (proPLA2) inhibited by two amide-type inhibitors, [(R)-2-dodecanoyl-amino-1-hexanolphosphocholine (DAHPc) and (R)-2-dodecanoylamino-1-hexanolphosphoglycol (DAHPg)], were determined to R = 0.208 and 0.215 using reflections with up to 2.1 A resolution, respectively. Both complex crystals lacked defined electron densities for the prosequence of the N-terminal and for a loop region consisting of residues 65-70, retaining the disordered feature observed in free proPLA2 despite stabilization due to complex formation. The polar and nonpolar moieties of the amide-type inhibitors were located in the calcium-binding pocket and in the N-terminal alpha-helical hydrophobic region of the enzyme, respectively. As for the amide group of the inhibitor, which is lacking in the true substrate, a strong hydrogen bond was formed between the NH of the inhibitor and the unprotonated N(delta1) atom of His-48, resulting in the tight binding of the inhibitor to proPLA2, as well as to PLA2. The 20-30 times more potent inhibitory activity of DAHPg than DAHPc toward PLA2 could be explained by hydrogen bond formation between the glycol OH of DAHPg and the carbonyl O of Asp-49. The seven residues of the N-terminal prosequence of proPLA2, though disordered, block the access of a water molecule to Ala-1 of PLA2 or change the hydrogen-bonding property of Ala-1 alpha-amino group, resulting in breakage of the water-mediated hydrogen-bond network which is commonly formed in PLA2. The results of molecular dynamics (MD) calculation in an aqueous solution at 300 K indicate that this, rather than the close contact between the prosequence and the residues 65-70 loop region, is the main reason why the latter region becomes flexible in proPLA2, compared with in PLA2.

Crystallization and preliminary X-ray study of the cathepsin B complexed with CA074, a selective inhibitor.

Cathepsin B from bovine spleen has been purified and crystallized as a complex with a specific inhibitor CA074 [N-(L-3-trans-propylcarbamoyloxirane-2-carbonyl)-L- isoleucyl-L-proline], using the hanging-drop method. The complex crystals obtained from 50 mM-citrate buffer (pH 3.5) belong to the tetragonal space group P4(1) (or P4(3)) with a = 73.06 A and c = 141.59 A, and diffract beyond 2.2 A resolution. There are two complex molecules per asymmetric unit giving a packing density of 3.37 A3/Da and indicating a high solvent content of 63.5%.

Crystal structure of amylomaltase from thermus aquaticus, a glycosyltransferase catalysing the production of large cyclic glucans.

Amylomaltase is involved in the metabolism of starch, one of the most important polysaccharides in nature. A unique feature of amylomaltase is its ability to catalyze the formation of cyclic amylose. In contrast to the well studied cyclodextrin glucanotransferases (CGTases), which synthesize cycloamylose with a ring size (degree of polymerization or DP) of 6-8, the amylomaltase from Thermus aquaticus produces cycloamyloses with a DP of 22 and higher. The crystal structure of amylomaltase from Thermus aquaticus was determined to 2.0 A resolution. It is a member of the alpha-amylase superfamily of enzymes, whose core structure consists of a (beta, alpha)(8) barrel. In amylomaltase, the 8-fold symmetry of this barrel is disrupted by several insertions between the barrel strands. The largest insertions are between the third and fifth barrel strands, where two insertions form subdomain B1, as well as between the second and third barrel strands, forming the alpha-helical subdomain B2. Whereas part of subdomain B1 is also present in other enzyme structures of the alpha-amylase superfamily, subdomain B2 is unique to amylomaltase. Remarkably, the C-terminal domain C, which is present in all related enzymes of the alpha-amylase family, is missing in amylomaltase. Amylomaltase shows a similar arrangement of the catalytic side-chains (two Asp residues and one Glu residue) as in previously characterized members of the alpha-amylase superfamily, indicating similar mechanisms of the glycosyl transfer reaction. In amylomaltase, a conserved loop of around eight amino acid residues is partially shielding the active center. This loop, which is well conserved among other amylomaltases, may sterically hinder the formation of small cyclic products.

Mode of binding of E-64-c, a potent thiol protease inhibitor, to papain as determined by X-ray crystal analysis of the complex.

The three-dimensional structure of the E-64-c-papain complex has been determined by X-ray crystal analysis at 2.5 A resolution (conventional R = 26.9%). The structure determined indicates that: (i) the C2 atom of the oxirane ring of E-64-c is covalently bound by the S gamma atom of Cys-25 of papain; (ii) this covalent bond formation results in a configurational conversion of the oxirane C2 atom from the S- to the R-form; and (iii) extensive hydrogen bonding and hydrophobic interactions are responsible for the specific interaction of the E-64-c molecule with papain.

Expression of a synthetic gene for initiation factor 4E-binding protein 1 in Escherichia coli and its interaction with eIF-4E and eIF-4E x m7GTP complex.

An artificial gene coding for the human initiation factor (eIF) 4E-binding protein 1 (4E-BP1) was chemically synthesized and cloned. Although the expression of the 4E-BP1 gene alone has not yet been accomplished, the gene was expressed in Escherichia coli [BL21(DE3)] as a fusion gene with the glutathione-S-transferase (GST) gene using a prokaryotic gene fusion vector (pGEX-4T-2), which contains a gene sequence coding the cleavage site for a specific protease, alpha-thrombin. The fusion gene product was purified to homogeneity by glutathione Sepharose-4B affinity column chromatography. It was shown by m7GTP- and glutathione-affinity chromatography that the binding ability of 4E-BP1 to eIF-4E is nearly the same as that to the eIF-4E x m7GTP complex, implying different binding sites of eIF-4E and its nonallosteric obligation for 4E-BP1 and mRNA cap structure. In contrast with the binding of eIF-4E to the mRNA cap structure, where some functional amino acids play an important role in the binding, the binding to 4E-BP1 was suggested to occur via multiple nonspecific interactions.

Crystallization and preliminary X-ray study of Agkistrodon halys blomhoffii phospholipase A2 complexed with a specific inhibitor.

Phospholipase A2 from the venom of Agkistrodon halys blomhoffii has been crystallized as a complex with a specific inhibitor, (S)-2-dodecanoyl-amino-3-hexanol-1-phosphoglycol. The complex crystals belong to the hexagonal space group, P6(1)22 (or P6(5)22), with cell dimensions of a = b = 61.13 A, and c = 173.15 A. The diffraction extends to at least 2.3 A resolution.

Molecular dynamics simulation of 1,2-dilauroyl-L-phosphatidylethanolamine binding to phospholipase A2: an attempt to explain the selective hydrolysis of substrate fatty acid ester at position 2.

To improve our understanding of why phospholipase A2 (PLA2) specifically catalyzes the hydrolysis of the fatty acid ester bond at position 2, not at position 1, of 1,2-diacyl-3-sn-phosphoglycerides, the binding of each fatty acid chain of 1,2-dilauroyl-L-phosphatidyl-ethanolamine (DLPE), a natural substrate, to bovine pancreas PLA2 was examined by molecular dynamics (MD) simulations. Two different binding modes were considered, i.e., the respective hydrocarbon chains of 1- and 2-lauroyl fatty acid esters were located at the PLA2 binding sites usually observed in the complex crystals (Form A2) and at the reverse sites (Form A1). Although the total energies of both forms fluctuated within nearly the same range during the 80 ps MD simulations, the binding mode of DLPE to the PLA2 catalytic site through the coordination to Ca2+ was much more advantageous in Form A2 than that in Form A1; significant deviation of the Ca2+ position from its starting structure was observed in the MD simulation of Form A1. The result suggests the importance of Ca2+ in the selective recognition and catalytic function of PLA2 toward the 2-positioned fatty acid ester of phosphoglyceride substrates.

Binding mode of CA074, a specific irreversible inhibitor, to bovine cathepsin B as determined by X-ray crystal analysis of the complex.

The binding mode of CA074 [N-(L-3-trans-propylcarbamoyl-oxirane-2-carbonyl)-L-isoleucyl-L-pr oline], a specific irreversible inhibitor, to bovine spleen cathepsin B was elucidated by X-ray crystal structure analysis of the complex at 2.2 A resolution (conventional R=0.185). Inconsistently with our model used for the development of CA074, the L-isoleucyl-L-proline and propylcarbamoyl moieties are located at the S' and S subsites, respectively. This unexpected binding is primarily due to (i) similar extended chain conformations (due to the same S configurations) at the oxirane C2 and C3 atoms of CA074 and (ii) the just fit formation of double hydrogen bonds between the carboxyl oxygens of L-proline and the imidazole nitrogens of His-110 and His-111 residues (these residues are missing in papain, the tertiary structure of which was used for the design of CA074). The oxirane C3 atom possessing the P' substituent is covalently bound to the Cys-29 Sgamma atom (C3-Sgamma=1.79 A) and the S configuration is maintained. The present result will provide useful information for characterizing the substrate-specificity of cathepsin B.

Crystallization and preliminary X-ray diffraction study of recombinant human eukaryotic initiation factor-4E.

Recombinant human eukaryotic initiation factor-4E (eIF-4E), purified by m7GTP-Sepharose 4B affinity chromatography, was used for crystallization. After concentration of the eIF-4E protein (7 mg/ml), the solution was subjected to crystallization by the hanging-drop method. Transparent needle crystals complexed with m7GTP were obtained from 50 mM 2-(N-morpholino)ethanesulfonic acid-KOH buffer (pH 6.5) containing 25% (w/v) polyethylene glycol 6000 and 0.2 M (NH4)2SO4. The crystals belong to tetragonal space group P4(1) or P4(3), of Z = 4, with unit-cell dimensions of a = 89.26, b = 89.26, and c = 38.51 angstrum, and diffract beyond 2.1 angstrum resolution. The Vm value was calculated to be 3.07 angstrum 3/Da, which indicates a solvent content of 59.9%.

Substrate specificity of bovine cathepsin B and its inhibition by CA074, based on crystal structure refinement of the complex.

The crystal structure of the bovine spleen cathepsin B (BSCB)-CA074 complex was refined to R = 0.152 using X-ray diffraction data up to 2.18 A resolution. BSCB is characterized by an extra Cys148-Cys252 disulfide bridge, as compared with rat and human CBs. Although the crystal structures of these enzymes showed similar overall folding, a difference was observed in the occluding loop, a structural element specific only to CB. Comparison of the torsion angles indicated the different flexibilities of their loop structures. The oxirane C6 atom of CA074 was covalently bonded to the Cys29 S(gamma) atom (C3-S(gamma)=1.81 A), where the S-configuration was transformed to the R-form. Concerning the oxirane carbon atom that participates in the covalent bonding with the Cys residue, an acceptable rule has been proposed. The substrate specificities at the Sn (n = 1-3) and Sn' (n=1 and 2) subsites of CB, together with the interaction features as to CA074, have been discussed in comparison with the crystal structure of the papain-CA028 (a CA074-related inhibitor) complex.

Function of the propeptide region in recombinant expression of active procathepsin L in Escherichia coli.

In order to determine the functional role of the procathepsin L propeptide region for the preparation of active recombinant rat cathepsin L (CL), cDNAs encoding two short-length propeptides (C-terminal 2 and 27 residues) and the full-length (96 residues) one plus the entire CL were expressed as two soluble fusion proteins with a fragment of maltose-binding protein and an insoluble fusion protein with glutathione-S-transferase in Escherichia coli, respectively. After refolding of the insoluble fusion protein, each gene product was purified to homogeneity by amylose or glutathione-Sepharose-4B affinity column, and digestion with factor Xa and alpha-thrombin under alkaline conditions (pH approximately 8.0) led to the elution of two pure short-length procathepsin Ls (PCLs) and a full-length one, respectively. The enzymatic activity, estimated by hydrolytic assaying of benzoxycarbonyl-Phe-Arg-7-(4-methyl)coumarylamide under acidic conditions (pH 5.5), indicated that the two short-length PCLs exhibited in a great loss of the activity, as compared with the full-length PCL. The CD spectra of the short-length PCLs were different from that of the full-length one. The present results clearly show that the full-length propeptide is essential for construction of the active tertiary structure of CL at the stage of recombinant protein expression, although the expression of CL itself in E. coli does not require the propeptide. Based on the tertiary structure of PCL, the propeptide region necessary for the construction of the CL active structure has been discussed.

Binding diversity of a noncovalent-type low-molecular-weight serine protease inhibitor and function of a catalytic water molecule: X-ray crystal structure of PKSI-527--inhibited trypsin.

PKSI-527 is a noncovalent-type low-molecular-weight inhibitor. The X-ray crystal structure of the trypsin-PKSI-527 complex revealed a binding mode (Form II) different from the previously reported one (Form I) [Nakamura, M. et al. (1995) Biochem. Biophys. Res. Commun. 213, 583--587]. In contrast to the previous case, the electron density of the inhibitor revealed the whole structure clearly. Each structural part of the inhibitor in Forms I and II was differently located at the active site, although the modes of binding of the terminal amino group to the Asp189 carboxyl group were similar. This binding diversity, which is a characteristic of the noncovalent-type low-molecular-weight inhibitor, provides a suitable example for estimating the possible mechanism toward the enzymatic inhibition, together with the structural basis necessary for a specific inhibitor. The mode of binding in Form II reflects the inhibitor-specific situation and is in contrast with the substrate-mimetic binding mode for Form I. Based on the generally accepted catalytic mechanism for serine protease, we propose that a water molecule located at the catalytic site plays an important role in blocking the catalytic function of the reactive Ser193 OH group.

Mutation of the cysteine residues in human initiation factor 4E: effects on mRNA cap binding ability.

To investigate the role of four Cys residues of eukaryotic initiation factor (eIF)-4E in the recognition of the mRNA cap structure, single, double and quadruple mutant genes which encoded the Ala residues in the place of the respective Cys residues were prepared using a synthetic human eIF-4E gene by the site-directed mutagenesis, and were expressed in E. coli with the same way as the wild type. The cap binding abilities of respective mutated eIF-4Es were compared with that of the wild-type by m7GTP affinity chromatography. The results suggest that, although all four of Cys residues participate in the recognition of the mRNA cap structure, they contribute indirectly to the stabilization of overall tertiary structure, especially of the cap binding pocket, rather than by direct interaction. A comparison among the cap binding abilities of single, double and quadruple mutants indicated no existence of internal disulfide bonds in eIF-4E.

X-ray crystal structure and molecular dynamics simulation of bovine pancreas phospholipase A2-n-dodecylphosphorylcholine complex.

The crystal structure of n-dodecylphosphorylcholine (n-C12PC)-bovine pancreas phospholipase A2 (PLA2) complex provided the following structural characteristics: (1) the dodecyl chain of n-C12PC was located at the PLA2 N-terminal helical region by hydrophobic interactions, which corresponds to the binding pocket of 2-acyl fatty acid chain (beta-chain) of the substrate phospholipid, (2) the region from Lys-53 to Lys-56 creates a choline-receiving pocket of n-C12PC and (3) the N-terminal group of Ala-1 shifts significantly toward the Tyr-52 OH group by the binding of the n-C12PC inhibitor. Since the accuracy of the X-ray analysis (R = 0.275 at 2.3 A resolution) was insufficient to establish these important X-ray insights, the complex structure was further investigated through the molecular dynamics (MD) simulation, assuming a system in aqueous solution at 310K. The MD simulation covering 176 ps showed that the structural characteristics observed by X-ray analysis are intrinsic and also stable in the dynamic state. Furthermore, the MD simulation made clear that the PLA2 binding pocket is large enough to permit the conformational fluctuation of the n-C12PC hydrocarbon chain.

Interaction mode of n-dodecylphosphorylcholine, a substrate analogue, with bovine pancreas phospholipase A2 as determined by X-ray crystal analysis.

Three-dimensional structure of a bovine pancreas phospholipase A2 (PLA2) crystal complexed with n-dodecylphosphorylcholine (n-C12PC), a substrate-type inhibitor, has been determined by the X-ray diffraction method. The present conventional R value is 0.275 at 2.3A resolution. The binding mode of n-C12PC to the PLA2 was clearly indicated, where the dodecyl chain was stably held by the hydrophobic contacts with the N-terminal region of PLA2 (Leu-2, Phe-5, and Ile-9), and the choline moiety was contacted with the hydrophobic space created by the side chains of Lys-53 and 56. The present result indicates that remarkable changes from the native PLA2 structure are caused at the N-terminal and middle (residues 60 to 70) regions by the binding of n-C12PC to the enzyme.

Molecular dynamics simulations of bovine cathepsin B and its complex with CA074.

To promote our better understanding of the dynamic stability of the bovine cathepsin B structure, which is characterized by an extra disulfide bond at Cys148-Cys252 from the other species, and of the binding stability of CA074 (a cathepsin B-specific inhibitor), molecular dynamics (MD) simulations were performed for the enzyme and its CA074 complex, assuming a system in aqueous solution at 300 K. The MD simulation covering 400 ps indicated that the existence of a Cys148-Cys252 disulfide bond increases the conformational flexibility of the occluding loop, although the conformational stability of the overall structure is little affected. The structural characteristics of the complex elucidated by X-ray analysis were suggested to be also intrinsic and stable in the dynamic state; the hydrogen bonding/electrostatic interactions between the main and side chains of CA074 and the Sn and Sn' subsites of the enzyme were maintained throughout the MD simulation. Furthermore, the simulation made clear that the binding of CA074 significantly restricted the conformational flexibility of the substrate binding region, especially the occluding loop, of cathepsin B. Statistical analyses during the simulation suggest that the selectivity of CA074 for cathepsin B stems from the tight P1'-S1' and P2'-S2' interactions, assisted in particular by double hydrogen bonds between the carboxyl two oxygens of the CA074 C-terminus and the imidazole NH groups of His110 and His111 residues.

Regulation of human eIF4E by 4E-BP1: binding analysis using surface plasmon resonance.

The interaction between recombinant human eukaryotic initiation factor (eIF)4E and recombinant glutathione S-transferase (GST)-fused human 4E-binding protein (BP)1 was analyzed by using the surface plasmon resonance method. The association rate of 4E-BP1 with eIF4E increased by about two orders of magnitude in the presence of m7GTP (a model compound of mRNA cap structure), but the dissociation rate was scarcely affected, indicating the cap-dependent binding of 4E-BP1 to eIF4E. On the other hand, phosphorylation of 4E-BP1 weakened its interaction with eIF4E whether m7GTP was present or not. However, phosphorylation of 4E-BP1 already associated with eIF4E or its m7GTP complex did not cause any change of the association, probably because of incomplete phosphorylation. This suggests that the regulation of eIF4E by 4E-BP phosphorylation is performed at its free state, not when it is in the associated state with eIF4E. Given these results, we discuss how 4E-BP regulates eIF4E at the first step of translation initiation.

Effect of mRNA cap structure on eIF-4E phosphorylation and cap binding analyses using Ser209-mutated eIF-4Es.

The in vitro phosphorylation of human recombinant eIF-4E by protein kinase C was most effective in the absence of m7GTP, supporting a 'performed complex model' as the mRNA binding step of initiation, i. e., eIF-4E first forms an initiation complex eIF-4F and is phosphorylated before interacting with mRNA. On the other hand, the comparison of m7GTP-binding ability of wild-type eIF-4E with those of four Ser209-mutated ones (S209A, S209D, S209E and S209K) showed that the addition of anionic charge on Ser209 increases the cap affinity of eIF-4E by repressing the release of the cap from the complex, not by increasing the complex formation, suggesting the importance of a retractable ionic bridge between Ser209 and Lys159 in controlling the cap binding by eIF-4E phosphorylation.

Revised amino acid sequence, crystallization, and preliminary x-ray diffraction analysis of acidic phospholipase A2 from the venom of Agkistrodon halys blomhoffii.

The complete amino acid sequence of acidic Agkistrodon halys blomhoffii phospholipase A2 has been redetermined by a combination of manual and automatic Edman degradations. Acidic A. halys blomhoffi phospholipase is a single polypeptide chain consisting of 122 amino acids and is highly homologous in sequence with corresponding regions of phospholipase A2 from a variety of sources. Prism crystals of acidic A. halys blomhoffii phospholipase have been reproducibly grown from 2-methyl-2,4-pentanediol solution adjusted to pH 8.0 with 50 mM Tris-HCl buffer in the presence of 10 mM CaCl2. The crystals belong to space group P6(1)22 or P6(5)22 with hexagonal unit cell dimensions of a = b = 76.22 A and C = 76.56 A. One molecule occupies the asymmetric unit of the crystal. The diffraction extends to at least 2.5 A.

Structural and thermodynamic behavior of eukaryotic initiation factor 4E in supramolecular formation with 4E-binding protein 1 and mRNA cap analogue, studied by spectroscopic methods.

The structural and thermodynamic behavior of the complex formation of eIF4E with either or both mRNA cap analogue (m7GTP, m7GpppA, or m7GpppG) and 4EBP1 has been investigated by spectroscopic measurements. Although the circular dichroism (CD) spectrum of eIF4E was little affected by the association with any cap analogue, the association constant of eIF4E with m7GpppA/G, estimated from the fluorescence quenching, was about 10 times larger than that with m7GTP. The van't Hoff analyses showed that the m7GpppA/G binding is enthalpy-driven with a large negative deltaH(o), and this is in contrast with the entropy-driven binding of m7GTP, where the positive deltaS(o) is large enough to overcome an increase of deltaH(o). This different behavior obviously originates in the interaction of the second nucleotide in m7GpppA with eIF4E, suggesting the importance of the nucleotide sequence linked to the m7Gppp terminal moiety, in addition to the specific interaction with the m7G base, for the recognition of mRNA cap structure by eIF4E. On the other hand, the CD spectra indicated that the binding of 4EBP1, an endogenous eIF4E-regulatory protein without having any defined secondary structure, shifted the m7GTP- or m7GpppA/G-bound eIF4E to an irregular structure, although such a structural change was not observed for eIF4E alone. The association constant of 4EBP1 with m7GTP- or m7GpppA/G-bound eIF4E was by two orders of magnitude larger than that with eIF4E alone. These results suggest the close interrelation in the supramolecular formation of 4EBP-eIF4E-mRNA cap structure.