Functions, structures and Triton X-100 effect for the catalytic subunits of heterodimeric phospholipases A2 from Vipera nikolskii venom.

Phospholipases A(2) (PLA(2)s) from snake venoms have diverse pharmacological functions including neurotoxicity, and more studies are necessary to understand relevant mechanisms. Here we report the different crystal structures for two enzymatically active basic subunits (HDP-1P and HDP-2P) of heterodimeric neurotoxic PLA(2)s isolated from Vipera nikolskii venom. Structural comparisons with similar PLA(2)s clearly show some flexible regions which might be important for the catalytic function and neurotoxicity. Unexpectedly, Triton X-100 molecule bound in the hydrophobic channel of HDP-1P and HDP-2P was observed, and its binding induced conformational changes in the Ca(2+) binding loop. Enzymatic activity measurements indicated that Triton X-100 decreased the activity of PLA(2), although with comparatively low inhibitory activity. For the first time exocytosis experiments in pancreatic beta cells were used to confirm the presynaptic neurotoxicity of relevant snake PLA(2). These experiments also indicated that Triton X-100 inhibited the influence of HDP-1P on exocytosis, but the inhibition was smaller than that of MJ33, a phospholipid-analogue inhibitor of PLA(2). Our studies performed at a cellular level are in good agreement with earlier findings that enzymatic activity of the snake presynaptic PLA(2) neurotoxins is essential for effective block of nerve terminals.

OASIS and molecular-replacement model completion.

A method of dual-space molecular-replacement model completion has been proposed which involves the programs ARP/wARP, REFMAC, OASIS and DM. OASIS is used in reciprocal space for phase refinement based on models built by ARP/wARP. For this purpose, the direct-method probability formula of breaking SAD/SIR phase ambiguities has been redefined. During the phase refinement, phi(h)('') in the expression phi(h) = phi(h)('') +/- |Delta phi(h)| is redefined as a reference phase calculated from a randomly selected 5% of the atoms in the current structure model, while |Delta phi(h)| is defined as the absolute difference between the phase of the current model and phi(h)(''). The probability formula P(+)(Delta phi(h)) = (1/2) + (1/2) tanh {sin |Delta phi(h)| x [Sigma (h('))m(h('))m(h - h('))kappa(h,h(')) sin(Phi'(3) + Delta phi(h'best) + Delta phi(h - h'best)) + chi sin delta(h)]} is then used to derive the sign of Delta phi(h). In this way the '0-2pi' phase problem is reduced to a 'plus or minus' sign problem. The redefinition implies that during the refinement phases close to the true values will probably be kept unchanged, while those distant from the true values will probably undergo a large shift. This is the desired property of phase refinement. The procedure has been tested using protein diffraction data without SAD/SIR signals. The results show that dual-space MR-model completion making use of OASIS is much more efficient than that without.

Structural and functional analysis of natrin, a venom protein that targets various ion channels.

Cysteine-rich secretory proteins (CRISPs) are secreted single-chain proteins found in different sources. Natrin is a member of the CRISP family purified from the snake venom of Naja naja atra, which has been reported as a BKca channel blocker. In our study, crystals of natrin were obtained in two different crystal forms and the structure of one of them was solved at a resolution of 1.68A. Our electrophysiological experiments indicated that natrin can block the ion channel currents of the voltage-gated potassium channel Kv1.3. Docking analyses of the interaction between natrin and Kv1.3 revealed a novel interaction pattern different from the two previously reported K(+) channel inhibition models termed "functional dyad" and "basic ring". These findings offered new insights into the function of natrin and how the specific interactions between CRISPs and different ion channels can be achieved.

Isolation and preliminary crystallographic studies of two new phospholipases A2 from Vipera nikolskii venom.

Snake-venom phospholipases A2 (PLA2s) represent a good model for studies of structure-function relationships, mainly because of their small size and diverse pharmacological and toxicological activities. To obtain new members of the abundant PLA2 family, the venom of the viper Vipera nikolskii was fractionated for the first time and two new proteins, VN5-3 and VN4-3, were isolated. Both proteins show phospholipase A2 activity and may possess neurotoxic activity. Based on the determined partial amino-acid sequences, the new proteins can be classified as basic Asp49 phospholipases A2. They were crystallized using the hanging-drop vapour-diffusion method and crystals of both proteins belong to space group R32, with similar unit-cell parameters: a = b = 76.29, c = 303.35 A for protein VN5-3 and a = b = 76.28, c = 304.39 A for protein VN4-3. Diffraction data sets to 3.0 and 2.2 A resolution were collected and processed for the VN5-3 and VN4-3 crystals, respectively. Preliminary analysis indicates that there are two molecules in the asymmetric unit for both crystals. Further crystallographic studies will help in understanding the structural basis for the multiple functions of snake-venom PLA2s.

Structure of a cardiotoxic phospholipase A(2) from Ophiophagus hannah with the "pancreatic loop".

The crystal structure of an acidic phospholipase A(2) from Ophiophagus hannah (king cobra) has been determined by molecular replacement at 2.6-A resolution to a crystallographic R factor of 20.5% (R(free)=23.3%) with reasonable stereochemistry. The venom enzyme contains an unusual "pancreatic loop." The conformation of the loop is well defined and different from those in pancreas PLA(2), showing its structural variability. This analysis provides the first structure of a PLA(2)-type cardiotoxin. The sites related to the cardiotoxic and myotoxic activities are explored and the oligomer observed in the crystalline state is described.

Structures of D-glyceraldehyde-3-phosphate dehydrogenase complexed with coenzyme analogues.

Crystal structures of GAPDH from Palinurus versicolor complexed with two coenzyme analogues, SNAD(+) and ADP-ribose, were determined by molecular replacement and refined at medium resolution to acceptable crystallographic factors and reasonable stereochemistry. ADP-ribose in the ADP-ribose-GAPDH complex adopts a rather extended conformation. The interactions between ADP-ribose and GAPDH are extensive and in a fashion dissimilar to the coenzyme NAD(+). This accounts for the strong inhibiting ability of ADP-ribose. The conformational changes induced by ADP-ribose binding are quite different to those induced by NAD(+) binding. This presumably explains the non-cooperative behaviour of the ADP-ribose binding. Unexpectedly, the SNAD(+)-GAPDH complex reveals pairwise asymmetry. The asymmetry is significant, including the SNAD(+) molecule, active-site structure and domain motion induced by the coenzyme analogue. In the yellow or red subunits [nomenclature of subunits is as in Buehner et al. (1974). J. Mol. Biol. 90, 25-49], SNAD(+) binds similarly, as does NAD(+) in holo-GAPDH. While, in the green or blue subunit, the SNAD(+) binds in a non-productive manner, resulting in a disordered thionicotinamide ring and rearranged active-site residues. The conformation seen in the yellow and red subunits of SNAD(+)-GAPDH is likely to represent the functional state of the enzyme complex in solution and thus accounts for the substrate activity of SNAD(+). A novel type of domain motion is observed for the binding of the coenzyme analogues to GAPDH. The possible conformational transitions involved in the coenzyme binding and the important role of the nicotinamide group are discussed.

Preliminary Crystallographic Analysis of Phospholipase A(2) from Naja naja kaouthia Lesson Venom.

An acidic phospholipase A(2) isolated from the venom of Naja naja kaouthia Lesson in Guangxi exhibits anticoagulative and hemolytic activities. In this work, the enzyme was crystallized by the method of hanging drop vapor diffusion. Two crystal forms were obtained and characterized by X-ray diffraction. One of them belonged to space group P 4 ( 3 ) 2 ( 1 )2 or P4(1)2(1)2 with unit cell parameters a b 8.797 nm, c 10.831 nm and there were three molecules per asymmetric unit the other belonged to space group P2(1)3 with unit cell parameters a b c 6.840 nm and there was one molecule per asymmetric unit. The diffraction data were collected up to 0.28 nm for each crystal form. The crystal properties of Naja naja verom phospholipase A(2) from different geographical regions are compared.

Structure Determination of Basic Phospholipase A(2) from the Venom of Agkistrodon halys Pallas in A New Monoclinic Crystal Form.

Basic phospholipase A(2) from the venom of Agkistrodon halys Pallas ( Agkistrodin blomhoffii brevicaudus ) exhibits hemolytic and anti-coagulant activities. A new monoclinic crystal form with four molecules per asymmetric unit was grown in the absence of n-octyl beta-o-glucopyranoside (beta-OG). The enzyme structure was determined by the molecular replacement method. The combined analysis of self- and cross- rotation function was used and non-crystallographic symmetry restraints were imposed to the structure refinement. The final model gave an acceptable crystallographic R factor and reasonable stereochemistry. Two molecules formed an interfacial-recognition-site linked dimer and two such dimers constituted a tetramer having pseudo 222 symmetry. Structural comparison with previously reported monoclinic forms, in which beta-OG was bound, showed that the variation of crystallization conditions had effects on the crystal packing, leading to significant changes of the cell parameters. Nevertheless, the structures of both the dimer and tetramer in the two crystal forms closely resembled to each other, indicating that the oligomers found in the monoclinic crystal forms were stable.

Cloning and Sequence Analysis of cDNAs Encoding Two Acidic PLA(2) from venom of Ophiophagus hannah(King Cobra), Guangxi Species.

Total RNA was extracted from venom glands of Ophiophagus hannah, Guangxi species. The cDNAs encoding PLA(2) were amplified by RT-PCR and cloned into the PUCm-T vector. The positive clones encoding two acidic PLA(2) (APLA(2)-1 and APLA(2)-2) were selected and bidirectionally sequenced. Their complete amino acid sequences were deduced and found to be identical to the known amino acid sequences. Their isoelectric points calculated by computer agreed with the values determined with their protein. Homology analysis indicated that the mature peptide of APLA(2)-1 had high homology with PLA(2) from venoms of Ophiophagus hannah, Fujian and Taiwan species, but APLA(2)-2 had lower homology. The most striking difference between APLA(2)-2 and other PLA(2) from Ophiophagus hannah venoms is the missing of a extra "pancreatic loop" at residues 62--66 in APLA(2)-2, and it may be related to their species evolution and biological activity.

Purification, Crystal Growth and Preliminary X-ray Analysis of a Phospholipase A(2) from Venom of Agkistrondon acutus.

An acidic phospholipase A(2) from Agkistrondon acutus venom has been purified to homogeneity via four steps using CM-Sepharose, two times DEAE-Sepharose, and Mono Q FPLC. The molecular weight of the protein was about 16.5 kD and the isoelectric point was 4.3. The purified enzyme showed a potent inhibitory effect on platelet aggregation induced by ADP in human platelet-enriched plasma. The enzyme was then crystallized by hanging drop diffusion method using 2-methyl-2, 4-pentanediol as a precipitant. Two kinds of single crystals suitable for X-ray crystallographic studies were obtained. X-ray crystallographic analysis showed that both crystal forms belong to monoclinic system and space group P2(1). The cell dimensions of form I crystals were a = 43.48 Aring;, b = 71.49 Aring;, c = 43.85 Aring; and beta = 116.32 deg; Those of form II crystals were a = 49.25 Aring;, b = 38.33 Aring;, c = 70.25 Aring; and beta = 99.20 deg;. Complete diffraction data sets have been collected to medium resolution for the two crystal forms.

Crystal Structure of Ca(2+) Ion-saturated Acidic Phospholipase A(2) From Agkistrodon halys Pallas.

The Ca(2+) ion is a cofactor for the catalysis of phospholipase A(2). The crystals of Ca(2+)-saturated acidic phospholipase A(2) from Agkistrodon halys Pallas were obtained by adding CaCl(2) during the crystallization to ensure the complete binding of Ca(2+). The synchrotron diffraction data were collected at 1.6 Aring; resolution. The structure was determined by difference Fouriers methods. The refined structure of Ca(2+)-saturated acidicPLA(2) resembles closely that of the native acidicPLA(2) with, however, some small conformational differences in the Ca(2+)-binding site and the C-terminal loop. The pentagonal bipyramidal configuration consisting of seven oxygen ligands of Ca(2+) ion appears more regular than that of the native acidicPLA(2). The small conformational changes induced by Ca(2+) implies that the main role of Ca(2+) ion is to stabilize the oxyanion in the tetrahedral intermediate formed during the catalysis by electrophilic interaction.

The crystallization and Preliminary Crystallographic Analysis of the Monoclinic Crystal Form of Basic Phospholipase A(2) from the Venom of Agkistrodon halys Pallas.

The basic phospholipase A(2) from the venom of Agkistrodon halys Pallas exhibits strong hemolytic activity. The enzyme has been crystallized by vapour diffusion techniques. Diffraction data of the crystal have been collected up to 2.5 Aring; resolution using the synchrotron radiation-imaging plate-Weissenberg camera system. The crystal parameters were calculated with an auto-indexing program. The crystal belongs to C2 space group with unit cell dimensions of alpha=100.38 Aring;, b=54.37 Aring;, c=117.38 Aring; and beta=120.71 deg;. Each asymmetric unit probably contains four or five molecules.