New antiarrhythmic targets to control intracellular calcium handling.

Sudden cardiac death due to ventricular arrhythmias is a major problem. Drug therapies to prevent SCD do not provide satisfying results, leading to the demand for new antiarrhythmic strategies. New targets include Ca(2+)/Calmodulin-dependent protein kinase II (CaMKII), the Na/Ca exchanger (NCX), the Ryanodine receptor (RyR, and its associated protein FKBP12.6 (Calstabin)) and the late component of the sodium current (I Na-Late ), all related to intracellular calcium (Ca(2+)) handling. In this review, drugs interfering with these targets (SEA-0400, K201, KN-93, W7, ranolazine, sophocarpine, and GS-967) are evaluated and their future as clinical compounds is considered. These new targets prove to be interesting; however more insight into long-term drug effects is necessary before clinical applicability becomes reality.

Determination of odour threshold concentration ranges for some disinfectants and disinfection by-products for an Australian panel.

Taste-and-odour complaints are a leading cause of consumer dissatisfaction with drinking water. The aim of this study was to determine odour threshold concentration ranges and descriptors, using a Western Australian odour panel, for chlorine, bromine, chlorine added to bromide ions, the four major regulated trihalomethanes (THMs), and combined THMs. An odour panel was established and trained to determine odour threshold concentration ranges for odorous compounds typically found in drinking water at 25 degrees C, using modified flavour profile analysis (FPA) techniques. Bromine and chlorine had the same odour threshold concentration ranges and were both described as having a chlorinous odour by a majority of panellists, but the odour threshold concentration range of bromine expressed in free chlorine equivalents was lower that that of chlorine. It is likely that the free chlorine equivalent residuals measured in many parts of distribution systems in Western Australia are comprised of some portion of bromine and that bromine has the potential to cause chlorinous odours at a lower free chlorine equivalent concentration than chlorine itself. In fact, bromine is the likely cause of any chlorinous odours in Western Australian distributed waters when the free chlorine equivalent concentration is between 0.04 and 0.1 mg L(-1). Odour threshold concentrations for the four individual THMs ranged from 0.06-0.16 mg L(-1), and the odour threshold concentration range was 0.10 + or - 0.09 mg L(-1) when the four THMs were combined (in equal mass concentrations). These concentrations are below the maximum guideline value for total THM concentration in Australia so odours from these compounds may possibly be observed in distributed waters. However, while the presence of THMs may contribute to any sweet/fragrant/floral and chemical/hydrocarbon odours in local drinking waters, the THMs are unlikely to contribute to chlorinous odours.

Crystal structure of the FMN-binding domain of human cytochrome P450 reductase at 1.93 A resolution.

The crystal structure of the FMN-binding domain of human NADPH-cytochrome P450 reductase (P450R-FMN), a key component in the cytochrome P450 monooxygenase system, has been determined to 1.93 A resolution and shown to be very similar both to the global fold in solution (Barsukov I et al., 1997, J Biomol NMR 10:63-75) and to the corresponding domain in the 2.6 A crystal structure of intact rat P450R (Wang M et al., 1997, Proc Nat Acad Sci USA 94:8411-8416). The crystal structure of P450R-FMN reported here confirms the overall similarity of its alpha-beta-alpha architecture to that of the bacterial flavodoxins, but reveals differences in the position, number, and length of the helices relative to the central beta-sheet. The marked similarity between P450R-FMN and flavodoxins in the interactions between the FMN and the protein, indicate a striking evolutionary conservation of the FMN binding site. The P450R-FMN molecule has an unusual surface charge distribution, leading to a very strong dipole, which may be involved in docking cytochrome P450 into place for electron transfer near the FMN. Several acidic residues near the FMN are identified by mutagenesis experiments to be important for electron transfer to P4502D6 and to cytochrome c, a clear indication of the part of the molecular surface that is likely to be involved in substrate binding. Somewhat different parts are found to be involved in binding cytochrome P450 and cytochrome c.

Towards a molecular understanding of phase separation in the lens: a comparison of the X-ray structures of two high Tc gamma-crystallins, gammaE and gammaF, with two low Tc gamma-crystallins, gammaB and gammaD.

gamma-Crystallins, although closely related in sequence, show intriguing differences in their temperature-dependent interactions: those that have a high or intermediate Tc for phase separation are cryoproteins whereas low Tc gamma-crystallins are not. To address the molecular basis of phase separation, X-ray crystallography has been used to define the structural differences between high and low Tc gamma-crystallins. A pre-requisite for this study was to clarify the assignment of bovine gene sequences to bovine gamma-crystallin proteins used for biophysical measurements. Based on nucleotide sequence analyses of gamma E and gamma F bovine crystallin genes, gamma F corresponds to the previously crystallised high Tc protein bovine gamma IVa and gamma E corresponds to the high Tc bovine protein fraction previously known as gamma IIIa. The gamma F sequence has enabled the completion of the refinement of the bovine gamma F crystal structure which shows that the molecule has an additional surface tryptophan explaining why gamma F has different spectroscopic properties from gamma B. A high Tc protein from rat lens, gamma E crystallin, has been crystallised and the X-ray structure solved at 2.3 A resolution. Comparison of the X-ray structures of two high Tc proteins, rat gamma E and bovine gamma F, with the structures of two low Tc proteins, bovine gamma B and bovine gamma D, shows that the main conformational change between high and low Tc proteins is in the cd surface loop of motif 3. All four structures have numerous ion pairs on their surfaces leading to a high surface charge density, yet with low overall charge. Comparison of the lattice contacts of the two high Tc proteins with the two low Tc gamma-crystallins indicates that these high Tc proteins utilise more amino-aromatic interactions such as between histidine and arginine. Comparison of the sequences of all the gamma-crystallins which have been characterised for phase separation temperature indicates that only residue Arg/Lys 163 uniquely distinguishes cryo from non-cryo gamma-crystallins and it is close to the altered surface loop. Although this region probably contributes to phase separation, Tc is likely to be a function of an overall global property that is responsive to overall charge distribution. Calculated dipole moments of native gamma-crystallins, low Tc gamma-crystallin sequences threaded into high Tc gamma-crystallin structures, and vice versa, show how both sequence and 3D structure contribute to this overall property. High Tc gamma-crystallins have on average higher Arg/Lys ratios and higher histidine content. It is hypothesised that this increases the proportion of surface static paired charged networks which thus reduces the repulsive hydration force and so increases the attractive interactions of the protein-rich phase in binary liquid phase separation.

Structure of bovine eye lens gammaD (gammaIIIb)-crystallin at 1.95 A.

The crystal structure of bovine lens gammaIIIb-crystallin at 2.5 A resolution previously reported was interpreted using a consensus sequence derived from related vertebrate sequences on the assumption that gammaIIIb-crystallin derived from the gammaC-crystallin gene. It has recently been shown that gammaIIIb is a product of the bovine gammaD gene. The structure of gammaIIIb has now been refined with the bovine gammaD sequence using new 1.95 A resolution synchrotron data. The crystallographic R factor was 20.4% for all 33 104 reflection data between 8.0 and 1.95 A measured at 277(1) K. The electron density fully supported the assignment of the gammaD sequence to gammaIIIb. The crystal belongs to space group P2(1)2(1)2(1) with two molecules of molecular mass 20 749 Da in the asymmetric unit in which 219 water molecules were located. The two-domain four-Greek-key motif highly symmetrical protein is very similar in structure to gammaB-crystallin (81% sequence identity). There is a single amino-acid deletion in gammaD in the linker region connecting the two domains. The intermolecular oganization in the crystal lattice is quite different from gammaB as a result of key mutations involving surface residues Leu51, Ile103 and His155. These point mutations will contribute to the intermolecular behaviour of the gamma-crystallins in the eye lens, where they are major components of the densely packed, high refractive index regions of the lens.

Crystallization and preliminary X-ray diffraction studies of human cytochrome P450 reductase.

The two functional domains of a cloned human fibroblast NADPH-cytochrome P450 reductase have been expressed in Escherichia coli and purified on the milligram scale for crystallization studies. One domain contains the cofactor FMN-binding site and the other contains the binding sites for cofactor FAD and substrate NADPH. Crystals of both domains have been obtained by the microbatch method. The crystals of the FMN domain belong to the monoclinic space group P21, with unit cell dimensions of a = 39.3 A, b = 51.5 A, c = 47.8 A, and beta = 105.7 degrees and have one molecule in the asymmetric unit. Diffraction data up to 2.3 A were collected with a merging residual on intensity of 9.3%. The crystals of the FAD/NADPH domain belong to the ortho-rhombic space group P212121 with unit cell dimensions of a = 55.9 A, b = 58.6 A, c = 131.1 A and have one molecule in the asymmetric unit. Diffraction data up to 2.6 A were collected with a merging residual on intensity of 8.0%.

The X-ray structures of two mutant crystallin domains shed light on the evolution of multi-domain proteins.

We use protein engineering and crystallography to simulate aspects of the early evolution of beta gamma-crystallins by observing how a single domain oligomerizes in response to changes in a sequence extension. The crystal structure of the C-terminal domain of gamma beta-crystallin with its four-residue C-terminal extension shows that the domain does not form a symmetric homodimer analogous to the two-domain pairing in beta gamma-crystallins. Instead the C-terminal extension now forms heterologous interactions with other domains leading to the solvent exposure of the natural hydrophobic interface with a consequent loss in protein solubility. However, this domain truncated by just the C-terminal tyrosine forms a symmetric homodimer of domains in the crystal lattice.

Amino acid differences at positions 10, 11, and 104 explain the profound catalytic differences between two murine pi-class glutathione S-transferases.

The glutathione S-transferases play a pivotal role in the detoxification of toxic and carcinogenic electrophiles. We have previously reported the isolation of two actively transcribed murine pi-class glutathione S-transferase genes. In this study the two proteins encoded by these genes, Gst p-1 and Gst p-2, were expressed in Escherichia coli and found to exhibit profoundly different catalytic activities, the activity of Gst p-2 toward a panel of electrophilic substrates being 1-3 orders of magnitude lower than that of Gst p-1. In order to establish the basis for the difference between these highly homologous proteins, mutants were generated where specific amino acids had been exchanged. Kinetic analysis of the wild-type and mutant enzymes revealed that the amino acid differences occurring at positions 10 (Val/Ser), 11 (Arg/Pro), and 104 (Val/Gly) are responsible for the reduced enzymatic activity of Gst p-2. This analysis together with computer graphics modeling for Gst p-2 indicated that these changes affected both substrate and glutathione binding to the enzyme.

The structure of avian eye lens delta-crystallin reveals a new fold for a superfamily of oligomeric enzymes.

The crystal structure of turkey delta-crystallin, a principal soluble components of the avian lens, has been determined to a resolution of 2.5 A. It is a tetramer, of 200,000 M(r), with 222 symmetry. The subunit has a new fold composed of three mainly alpha-helical domains. One domain is a bundle of five long helices which forms a 20-helix bundle at the core of the tetramer. delta-crystallin shares approximately 90% sequence identity with the enzyme argininosuccinate lyase (EC 4.3.2.1), indicating that it is an example of a 'hijacked' enzyme. It is also distantly related to the class II fumarases, aspartases, adenylosuccinases and 3-carboxy-cis,cis-muconate lactonising enzyme. The structure reveals a putative active-site cleft which is located on the boundary between three subunits of the tetramer. This is the first three-dimensional structure of a representative of this superfamily of enzymes.

Three-dimensional model and quaternary structure of the human eye lens protein gamma S-crystallin based on beta- and gamma-crystallin X-ray coordinates and ultracentrifugation.

A 3-dimensional model of the human eye lens protein gamma S-crystallin has been constructed using comparative modeling approaches encoded in the program COMPOSER on the basis of the 3-dimensional structure of gamma-crystallin and beta-crystallin. The model is biased toward the monomeric gamma B-crystallin, which is more similar in sequence. Bovine gamma S-crystallin was shown to be monomeric by analytical ultracentrifugation without any tendency to form assemblies up to concentrations in the millimolar range. The connecting peptide between domains was therefore built assuming an intramolecular association as in the monomeric gamma-crystallins. Because the linker has 1 extra residue compared with gamma B and beta B2, the conformation of the connecting peptide was constructed by using a fragment from a protein database. gamma S-crystallin differs from gamma B-crystallin mainly in the interface region between domains. The charged residues are generally paired, although in a different way from both beta- and gamma-crystallins, and may contribute to the different roles of these proteins in the lens.

Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.

Bacteriophage T4 beta-glucosyltransferase (EC 2.4.1.27) catalyses the transfer of glucose from uridine diphosphoglucose to hydroxymethyl groups of modified cytosine bases in T4 duplex DNA forming beta-glycosidic linkages. The enzyme forms part of a phage DNA protection system. We have solved and refined the crystal structure of recombinant beta-glucosyltransferase to 2.2 A resolution in the presence and absence of the substrate, uridine diphosphoglucose. The structure comprises two domains of similar topology, each reminiscent of a nucleotide binding fold. The two domains are separated by a central cleft which generates a concave surface along one side of the molecule. The substrate-bound complex reveals only clear electron density for the uridine diphosphate portion of the substrate. The UDPG is bound in a pocket at the bottom of the cleft between the two domains and makes extensive hydrogen bonding contacts with residues of the C-terminal domain only. The domains undergo a rigid body conformational change causing the structure to adopt a more closed conformation upon ligand binding. The movement of the domains is facilitated by a hinge region between residues 166 and 172. Electrostatic surface potential calculations reveal a large positive potential along the concave surface of the structure, suggesting a possible site for duplex DNA interaction.

Close packing of an oligomeric eye lens beta-crystallin induces loss of symmetry and ordering of sequence extensions.

beta-Crystallins are oligomeric eye lens proteins that are related to monomeric gamma-crystallins. The main sequence difference between the two families is the presence of sequence extensions in the beta-crystallins. A major question concerns the role that these extensions play in mediating interactions at the high protein concentrations found in the lens. The predominant beta-crystallin polypeptide, beta B2, can be crystallized in two different space groups, I222 and C222. The I222 crystal structure revealed that the protein packed as a tetramer with perfect 222 symmetry but that the extensions were disordered. The X-ray structure of the C222 lattice of beta B2 has now been refined at 3.3 A, the structure analysed and compared with the I222 lattice. The protein is also a tetramer with 222 symmetry in the C222 lattice but differs in that parts of the N-terminal extensions have been visualized. In the asymmetric unit of the C222 lattice there are four subunits, each comprising a single polypeptide chain, in which certain flexible loops in the N-terminal domains and the N-terminal extensions have various conformations. The tetramers in the C222 lattice are more tightly packed than in the I222 form. Analysis of the tetramer contacts shows that the sites of interaction break the 222 symmetry of the tetramers. The N-terminal extensions play a major role in directing interactions between tetramers. One of the N-terminal extensions interacts with a hydrophobic patch on the N-terminal domain of another tetramer. These crystallographic observations obtained over a physiological concentration range indicate how, in beta-crystallin oligomers, the N-terminal extensions of beta B2 can switch from interacting with water to interacting with protein depending on their relative concentrations. This could be useful in maintaining a gradient of refractive index.

X-ray analysis at 2.0 A resolution of mouse submaxillary renin complexed with a decapeptide inhibitor CH-66, based on the 4-16 fragment of rat angiotensinogen.

The structure of mouse submaxillary renin complexed with a decapeptide inhibitor, CH-66 (Piv-His-Pro-Phe-His-Leu-OH-Leu-Tyr-Tyr-Ser-NH2), where Piv denotes a pivaloyl blocking group, and -OH- denotes a hydroxyethylene (-(S)CHOH-CH2-) transition state isostere as a scissile bond surrogate, has been refined to an agreement factor of 0.18 at 2.0 A resolution. The positions of 10,038 protein atoms and 364 inhibitor atoms (4 independent protein inhibitor complexes), as well as of 613 solvent atoms, have been determined with an estimated root-mean-square (r.m.s.) error of 0.21 A. The r.m.s. deviation from ideality for bond distances is 0.026 A, and for angle distances is 0.0543 A. We have compared the three-dimensional structure of mouse renin with other aspartic proteinases, using rigid-body analysis with respect to shifts involving the domain comprising residues 190 to 302. In terms of the relative orientation of domains, mouse submaxillary renin is closest to human renin with only a 1.7 degrees difference in domain orientation. Porcine pepsin (the molecular replacement model) differs structurally from mouse renin by a 6.9 degrees domain rotation, whereas endothiapepsin, a fungal aspartic proteinase, differs by 18.8 degrees. The triple proline loop (residues 292 to 294), which is structurally opposite the active-site "flap" (residues 72 to 83), gives renin a superficial resemblance to the fold of the retroviral proteinases. The inhibitor is bound in an extended conformation along the active-site cleft, and the hydroxyethylene moiety forms hydrogen bonds with both catalytic aspartate carboxylates. The complex is stabilized by hydrogen bonds between the main chain of the inhibitor and the enzyme. All side-chains of the inhibitor are in van der Waals contact with groups in the enzyme and define ten specificity sub-sites. This study shows how renin has compact sub-sites due to the positioning of secondary structure elements, to complementary substitutions and to the residue composition of its loops close to the active site, leading to extreme specificity towards its prohormone substrate, angiotensinogen. We have analysed the micro-environment of each of the buried charged groups in order to predict their ionization states.

Crystallization and preliminary X-ray analysis of the superoxide dismutase from Mycobacterium tuberculosis.

The iron-dependent superoxide dismutase from Mycobacterium tuberculosis has been crystallized by the hanging drop method. The crystals belong to the P2(1) space group and have unit cell dimensions of a = 68.5 A, b = 85.6 A, c = 66.5 A, beta = 99.8 degrees. There are four molecules per asymmetric unit which, from analysis of data to 2.5 A, appear to be related by non-crystallographic 222 symmetry.

Structure of the bovine eye lens protein gammaB(gammaII)-crystallin at 1.47 A.

The molecular structure of calf gammaB-crystallin (previously called gammaII), a lens-specific protein, has been refined to a crystallographic R factor of 18.1% for all reflection data, between 8.0 and 1.47 A, 25 959 hkl measured at 293 (1) K. 230 water molecules have been defined by difference Fourier techniques and included in a restrained least-squares refinement. Difference Fourier maps clearly indicated the presence of multiple sites for the sulfur atoms of Cys 18 and Cys 22 which were therefore given coupled second-site occupancies during the refinement. The sulfur atom in the major position of Cys 22 is in the reduced state. Either of the Cys 18 sites can form a high-energy disulfide bridge with the minor position of Cys 22. The position of the carboxy terminus and many other surface side chains have been further defined including the RGD signal peptide. The hydration of the backbone and the interdomain region has been analysed. 27 water molecules make extensive contacts to a single protein molecule and thus contribute to its stability.

A model of the structure of human annexin VI bound to lipid monolayers.

Annexin VI is an eight repeat member of the annexin family of proteins which are both water soluble and bind to negatively charged phospholipids in a calcium-dependent manner. Here we present a model for annexin VI based on fitting the three-dimensional structure of two annexin V molecules (Huber (1990) EMBO J. 9, 3867-3874) to the two-dimensional stain-excluding density of lipid-bound annexin VI (Newman (1989) J. Mol. Biol. 206, 213-219). Both annexin VI lobes could only be fitted with their convex faces closest to the lipid monolayer. This supports the hypothesis that annexin-lipid binding is mediated by the interaction between calcium bound to the loops protruding from the convex protein surface and phospholipid headgroups.

X-ray analyses of peptide-inhibitor complexes define the structural basis of specificity for human and mouse renins.

X-ray analyses have defined the three-dimensional structures of crystals of mouse and human renins complexed with peptide inhibitors at resolutions of 1.9 and 2.8 A, respectively. The exquisite specificity of renin arises partly from ordered loop regions at the periphery of the binding cleft. Although the pattern of main-chain hydrogen bonding in other aspartic proteinase inhibitor complexes is conserved in renins, differences in the positions of secondary structure elements (particularly helices) also lead to improved specificity in renins for angiotensinogen substrates.

Structure of oligomeric beta B2-crystallin: an application of the T2 translation function to an asymmetric unit containing two dimers.

The molecular structure of the main subunit of the beta-crystallins, components of the vertebrate eye lens, has recently been solved by molecular replacement at 2.1 A resolution [Bax, Lapatto, Nalini, Driessen, Lindley, Mahadevan, Blundell & Slingsby (1990). Nature (London), 347, 776-780]. The protein, beta B2, is a dimer in solution, but a tetramer in the crystal with one subunit in the asymmetric unit of space group I222. Using the crystallographic dimer from this I-centred form the structure of a C222 crystal form of the beta B2 protein with four subunits in the asymmetric unit has now been solved by molecular replacement at 3.3 A. The solution involved the use of a new translation function for non-crystallographic symmetry, based on the T2 function of Crowther & Blow [Acta Cryst. (1967), 23, 544-548].