xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets

Two user-friendly computer programs are described for use in macromolecular X-ray crystallography, xdlMAPMAN provides an interface for electron-density map exchange between some of the most commonly used phase refinement, structure refinement and model- building programs. In addition, it contains several options to analyse and abstract such maps. xdlDATAMAN provides similar functionality for the analysis and manipulation of macromolecular reflection data sets. Both programs have a simple graphical user interface, and their source code has been put into the public domain.

Towards the automatic interpretation of macromolecular electron-density maps: qualitative and quantitative matching of protein sequence to map

The matching of the known polypeptide sequence to the electron density is a critical step in solving protein structures by the crystallographic method. Tools have been developed to help in defining the placement of the sequence, both qualitatively and quantitatively. They have been tested with good results on two proteins whose structures were solved by the MIR method.

A re-evaluation of the crystal structure of chloromuconate cycloisomerase

It is shown here that the reported 3 A crystal structure of chloromuconate cycloisomerase from Alcaligenes eutrophus [Hoier, Schlömann, Hammer, Glusker, Carrell, Goldman, Stezowski & Heinemann (1994). Acta Cryst. D50, 75-84] was refined in the incorrect space group I4. In addition, a stretch of about 25 residues near the N-terminus is out-of-register with the density in the original structure. From the coordinates and structure factors deposited in the Protein Data Bank (PDB), it was possible to determine the correct space group to be I422. The structure was then re-refined, using the original data reduced to I422, to a crystallographic free R factor of 0.264 at 3 A resolution (conventional R factor 0.189). With conservative refinement and rebuilding methods, the errors in the chain tracing could be identified and remedied. Since the two molecules per asymmetric unit in the original structure are actually related by crystallographic symmetry, the observed differences between them are artefacts. In particular, the differences between, and peculiarities of the metal-binding sites are unreal. This case shows the dangers of crystallographic refinement in cases with unfavourable data-to-parameter ratios, and the importance of reducing the number of parameters in such cases to prevent gross errors (for instance, by using NCS constraints). It also demonstrates how the evaluation and monitoring of model quality during the entire refinement and rebuilding process can be used to detect and remedy serious errors. Finally, it presents a strong case in favour of depositing not only model coordinates, but also experimental data (preferably, both merged and unmerged data).

Efficient rebuilding of protein structures

A computer program, called OOPS, is described which facilitates and speeds up the process of rebuilding a protein structure inside its electron density and reduces the chances of local errors persevering throughout the crystallographic protein structure determination process. The program uses a set of criteria to judge how reasonable each protein residue is and it generates macros for the macromolecular crystallographic model-building program O [Jones, Zou, Cowan & Kjeldgaard (1991). Acta Cryst. A47, 110-119] which, when executed, will take the crystallographer on a journey along all suspect residues.

Detection, delineation, measurement and display of cavities in macromolecular structures

A computer program, VOIDOO, is described which can be employed in the study of cavities such as they occur in macromolecular structures (in particular, in proteins). The program can be used to detect unknown cavities or to delineate known cavities, either of which may be connected to the outside of the molecule or molecular assembly under study. Optionally, output files can be requested that contain a description of the shape of the cavity which can be displayed by the crystallographic modelling program O. Additionally, VOIDOO can be used to calculate the volume of a molecule and to create a file containing data pertaining to the surface of the molecule which can also be displayed using O. Examples of the use of VOIDOO are given for P2 myelin protein, cellular retinol-binding protein and cellobiohydrolase II. Finally, operational definitions to discern different types of cavity are introduced and guidelines for assessing the accuracy and improving the comparability of cavity calculations are given.

Evidence for macular gravity receptor modulation of hypothalamic, limbic and autonomic nuclei

Mice lacking normal vestibular gravity reception show altered homeostatic, circadian and autonomic responses to hypergravity (+G) exposure. Using c-Fos as a marker of neuronal activation, the current study identifies CNS nuclei that may be critical for initiating and integrating such responses to changes in vestibular signaling. This experiment utilized the mutant C57BL/6JEi-het mouse (het), which lacks macular otoconia and thus gravity receptor function. Following 2 h of 2G (2x Earth's gravity) exposure (via centrifugation) the neuronal responses of the het mice were compared with wildtype mice similarly exposed to 2G, as well as het and wildtype 1G controls. Wildtype mice exposed to 2G demonstrated robust c-Fos expression in multiple autonomic, hypothalamic and limbic nuclei, including: the lateral septum, bed nucleus of the stria terminalis, amygdala, paraventricular hypothalamus, dorsomedial hypothalamus, arcuate, suprachiasmatic hypothalamus, intergeniculate leaflet, dorsal raphe, parabrachial and locus coeruleus. The het mice exposed to 2G demonstrated little to null c-Fos expression in these nuclei with a few exceptions and, in general, a similar pattern of c-Fos to 1G controls. Data from this study further support the existence of a complex and extensive influence of the neurovestibular system on homeostatic, circadian and possibly autonomic regulatory systems.

Training the "less-affected" forelimb after unilateral cortical infarcts interferes with functional recovery of the impaired forelimb in rats

PURPOSE

Unilateral lesions of the sensorimotor cortex (SMC) in adult rats cause major behavioral changes in the ipsilesional, "less-affected" forelimb. An increase in function and reliance on this forelimb can aid compensation for contralesional impairments, but may also promote disuse and reduced functionality of the impaired forelimb. We hypothesized that training focused on the ipsilesional forelimb following a unilateral SMC lesion would reduce the efficacy of later motor rehabilitative training of the impaired forelimb.

METHODS

Rats with ischemic SMC lesions were trained on a skilled reaching task with the ipsilesional forelimb (PriorT) or received control procedures (Cont) for 10 days. Both groups were then trained with the impaired forelimb on the same reaching task for 10 days.

RESULTS

In comparison with Cont, PriorT rats had little improvement on the reaching task with the impaired forelimb and had a more enduring disuse of the impaired forelimb for postural support behaviors. Lesion sizes were similar between groups.

CONCLUSIONS

Behavioral experience with the less-affected forelimb early after unilateral SMC lesions has the potential to increase disuse and dysfunction of the impaired forelimb, consistent with a training-induced exacerbation of learned non-use. These findings are suggestive of competitive processes in experience-dependent neural restructuring after brain damage.

Behavioral and neuroplastic effects of focal endothelin-1 induced sensorimotor cortex lesions

Previous studies have established the usefulness of endothelin-1 (ET-1) for the production of focal cerebral ischemia. The present study assessed the behavioral effects of focal ET-1-induced lesions of the sensorimotor cortex (SMC) in adult rats as well as cellular and structural changes in the contralateral homotopic motor cortex at early (2 days) and later (14 days) post-lesion time points. ET-1 lesions resulted in somatosensory and postural-motor impairments in the contralateral (to the lesion) forelimb as assessed on a battery of sensitive measures of sensorimotor function. The lesions also resulted in the development of a hyper-reliance on the ipsilateral forelimb for postural-support behaviors. In comparison to sham-operated rats, in layer V of the motor cortex opposite the lesions, there were time- and laminar-dependent increases in the surface density of dendritic processes immunoreactive for microtubule-associated protein 2, in the optical density of N-methyl-D-asparate receptor (NMDA) subunit 1 immunoreactivity, and in the numerical density of cells immunolabeled for Fos, the protein product of the immediate early gene c-fos. These findings corroborate and extend previous findings of the effects of electrolytic lesions of the SMC. It is likely that compensatory forelimb behavioral changes and transcallosal degeneration play important roles in these changes in the cortex opposite the lesion, similar to previously reported effects of electrolytic SMC lesions.

Addition of rosiglitazone to metformin is most effective in obese, insulin-resistant patients with type 2 diabetes

AIM

These analyses were undertaken to evaluate the efficacy of the insulin sensitizer rosiglitazone (RSG) when added to the therapy of obese type 2 diabetes mellitus patients (T2DM) taking near-maximal doses (2.5 g/day) of metformin (MET). In obese, insulin-resistant patients with T2DM who are inadequately controlled on MET, the addition of an agent that reduces insulin resistance may be a more rational and innovative approach than the addition of an insulin secretagogue.

METHODS

Data were pooled from two double-blind studies of RSG added to 2.5 g/day MET, involving a total of 550 T2DM patients. Patients were categorized as non-overweight, overweight and obese according to their baseline BMI using WHO criteria (<25 kgm(-2), 25-30 kgm(-2), >30 kgm(-2) respectively).

RESULTS

RSG improved glycaemia (HbA1c) and fasting plasma glucose (FPG) to a clinically significant extent in all three subgroups but the effect was most pronounced in the obese patients. Improvements in HOMA estimates of insulin resistance and beta-cell function were also greatest in the obese patients (4 mg: -16% and +19%; 8 mg: -37% and + 33% respectively), as were reductions in fasting insulin. The profile of adverse events was not demonstrably different in obese patients from the non-obese.

CONCLUSIONS

In obese type 2 diabetic patients inadequately controlled on MET alone, addition of rosiglitazone improves glycaemic control, insulin sensitivity and beta-cell function to a clinically important extent.

Primordial rhythmic bursting in embryonic cochlear ganglion cells

This study examined the nature of spontaneous discharge patterns in cochlear ganglion cells in embryonic day 13 (E13) to early E17 chicken embryos (stages 39-43). Neural recordings were made with glass micropipettes. No sound-driven activity was seen for the youngest embryos (maximum intensity 107 dB sound pressure level). Ganglion cells were labeled with biotinylated dextran amine in four embryos. In two animals, primary afferents projected to hair cells in the middle region along the length of the basilar papilla in which, in one cell, the terminals occupied a neural transverse position and, in the other, a more abneural location. Statoacoustic ganglion cells showing no spontaneous activity were seen for the first time in the chicken. The proportion of "silent" cells was largest at the youngest stages (stage 39, 67%). In active cells, mean spontaneous discharge rates [9.4 +/- 10.4 spikes (Sp)/sec; n = 44] were lower than rates for older embryos (19 +/- 17 Sp/sec) (Jones and Jones, 2000). Embryos at stages 39-41 evidenced even lower rates (4.2 +/- 5.0 Sp/sec). The most salient feature of spontaneous activity for stages 39-43 was a bursting discharge pattern in >75% of active neurons (33 of 44). Moreover, in 55% of these cells, there was a clear, slow, rhythmic bursting pattern. The proportion of cells showing rhythmic bursting was greatest at the youngest stages (39-42) and decreased to <30% at stage 43. Rate of bursting ranged from 1 to 54 bursts per minute. The presence of rhythmic bursting in cochlear ganglion cells at E13-E17 provides an explanation for the existence of such patterns in central auditory relays. The bursting patterns may serve as a patterning signal for central synaptic refinements in the auditory system during development.

Vestibular ontogeny: measuring the influence of the dynamic environment

In comparison to other special senses, we are only meagerly informed about the development of vestibular function and the mechanisms that may operate to control or influence the course of vestibular ontogeny. Perhaps one contributing factor to this disparity is the difficulty of evaluating vestibular sense organs directly and noninvasively. The present report describes a recently developed direct noninvasive vestibular function test that can be used to address many basic questions about the developing vestibular system. More particularly, the test can be used to examine the effects of the dynamic environment (e.g. gravitational field and vibration) on vestibular ontogeny.

Effects of microgravity on vestibular ontogeny: direct physiological and anatomical measurements following space flight (STS-29)

Does space flight change gravity receptor development? The present study measured vestibular form and function in birds flown as embryos for 5 days in earth orbit (STS-29). No major changes in vestibular gross morphology were found. Vestibular response mean amplitudes and latencies were unaffected by space flight. However, the results of measuring vestibular thresholds were mixed and abnormal responses in 3 of the 8 flight animals raise important questions.

Computational identification of noncoding RNAs in E. coli by comparative genomics

Some genes produce noncoding transcripts that function directly as structural, regulatory, or even catalytic RNAs [1, 2]. Unlike protein-coding genes, which can be detected as open reading frames with distinctive statistical biases, noncoding RNA (ncRNA) gene sequences have no obvious inherent statistical biases [3]. Thus, genome sequence analyses reveal novel protein-coding genes, but any novel ncRNA genes remain invisible. Here, we describe a computational comparative genomic screen for ncRNA genes. The key idea is to distinguish conserved RNA secondary structures from a background of other conserved sequences using probabilistic models of expected mutational patterns in pairwise sequence alignments. We report the first whole-genome screen for ncRNA genes done with this method, in which we applied it to the "intergenic" spacers of Escherichia coli using comparative sequence data from four related bacteria. Starting from >23,000 conserved interspecies pairwise alignments, the screen predicted 275 candidate structural RNA loci. A sample of 49 candidate loci was assayed experimentally. At least 11 loci expressed small, apparently noncoding RNA transcripts of unknown function. Our computational approach may be used to discover structural ncRNA genes in any genome for which appropriate comparative genome sequence data are available.

Bouveret's syndrome presenting as upper gastrointestinal hemorrhage without hematemesis

A 74-year-old woman with a recent diagnosis of peptic ulcer disease diagnosed by endoscopy after presentation with an episode of upper gastrointestinal bleeding returned 6 1/2 weeks later with a 5-day history of nausea and vomiting without associated symptoms. An ultrasound was nondiagnostic except for a large gallstone and a poorly visualized gallbladder. Repeat endoscopy revealed a hard mass that was presumed to have formed secondarily to an ulcer-induced stricture, and a 6-cm filling defect just proximal to the duodenal bulb was seen on a preoperative upper gastrointestinal series. At laparotomy the mass was actually a large gallstone and two smaller stones, which had eroded into and become impacted in the duodenal bulb creating a gastric outlet obstruction. The stones were extracted via a duodenotomy, and the remaining portion of the gallbladder was removed with repair of the cholecystoduodenal fistula. The patient was discharged home after an uncomplicated postoperative course. Gastric outlet obstruction by a duodenal gallstone is a condition known as Bouveret's syndrome, which is a rare complication of gallstone disease. Upper gastrointestinal hemorrhage is an especially rare form of presentation.

Molray--a web interface between O and the POV-Ray ray tracer

A publicly available web-based interface is presented for producing high-quality ray-traced images and movies from the molecular-modelling program O [Jones et al. (1991), Acta Cryst. A47, 110-119]. The interface allows the user to select O-plot files and set parameters to create standard input files for the popular ray-tracing renderer POV-Ray, which can then produce publication-quality still images or simple movies. To ensure ease of use, we have made this service available to the O user community via the World Wide Web. The public Molray server is available at http://xray.bmc.uu.se/molray.

Binding site differences revealed by crystal structures of Plasmodium falciparum and bovine acyl-CoA binding protein

Acyl-CoA binding protein (ACBP) maintains a pool of fatty acyl-CoA molecules in the cell and plays a role in fatty acid metabolism. The biochemical properties of Plasmodium falciparum ACBP are described together with the 2.0 A resolution crystal structures of a P. falciparum ACBP-acyl-CoA complex and of bovine ACBP in two crystal forms. Overall, the bovine ACBP crystal structures are similar to the NMR structures published previously; however, the bovine and parasite ACBP structures are less similar. The parasite ACBP is shown to have a different ligand-binding pocket, leading to an acyl-CoA binding specificity different from that of bovine ACBP. Several non-conservative differences in residues that interact with the ligand were identified between the mammalian and parasite ACBPs. These, together with measured binding-specificity differences, suggest that there is a potential for the design of molecules that might selectively block the acyl-CoA binding site.

Engineering of a glycosidase Family 7 cellobiohydrolase to more alkaline pH optimum: the pH behaviour of Trichoderma reesei Cel7A and its E223S/ A224H/L225V/T226A/D262G mutant

The crystal structures of Family 7 glycohydrolases suggest that a histidine residue near the acid/base catalyst could account for the higher pH optimum of the Humicola insolens endoglucanase Cel7B, than the corresponding Trichoderma reesei enzymes. Modelling studies indicated that introduction of histidine at the homologous position in T. reesei Cel7A (Ala(224)) required additional changes to accommodate the bulkier histidine side chain. X-ray crystallography of the catalytic domain of the E223S/A224H/L225V/T226A/D262G mutant reveals that major differences from the wild-type are confined to the mutations themselves. The introduced histidine residue is in plane with its counterpart in H. insolens Cel7B, but is 1.0 A (=0.1 nm) closer to the acid/base Glu(217) residue, with a 3.1 A contact between N(epsilon2) and O(epsilon1). The pH variation of k(cat)/K(m) for 3,4-dinitrophenyl lactoside hydrolysis was accurately bell-shaped for both wild-type and mutant, with pK(1) shifting from 2.22+/-0.03 in the wild-type to 3.19+/-0.03 in the mutant, and pK(2) shifting from 5.99+/-0.02 to 6.78+/-0.02. With this poor substrate, the ionizations probably represent those of the free enzyme. The relative k(cat) for 2-chloro-4-nitrophenyl lactoside showed similar behaviour. The shift in the mutant pH optimum was associated with lower k(cat)/K(m) values for both lactosides and cellobiosides, and a marginally lower stability. However, k(cat) values for cellobiosides are higher for the mutant. This we attribute to reduced non-productive binding in the +1 and +2 subsites; inhibition by cellobiose is certainly relieved in the mutant. The weaker binding of cellobiose is due to the loss of two water-mediated hydrogen bonds.

The X-ray crystal structure of the Trichoderma reesei family 12 endoglucanase 3, Cel12A, at 1.9 A resolution

We present the three-dimensional structure of Trichoderma reesei endoglucanase 3 (Cel12A), a small, 218 amino acid residue (24.5 kDa), neutral pI, glycoside hydrolase family 12 cellulase that lacks a cellulose-binding module. The structure has been determined using X-ray crystallography and refined to 1.9 A resolution. The asymmetric unit consists of six non-crystallographic symmetry-related molecules that were exploited to improve initial multiple isomorphous replacement phasing, and subsequent structure refinement. The enzyme contains one disulfide bridge and is glycosylated at Asp164 by a single N-acetyl glucosamine residue. The protein has the expected fold for a glycoside hydrolase clan-C family 12 enzyme. It contains two beta-sheets, of six and nine strands, packed on top of one another, and one alpha-helix. The concave surface of the nine-stranded beta-sheet forms a large substrate-binding groove in which the active-site residues are located. In the active site, we find a carboxylic acid trio, similar to that of glycoside hydrolase families 7 and 16. The strictly conserved Asp99 hydrogen bonds to the nucleophile, the invariant Glu116. The binding crevice is lined with both aromatic and polar amino acid side-chains which may play a role in substrate binding. The structure of the fungal family 12 enzyme presented here allows a complete structural characterization of the glycoside hydrolase-C clan.

Compound gravity receptor polarization vectors evidenced by linear vestibular evoked potentials

The utricle and saccule are gravity receptor organs of the vestibular system. These receptors rely on a high-density otoconial membrane to detect linear acceleration and the position of the cranium relative to Earth's gravitational vector. The linear vestibular evoked potential (VsEP) has been shown to be an effective non-invasive functional test specifically for otoconial gravity receptors (Jones et al., 1999). Moreover, there is some evidence that the VsEP can be used to independently test utricular and saccular function (Taylor et al., 1997; Jones et al., 1998). Here we characterize compound macular polarization vectors for the utricle and saccule in hatchling chickens. Pulsed linear acceleration stimuli were presented in two axes, the dorsoventral (DV, +/- Z axis) to isolate the saccule, and the interaural (IA, +/- Y axis) to isolate the utricle. Traditional signal averaging was used to resolve responses recorded from the surface of the skull. Latency and amplitude of eighth nerve components of the linear VsEP were measured. Gravity receptor responses exhibited clear preferences for one stimulus direction in each axis. With respect to each utricular macula, lateral translation in the IA axis produced maximum ipsilateral response amplitudes with substantially greater amplitude intensity (AI) slopes than medially directed movement. Downward caudal motions in the DV axis produced substantially larger response amplitudes and AI slopes. The results show that the macula lagena does not contribute to the VsEP compound polarization vectors of the sacculus and utricle. The findings suggest further that preferred compound vectors for the utricle depend on the pars externa (i.e. lateral hair cell field) whereas for the saccule they depend on pars interna (i.e. superior hair cell fields). These data provide evidence that maculae saccule and utricle can be selectively evaluated using the linear VsEP.

Initial sequencing and analysis of the human genome

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Structural basis for enantiomer binding and separation of a common beta-blocker: crystal structure of cellobiohydrolase Cel7A with bound (S)-propranolol at 1.9 A resolution

Cellobiohydrolase Cel7A (previously called CBH 1), the major cellulase produced by the mould fungus Trichoderma reesei, has been successfully exploited as a chiral selector for separation of stereo-isomers of some important pharmaceutical compounds, e.g. adrenergic beta-blockers. Previous investigations, including experiments with catalytically deficient mutants of Cel7A, point unanimously to the active site as being responsible for discrimination of enantiomers. In this work the structural basis for enantioselectivity of basic drugs by Cel7A has been studied by X-ray crystallography. The catalytic domain of Cel7A was co-crystallised with the (S)-enantiomer of a common beta-blocker, propranolol, at pH 7, and the structure of the complex was determined and refined at 1. 9 A resolution. Indeed, (S)-propranolol binds at the active site, in glucosyl-binding subsites -1/+1. The catalytic residues Glu212 and Glu217 make tight salt links with the secondary amino group of (S)-propranolol. The oxygen atom attached to the chiral centre of (S)-propranolol forms hydrogen bonds to the nucleophile Glu212 O(epsilon1) and to Gln175 N(epsilon2), whereas the aromatic naphthyl moiety stacks with the indole ring of Trp376 in site +1. The bidentate charge interaction with the catalytic glutamate residues is apparently crucial, since no enantioselectivity has been obtained with the catalytically deficient mutants E212Q and E217Q. Activity inhibition experiments with wild-type Cel7A were performed in conditions close to those used for crystallisation. Competitive inhibition constants for (R)- and (S)-propranolol were determined at 220 microM and 44 microM, respectively, corresponding to binding free energies of 20 kJ/mol and 24 kJ/mol, respectively. The K(i) value for (R)-propranolol was 57-fold lower than the highest concentration, 12.5 mM, used in co-crystallisation experiments. Still several attempts to obtain a complex with the (R)-enantiomer have failed. By using cellobiose as a selective competing ligand, the retention of the enantiomers of propranolol on the chiral stationary phase (CSP) based on Cel7A mutant D214N were resolved into enantioselective and non- selective binding. The enantioselective binding was weaker for both enantiomers on D214N-CSP than on wild-type-CSP.

The relationship between tail biting in pigs, docking procedure and other management practices

The tail length (docked, tipped or undocked) and tail status (bitten or unbitten) of 27,870 pigs from 450 units was recorded at six UK abattoirs. A farm survey of the final finishing stage was used to investigate the relationship between management practice and tail biting. This showed that docking was the most important factor influencing the probability of being not bitten, with 2.4% of docked and 8.5% of long-tailed pigs being tail-bitten. The following factors reduced the probability of long-tailed pigs being tail-bitten; light straw provision, use of natural ventilation or artificially controlled natural ventilation (ACNV), mixed sex grouping, meal or liquid feeding, and use of double or multi-space feeders. Docked and long-tailed pigs provided with light straw and natural ventilation/ACNV had levels of tail biting of 1.2% and 4.3% respectively; 3.9% of docked pigs with artificial ventilation and no straw were tail-bitten. Long-tailed pigs fed via double or multi-space feeders also had 3.9% of tails bitten.