X-ray structure of TMP kinase from Mycobacterium tuberculosis complexed with TMP at 1.95 A resolution

The X-ray structure of Mycobacterium tuberculosis TMP kinase at 1.95 A resolution is described as a binary complex with its natural substrate TMP. Its main features involve: (i) a clear magnesium-binding site; (ii) an alpha-helical conformation for the so-called LID region; and (iii) a high density of positive charges in the active site. There is a network of interactions involving highly conserved side-chains of the protein, the magnesium ion, a sulphate ion mimicking the beta phosphate group of ATP and the TMP molecule itself. All these interactions conspire in stabilizing what appears to be the closed form of the enzyme. A complete multialignment of all (32) known sequences of TMP kinases is presented. Subtle differences in the TMP binding site were noted, as compared to the Escherichia coli, yeast and human enzyme structures, which have been reported recently. These differences could be used to design specific inhibitors of this essential enzyme of nucleotide metabolism. Two cases of compensatory mutations were detected in the TMP binding site of eukaryotic and prokaryotic enzymes. In addition, an intriguing high value of the electric field is reported in the vicinity of the phosphate group of TMP and the putative binding site of the gamma phosphate group of ATP.

Crystallization of the catalytic domain of murine terminal deoxynucleotidyl transferase

The catalytic domain of murine terminal deoxynucleotidyl transferase (TdT) has been crystallized in the space group P2(1)2(1)2(1), with unit-cell parameters a = 47.1, b = 86.2, c = 111.7 A. The crystals diffract to a resolution of 2.4 A using synchrotron radiation and a full data set has been collected from the native crystals. The enzyme was shown to be active in the crystalline state.

General formalism for phase combination and phase refinement: a statistical thermodynamics approach in reciprocal space

The mean-field optimization methodology has been used to recast in a single formalism the problem of phase optimization using an arbitrary energy function in the presence of an experimentally determined phase probability distribution function. It results naturally in the generalization of the notions of figure of merit and centroid phase where the weight of the energy refinement is controlled by an effective temperature in a self-consistent manner. In the limit of high temperature, the formalism reduces of course to the Blow & Crick [Acta Cryst. (1959), 12, 794-802] classical treatment. If a model is available, Sim's [Acta Cryst. (1960), 13, 511-512] weighting scheme for a combined map appears as the first step of a refinement to be conducted until self-consistency is achieved. Assuming that MIR phases exist and that they agree reasonably well with the phases of the model, a first-order expansion gives an estimate of the changes of weights and phases to be performed for the Fourier synthesis. This provides for a new way of doing phase combination that might prove useful in challenging cases of model refinement, e.g. in large macromolecular complexes. Thermodynamic considerations have been used to discuss the best determination of weights in phase refinement; they also suggest that a variational expression of maximum likelihood is best suited as a target for refinement because it is the free energy of the system. The formalism readily allows use of solvent flattening, density averaging and the atomicity criterion to refine phases, and automatically assigns a figure of merit to each reflection. Numerical tests of the method are presented in an attempt to resolve the phase-ambiguity problem of protein crystallography in the centrosymmetric P¿1¿ space group using an energy derived from the Sayre equation.

Resolution of the phase-ambiguity problem in the centrosymmetric P [1] space group by Monte Carlo methods

Simulated-annealing methods have been used to resolve the phase-ambiguity problem in the centrosymmetric P¿bar¿1¿ space group. First, an energy function based on the Sayre equation is introduced and a formal comparison with classical spin systems is drawn. The energy landscape is studied in detail and the validity of several energy criteria thoroughly tested. Classical Monte Carlo methods proved to be successful using a multistart optimization of the Sayre score, along with the additional monitoring of other energetic criteria. These involved the Terwilliger map quality index in reciprocal space in the absence of envelope information, and an envelope score if the shape of the molecule is known. The inherent phase-ambiguity problem of the P¿bar¿1¿ space group was therefore technically solved by Monte Carlo methods. The method should also work to resolve phase ambiguity in the SIR method of protein crystallography.

Solution structural studies and low-resolution model of the Schizosaccharomyces pombe sap1 protein

Sap1 is a DNA-binding protein involved in controlling the mating type switch in fission yeast Schizosaccharomyces pombe. In the absence of any significant sequence similarity with any structurally known protein, a variety of biophysical techniques has been used to probe the solution low-resolution structure of the sap1 protein. First, sap1 is demonstrated to be an unusually elongated dimer in solution by measuring the translational diffusion coefficient with two independent techniques: dynamic light-scattering and ultracentrifugation. Second, sequence analysis revealed the existence of a long coiled-coil region, which is responsible for dimerization. The length of the predicted coiled-coil matches estimates drawn from the hydrodynamic experimental behaviour of the molecule. In addition, the same measurements done on a shorter construct with a coiled-coil region shortened by roughly one-half confirmed the localization of the long coiled-coil region. A crude T-shape model incorporating all these information was built. Third, small-angle X-ray scattering (SAXS) of the free molecule provided additional evidence for the model. In particular, the P(r) curve strikingly demonstrates the existence of long intramolecular distances. Using a novel 3D reconstruction algorithm, a low resolution 3D model of the protein has been independently constructed that matches the SAXS experimental data. It also fits the translation diffusion coefficients measurements and agrees with the first T-shaped model. This low-resolution model has clearly biologically relevant new functional implications, suggesting that sap1 is a bifunctional protein, with the two active sites being separated by as much as 120 A; a tetrapeptide repeated four times at the C terminus of the molecule is postulated to be of utmost functional importance.

Aspartyl tRNA-synthetase from Escherichia coli: flexibility and adaptability to the substrates

The crystal structure of aspartyl-tRNA synthetase from Escherichia coli has been determined to a resolution of 2.7 A. The structure is compared to the same enzyme co-crystallized with tRNA(Asp) and containing aspartyl adenylate or ATP. The asymmetric unit contains three monomers of the enzyme. While most parts of the protein show no significant differences in the three monomers, a few regions cannot be superimposed. Those regions are characterized by a high B-factor, and consist mostly of loops that make contacts with the tRNA in the complexes. The flexibility of the protein is seen at a global level, by the observation of a 10 to 15 degrees rotation of the N-terminal and insertion domains upon tRNA binding, and at the level of the individual amino acid residues, by main-chain and side-chain rearrangements. In contrast to these induced-fit conformational changes, a few residues essential for the tRNA anticodon or aspartyl-adenylate recognition exist in a predefined conformation, ensured by specific interactions within the protein.

Crystallization and preliminary X-ray analysis of the thymidylate kinase from Mycobacterium tuberculosis

Mycobacterium tuberculosis thymidylate kinase complexed with the substrate deoxythymidine monophosphate was crystallized in the hexagonal space group P6(5)22 or P6(1)22, with unit-cell parameters a = b = 76.62, c = 134.38 A and one single monomer of 23 kDa in the asymmetric unit. Cryo-cooled crystals diffract at 1.94 A resolution using synchrotron radiation.

Calponin modulates the exclusion of Otx-expressing cells from convergence extension movements

Otx2, a vertebrate homologue of the Drosophila orthodenticle gene, coordinates two processes in early embryonic development. Not only does it specify cell fate in the anterior regions of the embryo, it also prevents the cells that express it from participating in the convergence extension movements that shape the rest of the body axis. Here we show that, in Xenopus, this latter function is mediated by XclpH3, transcription of which is directly stimulated by Xotx2. XclpH3 is a Xenopus homologue of the mammalian calponin gene, the product of which binds both actin and myosin and prevents the generation of contractile force by actin filaments.

Role of fibroblast growth factor during early midbrain development in Xenopus

Genes encoding fibroblast growth factors (FGFs) are expressed in early Xenopus neurulae in the prospective midbrain-hindbrain boundary (MHB) region of the neural plate. These expression domains overlap those of XWnt-1 and XEn-2, raising the question of the role of FGF signalling in the regulation of these genes, and more generally about the function of FGF during Xenopus midbrain development. We report that explants from the prospective MHB grafted into the anterior neural plate in midneurula stage embryos induce XWnt-1 expression and, at a lower frequency, XEn-2 expression in the vicinity of the graft. Such a process is likely to involve FGF signalling. Implantation of FGF4- or FGF8-soaked beads in the prospective forebrain at neurula and tailbud stages causes the up-regulation of XWnt-1 and XEn-2 in the dorsal and lateral region of the anterior midbrain. This effect is not relayed by endogenous FGF genes since exogenous FGFs inhibit the expression of endogenous XFGF3 or XFGF8. However, consequences of grafting MHB or implanting FGF4 or FGF8 beads on tadpole brain development are different. MHB grafts induce ectopic mesencephalic structures, strongly suggesting that a region homologous to the isthmic organizer of amniotes is specified as early as the midneurula stage. In contrast, exogenous FGFs do not cause the formation of ectopic mesencephalic structures but an overgrowth of mesencephalon and diencephalon. We propose that FGF signals from the prospective MHB play a crucial role in the spatial regulation of XWnt-1 and XEn-2 expression in the posterior midbrain, but that the full organizing activity of the MHB involves other factors in combination with FGF.

Medial cell mixing during axial morphogenesis of the amphibian embryo requires cadherin function

A truncated form of Xenopus E-cadherin (deltaE-cad) comprising the cytoplasmic and transmembrane domains was overexpressed generating a dominant negative mutation in the urodelan amphibian embryo Pleurodeles waltl. deltaE-cad mRNA and rhodamine-lysinated-dextran (RLDx) cell lineage tracer were microinjected into 32-cell stage blastomeres which contribute principally to the notochord and central nervous system. deltaE-cad expression causes defects in forebrain and hindbrain formation coupled with the development of supernumerary vesicles. Duplication of the notochord also occurs due to the retardation of medial cell intercalation with correlated duplications of spinal cord and somites. These results emphasize the role of cadherins in mediating cell-cell adhesion in early amphibian embryogenesis. They extend to Pleurodeles the observations made in Xenopus, illustrating that despite differences in morphogenetic processes, the molecular mechanisms are conserved in these two species.

Sur2 mutations of Arabidopsis thaliana define a new locus involved in the control of auxin homeostasis

A new auxin homeostasis gene in Arabidopsis called SUR2 has been identified. This gene, mapped to the bottom of chromosome 4, is defined by two recessive nuclear mutants designated superroot2 (sur2), which display several abnormalities reminiscent of auxin effects. A number of these characteristics are similar to the phenotype of the previously described auxin-overproducing mutant superroot1 (sur1); however, several lines of evidences reveal that the SUR2 gene defines a new key point in the regulation of endogenous auxin concentrations. The phenotype of the sur1 sur2 double mutant is additive. Analysis by gas chromatography coupled to mass spectrometry indicated increased levels of free indole-3-acetic acid correlated with a decreased level of bound auxin in the sur2 mutant. These results suggest that SUR2 may be involved in the control of auxin conjugation.

Higher activity of an aldehyde oxidase in the auxin-overproducing superroot1 mutant of Arabidopsis thaliana

Aldehyde oxidase (AO; EC 1.2.3.1) activity was measured in seedlings of wild type or an auxin-overproducing mutant, superroot1 (sur1), of Arabidopsis thaliana. Activity staining for AO after native polyacrylamide gel electrophoresis separation of seedling extracts revealed that there were three major bands with AO activity (AO1-3) in wild-type and mutant seedlings. One of them (AO1) had a higher substrate preference for indole-3-aldehyde. This AO activity was significantly higher in sur1 mutant seedlings than in the wild type. The difference in activity was most apparent 7 d after germination, the same time required for the appearance of the remarkable sur1 phenotype, which includes epinastic cotyledons, elongated hypocotyls, and enhanced root development. Higher activity was observed in the root and hypocotyl region of the mutant seedlings. We also assayed the indole-3-acetaldehyde oxidase activity in extracts by high-performance liquid chromatography detection of indole-3-acetic acid (IAA). The activity was about 5 times higher in the extract of the sur1 seedlings, indicating that AO1 also has a substrate preference for abscisic aldehyde. Treatment of the wild-type seedlings with picloram or IAA caused no significant increase in AO1 activity. This result suggested that the higher activity of AO1 in sur1 mutant seedlings was not induced by IAA accumulation and, thus, strongly supports the possible role of AO1 in IAA biosynthesis in Arabidopsis seedlings.

The native sequence determines sidechain packing in a protein, but does optimal sidechain packing determine the native sequence?

Globular proteins have highly compact structures and the corresponding packing interactions are widely considered as the principal determinant of the native structure. It is therefore important that theoretical approaches to protein design explicitly take in account packing, which requires that a full atomic representation of the designed protein is maintained. As a first step towards this goal, we have developed in this report an inverse folding algorithm with the aim of specifically designing amino acid sequences which optimise sidechain packing for a given protein fold. The design is performed by a global Monte Carlo optimisation in sequence space, with constant amino acid composition and a full-atom representation of the various protein models. Packing is defined by a Lennard-Jones potential. The program was tested by designing stable sequence variants for the chymotrypsin inhibitor fold. The final protein models showed an increase in intramolecular atomic contacts and a decrease in the overall volume compared to the native structure. Starting from the backbone only of the target structure, the algorithm did gradually retrieve reliable though limited sequence information. Higher compatibility might be achieved by improving the potential, however our results suggest that packing interactions are an essential element of a yet-to-be-defined successful energy function for protein design.

The inverse protein folding problem: self consistent mean field optimisation of a structure specific mutation matrix

The goal of the inverse folding problem is to supply a list of sequences compatible with a known protein structure. If two-body interactions are taken into account in energy calculations, an exhaustive exploration of the energy landscape in sequence space cannot be achieved because of the huge number of possible combinations. To circumvent this problem, we propose a method in which multiple copies corresponding to every possible side-chain type are attached to each C alpha position in the protein. The weights of each copy (stored in the sequence matrix SM) are refined using mean field theory: each side-chain copy interacts with the mean field generated by all possible side-chain copies at neighbouring positions, weighted by their respective probabilities. The potential energy is simply taken to be amino acid pair potentials of mean force. The method converges in a few cycles to a self-consistent solution. The refined matrix does not depend on the starting point; therefore the method succeeds in removing memory effects. Starting solely from the backbone of the known structure, and without information from the initial sequence, the final sequence matrix SM is shown to be able to retrieve significant sequence information, as observed through a series of structure-recognizes-sequence(s) computer experiments. The issue of specificity is discussed in detail.

Fates of the blastomeres of the 32-cell stage Pleurodeles waltl embryo

Cell fate of the blastomeres at the 32-cell stage in the Pleurodeles waltl embryo was analyzed by injection of rhodamine or fluorescein lysinated-dextran (RLDx or FLDx). At the tailbud stage, the progeny of each blastomere contributed to more than one germ layer with unequal distribution along the anteroposterior and dorsoventral axis. Such a regionalized positioning of the descendants of the 32-cell blastomeres was found in the neuroectoderm, the epidermis, the notochord, the somites, the lateral plate, and the endoderm, but not in the head mesenchyme, the pronephros, or the blood islands. Results of double labeling of juxtaposed blastomeres showed that cell mixing and rearrangement take place during organ formation. Results are compared with those of the 32-cell stage fate map in Xenopus and Rana and reveal the more restricted fate of 32-cell stage blastomeres in Pleurodeles germ layers.

A comparison of two-dimensional electrophoresis data with phenotypical traits in Arabidopsis leads to the identification of a mutant (cri1) that accumulates cytokinins

Total proteins extracted from developmental mutants of Arabidopsis thaliana (L.) Heyhn. and from wild-type plants cultivated in the presence of various hormones were analyzed by two-dimensional (2-D) gel electrophoresis. Computer analysis of 2-D gels followed by a statistical treatment of data allowed us to build a phenogram that describes the biochemical distances between the different genotypes. Analysis of the 2-D electrophoresis data allowed us to discriminate mutants in agreement with phenotypical and physiological traits. This biochemical analysis helped us to develop a working hypothesis which led us to show that one developmental mutant (cri1) overaccumulates cytokinins.

Cristal mutations in Arabidopsis confer a genetically heritable, recessive, hyperhydric phenotype

A new class of recessive Arabidopsis mutants, designated cristal (cri) has been isolated which display several abnormalities reminiscent of hyperhydric symptoms. These characteristics include translucent and wrinkled cotyledons and leaves, abnormal chloroplast organization, a reduced amount of chlorophyll, a reduced dry weight and a decreased number of palisade cells in the leaves accompanied by an increase of intercellular space, and therefore give a vitreous appearance to the aerial part. The phenotype is also dependent on the culture medium water potential. The cri1 gene was mapped on chromosome 4 close to the DHS1 marker.

Cloning and characterisation of a gene from Plasmodium vivax and P. knowlesi: homology with valine-tRNA synthetase

We have previously described a lambdagt11 clone detected by immune screening with a monoclonal antibody (mAb) A12. This mAb is capable of completely blocking Plasmodium vivax transmission in the mosquito vector. An epitope recognised by A12 was mapped to six amino acids (aa) within the translated sequence of this clone. Here, we describe the complete sequence of the gene within which we mapped this epitope. Surprisingly, the translated sequence of the full-length open reading frame shows homology with that of valine-tRNA synthetases (Val-tRS) from other organisms. DNA cross-hybridisation with several of these species was observed by Southern blot. In addition, the corresponding gene has been obtained from the closely related simian malaria parasite, P. knowlesi. The two aa sequences show 66% identity and yet are very divergent from other Val-tRS sequences, apart from conserved blocks related to functional activity. Multiple sequence alignments reflect this dichotomy, as do predicted differences in antigenicity.

What mechanisms drive cell migration and cell interactions in Pleurodeles?

Embryogenesis implies a strict control of cell interaction and cell migration. The spatial and temporal regulation of morphogenetic movements occurring during gastrulation is directly dependent on the early cell interactions that take place in the blastula. The newt Pleurodeles waltl is a favorable model for the study of these early morphogenetic events. The combination of orthotopic grafting and fluorescent lineage tracers has led to precise early gastrula mesoderm fate maps. It is now clear that there are no sharp boundaries between germ layers at the onset of gastrulation but rather diffuse transition zones. The coordination of cell movements during gastrulation is closely related to the establishment of dorsoventral polarity. Ventralization by U.V. irradiation or dorsalization by lithium treatment modifies the capacity for autonomous migration on the fibronectin coated substratum of marginal zone cells accordingly. It is now firmly established that mesodermal cells need to adhere to a fibrillar extracellular matrix (ECM) to undergo migration during gastrulation. Extracellular fibrils contain laminin and fibronectin (FN). Interaction of cells with ECM involves receptors of the beta 1 integrin family. A Pleurodeles homolog of the alpha v integrin subunit has been recently identified. Protein alpha v expression is restricted to the surface of mesodermal cells during gastrulation. Integrin-mediated interactions of cells with FN are essential for ECM assembly and mesodermal cell migration. Intracellular injection of antibodies to the cytoplasmic domain of beta 1 into early cleavage embryos causes inhibition of FN fibril formation. Intrablastocoelic injections of several probes including antibodies to FN or integrin alpha 5 beta 1, competitive peptides to the major cell binding site of FN or the antiadhesive protein tenascin all block mesodermal cell migration. This results in a complete arrest of gastrulation indicating that mesodermal cell migration is a major driving force in urodele gastrulation. It is now possible to approach the role of fibroblast growth factor (FGF) during cell interactions taking place in urodele embryos. Four different FGF receptors (FGFR) have been cloned in Pleurodeles. Each of them has a unique mRNA expression pattern. FGFR-1, FGFR-3, and the variant of FGFR-2 containing the IIIb exon are maternally expressed and might be involved in mesodermal induction. During gastrulation, FGFR-3 and FGFR-4 have a restricted pattern of expression, whereas FGFR-1 mRNA is nearly uniformly distributed. Splicing variants FGFR-2IIIb and FGFR-2IIIc have exclusive expression patterns during neurulation. IIIb is expressed in epidermis and IIIc in neural tissue, suggesting a function in the differentiation of ectodermal derivatives.

Mean-field minimization methods for biological macromolecules

Simulations of macromolecular structures involve the minimization of a potential-energy function that presents many local minima. Mean-field theory provides a tool that enables us to escape these minima, by enhancing sampling in conformational space. The number of applications of this technique has increased significantly over the past year, enabling problems with protein-homology modelling and inverted protein structure prediction to be solved.

Partition of aminoacyl-tRNA synthetases in two different structural classes dating back to early metabolism: implications for the origin of the genetic code and the nature of protein sequences

We describe, on the molecular level, a possible fuzzy and primordial translation apparatus capable of synthesizing polypeptides from nucleic acids in a world containing a mixture of coevolving molecules of RNA and proteins already arranged in metabolic cycles (including cofactors). Close attention is paid to template-free systems because they are believed to be the immediate ancestors of this primordial translation apparatus. The two classes of aminoacyl-tRNA synthetases (aaRSs), as seen today, are considered as the remnants of such a simple imprecise translation apparatus and are used as guidelines for the construction of the model. Earlier theoretical work by Bedian on a related system is invoked to show how specificity and stability could have been achieved automatically and rather quickly, starting from such an imprecise system, i.e., how the encoded synthesis of proteins could have appeared. Because of the binary nature of the underlying proto-code, the first genetically encoded proteins would then have been alternating copolymers with a high degree of degeneracy, but not random. Indeed, a clear signal for alternating hydrophobic and hydrophilic residues in present-day protein sequences can be detected. Later evolution of the genetic code would have proceeded along lines already discussed by Crick. However, in the initial stages, the translation apparatus proposed here is in fact very similar to the one postulated by Woese, only here it is given a molecular framework. This hypothesis departs from the paradigm of the RNA world in that it supposes that the origin of the genetic code occurred after the apparition of some functional (statistical) proteins first. Implications for protein design are also discussed.

Superroot, a recessive mutation in Arabidopsis, confers auxin overproduction

We have isolated seven allelic recessive Arabidopsis mutants, designated superroot (sur1-1 to sur1-7), displaying several abnormalities reminiscent of auxin effects. These characteristics include small and epinastic cotyledons, an elongated hypocotyl in which the connection between the stele and cortical and epidermal cells disintegrates, the development of excess adventitious and lateral roots, a reduced number of leaves, and the absence of an inflorescence. When germinated in the dark, sur1 mutants did not develop the apical hook characteristic of etiolated seedlings. We were able to phenocopy the Sur1- phenotype by supplying auxin to wild-type seedlings, to propagate sur1 explants on phytohormone-deficient medium, and to regenerate shoots from these explants by the addition of cytokinins alone to the culture medium. Analysis by gas chromatography coupled to mass spectrometry indicated increased levels of both free and conjugated indole-3-acetic acid. sur1 was crossed to the mutant axr2 and the altered-auxin response mutant ctr1. The phenotype of both double mutants was additive. The sur1 gene was mapped on chromosome 2 at 0.5 centimorgans from the gene encoding phytochrome B.

Superroot, a recessive mutation in Arabidopsis, confers auxin overproduction

We have isolated seven allelic recessive Arabidopsis mutants, designated superroot (sur1-1 to sur1-7), displaying several abnormalities reminiscent of auxin effects. These characteristics include small and epinastic cotyledons, an elongated hypocotyl in which the connection between the stele and cortical and epidermal cells disintegrates, the development of excess adventitious and lateral roots, a reduced number of leaves, and the absence of an inflorescence. When germinated in the dark, sur1 mutants did not develop the apical hook characteristic of etiolated seedlings. We were able to phenocopy the Sur1- phenotype by supplying auxin to wild-type seedlings, to propagate sur1 explants on phytohormone-deficient medium, and to regenerate shoots from these explants by the addition of cytokinins alone to the culture medium. Analysis by gas chromatography coupled to mass spectrometry indicated increased levels of both free and conjugated indole-3-acetic acid. sur1 was crossed to the mutant axr2 and the altered-auxin response mutant ctr1. The phenotype of both double mutants was additive. The sur1 gene was mapped on chromosome 2 at 0.5 centimorgans from the gene encoding phytochrome B.

Structure of phenylalanyl-tRNA synthetase from Thermus thermophilus

The crystal structure of phenylalanyl-tRNA synthetase from Thermus thermophilus, solved at 2.9 A resolution, displays (alpha beta)2 subunit organization. Unexpectedly, both the catalytic alpha- and the non-catalytic beta-subunits comprise the characteristic fold of the class II active-site domains. The alpha beta heterodimer contains most of the building blocks so far identified in the class II synthetases. The presence of an RNA-binding domain, similar to that of the U1A spliceosomal protein, in the beta-subunit is indicative of structural relationships among different families of RNA-binding proteins. The structure suggests a plausible catalytic mechanism which explains why the primary site of tRNA aminoacylation is different from that of the other class II enzymes.

Atomic environment energies in proteins defined from statistics of accessible and contact surface areas

Atomic contact potentials are derived by statistical analysis of atomic surface contact areas versus atom type in a database of non-homologous protein structures. The atomic environment is characterized by the surface area accessible to solvent and the surface of contacts with polar and non-polar atoms. Four types of atoms are considered, namely neutral polar atoms from protein backbones and from protein side-chains, non-polar atoms and charged atoms. Potential energies delta Ej(E) are defined from the preference for an atom of type j to be in a given environment E compared to the expected value if everything was random; Boltzmann's law is then used to transform these preferences into energies. These new potentials very clearly discriminate misfolded from correct structural models. The performance of these potentials are critically assessed by monitoring the recognition of the native fold among a large number of alternative structural folding types (the hide-and-seek procedure), as well as by testing if the native sequence can be recovered from a large number of randomly shuffled sequences for a given 3D fold (a procedure similar to the inverse folding problem). We suggest that these potentials reflect the atomic short range non-local interactions in proteins. To characterise atomic solvation alone, similar potentials were derived as a function of the percentage of solvent-accessible area alone. These energies were found to agree reasonably well with the solvation formalism of Eisenberg and McLachlan.

Aminoacyl-tRNA synthetases

Detailed mechanisms for each step of the reaction catalyzed by both class I and class II aminoacyl-tRNA synthetases have been proposed on the basis of crystallographic data of aminoacyl-tRNA synthetases in complex with their different substrates. Despite the very different topologies of the two classes, there are striking and unanticipated chemical similarities between their active sites and proposed mechanisms.

A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling

A new computational procedure which simultaneously provides gap closure and side-chain positioning in homology modelling is described. It uses a database search scheme to generate fragments to model gaps, a rotamer library to define side-chain conformations, and iteratively refines a conformational matrix CM, such that its elements CM(i,j,o) and CM(i,j,k) give the probabilities that the backbone of residue i adopts the conformation described by fragment j and that its side-chain adopts the conformation of its possible rotamer k. Each residue experiences the average of all possible environments, weighted by their respective probabilities. The method converges, thereby deserving the name of 'self consistent mean field' approach.

Synthesis and recognition of aspartyl-adenylate by Thermus thermophilus aspartyl-tRNA synthetase

The crystal structures of Thermus thermophilus aspartyl-tRNA synthetase and of its complex with ATP, Mg2+ and aspartic acid, show in situ formation of the amino acid adenylate and furnish experimental evidence for the modes of recognition of aspartic acid and ATP. The amino acid fits in a predefined specific site in which it replaces water molecules without significant conformational changes of the binding residues. This mode of selection is reminiscent of the lock and key concept. The pocket is closed by the movement of a histidine side chain from a neighbouring loop acting as a valve. ATP binding is driven by the stacking of the adenine upon the otherwise fixed aromatic ring of the class-II-invariant phenylalanine Phe235. Specific recognition is achieved by interactions with the flexible side chains of other class-II-conserved residues. Conformational changes have been identified which allow the description of a reaction pathway including both lock-and-key and induced-fit interactions. This pathway can presumably be extended to all class II aaRS.

Crystallization and X-ray crystallographic analysis of recombinant chicken poly(ADP-ribose) polymerase catalytic domain produced in Sf9 insect cells

Poly (ADP-ribose) polymerase (PARP) participates in the immediate response in mammalian cells exposed to DNA-damaging agents. Recombinant baculovirus harboring the cDNA of the chicken PARP catalytic domain (40 kDa) have been used to infect Spodoptera frugiperda (Sf9) insect cells. The recombinant polypeptide (30 mg per 1 x 10(9) cells) was purified to homogeneity by 3-aminobenzamide affinity chromatography. The enzymatic properties of the recombinant domain were similar to those of the native fragment. Crystals of the purified recombinant catalytic domain were grown by vapor diffusion. The crystals belong to space group P2(1)2(1)2(1) with unit cell dimensions of a = 59.2 A, b = 65.0 A, c = 96.9 A. They are suitable for X-ray analysis and diffract to 2.0 A.

Polar and nonpolar atomic environments in the protein core: implications for folding and binding

Hydrophobic interactions are believed to play an important role in protein folding and stability. Semi-empirical attempts to estimate these interactions are usually based on a model of solvation, whose contribution to the stability of proteins is assumed to be proportional to the surface area buried upon folding. Here we propose an extension of this idea by defining an environment free energy that characterizes the environment of each atom of the protein, including solvent, polar or nonpolar atoms of the same protein or of another molecule that interacts with the protein. In our model, the difference of this environment free energy between the folded state and the unfolded (extended) state of a protein is shown to be proportional to the area buried by nonpolar atoms upon folding. General properties of this environment free energy are derived from statistical studies on a database of 82 well-refined protein structures. This free energy is shown to be able to discriminate misfolded from correct structural models, to provide an estimate of the stabilization due to oligomerization, and to predict the stability of mutants in which hydrophobic residues have been substituted by site-directed mutagenesis, provided that no large structural modifications occur.

Superficial cells in the early gastrula of Rana pipiens contribute to mesodermal derivatives

We have studied the fate of presumptive mesodermal cells in the early Rana pipiens gastrula. We labeled superficial cells of the early gastrula with 125I. We also labeled all cells in a gastrula with rhodamine-lysine-dextran cell lineage tracer and superficial cells with 125I and then grafted small pieces of the marginal zone orthotopically into unlabeled host embryos. Labeled progeny were identified in sectioned embryos at the tail bud stage. The use of double-labeled grafts allowed us to study the relative contributions by superficial and deep cells to different derivatives. We found that the notochord and somite regions are both derived from the superficial and deep portions of circumblastoporal regions. In contrast, pronephros, lateral plate, cardiac anlagen, and blood cells only arise from deep cells in circumblastoporal regions. Such observations indicate that the fate map for R. pipiens is different from that of Xenopus laevis, where mesodermal derivatives appear to be restricted to the deep layers, and from that of Pleurodeles waltl, where all mesodermal derivatives are formed both from superficial and deep layers. We also have shown that from the neurula stage there is substantial mixing between cells due to the ingression of cells in the dorsal region so that superficial labeled cells, initially located in the roof of the archenteron, contribute to ventral regions of both the somites and notochord.

Crystal structure of a prokaryotic aspartyl tRNA-synthetase

The crystal structure of Thermus thermophilus aspartyl tRNA-synthetase (AspRS) refined at 2.5 A resolution is described. This molecular structure is a textbook illustration of the modular organization of aminoacyl-tRNA synthetases. In addition to the three domains found in yeast AspRS, each monomer exhibits a module specific to prokaryotic enzymes, which corresponds to a helix-turn-helix motif in yeast AspRS, a domain implicated in the stabilization of the complex with tRNA. Its topology matches that of the histidine-containing phosphocarrier HPr which has been linked recently to another group of proteins containing the ferredoxin fold. We propose a more extensive alignment of these folds, which involves a circular permutation of the sequences and changes the point of entry of the whole domain. The C-terminal extension, another prokaryotic characteristic, leads to a significant increase in the network of interaction at the dimer interface. Some potential communication pathways suggest how a transfer of information between the two active sites of the homodimer might occur. Most of the residues involved belong to the class II-specific motifs in correlation with the dimeric state of nearly all class II enzymes. The T. thermophilus enzyme exhibits some features not found in any of the six other known AspRSs from mesophilic organisms.

Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy

Understanding the relations between the conformation of the side-chains and the backbone geometry is crucial for structure prediction as well as for homology modelling. To attempt to unravel these rules, we have developed a method which allows us to predict the position of the side-chains from the co-ordinates of the main-chain atoms. This method is based on a rotamer library and refines iteratively a conformational matrix of the side-chains of a protein, CM, such that its current element at each cycle CM (ij) gives the probability that side-chain i of the protein adopts the conformation of its possible rotamer j. Each residue feels the average of all possible environments, weighted by their respective probabilities. The method converges in only a few cycles, thereby deserving the name of self consistent mean field method. Using the rotamer with the highest probability in the optimized conformational matrix to define the conformation of the side-chain leads to the result that on average 72% of chi 1, 75% of chi 2 and 62% of chi 1 + 2 are correctly predicted for a set of 30 proteins. Tests with six pairs of homologous proteins have shown that the method is quite successful even when the protein backbone deviates from the correct conformation. The second application of the optimized conformational matrix was to provide estimates of the conformational entropy of the side-chains in the folded state of the protein. The relevance of this entropy is discussed.

Rift Valley fever virus L segment: correction of the sequence and possible functional role of newly identified regions conserved in RNA-dependent polymerases

The sequence of Rift Valley fever virus L segment that we published in a previous paper was erroneous in the 3'-terminal region of the antigenomic RNA molecule. Here, we have shown that the L segment is in fact 6404 nucleotides long and encodes a polypeptide of 237.7K in the viral complementary sense. Sequence comparisons performed between the RNA-dependent RNA polymerases of 22 negative-stranded RNA viruses revealed the existence of two novel regions located at the amino termini of the proteins and conserved only in the polymerases of bunya- and arenaviruses. In the region conserved in all RNA-dependent polymerases, corresponding to the so-called 'polymerase module', we identified a new motif, designated premotif A, common to all RNA-dependent polymerases, as well as amino acids located in the region between motifs preA and A which are strictly conserved for segmented negative-stranded RNA viruses. Using the recently released coordinates of human immunodeficiency virus reverse transcriptase and the alignment between all RNA-dependent polymerases in the 'polymerase module', we have determined the position of the conserved residues in these polymerases and discuss their possible functions in light of the available structural information.

The aminoacyl-tRNA synthetase family: modules at work

The combined use of molecular and structural biology techniques has proved very efficient in elucidating structure-function relationships in aminoacyl-tRNA synthetases. Our present understanding of this family of enzymes is based on two main unifying principles: (i) division into two different classes, corresponding to two different modes of ATP binding and attachment of the activated amino acid to the last nucleotide of tRNA (either 2'OH or 3'OH of the ribose) by two different catalytic mechanisms and two structural domains with completely different folding, and (ii) the modular organization into separate and additional domains that we are just beginning to understand. Sequence analysis complements very nicely existing structural, biochemical and genetic results and makes them more general, leading to verifiable predictions.

Crystal structure of cleaved bovine antithrombin III at 3.2 A resolution

The crystal structure of cleaved antithrombin III (ATIII) has been determined to 3.2 A resolution by single isomorphous replacement, real space density modification and phase extension protocols. The heavy-atom sites and the first molecular envelope were determined owing to the molecular replacement solution previously reported and partially refined. Refinement of the two molecules of the asymmetric unit led to a crystallographic R-factor of 0.212 for all reflections between 8.0 and 3.2 A, without inclusion of water molecules. The root-mean-square deviation from ideal values is, respectively, 0.015 A and 3.6 degrees for bond lengths and bond angles. The topology of the molecule closely resembles that of cleaved serpins inhibitors with the two residues forming the reactive bond at opposite ends of the molecule. The most significant difference between ATIII and alpha 1-antitrypsin lies in the 45 residue N-terminal extension in ATIII which contribute to the definition of the heparin binding site. This loop region at the surface of the molecule is held by two disulphide bridges to the protein core and exhibits high temperature factor values. It forms a valley which restrains the possibilities for binding of heparin. Docking of the pentasaccharide unit which represents the minimum fragment of heparin able to bind to ATIII indicates a possible role for arginine 14 in the interaction of heparin and the protein.

Identification of potential active-site residues in the human poly(ADP-ribose) polymerase

The carboxyl-terminal catalytic domain of the human poly(ADP-ribose) polymerase (PARP) exhibits sequence homology with the NAD(P)(+)-dependent leucine and glutamate dehydrogenases. To clarify the role played by some conserved residues between PARP and NAD(P)(+)-dependent dehydrogenases, point mutations were introduced into the whole enzyme context. Non-conservative mutations of Lys-893 (K893I) and Asp-993 (D993A) completely inactivate human PARP, whereas conservative and nonconservative mutations of Asp-914 (D914E and D914A, respectively) and Lys-953 (K953R and K953I, respectively) partially alter PARP activity. The consequences of conservative substitution of Lys-893 and Asp-993 on the kinetic properties of human poly(ADP-ribose) polymerase enzyme and the polymer it synthesizes suggest that these 2 amino acids are directly involved in the covalent attachment of the first ADP-ribosyl residue from NAD+ onto the acceptor amino acid. In addition, the recent resolution of the three-dimensional structure of the NAD(+)-linked glutamate dehydrogenase from Clostridium symbiosum (Baker, P.J., Britton, K.L., Engel, P.C., Farrants, G.W., Lilley, K.S., Rice, D.W., and Stillman, T.J. (1992) Proteins 12, 75-86) strongly supports our alignment with leucine and glutamate dehydrogenases and provides an interesting structural framework for the analysis of our results of site-directed mutagenesis.

Three-dimensional structure of phenylalanyl-transfer RNA synthetase from Thermus thermophilus HB8 at 0.6-nm resolution

The three-dimensional structure of the heterodimeric alpha 2 beta 2 enzyme phenylalanyl-tRNA synthetase from Thermus thermophilus HB8 has been determined by X-ray crystallography, using the multiple-isomorphous-replacement method at 0.6 nm resolution. Trigonal crystals of space group P3(2)21 have cell dimensions a = b = 17.6 nm and c = 14.2 nm. Assuming one heterodimeric molecule/asymmetric unit, the ratio of unit cell volume/molecular mass was V = 0.00244 nm3/Da, which is in the middle of the range normally observed. However, after a rotation-function calculation and measurement of the density of the native crystals, we postulate the existence of only the alpha beta dimer in the asymmetric units. This implies 73% solvent content in the unit cell. Three heavy-atom derivatives [K2PtCl4, KAu(CN)2 and Hg(CH3COO)2] and the solvent-flattening procedure were used for electron-density-map calculations. This map confirmed our hypothesis and revealed a remarkably large space filled by solvent, with alpha beta dimer only in the asymmetric unit. The phenylalanyl-tRNA synthetase from T. thermophilus molecule has a 'quasi-linear' subunit organization. As can be concluded at this level of resolution, there is no contact between small alpha subunits in the functional heterodimer.

A fate map of superficial and deep circumblastoporal cells in the early gastrula of Pleurodeles waltl

We have determined the fate of presumptive mesodermal cells in the early Pleurodeles waltl gastrula. We labeled all cells in a gastrula with RLDx cell lineage tracer and superficial cells with 125I and then grafted small pieces of the marginal zone orthotopically into unlabeled host embryos. Labeled progeny were identified in sectioned embryos at the tail bud stage. The use of double-labeled grafts allowed us to study the relative contributions by superficial and deep cells to different derivatives. We found that the presumptive regions are generally distributed according to classical fate maps for urodeles but that the boundaries between presumptive regions are indistinct, due to extensive intermingling between cells at the edges of grafted regions. We have shown that there is a high dorsal to low ventral gradient of mixing between superficial and deep cells.

The amphibian embryo: an experimental model for the in vivo analysis of interactions between embryonic cells and extracellular matrix molecules

The early amphibian embryo provides an attractive model for the in vivo analysis of cell interactions with extracellular matrix components. During gastrulation, mesodermal cells use an anastomosing network of extracellular fibrils as substratum for their migration. These fibrils contain glycosaminoglycans and non collagenous proteins including laminin and fibronectin. The function of these extracellular components in the mesodermal cell migration process has been inferred from grafting experiments and microinjection of probes such as specific antibodies or GRGDS-containing peptides. Using the amphibian embryo as an experimental system, combination of microsurgical, cell behavioral and molecular approaches will provide new insights into cell-extracellular matrix interactions directing morphogenetic cell movements.

Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs

The aminoacyl-transfer RNA synthetases (aaRS) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology. Out of the 18 known aaRS, only 9 referred to as class I synthetases (GlnRS, TyrRS, MetRS, GluRS, ArgRS, ValRS, IleRS, LeuRS, TrpRS), display two short common consensus sequences ('HIGH' and 'KMSKS') which indicate, as observed in three crystal structures, the presence of a structural domain (the Rossman fold) that binds ATP. We report here the sequence of Escherichia coli ProRS, a dimer of relative molecular mass 127,402, which is homologous to both ThrRS and SerRS. These three latter aaRS share three new sequence motifs with AspRS, AsnRS, LysRS, HisRS and the beta subunit of PheRS. These three motifs (motifs 1, 2 and 3), in a search through the entire data bank, proved to be specific for this set of aaRS (referred to as class II). Class II may also contain AlaRS and GlyRS, because these sequences have a typical motif 3. Surprisingly, this partition of aaRS in two classes is found to be strongly correlated on the functional level with the acylation occurring either on the 2' OH (class I) or 3' OH (class II) of the ribose of the last nucleotide of tRNA.