Characterization of SP1, a stress-responsive,boiling-soluble,homo-oligomeric protein from aspen

In flowering plants, the vegetative nucleus and the two sperm cells are proposed to form a functional assemblage, the male germ unit (MGU). Here, we describe the developmental pathway of MGU assembly in Arabidopsis and report two classes of mutations that affect the integrity and/or the positioning of the MGU in the mature pollen grain. In germ unit malformed (gum) mutants, the vegetative nucleus is positioned adjacent to the pollen grain wall, separate from the two sperm cells, whereas in MGU displaced (mud) mutants, the intact MGU is displaced to the pollen grain wall. mud and gum mutants correspond to male-specific gametophytic mutations that also reduce pollen fitness. Genetic mapping showed that the gum1 and gum2 mutations are genetically linked, possibly allelic, whereas the mud1 and mud2 mutations correspond to two unlinked loci mapping on different chromosomes. The hierarchical relationship between mud and gum mutations was investigated by phenotypic analysis of double mutants. gum1 appeared to act earlier than mud1 and mud2, affecting initial MGU assembly and its stability during pollen maturation. In contrast, mud1 and mud2 mutations appear to act only on MGU positioning during final maturation. From in planta analyses of pollen germination in mud and gum mutants, we conclude that the initial proximity and positioning of MGU components is not required for their entrance into the pollen tube, but the efficiency of MGU translocation is reduced.     

Structural adaptation of a thermostable biotin-binding protein in a psychrophilic environment

Shwanavidin is an avidin-like protein from the marine proteobactrium Shewanella denitrificans, which exhibits an innate dimeric structure while maintaining high affinity toward biotin. A unique residue (Phe-43) from the L3,4 loop and a distinctive disulfide bridge were shown to account for the high affinity toward biotin. Phe-43 emulates the function and position of the critical intermonomeric Trp that characterizes the tetrameric avidins but is lacking in shwanavidin. The 18 copies of the apo-monomer revealed distinctive snapshots of L3,4 and Phe-43, providing rare insight into loop flexibility, binding site accessibility, and psychrophilic adaptation. Nevertheless, as in all avidins, shwanavidin also displays high thermostability properties. The unique features of shwanavidin may provide a platform for the design of a long sought after monovalent form of avidin, which would be ideal for novel types of biotechnological application.     

Structural modeling and characterization of a thermostable lipase from Bacillus stearothermophilus P1

The moderate thermophilic bacterium Bacillus stearothermophilus P1 expresses a thermostable lipase that was active and stable at the high temperature. Based on secondary structure predictions and secondary structure-driven multiple sequence alignment with the homologous lipases of known three-dimensional (3-D) structure, we constructed the 3-D structure model of this enzyme and the model reveals the topological organization of the fold, corroborating our predictions. We hypothesized for this enzyme the alpha/beta-hydrolase fold typical of several lipases and identified Ser-113, Asp-317, and His-358 as the putative members of the catalytic triad that are located close to each other at hydrogen bond distances. In addition, the strongly inhibited enzyme by 10 mM PMSF and 1-hexadecanesulfonyl chloride was indicated that it contains a serine residue which plays a key role in the catalytic mechanism. It was also confirmed by site-directed mutagenesis that mutated Ser-113, Asp-317, and His-358 to Ala and the activity of the mutant enzyme was drastically reduced.     

Structural features and functional domains of amassin-1, a cell-binding olfactomedin protein.

Amassin-1 mediates a rapid cell adhesion that tightly adheres sea urchin coelomocytes (body cavity immunocytes) together. Three major structural regions exist in amassin-1: a short beta region, 3 coiled coils, and an olfactomedin domain. Amassin-1 contains 8 disulfide-bonded cysteines that, upon reduction, render it inactive. Truncated forms of recombinant amassin-1 were expressed and purified from Pichia pastoris and their disulfide bonding and biological activities investigated. Expressed alone, the olfactomedin domain contained 2 intramolecular disulfide bonds, existed in a monomeric state, and inhibited amassin-1-mediated clotting of coelomocytes by a calcium-dependent cell-binding activity. The N-terminal beta region, containing 3 cysteines, was not required for clotting activity. The coiled coils may dimerize amassin-1 in a parallel orientation through a homodimerizing disulfide bond. Neither amassin-1 fragments that were disulfide-linked as dimers or that were engineered to exist as dimers induced coelomocytes clotting. Clotting required higher multimeric states of amassin-1, possibly tetramers, which occurred through the N-terminal beta region and (or) the first segment of coiled coils.     

Homology model of a novel thermostable xylanase from Bacillus subtilis-AK1

Xylanases are glycosyl hydrolases that catalyze the hydrolysis of internal beta-1,4 glycosidic bonds of xylan, the major hemi-cellulose component of the plant cell wall. Enzymes such as xylanases are used considerably in industries. Their industrial usage is especially attractive since they can replace some of the environmental pollutants. We have earlier isolated a family 11-xylanase gene from Bacillus subtilis-AK1, which is active at high temperature as well as at alkaline pH. In order to understand the factors liable for the adaptation of this enzyme, three dimensional model of B. subtilis-AK1 xylanase has now been obtained by homology modeling. Modeling was carried out using Molecular Operating Environment (MOE) software developed by Chemical Computing Group Inc., running on Pentium IV workstation. The model showed that B. subtilis-AK1 xylanase having molecular weight around 20 kDa contains in its fold an alpha-helix and two beta-sheets packed against each other forming a beta-sandwich. The conserved active site amino acids E78R, Y80L were mutated in this novel B. subtilis-AK1 strain, but the protein folding and the function was maintained with high thermal stability. Several minor modifications appeared to be responsible for the increased thermo stability of AK1. Docking studies of the substrate xylan with -AK1 shows the possibility of the Arg 78 acting as the nucleophile instead of Glu 78.     

Structural features of the maize sus1 gene and protein.

Genomic clones, cDNA clones, and protein of the maize (Zea mays L.) Suc synthase1 (sus1) gene were isolated and sequenced. Termini (5' and 3') of the transcribed unit were identified. The SUS1 protein was purified from tissue culture cells as a phosphorylated protein. The overall structure of sus1 is virtually identical with that of the paralogous gene, shrunken1 (sh1); however, the last intron of sh1 is missing in sus1. This intron bears much sequence similarity with the adjacent exon, suggesting that the intron arose from an internal duplication. Although the placement of the other 14 introns is identical in both genes, the introns exhibit markedly greater differences in size and sequence relative to that shown by the exons. An explanation for the differential rate of divergence of exons and introns is selection pressure for gene function. Additionally, comparisons of coding regions of plant sucrose synthases show that sh1-like and sus1-like genes can be found in all monocots so far analyzed. These latter observations point to an important role played by both genes in this group of plants.     

Structural basis for the selective inhibition of JNK1 by the scaffolding protein JIP1 and SP600125

The c-jun N-terminal kinase (JNK) signaling pathway is regulated by JNK-interacting protein-1 (JIP1), which is a scaffolding protein assembling the components of the JNK cascade. Overexpression of JIP1 deactivates the JNK pathway selectively by cytoplasmic retention of JNK and thereby inhibits gene expression mediated by JNK, which occurs in the nucleus. Here, we report the crystal structure of human JNK1 complexed with pepJIP1, the peptide fragment of JIP1, revealing its selectivity for JNK1 over other MAPKs and the allosteric inhibition mechanism. The van der Waals contacts by the three residues (Pro157, Leu160, and Leu162) of pepJIP1 and the hydrogen bonding between Glu329 of JNK1 and Arg156 of pepJIP1 are critical for the selective binding. Binding of the peptide also induces a hinge motion between the N- and C-terminal domains of JNK1 and distorts the ATP-binding cleft, reducing the affinity of the kinase for ATP. In addition, we also determined the ternary complex structure of pepJIP1-bound JNK1 complexed with SP600125, an ATP-competitive inhibitor of JNK, providing the basis for the JNK specificity of the compound.     

Structural characteristics of thermostable immunogenic outer membrane protein from Salmonella enterica serovar Typhi

In this work, we explored the acid-induced unfolding pathway of non-porin outer membrane protein (OMP), an immunogenic protein from Salmonella Typhi, by monitoring the conformational changes over a pH range of 1.0–7.0 by circular dichroism, intrinsic fluorescence, ANS binding, acrylamide quenching, and dynamic light scattering. The spectroscopic measurements showed that OMP in its native state at pH 7.0 exists in more stable and compact conformation. In contrast, at pH 2.0, OMP retains substantial amount of secondary structure, disrupted side chain interactions, increased hydrodynamic radii, and nearly four-fold increase in ANS fluorescence with respect to the native state, indicating that MG state exists at pH 2.0. Quenching of tryptophan fluorescence by acrylamide further confirmed the accumulation of a partially unfolded state between native and unfolded state. The effect of pH on the conformation and thermostability of OMP points towards its heat resistance at neutral pH (T _m?~?69 °C at pH 7.0, monitored by change in MRE_{222 nm}). Acid unfolded state was also characterized by the lack of a cooperative thermal transition. All these results suggested that acid-induced unfolded state of OMP at pH 2.0 represented the molten globule state. The chemical denaturation studies with GuHCl and urea as denaturants showed dissimilar results. The chemical unfolding experiments showed that in both far-UV CD and fluorescence measurements, GuHCl is more efficient than urea. GuHCl is characterized by low C _m (~1 M), while urea is characterized by high C _m (~3 M). The fully unfolded states were reached at 2 M GuHCl and 4 M urea concentration, respectively. This study adds to several key considerations of importance in the development of therapeutic agents against typhoid fever for clinical purposes.     

A new thermostable proteinase from Thermoactinomyces SP.27a. Cloning and gene expression

A library of Thermoactinomyces sp. 27a, producer of thermostable proteases of different groups, has been created. Gene coding for thermostable neutral proteinase was cloned and expressed in Bac. subtilis cells. Restriction map for cloned DNA fragment was created and physicochemical parameters of recombinant proteinase were characterized. The thermostability and optimum of proteolytic activity of the enzyme was lower than in the natural Thermoactinomyces sp. strain, which can be due to heterologous expression of the gene coding for thermostable protein in the mesophilic host.     

Proteolysis of abnormal prion protein with a thermostable protease from Thermococcus kodakarensis KOD1

The abnormal prion protein (scrapie-associated prion protein, PrP^Sc) is considered to be included in the group of infectious agents of transmissible spongiform encephalopathies. Since PrP^Sc is highly resistant to normal sterilization procedures, the decontamination of PrP^Sc is a significant public health issue. In the present study, a hyperthermostable protease, Tk-subtilisin, was used to degrade PrP^Sc. Although PrP^Sc is known to be resistant toward proteolytic enzymes, Tk-subtilisin was able to degrade PrP^Sc under extreme conditions. The level of PrP^Sc in brain homogenates was found to decrease significantly in vitro following Tk-subtilisin treatment at 100 °C, whereas some protease-resistant fractions remain after proteinase K treatment. Rather small amounts of Tk-subtilisin (0.3 U) were required to degrade PrP^Sc at 100 °C and pH 8.0. In addition, Tk-subtilisin was observed to degrade PrP^Sc in the presence of sodium dodecyl sulfate or other industrial surfactants. Although several proteases degrading PrP^Sc have been reported, practical decontamination procedures using enzymes are not available. This report aims to provide basic information for the practical use of a proteolytic enzyme for PrP^Sc degradation.     

Structural features of the C-terminus from the human neurokinin-1 receptor

The neurokinin-1 receptor (NK1R) is a G-protein coupled receptor found in the central and peripheral nervous systems of vertebrates, and is responsible for many physiological processes. The C-terminus domain seems to be essential for coupling to the corresponding G-protein and β-arrestin, and is important for receptor desensitization, internalization and recycling. We have focused our study on expression of the human NK1R (hNK1R) C-terminus in Escherichia coli, and its purification and characterization, in order to elucidate its structural properties. CD and Fourier transform infrared spectroscopy showed that the hNK1R C-terminus, rather than having a random structure, has well-defined secondary-structure patterns. The presence of three tyrosine residues in the primary sequence of the hNK1R C-terminus facilitated the use of UV and fluorescence spectroscopy techniques which revealed tyrosine fluorescence and UV absorption at anomalous wavelengths. In their entirety, the results show that the hNK1R C-terminus has clearly defined secondary (25% α-helix, 27% unordered structure and 48% β-sheets and β-turns) and tertiary structures which, it is believed, are tightly related to its multiple functions.     

Structural insight into the ligand specificity of a thermostable family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum

The digestion of the plant cell wall requires the concerted action of a diverse repertoire of enzyme activities. An important component of these hydrolase consortia are arabinofuranosidases, which release L-arabinofuranose moieties from a range of plant structural polysaccharides. The anaerobic bacterium Clostridium thermocellum, a highly efficient plant cell wall degrader, possesses a single alpha-L-arabinofuranosidase (EC 3.2.1.55), CtAraf51A, located in GH51 (glycoside hydrolase family 51). The crystal structure of the enzyme has been solved in native form and in 'Michaelis' complexes with both alpha-1,5-linked arabinotriose and alpha-1,3 arabinoxylobiose, both forming a hexamer in the asymmetric unit. Kinetic studies reveal that CtAraf51A, in contrast with well-characterized GH51 enzymes including the Cellvibrio japonicus enzyme [Beylot, McKie, Voragen, Doeswijk-Voragen and Gilbert (2001) Biochem. J. 358, 607-614], catalyses the hydrolysis of alpha-1,5-linked arabino-oligosaccharides and the alpha-1,3 arabinosyl side chain decorations of xylan with equal efficiency. The paucity of direct hydrogen bonds with the aglycone moiety and the flexible conformation adopted by Trp(178), which stacks against the sugar at the +1 subsite, provide a structural explanation for the plasticity in substrate specificity displayed by the clostridial arabinofuranosidase.     

Structural model of a complex between the heterotrimeric G protein, Gsalpha, and tubulin

A number of studies have demonstrated interplay between the cytoskeleton and G protein signaling. Many of these studies have determined a specific interaction between tubulin, the building block of microtubules, and G proteins. The alpha subunits of some heterotrimeric G proteins, including Gsalpha, have been shown to interact strongly with tubulin. Binding of Galpha to tubulin results in increased dynamicity of microtubules due to activation of GTPase of tubulin. Tubulin also activates Gsalpha via a direct transfer of GTP between these molecules. Structural insight into the interaction between tubulin and Gsalpha was required, and was determined, in this report, through biochemical and molecular docking techniques. Solid phase peptide arrays suggested that a portion of the amino terminus, alpha2-beta4 (the region between switch II and switch III) and alpha3-beta5 (just distal to the switch III region) domains of Gsalpha are important for interaction with tubulin. Molecular docking studies revealed the best-fit models based on the biochemical data, showing an interface between the two molecules that includes the adenylyl cyclase/Gbetagamma interaction regions of Gsalpha and the exchangeable nucleotide-binding site of tubulin. These structural models explain the ability of tubulin to facilitate GTP exchange on Galpha and the ability of Galpha to activate tubulin GTPase.     

Structural features of protein folding nuclei

A crucial event of protein folding is the formation of a folding nucleus. We demonstrate the presence of a considerable coincidence between the location of folding nuclei and the location of so-called "root structural motifs", which have unique overall folds and handedness. In the case of proteins with a single root structural motif, the involvement in the formation of a folding nucleus is in average significantly higher for amino acids residues that are in root structural motifs, compared to residues in other parts of the protein. The tests carried out revealed that the observed difference is statistically reliable. Thus, a structural feature that corresponds to the protein folding nucleus is now found.     

Isolation, purification, and characterization of a thermostable xylanase from a novel strain, Paenibacillus campinasensis G1-1

High levels of xylanase activity (143.98 IU/ml) produced by the newly isolated Paenibacillus campinasensis G1-1 were detected when it was cultivated in a synthetic medium. A thermostable xylanase, designated XynG1-1, from P. campinasensis G1-1 was purified to homogeneity by Octyl-Sepharose hydrophobic-interaction chromatography, Sephadex G75 gel-filter chromatography, and Q-Sepharose ion-exchange chromatography, consecutively. By multistep purification, the specific activity of XynG1-1 was up to 1,865.5 IU/mg with a 9.1-fold purification. The molecular mass of purified XynG1-1 was about 41.3 kDa as estimated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Sequence analysis revealed that XynG1-1 containing 377 amino acids encoded by 1,134 bp genomic sequences of P. campinasensis G1-1 shared 96% homology with XylX from Paenibacillus campinasensis BL11 and 77%~78% homology with xylanases from Bacillus sp. YA- 335 and Bacillus sp. 41M-1, respectively. The activity of XynG1-1 was stimulated by Ca2+, Ba2+, DTT, and beta- mercaptoethanol, but was inhibited by Ni2+, Fe2+, Fe3+, Zn2+, SDS, and EDTA. The purified XynG1-1 displayed a greater affinity for birchwood xylan, with an optimal temperature of 60 degrees C and an optimal pH of 7.5. The fact that XynG1-1 is cellulose-free, thermostable (stability at high temperature of 70 degrees C~80 degrees C), and active over a wide pH range (pH 5.0~9.0) suggests that the enzyme is potentially valuable for various industrial applications, especially for pulp bleaching pretreatment.     

Structural features of the sulphated polysaccharide from a green seaweed,Caulerpa taxifolia

A sulphated heteropolysaccharide was isolated from a green seaweed, Caulerpa taxifolia, by extraction with acid and purified via its copper complex. Methylation analysis of both the sulphated and desulphated polysaccharides revealed the presence of 1,4-linked xylose, 1,6-linked galactose, 1,4,6-linked mannose and non-reducing galactose end group units which are all devoid of sulphate groups. In addition 1,4-linked galactose units sulphated at C-3 are also present. Quantitative periodate oxidation showed a consumption of 1.30 and 1.60 moles of oxidant per anhydrosugar unit in the sulphated and desulphated polysaccharides respectively. The oxo-polysaccharides after reduction and hydrolysis revealed the presence of glycerol, erythritol and unoxidized galactose in the mol ratio 11.6:5.1:4.9 and 11.2:5.0:1.0 respectively, besides threitol (3.9 mol) in the desulphated polysaccharide.     

Structural and functional studies on a thermostable polyethylene terephthalate degrading hydrolase from Thermobifida fusca

Bacterial cutinases are promising catalysts for the modification and degradation of the widely used plastic polyethylene terephthalate (PET). The improvement of the enzyme for industrial purposes is limited due to the lack of structural information for cutinases of bacterial origin. We have crystallized and structurally characterized a cutinase from Thermobifida fusca KW3 (TfCut2) in free as well as in inhibitor-bound form. Together with our analysis of the thermal stability and modelling studies, we suggest possible reasons for the outstanding thermostability in comparison to the less thermostable homolog from Thermobifida alba AHK119 and propose a model for the binding of the enzyme towards its polymeric substrate. The TfCut2 structure is the basis for the rational design of catalytically more efficient enzyme variants for the hydrolysis of PET and other synthetic polyesters.     

Structural features and chaperone activity of the NudC protein family

The NudC family consists of four conserved proteins with representatives in all eukaryotes. The archetypal nudC gene from Aspergillus nidulans is a member of the nud gene family that is involved in the maintenance of nuclear migration. This family also includes nudF, whose human orthologue, Lis1, codes for a protein essential for brain cortex development. Three paralogues of NudC are known in vertebrates: NudC, NudC-like (NudCL), and NudC-like 2 (NudCL2). The fourth distantly related member of the family, CML66, contains a NudC-like domain. The three principal NudC proteins have no catalytic activity but appear to play as yet poorly defined roles in proliferating and dividing cells. We present crystallographic and NMR studies of the human NudC protein and discuss the results in the context of structures recently deposited by structural genomics centers (i.e., NudCL and mouse NudCL2). All proteins share the same core CS domain characteristic of proteins acting either as cochaperones of Hsp90 or as independent small heat shock proteins. However, while NudC and NudCL dimerize via an N-terminally located coiled coil, the smaller NudCL2 lacks this motif and instead dimerizes as a result of unique domain swapping. We show that NudC and NudCL, but not NudCL2, inhibit the aggregation of several target proteins, consistent with an Hsp90-independent heat shock protein function. Importantly, and in contrast to several previous reports, none of the three proteins is able to form binary complexes with Lis1. The availability of structural information will be of help in further studies on the cellular functions of the NudC family.     

Cloning, purification and characterization of a thermostable carboxylesterase from Anoxybacillus sp. PDF1

The gene encoding a carboxylesterase from Anoxybacillus sp., PDF1, was cloned and sequenced. The recombinant protein was expressed in Escherichia coli BL21, under the control of isopropyl-β-D-thiogalactopyranoside-inducible T7 promoter. The enzyme, designated as PDF1Est, was purified by heat shock and ion-exchange column chromatography. The molecular mass of the native protein, as determined by SDS-PAGE, was about 26 kDa. PDF1Est was active under a broad pH range (pH 5.0-10.0) and a broad temperature range (25-90 °C), and it had an optimum pH of 8.0 and an optimum temperature of 60 °C. The enzyme was thermostable carboxylesterase, and did not lose any activity after 30 min of incubation at 60 °C. The enzyme exhibited a high level of activity with p-nitrophenyl butyrate with apparent K(m), V(max), and K(cat) values of 0.348 ± 0.030 mM, 3725.8 U/mg, and 1500 ± 54.50/s, respectively. The effect of some chemicals on the esterase activity indicated that Anoxybacillus sp. PDF1 produce an carboxylesterase having serine residue in active site and -SH groups in specific sites, which are required for its activity.     

Design of a thermostable cell adhesion protein

The design principle of a thermostable functional protein has been proposed by demonstrating genetic engineering synthesis of a thermostable cell adhesion protein. The cell adhesive peptide sequence, Arg-Gly-Asp (RGD), was incorporated into the elastin-based polyhexapeptide, whose repeating unit is Ala-Pro-Gly-Val-Gly-Val (APGVGV). The resulting protein possesses cell adhesion activity approximately 80% of fibronectin. After autoclaving at 120°C for 20 min, the protein retained over 90% of cell adhesion activity, while the activity of autoclaved fibronectin decreased to 50%.