The 1.8 A crystal structure of winged bean albumin 1, the major albumin from Psophocarpus tetragonolobus (L.) DC

Modeling to Understand Plant Protein Structure-Function Relationships-Implications for Seed Storage Proteins

Proteins are among the most important molecules on Earth. Their structure and aggregation behavior are key to their functionality in living organisms and in protein-rich products. Innovations, such as increased computer size and power, together with novel simulation tools have improved our understanding of protein structure-function relationships. This review focuses on various proteins present in plants and modeling tools that can be applied to better understand protein structures and their relationship to functionality, with particular emphasis on plant storage proteins. Modeling of plant proteins is increasing, but less than 9% of deposits in the Research Collaboratory for Structural Bioinformatics Protein Data Bank come from plant proteins. Although, similar tools are applied as in other proteins, modeling of plant proteins is lagging behind and innovative methods are rarely used. Molecular dynamics and molecular docking are commonly used to evaluate differences in forms or mutants, and the impact on functionality. Modeling tools have also been used to describe the photosynthetic machinery and its electron transfer reactions. Storage proteins, especially in large and intrinsically disordered prolamins and glutelins, have been significantly less well-described using modeling. These proteins aggregate during processing and form large polymers that correlate with functionality. The resulting structure-function relationships are important for processed storage proteins, so modeling and simulation studies, using up-to-date models, algorithms, and computer tools are essential for obtaining a better understanding of these relationships.

Functional genomics studies of Rhipicephalus (Boophilus) annulatus ticks in response to infection with the cattle protozoan parasite, Babesia bigemina

Ticks are obligate haematophagous ectoparasites of wild and domestic animals as well as humans, considered to be second worldwide to mosquitoes as vectors of human diseases, but the most important vectors of disease-causing pathogens in domestic and wild animals. Babesia spp. are tick-borne pathogens that cause a disease called babesiosis in a wide range of animals and in humans. In particular, Babesia bovis and Babesia bigemina are transmitted by cattle ticks, Rhipicephalus (Boophilus) annulatus and Rhipicephalus microplus, which are considered the most important cattle ectoparasites with major economic impacts on cattle production. The objectives of this study were to identify R. annulatus genes differentially expressed in response to infection with B. bigemina. Functional analyses were conducted on selected genes by RNA interference in both R. annulatus and R. microplus ticks. Eight hundred randomly selected suppression-subtractive hybridisation library clones were sequenced and analysed. Molecular function Gene Ontology assignments showed that the obtained tick sequences encoded for proteins with different cellular functions. Differentially expressed genes with putative functions in tick-pathogen interactions were selected for validation of SSH results by real-time reverse transcription-PCR. Genes encoding for TROSPA, calreticulin, ricinusin and serum amyloid A were over-expressed in B. bigemina-infected ticks while Kunitz-type protease inhibitor 5 mRNA levels were down-regulated in infected ticks. Functional analysis of differentially expressed genes by double stranded RNA-mediated RNAi showed that under the conditions of the present study knockdown of TROSPA and serum amyloid A significantly reduced B. bigemina infection levels in R. annulatus while in R. microplus, knockdown of TROSPA, serum amyloid A and calreticulin also reduced pathogen infection levels when compared with controls. Several studies have characterised the tick-pathogen interface at the molecular level. However, to our knowledge this is the first report of functional genomics studies in R. annulatus infected with B. bigemina. The results reported here increase our understanding of the role of tick genes in Babesia infection/multiplication.

Enterolobium contortisiliquum trypsin inhibitor (EcTI), a plant proteinase inhibitor, decreases in vitro cell adhesion and invasion by inhibition of Src protein-focal adhesion kinase (FAK) signaling pathways

Tumor cell invasion is vital for cancer progression and metastasis. Adhesion, migration, and degradation of the extracellular matrix are important events involved in the establishment of cancer cells at a new site, and therefore molecular targets are sought to inhibit such processes. The effect of a plant proteinase inhibitor, Enterolobium contortisiliquum trypsin inhibitor (EcTI), on the adhesion, migration, and invasion of gastric cancer cells was the focus of this study. EcTI showed no effect on the proliferation of gastric cancer cells or fibroblasts but inhibited the adhesion, migration, and cell invasion of gastric cancer cells; however, EcTI had no effect upon the adhesion of fibroblasts. EcTI was shown to decrease the expression and disrupt the cellular organization of molecules involved in the formation and maturation of invadopodia, such as integrin β1, cortactin, neuronal Wiskott-Aldrich syndrome protein, membrane type 1 metalloprotease, and metalloproteinase-2. Moreover, gastric cancer cells treated with EcTI presented a significant decrease in intracellular phosphorylated Src and focal adhesion kinase, integrin-dependent cell signaling components. Together, these results indicate that EcTI inhibits the invasion of gastric cancer cells through alterations in integrin-dependent cell signaling pathways.

The plasticity of the β-trefoil fold constitutes an evolutionary platform for protease inhibition

Proteases carry out a number of crucial functions inside and outside the cell. To protect the cells against the potentially lethal activities of these enzymes, specific inhibitors are produced to tightly regulate the protease activity. Independent reports suggest that the Kunitz-soybean trypsin inhibitor (STI) family has the potential to inhibit proteases with different specificities. In this study, we use a combination of biophysical methods to define the structural basis of the interaction of papaya protease inhibitor (PPI) with serine proteases. We show that PPI is a multiple-headed inhibitor; a single PPI molecule can bind two trypsin units at the same time. Based on sequence and structural analysis, we hypothesize that the inherent plasticity of the β-trefoil fold is paramount in the functional evolution of this family toward multiple protease inhibition.

Evidence that highly conserved residues of Delonix regia trypsin inhibitor are important for activity

Delonix regia trypsin inhibitor (DrTI) consists of a single-polypeptide chain with a molecular mass of 22 kDa and containing two disulfide bonds (Cys44-Cys89 and Cys139-Cys149). Sequence comparison with other plant trypsin inhibitors of the Kunitz family reveals that DrTI contains a negatively charged residue (Glu68) at the reactive site rather than the conserved Arg or Lys found in other Kunitz-type trypsin inhibitors. Site-directed mutagenesis yielded five mutants containing substitutions at the reactive site and at one of the disulfide bonds. Assay of the recombinant proteins showed mutant Glu68Leu and Glu68Lys to have only 4-5% of the wild-type activity. These provide evidence that the Glu68 residue is the reactive site for DrTI and various other Kunitz-type trypsin inhibitors. The Cys139Gly mutant lost its inhibitory activity, whereas the Cys44Gly mutant did not, indicating that the second disulfide bond (Cys139-Cys149) is critical to DrTI inhibitory activity, while the first disulfide bond (Cys44-Cys89) is not required.

Functional analysis of the Kunitz trypsin inhibitor family in poplar reveals biochemical diversity and multiplicity in defense against herbivores

We investigated the functional and biochemical variability of Kunitz trypsin inhibitor (KTI) genes of Populus trichocarpa x Populus deltoides. Phylogenetic analysis, expressed sequence tag databases, and western-blot analysis confirmed that these genes belong to a large and diverse gene family with complex expression patterns. Five wound- and herbivore-induced genes representing the diversity of the KTI gene family were selected for functional analysis and shown to produce active KTI proteins in Escherichia coli. These recombinant KTI proteins were all biochemically distinct and showed clear differences in efficacy against trypsin-, chymotrypsin-, and elastase-type proteases, suggesting functional specialization of different members of this gene family. The in vitro stability of the KTIs in the presence of reducing agents and elevated temperature also varied widely, emphasizing the biochemical differences of these proteins. Significantly, the properties of the recombinant KTI proteins were not predictable from primary amino acid sequence data. Proteases in midgut extracts of Malacosoma disstria, a lepidopteran pest of Populus, were strongly inhibited by at least two of the KTI gene products. This study suggests that the large diversity in the poplar (Populus spp.) KTI family is important for biochemical and functional specialization, which may be important in the maintenance of pest resistance in long-lived plants such as poplar.

Global transcript profiling of potato tuber using LongSAGE

Solanum tuberosum (potato) is the fourth major crop worldwide and is used for food, feed and biotechnological applications. To fully realize the biosynthetic potential for the production of starch, protein and metabolites, we conducted an extensive quantitative profiling of the expressed genes of mature potato tuber. A total of 58,322 serial analysis of gene expression (SAGE) tags of 19 nucleotides (nt), representing 22,233 different tags, were analysed. The 695 tags seen 10 or more times were assigned a tentative function by comparison with homologous genes. The identities of 12 'known' and 12 'unknown' transcripts were confirmed by rapid amplification of cDNA ends (RACE) cloning using the 19 nt tag as a primer. The SAGE and expressed sequence tag (EST) profiles of potato tuber were compared. Transcripts for four types of protease inhibitor, a metallothionein and a lipoxygenase were more prominent than patatin isoforms.

Novel protein from Labramia bojeri A. DC. seeds homologue to Kunitz-type trypsin inhibitor with lectin-like properties

This study starts by isolating and characterizing the first protein from Labramia bojeri seeds, which belong to the Sapotaceae family. The purified lectin analyzed by SDS-PAGE with and without beta-mercaptoethanol shows two protein bands (M(r) = 19 and 20 kDa), which cannot be resolved. Protein bands have shown similar characteristics as molecular masses, determined by gel filtration and native gel; N-terminal sequences presented a difference in their isoelectric points. We have suggested that those protein bands might be variants of the protein named Labramin. The sequence database search has shown that the N-terminal sequence of Labramin presented a high degree of homology to Kunitz-type trypsin inhibitor (82-52%) despite no trypsin inhibition activity detection. The lectin-like form from Labramin was better inhibited by glycoproteins and has also presented growth inhibition of the fungus Colletotrichum lindemuthianum and the yeast Saccharomyces cerevisiae, but it has not presented an apparent effect on Fusarium oxysporum.

Crystal structure of the Kunitz (STI)-type inhibitor from Delonix regia seeds

The three-dimensional structure of a novel Kunitz (STI) family member, an inhibitor purified from Delonix regia seeds (DrTI), was solved by molecular replacement method and refined, respectively, to R(factor) and R(free) values of 21.5% and 25.3% at 1.75A resolution. The structure has a classical beta-trefoil fold, however, differently from canonical Kunitz type (STI) inhibitors, its reactive site loop has an insertion of one residue, Glu68, between the residues P1 and P2. Surprisingly, DrTI is an effective inhibitor of trypsin and human plasma kallikrein, but not of chymotrypsin and tissue kallikrein. Putative structural grounds of such specificity are discussed.

Three-dimensional structure of an unusual Kunitz (STI) type trypsin inhibitor from Copaifera langsdorffii

The crystallographic structure of a novel trypsin inhibitor (CTI) from Copaifera langsdorffii is reported. The structure was solved by MIRAS procedure and refined to a crystallographic residual of 17.3% (R(free) = 20.3%) at 1.8 A resolution. Two isomorphous derivatives were obtained by quick cryo-soaking approach. CTI is the first structure of a member of Kunitz (STI) family formed by two noncovalently bound polypeptide chains and only one disulfide bridge. A standard Kunitz-type inhibitor has a single polypeptide chain and two disulfide bridges. Structural features granting CTI high inhibitory activity are discussed.

Overlapping binding sites for trypsin and papain on a Kunitz-type proteinase inhibitor from Prosopis juliflora

Proteinase inhibitors are among the most promising candidates for expression by transgenic plants and consequent protection against insect predation. However, some insects can respond to the threat of the proteinase inhibitor by the production of enzymes insensitive to inhibition. Inhibitors combining more than one favorable activity are therefore strongly favored. Recently, a known small Kunitz trypsin inhibitor from Prosopis juliflora (PTPKI) has been shown to possess unexpected potent cysteine proteinase inhibitory activity. Here we show, by enzyme assay and gel filtration, that, unlike other Kunitz inhibitors with dual activities, this inhibitor is incapable of simultaneous inhibition of trypsin and papain. These data are most readily interpreted by proposing overlapping binding sites for the two enzymes. Molecular modeling and docking experiments favor an interaction mode in which the same inhibitor loop that interacts in a canonical fashion with trypsin can also bind into the papain catalytic site cleft. Unusual residue substitutions at the proposed interface can explain the relative rarity of twin trypsin/papain inhibition. Other changes seem responsible for the relative low affinity of PTPKI for trypsin. The predicted coincidence of trypsin and papain binding sites, once confirmed, would facilitate the search, by phage display for example, for mutants highly active against both proteinases.

Site-directed mutagenesis evidence for a negatively charged trypsin inhibitory loop in sweet potato sporamin

Sporamin, a sweet potato tuberous storage protein, has trypsin inhibitory activity. Sequence comparison with other plant trypsin inhibitors (TIs) of the Kunitz family reveals that, instead of the conserved Arg or Lys found in other Kunitz TIs, sporamin contains a negatively charged residue (Asp70 or Glu72) at the P1 reactive site. Using site-directed mutagenesis, six mutants were generated containing substitutions at the reactive site and at one of the disulfide bonds, and the recombinant proteins were assayed for TI activity. Mutants Asp70Val and Glu72Arg were found to have only 2-3% of the wild-type activity. These results provide the first evidence for a negatively charged trypsin inhibitory loop and a new mechanism of trypsin inhibition in the Kunitz family.

The role of Asn14 in the stability and conformation of the reactive-site loop of winged bean chymotrypsin inhibitor: crystal structures of two point mutants Asn14-->Lys and Asn14-->Asp

A double-headed chymotrypsin inhibitor, WCI, from winged bean seeds was cloned for structural and biochemical studies. The inhibitor was subjected to two point mutations at a conserved position, Asn14. This residue, known to have a pivotal role in stabilizing the first reactive-site loop (Gln63-Phe68) of the inhibitor, is highly conserved in the sequences of the other members of Kunitz (STI) family as well as in the sequences of Kazal family of serine protease inhibitors. The mutants, N14K and N14D, were subjected to biochemical assay and their characteristics were compared with those of the recombinant inhibitor (rWCI). Crystallographic studies of the recombinant and the mutant proteins are discussed. These studies were primarily aimed at understanding the importance of the protein scaffolding towards the conformational rigidity of the reactive-site loop. Our analysis reveals that, as the Lys14 side chain takes an unusual fold in N14K and the Asp14 side chain in N14D interacts with the loop residues by water-mediated hydrogen bonds, the canonical conformation of the loop has remained effectively intact in both the mutant structures. However, minor alterations such as a 2-fold increase in the inhibitory affinity towards the cognate enzyme were observed.

Refined crystal structure (2.3 A) of a double-headed winged bean alpha-chymotrypsin inhibitor and location of its second reactive site

The crystal structure of a double-headed alpha-chymotrypsin inhibitor, WCI, from winged bean seeds has now been refined at 2.3 A resolution to an R-factor of 18.7% for 9,897 reflections. The crystals belong to the hexagonal space group P6(1)22 with cell parameters a = b = 61.8 A and c = 212.8 A. The final model has a good stereochemistry and a root mean square deviation of 0.011 A and 1.14 degrees from ideality for bond length and bond angles, respectively. A total of 109 ordered solvent molecules were localized in the structure. This improved structure at 2.3 A led to an understanding of the mechanism of inhibition of the protein against alpha-chymotrypsin. An analysis of this higher resolution structure also helped us to predict the location of the second reactive site of the protein, about which no previous biochemical information was available. The inhibitor structure is spherical and has twelve anti-parallel beta-strands with connecting loops arranged in a characteristic beta-trefoil fold common to other homologous serine protease inhibitors in the Kunitz (STI) family as well as to some non homologous functionally unrelated proteins. A wide variation in the surface loop regions is seen in the latter ones.