Determination of a high precision structure of a novel protein, Linum usitatissimum trypsin inhibitor (LUTI), using computer-aided assignment of NOESY cross-peaks

Characterization of a thermostable, protease-tolerant inhibitor of α-glycosidase from carrot: A potential oral additive for treatment of diabetes

Inhibiting α-glucosidase activity is important in controlling postprandial hyperglycemia and, thus, helping to manage type-2 diabetes mellitus (T2DM). In the present study, we purified a hypothetical protein of carrots called DCHP (Daucus Carrot hypoglycemic peptide), and their inhibitory effects on α-glucosidase, as well as related mechanisms, were investigated. The recombinant DCHP protein with a molecular weight of 8 kDa showed strong inhibitory activity against α-glycosidase and maintained good stability in solution. DCHP exhibited no inhibitory activity but was tolerant to trypsin and chymotrypsin. Cellular experiments demonstrated that glucose consumption and lactic acid production increased rapidly when treated with DCHP in Caco-2 and HepG2 cells. DCHP crystal was generated, and the crystal structure, which was similar to that of rBTI and consisted of a central α-helix and a two-stranded β-sheet with a unique loop region. The interaction between DCHP and α-glycosidase was investigated by molecular docking and site-directed mutation, which revealed that Glu43, Pro46, Thr47 Thr48 and Gln49 are the key residues in DCHP that inhibit α-glycosidase activity. This work provides potential bioactive peptides as functional foods or nutraceutical supplements in preventing and managing T2DM.

A Review on Pharmacological and Clinical Aspects of Linum usitatissimum L

INTRODUCTION AND BACKGROUND

Linum usitatissimum L., known as common Flax or linseed, from the family Linnaceae, has long been cultivated in different nations due to its applications in medicine and industry. The present study aims to collect nearly all available information about chemical constituents of Flax, as well as pharmacological properties and confirmed clinical usages of it.

METHODS

We searched through databases such as Scopus and PubMed for relevant literature using the keywords: Linum usitatissimum, pharmacology and phytochemical from the beginning to 13 Aug 2017. Nearly 60 relevant papers, relating to a pharmacological and phytochemical constituent of L. usitatissimum were selected.

RESULTS AND DISCUSSION

According to our researches, various properties were attributed to L. usitatisimum including antioxidant, immunomodulatory, anti-inflammatory, antimicrobial, antiprotozoal, insecticidal, analgesic, anti-hyperlipidemia, anti-hyperglycemic, anti-tumor, wound healing and Feticidal activities. There were also many reports on disease prevention and healing properties of the flax. Diseases like: GI disorders, cardiovascular, urogenital, respiratory diseases and some neurological syndromes were mentioned to be treated by Flax. The application of Flax in drug formulations was also investigated.

CONCLUSION

Despite so much animal studies that have been accomplished, there have not been enough clinical trials done on pharmacological properties of L. usitatissimum. Therefore, this study could be considered as a concise and up to date overview for further facile studies and clinical trials over the valuable plant, L. usitatissimum.

Ethnomedicinal plants used to treat skin diseases by Tharu community of district Udham Singh Nagar, Uttarakhand, India

ETHNOPHARMACOLOGICAL RELEVANCE

Tharu community is the largest primitive indigenous community of the Uttarakhand, India. In this article we have scientifically enumerated medicinal plants and herbal preparations used by the Tharu community to treat various skin diseases, and discussed dermatological properties of these plants in the light of previous ethnomedicinal, microbiological, pharmacological, toxicological, phytochemical and clinical studies.

MATERIALS AND METHODS

Ethnomedicinal survey was conducted in different villages of Tharu community located in district Udham Singh Nagar, Uttarakhand, India. Ethnomedicinal information on plants used to treat various skin diseases was collected from 122 individuals (93 males and 29 females), including 35 experienced herbal practitioners and 87 local villagers. For each of the recorded plant species the use value (UV) and fidelity level (FL) was calculated. The informant consensus factor (Fic) was also calculated to find out the homogeneity in the information given by the informants.

RESULTS

A total of 90 plant species belonging to 86 genera and 48 families were used by the Tharu community to treat various skin diseases viz., wounds (38 spp.), boils (32 spp.), cuts (18 spp.), leprosy (11 spp.), eczema (10 spp.), itching (7 spp.), ringworm (5 spp.), burns (4 spp.), leucoderma (4 spp.), cracked heels (2 spp.), dandruff (3 spp.), body infection (2 spp.), chilblains (2 spp.), hair fall (2 spp.) and toes infection (2 spp.). Information on botanical name, family, vernacular name, ailments treated, mode and dose of herbal preparations, UV and FL values are provided for each of the recorded species. According to UV value most preferred plant species used to treat skin diseases by Tharu community was Ricinus communis L. followed by Tridax procumbens (L.) L., Azadirachta indica A. Juss., Ageratum conyzoides and Allium cepa L.

CONCLUSIONS

The present study has revealed significant information on various medicinal plants used to treat skin diseases by Tharu community. Literature review has confirmed most of the claims made by the Tharu community regarding treatment of various skin diseases by the reported plants. The literature review has also revealed that products from very few of the reported plants are available in market, while most of the reported plants are still under preclinical or clinical trials. There are various known phytochemicals, and antibiotic, antibacterial, antiviral and antifungal agents present in these plants which may be synthesized or transformed to make pharmaceuticals. Some of the reported plants have shown promising results in preclinical trails and there is a need of clinical trials to see their safety and efficacy in treating various skin diseases. These plants may be targeted for development of new medicines, ointments or drugs for the treatment of skin diseases. However further toxicological, preclinical and clinical studies are needed to validate claims about little worked out plant species reported in the present study viz., Sida cordata (Burm. F.) Borss. Waalk., Millettia extensa (Benth.) Baker, Caesulia axillaris Roxb., Ehretia laevis Roxb., Vanda tessellate (Roxb.) Hook. Ex G.Don. and Eualaliopsis binata (Retz.) C.E. Hubb. Further studies on these plants are recommended to assess their potential in development of new skin care products.

X-ray structure analysis and characterization of AFUEI, an elastase inhibitor from Aspergillus fumigatus

Elastase from Aspergillus sp. is an important factor for aspergillosis. AFUEI is an inhibitor of the elastase derived from Aspergillus fumigatus. AFUEI is a member of the I78 inhibitor family and has a high inhibitory activity against elastases of Aspergillus fumigatus and Aspergillus flavus, human neutrophil elastase and bovine chymotrypsin, but does not inhibit bovine trypsin. Here we report the crystal structure of AFUEI in two crystal forms. AFUEI is a wedge-shaped protein composed of an extended loop and a scaffold protein core. The structure of AFUEI shows remarkable similarity to serine protease inhibitors of the potato inhibitor I family, although they are classified into different inhibitor families. A structural comparison with the potato I family inhibitors suggests that the extended loop of AFUEI corresponds to the binding loop of the potato inhibitor I family, and AFUEI inhibits its cognate proteases through the same mechanism as the potato I family inhibitors.

Conformational changes of rBTI from buckwheat upon binding to trypsin: implications for the role of the P(8)' residue in the potato inhibitor I family

BWI-1 (buckwheat trypsin inhibitor), a member of the potato inhibitor I family, suppresses the growth of T-acute lymphoblastic leukemia cells and induces apoptosis in human solid tumor cell lines. Here, we report the crystal structure of rBTI (recombinant buckwheat trypsin inhibitor), a recombinant protein of BWI-1, at 1.84 Å resolution and the structure of rBTI in complex with bovine trypsin at 2.26 Å resolution. A conformational change of Trp53 at the P(8)' position in rBTI was observed upon its binding to trypsin, which is not seen in other members of the potato inhibitor I family reported previously. The role of the P(8)' residue in the potato inhibitor I family was examined by measuring the association and dissociation rates of four rBTI mutants with different substitutions at the P(2) and P(8)' positions when binding to trypsin. One of the mutants, P44T, was found to be a much stronger inhibitor than wild-type rBTI, with a picomolar (pM) dissociation constant. Our results could provide valuable insights for designing a new rBTI-based antitumor drug in the future.

"Fuzzy oil drop" model applied to individual small proteins built of 70 amino acids

The proteins composed of short polypeptides (about 70 amino acid residues) representing the following functional groups (according to PDB notation): growth hormones, serine protease inhibitors, antifreeze proteins, chaperones and proteins of unknown function, were selected for structural and functional analysis. Classification based on the distribution of hydrophobicity in terms of deficiency/excess as the measure of structural and functional specificity is presented. The experimentally observed distribution of hydrophobicity in the protein body is compared to the idealized one expressed by a three-dimensional Gauss function. The differences between these two distributions reveal the specificity of structural/functional characteristics of the protein. The residues of hydrophobicity deficiency versus the idealized distribution are assumed to indicate cavities with the potential to bind ligands, while the residues of hydrophobicity excess are interpreted as potentially participating in protein-protein complexation. The distribution of hydrophobicity irregularity seems to be specific for particular structures and functions of proteins. A comparative analysis of such profiles is carried out to identify the potential biological activity of proteins of unknown function.

LTCI, a novel chymotrypsin inhibitor of the potato I family from the earthworm Lumbricus terrestris. Purification, cDNA cloning, and expression

A novel chymotrypsin inhibitor of the potato I protease inhibitor family from the earthworm Lumbricus terrestris was purified. The inhibitor, named LTCI, was isolated by methanol extraction, affinity chromatography on immobilized methylchymotrypsin, and ion exchange chromatography followed by RP-HPLC. The 7076 Da inhibitor consists of a single polypeptide chain of 64-amino-acid residues without disulfide bridges. LTCI is the first of the potato I protease inhibitors with Tyr in position P1 of the reactive site. cDNA analysis revealed that LTCI is produced as a 86-amino-acid precursor with a 22-amino-acid secretory signal peptide. RT-PCR analysis demonstrates that LTCI mRNA is expressed in body wall, intestine, and coelomocytes. The recombinant LTCI was produced in Escherichia coli as a fusion protein with intein and chitin binding domain using IMPACT-CN system.

CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology

The identification of evolutionarily conserved features of protein structures can provide insights into their functional and structural properties. Three methods have been developed and implemented as WWW tools, CAMPO, SCR_FIND and CHC_FIND, to analyze evolutionarily conserved residues (ECRs), structurally conserved regions (SCRs) and conserved hydrophobic contacts (CHCs) in protein families and superfamilies, on the basis of their 3D structures and the homologous sequences available. The programs identify protein segments that conserve a similar main-chain conformation, compute residue-to-residue hydrophobic contacts involving only apolar atoms common to all the 3D structures analyzed and allow the identification of conserved amino-acid sites among protein structures and their homologous sequences. The programs also allow the visualization of SCRs, CHCs and ECRs directly on the superposed structures and their multiple structural and sequence alignments. Tools and tutorials explaining their usage are available at , and .

The distribution of serine proteinase inhibitors in seeds of the Asteridae

The Asteridae is one of the most successful clades of flowering plants comprising some 80,000 species. Despite this diversity, analysis of seeds from 398 species (representing 8 orders, 32 families and 181 genera) showed just two major types of serine proteinase inhibitors (PI). PIs of the potato inhibitor I family were widely distributed. These had M(r) of 7000-7500 and were inhibitory to subtilisin and one or more other proteinases (but only rarely elastase). The second major group was TI related to the well-characterised Bowman-Birk inhibitors of legume seeds but these varied widely in their sequences and structure. In addition to these two groups of inhibitors, seeds of the Solanaceae also often contained PI of the potato inhibitor II family while some other asterids contained inhibitors whose relationships were not established.

Solution structure of IsTX

The novel sex-specific potassium channel inhibitor IsTX, a 41-residue peptide, was isolated from the venom of male Opisthacanthus madagascariensis. Two-dimensional NMR techniques revealed that the structure of IsTX contains a cysteine-stabilized alpha/beta-fold. IsTX is classified, based on its sequential and structural similarity, in the scorpion short toxin family alpha-KTx6. The alpha-KTx6 family contains a single alpha-helix and two beta-strands connected by four disulfide bridges and binds to voltage-gated K(+) channels and apamin-sensitive Ca(2+)-activated K(+) channels. The three-dimensional structure of IsTX is similar to that of Heterometrus spinifer toxin (HsTX1). HsTX1 blocks the Kv1.3 channel at picomolar concentrations, whereas IsTX has much lower affinities (10 000-fold). To investigate the structure-activity relationship, the geometry of sidechains and electrostatic surface potential maps were compared with HsTX1. As a result of the comparison of the primary structures, Lys27 of IsTX was conserved at the same position in HsTX1. The analogous Lys23 of HsTX1, the most critical residue for binding to potassium channels, binds to the channel pore. However, IsTX has fewer basic residues to interact with acidic channel surfaces than HsTX1. MALDI-TOF MS analysis clearly indicated that IsTX was found in male scorpion venom, but not in female. This is the first report that scorpion venom contains sex-specific compounds.

NMR structures of two variants of bovine pancreatic trypsin inhibitor (BPTI) reveal unexpected influence of mutations on protein structure and stability

Here we determined NMR solution structures of two mutants of bovine pancreatic trypsin inhibitor (BPTI) to reveal structural reasons of their decreased thermodynamic stability. A point mutation, A16V, in the solvent-exposed loop destabilizes the protein by 20 degrees C, in contrast to marginal destabilization observed for G, S, R, L or W mutants. In the second mutant introduction of eight alanine residues at proteinase-contacting sites (residues 11, 13, 17, 18, 19, 34, 37 and 39) provides a protein that denatures at a temperature about 30 degrees C higher than expected from additive behavior of individual mutations. In order to efficiently determine structures of these variants, we applied a procedure that allows us to share data between regions unaffected by mutation(s). NOAH/DYANA and CNS programs were used for a rapid assignment of NOESY cross-peaks, structure calculations and refinement. The solution structure of the A16V mutant reveals no conformational change within the molecule, but shows close contacts between V16, I18 and G36/G37. Thus, the observed 4.3kcal/mol decrease of stability results from a strained local conformation of these residues caused by introduction of a beta-branched Val side-chain. Contrary to the A16V mutation, introduction of eight alanine residues produces significant conformational changes, manifested in over a 9A shift of the Y35 side-chain. This structural rearrangement provides about 6kcal/mol non-additive stabilization energy, compared to the mutant in which G37 and R39 are not mutated to alanine residues.

Hydrogen bonds in human ubiquitin reflected in temperature coefficients of amide protons

Analysis of amide proton temperature coefficients (deltasigma(HN)/DeltaT) in human ubiquitin shows their usefulness in indicating hydrogen bonds. The availability of a very accurate solution structure of ubiquitin enables the precise determination of hydrogen bonds and increases the reliability of the analysis of chemical shift temperature gradients. Values of deltasigma(HN)/DeltaT more positive than -4.6 ppb/K are very good indicators of hydrogen bonds. Additionally, a weak temperature dependence of non-hydrogen-bonded amides was observed for amide protons that are significantly shifted upfield. We observed that temperature gradients of amide protons involved in short hydrogen bonds are related to donor-acceptor distances.

Correlation of binding-loop internal dynamics with stability and function in potato I inhibitor family: relative contributions of Arg(50) and Arg(52) in Cucurbita maxima trypsin inhibitor-V as studied by site-directed mutagenesis and NMR spectroscopy

The side chains of Arg(50) and Arg(52) at positions P(6)' and P(8)', respectively, anchor the binding loop to the protein scaffold by means of hydrogen bonds in Cucurbita maxima trypsin inhibitor-V (CMTI-V), a potato I family member. Here, we have investigated the relative contributions of Arg(50) and Arg(52) to the binding-loop flexibility and stability by determining changes in structure, dynamics, and proteolytic stability as a consequence of individually mutating them into an alanine. We have compared chemical shift assignments of main-chain hydrogens and nitrogens, and (1)H-(1)H interresidue nuclear Overhauser effects (NOEs) for the two mutants with those of the wild-type protein. We have also measured NMR longitudinal and transverse relaxation rates and (15)N-(1)H NOE enhancements for all backbone and side-chain NH groups and calculated the model-free parameters for R50A-rCMTI-V and R52A-rCMTI-V. The three-dimensional structures and backbone dynamics of the protein scaffold region remain very similar for both mutants, relative to the wild-type protein. The flexibility of the binding loop is increased in both R50A- and R52A-rCMTI-V. In R52A-rCMTI-V, the mean generalized order parameter (<S(2)>) of the P(6)-P(1) residues of the binding loop (39-44) decreases to 0.68 +/- 0.02 from 0.76 +/- 0.04 observed for the wild-type protein. However, in R50A-rCMTI-V, the flexibility of the whole binding loop increases, especially that of the P(1)'-P(3)' residues (45-47), whose <S(2)> value drops dramatically to 0.35 +/- 0.03 from 0.68 +/- 0.03 determined for rCMTI-V. More strikingly, S(2) values of side-chain N epsilon Hs reveal that, in the R50A mutant, removal of the R50 hydrogen bond results in the loss of the R52 hydrogen bond too, whereas in R52A, the R50 hydrogen bond remains unaffected. Kinetic data on trypsin-catalyzed hydrolysis of the reactive-site peptide bond (P(1)-P(1)') suggest that the activation free energy barrier of the reaction at 25 degrees C is reduced by 2.1 kcal/mol for R50A-rCMTI-V and by 1.5 kcal/mol for R52A-rCMTI-V, relative to rCMTI-V. Collectively, the results suggest that although both the P(6') and P(8)' anchors are required for optimal inhibitor function and stability in the potato I family, the former is essential for the existence of the latter and has greater influence on the binding-loop structure, dynamics, and stability.

Isolation and amino acid sequence of a serine proteinase inhibitor from common flax (Linum usitatissimum) seeds

LUTI (Linum usitatissimum trypsin inhibitor), a member of the potato inhibitor I family, has been isolated from seeds of flax by ethanol fractionation, ion exchange chromatography on CM-Sephadex C-25, affinity purification on immobilized methylchymotrypsin (alpha-chymotrypsin in which His57 has been converted to 3-methylhistidine) in the presence of 5M NaCl, and finally by reversed-phase HPLC. The 7655 Da inhibitor consists of a single polypeptide chain of 69 residues with one disulfide bridge. The molecule is acetylated at the N terminus. Its primary structure has been determined after limited proteolysis of the native molecule with trypsin at the reactive site, cleavage with cyanogen bromide or arginyl endopeptidase (Arg-gingipain), and alcoholytic deacetylation of the N-terminally blocked serine. The association constants (K(a)) of LUTI with bovine beta-trypsin and alpha-chymotrypsin are 3.58x10(10) M(-1) and 5.02x10(5) M(-1), respectively. High NaCl concentration (3M) increased the association constant of LUTI with alpha-chymotrypsin to 6.64x10(7) M(-1). To our knowledge, LUTI is the first serine-proteinase-type inhibitor isolated from a plant of the Linaceae family.