Crystal structure of barley limit dextrinase-limit dextrinase inhibitor (LD-LDI) complex reveals insights into mechanism and diversity of cereal type inhibitors

Impacts of Sourdough Technology on the Availability of Celiac Peptides from Wheat α- and γ-Gliadins: In Silico Approach

Celiac peptide-generating α- and γ-gliadins consist of a disordered N-terminal domain extended by an α-helical-folded C-terminal domain. Celiac peptides, primarily located along the disordered part of α- and γ-gliadin molecules, are nicely exposed and directly accessible to proteolytic enzymes occurring in the gastric (pepsin) and intestinal (trypsin, chymotrypsin) fluids. More than half of the potential celiac peptides identified so far in gliadins exhibit cleavage sites for pepsin. However, celiac peptides proteolytically truncated by one or two amino acid residues could apparently retain some activity toward HLA-DQ2 and HLA-DQ8 receptors in docking experiments. Together with the uncleaved peptides, these still active partially degraded CD peptides account for the incapacity of the digestion process to inactivate CD peptides from gluten proteins. In contrast, sourdough fermentation processes involve other proteolytic enzymes susceptible to the deep degradation of celiac peptides. In particular, sourdough supplemented by fungal prolyl endoproteases enhances the degrading capacities of the sourdough fermentation process toward celiac peptides. Nevertheless, since tiny amounts of celiac peptides sufficient to trigger deleterious effects on CD people can persist in sourdough-treated bread and food products, it is advisable to avoid consumption of sourdough-treated food products for people suffering from celiac disease. As an alternative, applying the supplemented sourdough process to genetically modified low gluten or celiac-safe wheat lines should result in food products that are safer for susceptible and CD people.

Structure, Function and Protein Engineering of Cereal-Type Inhibitors Acting on Amylolytic Enzymes

Numerous plants, including cereals, contain seed proteins able to inhibit amylolytic enzymes. Some of these inhibitors, the CM-proteins (soluble in chloroform:methanol mixtures)—also referred to as cereal-type inhibitors (CTIs)—are the topic of this review. CM-proteins were first reported 75 years ago. They are small sulfur-rich proteins of the prolamine superfamily embracing bifunctional α-amylase/trypsin inhibitors (ATIs), α-amylase inhibitors (AIs), limit dextrinase inhibitors (LDIs), and serine protease inhibitors. Phylogenetically CM-proteins are predicted across poaceae genomes and many isoforms are identified in seed proteomes. Their allergenicity and hence adverse effect on humans were recognized early on, as were their roles in plant defense. Generally, CTIs target exogenous digestive enzymes from insects and mammals. Notably, by contrast LDI regulates activity of the endogenous starch debranching enzyme, limit dextrinase, during cereal seed germination. CM-proteins are four-helix bundle proteins and form enzyme complexes adopting extraordinarily versatile binding modes involving the N-terminal and different loop regions. A number of these inhibitors have been characterized in detail and here focus will be on target enzyme specificity, molecular recognition, forces and mechanisms of binding as well as on three-dimensional structures of CM-protein–enzyme complexes. Lastly, prospects for CM-protein exploitation, rational engineering and biotechnological applications will be discussed.

Interplay of starch debranching enzyme and its inhibitor is mediated by Redox-Activated SPL transcription factor

•

We have first time described that pullulanase inhibitor is under control of SPL transcriptional factor in barley.

•

SPL3 mediated transcriptional regulation of pullulanase inhibitor is redox-dependent.

•

Antagonistic relationship between pullulanase and its inhibitors is epigenetically guided via miR156 targeted SPL3.

The germination process is of central importance across the cultivated species involving several key enzymes for mobilization of stored food reserves. Pullulanase (PUL), a starch-debranching enzyme, plays an important role in mobilizing stored endosperm food reserves during germination. Pullulanase inhibitor (PULI) hinders PUL’s activity through an unknown mechanism. Barley has one PUL and two PULI genes. During the time-dependent processes of seed germination, only PULI-1 expression shows an antagonistic relationship with that of PUL. Our data have indicated that the expression of PULI-1 is modulated by SPL (Squamosa-promoter-binding Protein Like) transcription factors, known to be targeted by miR156. We show that the binding of recombinant HvSPL3 protein to the PULI-1 promoter occurs under reducing, but not under oxidizing conditions. Replacement of Cys residues with threonine in HvSPL3 abolishes the binding, indicating an essential role of the redox state in the expression of PULI. Our findings may have important implications for the industrial use of starch.

Exploring the factors that affect the themostability of barley limit dextrinase - Inhibitor complex

Barley Limit dextrinase (Hordeum vulgare HvLD) is the unique endogenous starch-debranching enzyme, determining the production of a high degree of fermentation. The activity of HvLD is regulated by an endogenous LD inhibitor protein (LDI). In beer production, free LD is easy to inactivate in mashing process under the condition of high temperature. The binding of LD with LDI protects it against heat inactivation. Exploring the factors affecting the themostability of HvLD-LDI complex is important for beer production. In this work, the themostability of HvLD-LDI complex at different NaCl concentrations and temperatures were explored by molecular dynamics simulation and binding free energy calculation. In NaCl solution, the complex exhibits higher conformational stability at 343 K and 363 K than those in pure water. Root mean square fluctuation (RMSF) analysis identified the thermal sensitive regions of HvLD and LDI. The binding free energy results suggest that the LD-LDI complex is more stable in NaCl solution than those in pure water at high temperature. The residues with high contribution to the complex were identified. The structural and dynamic details will help us to understand the driving forces that lead to the themostability of HvLD-LDI complex at different temperatures and different salt concentrations, which will facilitate the optimization conditions of beer production for maintaining the thermal stability and activity of HvLD.

Microbial starch debranching enzymes: Developments and applications

Starch debranching enzymes (SDBEs) hydrolyze the α-1,6 glycosidic bonds in polysaccharides such as starch, amylopectin, pullulan and glycogen. SDBEs are also important enzymes for the preparation of sugar syrup, resistant starch and cyclodextrin. As the synergistic catalysis of SDBEs and other starch-acting hydrolases can effectively improve the raw material utilization and production efficiency during starch processing steps such as saccharification and modification, they have attracted substantial research interest in the past decades. The substrate specificities of the two major members of SDBEs, pullulanases and isoamylases, are quite different. Pullulanases generally require at least two α-1,4 linked glucose units existing on both sugar chains linked by the α-1,6 bond, while isoamylases require at least three units of α-1,4 linked glucose. SDBEs mainly belong to glycoside hydrolase (GH) family 13 and 57. Except for GH57 type II pullulanse, GH13 pullulanases and isoamylases share plenty of similarities in sequence and structure of the core catalytic domains. However, the N-terminal domains, which might be one of the determinants contributing to the substrate binding of SDBEs, are distinct in different enzymes. In order to overcome the current defects of SDBEs in catalytic efficiency, thermostability and expression level, great efforts have been made to develop effective enzyme engineering and fermentation strategies. Herein, the diverse biochemical properties and distinct features in the sequence and structure of pullulanase and isoamylase from different sources are summarized. Up-to-date developments in the enzyme engineering, heterologous production and industrial applications of SDBEs is also reviewed. Finally, research perspective which could help understanding and broadening the applications of SDBEs are provided.

An ultra-high affinity protein-protein interface displaying sequence-robustness

Protein-protein interactions are crucial in biology and play roles in for example, the immune system, signaling pathways, and enzyme regulation. Ultra-high affinity interactions (K_d <0.1 nM) occur in these systems, however, structures and energetics behind stability of ultra-high affinity protein-protein complexes are not well understood. Regulation of the starch debranching barley limit dextrinase (LD) and its endogenous cereal type inhibitor (LDI) exemplifies an ultra-high affinity complex (K_d of 42 pM). In this study the LD-LDI complex is investigated to unveil how robust the ultra-high affinity is to LDI sequence variation at the protein-protein interface and whether alternative sequences can retain the ultra-high binding affinity. The interface of LD-LDI was engineered using computational protein redesign aiming at identifying LDI variants predicted to retain ultra-high binding affinity. These variants present a very diverse set of mutations going beyond conservative and alanine substitutions typically used to probe interfaces. Surface plasmon resonance analysis of the LDI variants revealed that high affinity of LD-LDI requires interactions of several residues at the rim of the protein interface, unlike the classical hotspot arrangement where key residues are found at the center of the interface. Notably, substitution of interface residues in LDI, including amino acids with functional groups different from the wild-type, could occur without loss of affinity. This demonstrates that ultra-high binding affinity can be conferred without hotspot residues, thus making complexes more robust to mutational drift in evolution. The present mutational analysis also demonstrates how energetic coupling can emerge between residues at large distances at the interface.

Structural basis of carbohydrate binding in domain C of a type I pullulanase fromPaenibacillus barengoltzii

Pullulanase (EC 3.2.1.41) is a well known starch-debranching enzyme that catalyzes the cleavage of α-1,6-glycosidic linkages in α-glucans such as starch and pullulan. Crystal structures of a type I pullulanase fromPaenibacillus barengoltzii(PbPulA) and ofPbPulA in complex with maltopentaose (G5), maltohexaose (G6)/α-cyclodextrin (α-CD) and β-cyclodextrin (β-CD) were determined in order to better understand substrate binding to this enzyme.PbPulA belongs to glycoside hydrolase (GH) family 13 subfamily 14 and is composed of three domains (CBM48, A and C). Three carbohydrate-binding sites identified inPbPulA were located in CBM48, near the active site and in domain C, respectively. The binding site in CBM48 was specific for β-CD, while that in domain C has not been reported for other pullulanases. The domain C binding site had higher affinity for α-CD than for G6; a small motif (FGGEH) seemed to be one of the major determinants for carbohydrate binding in this domain. Structure-based mutations of several surface-exposed aromatic residues in CBM48 and domain C had a debilitating effect on the activity of the enzyme. These results suggest that both CBM48 and domain C play a role in binding substrates. The crystal forms described contribute to the understanding of pullulanase domain–carbohydrate interactions.

Understanding Thermostability Factors of Barley Limit Dextrinase by Molecular Dynamics Simulations

Limit dextrinase (LD) is the only endogenous starch-debranching enzyme in barley (Hordeum vulgare, Hv), which is the key factor affecting the production of a high degree of fermentation. Free LD will lose its activity in the mashing process at high temperature in beer production. However, there remains a lack of understanding on the factor affecting the themostability of HvLD at the atomic level. In this work, the molecular dynamics simulations were carried out for HvLD to explore the key factors affecting the thermal stability of LD. The higher value of root mean square deviation (RMSD), radius of gyration (R_g), and surface accessibility (SASA) suggests the instability of HvLD at high temperatures. Intra-protein hydrogen bonds and hydrogen bonds between protein and water decrease at high temperature. Long-lived hydrogen bonds, salt bridges, and hydrophobic contacts are lost at high temperature. The salt bridge interaction analysis suggests that these salt bridges are important for the thermostability of HvLD, including E568–R875, D317–R378, D803–R884, D457–R214, D468–R395, D456–R452, D399–R471, and D541–R542. Root mean square fluctuation (RMSF) analysis identified the thermal-sensitive regions of HvLD, which will facilitate enzyme engineering of HvLD for enhanced themostability.

Starch-binding domains as CBM families-history, occurrence, structure, function and evolution

The term "starch-binding domain" (SBD) has been applied to a domain within an amylolytic enzyme that gave the enzyme the ability to bind onto raw, i.e. thermally untreated, granular starch. An SBD is a special case of a carbohydrate-binding domain, which in general, is a structurally and functionally independent protein module exhibiting no enzymatic activity but possessing potential to target the catalytic domain to the carbohydrate substrate to accommodate it and process it at the active site. As so-called families, SBDs together with other carbohydrate-binding modules (CBMs) have become an integral part of the CAZy database (http://www.cazy.org/). The first two well-described SBDs, i.e. the C-terminal Aspergillus-type and the N-terminal Rhizopus-type have been assigned the families CBM20 and CBM21, respectively. Currently, among the 85 established CBM families in CAZy, fifteen can be considered as families having SBD functional characteristics: CBM20, 21, 25, 26, 34, 41, 45, 48, 53, 58, 68, 69, 74, 82 and 83. All known SBDs, with the exception of the extra long CBM74, were recognized as a module consisting of approximately 100 residues, adopting a β-sandwich fold and possessing at least one carbohydrate-binding site. The present review aims to deliver and describe: (i) the SBD identification in different amylolytic and related enzymes (e.g., CAZy GH families) as well as in other relevant enzymes and proteins (e.g., laforin, the β-subunit of AMPK, and others); (ii) information on the position in the polypeptide chain and the number of SBD copies and their CBM family affiliation (if appropriate); (iii) structure/function studies of SBDs with a special focus on solved tertiary structures, in particular, as complexes with α-glucan ligands; and (iv) the evolutionary relationships of SBDs in a tree common to all SBD CBM families (except for the extra long CBM74). Finally, some special cases and novel potential SBDs are also introduced.

Industrially produced pullulanases with thermostability: Discovery, engineering, and heterologous expression

Pullulanases (EC 3.2.1.41) are well-known starch-debranching enzymes widely used to hydrolyze α-1,6-glucosidic linkages in starch, pullulan, amylopectin, and other oligosaccharides, with application potentials in food, brewing, and pharmaceutical industries. Although extensive studies are done to discover and express pullulanases, only few are available with desirable characteristics for industrial applications. This raises the challenge to mine new enzyme sources, engineer proteins based on sequence/structure, and regulate expressions. We review here the identification of extremophilic and mesophilic microbes as sources of industrial pullulanases with desirable characteristics, including acid-resistance, thermostability, and psychrotrophism. We present current advances in site-directed mutagenesis and sequence/structure-guided protein engineering of pullulanases. In addition, we discuss heterologous expression of pullulanases in prokaryotic and eukaryotic microbial systems, and address the effectiveness of the expression elements and their regulation of enzyme production. Finally, we indicate future research needs to develop desired industrial pullulanases.

Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin

Crystal structures of Klebsiella pneumoniae pullulanase (KPP) in complex with α-cyclodextrin (α-CD), β-cyclodextrin (β-CD) and γ-cyclodextrin (γ-CD) were refined at around 1.98–2.59 Å resolution from data collected at SPring-8. In the structures of the complexes obtained with 1 mM α-CD or γ-CD, one molecule of CD was found at carbohydrate-binding module 41 only (CBM41). In the structures of the complexes obtained with 1 mM β-CD or with 10 mM α-CD or γ-CD, two molecules of CD were found at CBM41 and in the active-site cleft, where the hydrophobic residue of Phe746 occupies the inside cavity of the CD rings. In contrast to α-CD and γ-CD, one β-CD molecule was found at the active site only in the presence of 0.1 mM β-CD. These results were coincident with the solution experiments, which showed that β-CD inhibits this enzyme more than a thousand times more potently than α-CD and γ-CD. The strong inhibition of β-CD is caused by the optimized interaction between β-CD and the side chain of Phe746. The increased K i values of the F746A mutant for β-CD supported the importance of Phe746 in the strong interaction of pullulanase with β-CD.

Interfering with the high-affinity interaction between wheat amylase trypsin inhibitor CM3 and toll-like receptor 4: in silico and biosensor-based studies

Wheat amylase/trypsin bi-functional inhibitors (ATIs) are protein stimulators of innate immune response, with a recently established role in promoting both gastrointestinal and extra-gastrointestinal inflammatory syndromes. These proteins have been reported to trigger downstream intestinal inflammation upon activation of TLR4, a member of the Toll-like family of proteins that activates signalling pathways and induces the expression of immune and pro-inflammatory genes. In this study, we demonstrated the ability of ATI to directly interact with TLR4 with nanomolar affinity, and we kinetically and structurally characterized the interaction between these macromolecules by means of a concerted approach based on surface plasmon resonance binding analyses and computational studies. On the strength of these results, we designed an oligopeptide capable of preventing the formation of the complex between ATI and the receptor.

Structure and function of α-glucan debranching enzymes

α-Glucan debranching enzymes hydrolyse α-1,6-linkages in starch/glycogen, thereby, playing a central role in energy metabolism in all living organisms. They belong to glycoside hydrolase families GH13 and GH57 and several of these enzymes are industrially important. Nine GH13 subfamilies include α-glucan debranching enzymes; isoamylase and glycogen debranching enzymes (GH13_11); pullulanase type I/limit dextrinase (GH13_12-14); pullulan hydrolase (GH13_20); bifunctional glycogen debranching enzyme (GH13_25); oligo-1 and glucan-1,6-α-glucosidases (GH13_31); pullulanase type II (GH13_39); and α-amylase domains (GH13_41) in two-domain amylase-pullulanases. GH57 harbours type II pullulanases. Specificity differences, domain organisation, carbohydrate binding modules, sequence motifs, three-dimensional structures and specificity determinants are discussed. The phylogenetic analysis indicated that GH13_39 enzymes could represent a "missing link" between the strictly α-1,6-specific debranching enzymes and the enzymes with dual specificity and α-1,4-linkage preference.

Iminosugar inhibitors of carbohydrate-active enzymes that underpin cereal grain germination and endosperm metabolism

Starch is a major energy store in plants. It provides most of the calories in the human diet and, as a bulk commodity, it is used across broad industry sectors. Starch synthesis and degradation are not fully understood, owing to challenging biochemistry at the liquid/solid interface and relatively limited knowledge about the nature and control of starch degradation in plants. Increased societal and commercial demand for enhanced yield and quality in starch crops requires a better understanding of starch metabolism as a whole. Here we review recent advances in understanding the roles of carbohydrate-active enzymes in starch degradation in cereal grains through complementary chemical and molecular genetics. These approaches have allowed us to start dissecting aspects of starch degradation and the interplay with cell-wall polysaccharide hydrolysis during germination. With a view to improving and diversifying the properties and uses of cereal grains, it is possible that starch degradation may be amenable to manipulation through genetic or chemical intervention at the level of cell wall metabolism, rather than simply in the starch degradation pathway per se.