Conformational analysis and molecular modelling of the branching point of amylopectin

Starch structure and nutritional functionality - Past revelations and future prospects

Starch exists naturally as insoluble semi-crystalline granules assembled by amylose and amylopectin. Acknowledging the pioneers, we have reviewed the major accomplishments in the area of starch structure from the early 18th century and further established the relation of starch structure to nutritional functionality. Although a huge array of work is reported in the area, the review identified that some features of starch are still not fully understood and needs further elucidation. With the rise of diet-related diseases, it has never been more important to understand starch structure and use that knowledge to improve the nutritional value of the world's principal energy source.

Cold plasma technologies: Their effect on starch properties and industrial scale-up for starchmodification

Native starches have limited applications in the food industry due to their unreactive and insoluble nature. Cold plasma technology, including plasma-activated water (PAW), has been explored to modify starches to enhance their functional, thermal, molecular, morphological, and physicochemical properties. Atmospheric cold plasma and low-pressure plasma systems have been used to alter starches and have proven successful. This review provides an in-depth analysis of the different cold plasma setups employed for starch modifications. The effect of cold plasma technology application on starch characteristics is summarized. We also discussed the potential of plasma-activated water as a novel alternative for starch modification. This review provides information needed for the industrial scale-up of cold plasma technologies as an eco-friendly method of starch modification.

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Cold plasma technology could be an effective, sustainable alternative for starch modification.

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The extent of modification of starches from different botanical sources depends on the type of cold plasma technology used.

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For mainstream adoption of cold plasma modified starches, research on safety and consumer perception must be conducted.

Starch granule size: Does it matter?

Nature has developed starch granules varying in size from less than 1 μm to more than 100 μm. The granule size is an important factor affecting the functional properties and the applicability of starch for food and non-food applications. Within the same botanical species, the range of starch granule size can be up to sevenfold. This review critically evaluated the biological and environmental factors affecting the size of starch granules, the methods for the separation of starch granules and the measurement of size distribution. Further, the structure at different length scales and properties of starch-based on the granule size is elucidated by specifying the typical applications of granules with varying sizes. An amylopectin cluster model showing the arrangement of amylopectin from inside toward the granule surface is proposed with the hypothesis that the steric hindrance for the growth of lamellar structure may limit the size of starch granules.

Understanding Starch Structure: Recent Progress

Starch is a major food supply for humanity. It is produced in seeds, rhizomes, roots and tubers in the form of semi-crystalline granules with unique properties for each plant. Though the size and morphology of the granules is specific for each plant species, their internal structures have remarkably similar architecture, consisting of growth rings, blocklets, and crystalline and amorphous lamellae. The basic components of starch granules are two polyglucans, namely amylose and amylopectin. The molecular structure of amylose is comparatively simple as it consists of glucose residues connected through α-(1,4)-linkages to long chains with a few α-(1,6)-branches. Amylopectin, which is the major component, has the same basic structure, but it has considerably shorter chains and a lot of α-(1,6)-branches. This results in a very complex, three-dimensional structure, the nature of which remains uncertain. Several models of the amylopectin structure have been suggested through the years, and in this review two models are described, namely the “cluster model” and the “building block backbone model”. The structure of the starch granules is discussed in light of both models.

Crop-derived polysaccharides as binders for high-capacity silicon/graphite-based electrodes in lithium-ion batteries

Rice to power: Amylopectin is a major component of agricultural products such as corn, potato, and rice. Silicon-graphite electrodes are prepared by using slurries of these polysaccharides as binders. Compared to the conventionally used binder PVdF, they exhibit drastically improved electrode performance in Li cells. The improved performance is coupled to the degree of branching.

Characterization of water binding and dehydration in gelatinized starch

Using near-infrared spectroscopy and thermogravimetry coupled with differential scanning calorimetry (TG-DSC), we investigated the characteristics of water in starch and the effects of the inner structure of starch on dehydration. The results directly show that the dehydration process is significantly more favorable in native starch than in gelatinized starch. When the starch was heated to 100 °C, the water retention in gelatinized starch was 22.35 per total water content, much greater than that in native starch (4.3%). The hydrogen bond network that changes from native starch to gelatinized starch was simultaneously explored, and the weaker hydrogen bonds were found to be predominant in the hydrogen bond network of gelatinized starch.

Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling

Explicit-solvent molecular dynamics (MD) simulations of the 11 glucose-based disaccharides in water at 300K and 1bar are reported. The simulations were carried out with the GROMOS 45A4 force-field and the sampling along the glycosidic dihedral angles phi and psi was artificially enhanced using the local elevation umbrella sampling (LEUS) method. The trajectories are analyzed in terms of free-energy maps, stable and metastable conformational states (relative free energies and estimated transition timescales), intramolecular H-bonds, single molecule configurational entropies, and agreement with experimental data. All disaccharides considered are found to be characterized either by a single stable (overwhelmingly populated) state ((1-->n)-linked disaccharides with n=1, 2, 3, or 4) or by two stable (comparably populated and differing in the third glycosidic dihedral angle omega ; gg or gt) states with a low interconversion barrier ((1-->6)-linked disaccharides). Metastable (anti-phi or anti-psi) states are also identified with relative free energies in the range of 8-22 kJ mol(-1). The 11 compounds can be classified into four families: (i) the alpha(1-->1)alpha-linked disaccharide trehalose (axial-axial linkage) presents no metastable state, the lowest configurational entropy, and no intramolecular H-bonds; (ii) the four alpha(1-->n)-linked disaccharides (n=1, 2, 3, or 4; axial-equatorial linkage) present one metastable (anti-psi) state, an intermediate configurational entropy, and two alternative intramolecular H-bonds; (iii) the four beta(1-->n)-linked disaccharides (n=1, 2, 3, or 4; equatorial-equatorial linkage) present two metastable (anti-phi and anti-psi) states, an intermediate configurational entropy, and one intramolecular H-bond; (iv) the two (1-->6)-linked disaccharides (additional glycosidic dihedral angle) present no (isomaltose) or a pair of (gentiobiose) metastable (anti-phi) states, the highest configurational entropy, and no intramolecular H-bonds. The observed conformational preferences appear to be dictated by four main driving forces (ring conformational preferences, exo-anomeric effect, steric constraints, and possible presence of a third glycosidic dihedral angle), leaving a secondary role to intramolecular H-bonding and specific solvation effects. In spite of the weak conformational driving force attributed to solvent-exposed H-bonds in water (highly polar protic solvent), intramolecular H-bonds may still have a significant influence on the physico-chemical properties of the disaccharide by decreasing its hydrophilicity. Along with previous work, the results also complete the suggestion of a spectrum of approximate transition timescales for carbohydrates up to the disaccharide level, namely: approximately 30 ps (hydroxyl groups), approximately 1 ns (free lactol group, free hydroxymethyl groups, glycosidic dihedral angleomega in (1-->6)-linked disaccharides), approximately 10 ns to 2 micros (ring conformation, glycosidic dihedral angles phi and psi). The calculated average values of the glycosidic torsional angles agree well with the available experimental data, providing validation for the force-field and simulation methodology employed.

Synthesis of triazole-linked pseudo-starch fragments

Rapid assembly of starch fragment analogues was achieved using 'click chemistry'. Specifically, a pentadecasaccharide and two hexadecasaccharide mimics containing two parallel maltoheptaosyl chains linked via [1,2,3]-triazoles to glucose or maltose core were synthesised using Cu(I)-catalyzed [3+2] dipolar cycloaddition of azidosaccharides and 4,6-di-O-propargylated methyl alpha-d-glucopyranoside and 6,6'- and 4',6'-di-O-propargylated p-methoxyphenyl beta-maltoside.

Oligosaccharide binding to barley alpha-amylase 1

Enzymatic subsite mapping earlier predicted 10 binding subsites in the active site substrate binding cleft of barley alpha-amylase isozymes. The three-dimensional structures of the oligosaccharide complexes with barley alpha-amylase isozyme 1 (AMY1) described here give for the first time a thorough insight into the substrate binding by describing residues defining 9 subsites, namely -7 through +2. These structures support that the pseudotetrasaccharide inhibitor acarbose is hydrolyzed by the active enzymes. Moreover, sugar binding was observed to the starch granule-binding site previously determined in barley alpha-amylase isozyme 2 (AMY2), and the sugar binding modes are compared between the two isozymes. The "sugar tongs" surface binding site discovered in the AMY1-thio-DP4 complex is confirmed in the present work. A site that putatively serves as an entrance for the substrate to the active site was proposed at the glycone part of the binding cleft, and the crystal structures of the catalytic nucleophile mutant (AMY1D180A) complexed with acarbose and maltoheptaose, respectively, suggest an additional role for the nucleophile in the stabilization of the Michaelis complex. Furthermore, probable roles are outlined for the surface binding sites. Our data support a model in which the two surface sites in AMY1 can interact with amylose chains in their naturally folded form. Because of the specificities of these two sites, they may locate/orient the enzyme in order to facilitate access to the active site for polysaccharide chains. Moreover, the sugar tongs surface site could also perform the unraveling of amylose chains, with the aid of Tyr-380 acting as "molecular tweezers."

“Click chemistry”en route to pseudo-starch

Rapid assembly of starch fragment analogues was achieved using "click chemistry". Specifically, two hexadecasaccharide mimics containing two parallel maltoheptaosyl chains linked via [1,2,3]-triazoles to a maltose core were synthesized using Cu(i)-catalyzed [3 + 2] dipolar cycloaddition of azido saccharides and 6,6'- and 4',6'-dipropargylated p-methoxyphenyl maltoside.

Comparative Study of Small Linear and Branched α-Glucans Using Size Exclusion Chromatography and Static and Dynamic Light Scattering

A series of synthesized small linear and branched alpha-glucans has been studied by dynamic light scattering and combined size exclusion chromatography, refractive index measurement and static light scattering. The alpha-glucan molecules studied were maltose, maltotriose, maltopentaose, maltohexaose, maltoheptaose, panose, 6'-alpha-maltosyl-maltotriose, methyl 6'-alpha-maltosyl-maltotrioside, 6' '-alpha-maltosyl-maltotetraose, 6' ''-alpha-maltotriosyl-maltohexaose, and 6,6' '' '-bis(alpha-maltosyl)-maltohexaose. The alpha-glucan oligosaccharides appeared to be very flexible molecules having a variety of conformations and self-associating into noncovalent dimers and trimers (referring to the single molecule). The size distributions were narrow (compared to pullulan) indicating that the alpha-glucan oligosaccharides are relatively compact molecules. The branched oligomers that include one or more flexible alpha-(1 --> 6) linkages exhibit size distributions corresponding to more compact conformations than their linear counterparts. This observation may be explained by intermolecular interactions or water bridges facilitated by the additional flexibility of these molecules. For the branched maltohexaose, a significant noncovalent trimer formation was observed, whereas in all other cases, noncovalent dimers were formed. Model calculations suggest that both the linear and branched oligomers containing 5-10 alpha-glucose units exist predominantly in a partial or full single turn helix in agreement with the glycosidic linkage preferences derived for these molecules.

Comparative structure and physicochemical properties of Ilpumbyeo, a high-quality japonica rice, and its mutant, Suweon 464

A new rice mutant Suweon 464 (S-464) derived from a high-quality rice, Ilpumbyeo (IP), revealed a striking difference in cooking quality from IP. The physicochemical properties of S-464 and IP were compared. S-464 was unusually high in amylose and fiber contents, had B-type crystallinity of starch, and had a markedly lower proportion of short chains in the distribution of glucan-chain fractions of debranched starch as compared with IP. Scanning electron microscopy revealed that starch granules of S-464 were much smaller in size than those of IP and that many of them were not separated from amyloplasts. The physicochemical properties of S-464 would contribute to poor gelatinization, lower swelling power, higher hardness, and less stickiness when cooked. Although S-464 may not be desirable for cooked rice, the mutant could be an excellent candidate for other processed food products on the basis of its unusual properties of starch and high fiber, protein, and lipid contents.

The phase transformations in starch during gelatinisation: a liquid crystalline approach

The analogy between starch and a chiral side-chain polymeric liquid crystal is examined in relation to the processes involved during gelatinisation. There are three important parameters for characterisation of the molecular phase behaviour of the amylopectin: the lamellar order parameter (psi), the orientational order parameter of the amylopectin double helices (phi), and the helicity of the sample (h, the helix/coil ratio, a measure of the helix-coil transition of the double helices). The coupling between the double helices and the backbone through the flexible spacers is affected dramatically by the water content and it is this factor which dictates the particular phase adopted by the amylopectin inside the starch granule as a function of temperature. SAXS, WAXS and 13C CP/MAS NMR are used to examine these phenomena in excess water. Furthermore, previous experimental evidence pertaining to the limiting water case is reviewed with respect to this new theoretical framework.

The relationship between internal chain length of amylopectin and crystallinity in starch

Molecular models of amylopectin were created and investigated by computer simulation. First, single and double helices of various lengths were constructed. The 1 --> 6 branching in double and single helices of amylopectin was studied. Subunits of single helices, double helices, and branch points were used as building blocks of larger systems. The possible makeup of amylopectin unit clusters was investigated via a series of models, including single-single, double-single, and double-double helix systems. The lengths of the single helix section that linked two branch points (internal chains) was systematically varied between values of 0-10 glucose residues. It was found that certain internal chain lengths lead to parallel double helices. Thus, it was postulated that the length of internal chains may determine the degree of local crystallinity. Furthermore, it was noted that some of the low-energy arrangement of double helices could be superimposed on either the two adjacent and nonadjacent double helices of crystalline A and B starch polymorphs. In other cases, the distance between the double helices is so large that it may in fact be a model for branching between two amylopectin crystals or unit clusters. Results obtained through this work were corroborated, where possible, with information available from crystallographic, branching, and enzymatic studies.

X-ray diffraction of food polysaccharides

The morphologies of food polysaccharides described in this chapter illustrate the power of x-ray fiber diffraction in conjunction with computer modeling and sophisticated refinement techniques. On the other hand, the lack of information on structures such as xanthan reflects the inadequacy of the experimental techniques used to date. But the demands from academic and industrial sectors to investigate the molecular interactions in multicomponent systems, including protein-protein, protein-polysaccharide, polysaccharide-polysaccharide, and other complexes, are high and growing, because they have important food applications. These complexes are structurally more difficult than those solved in the past 40 years and it is improbable that any chosen system will be amenable for crystallographic investigation, crystals or fibers. Modern research facilities that include two-dimensional area detectors, millisecond exposures with synchrotron x-ray radiation, interactive computer graphics, sophisticated molecular dynamics calculations, unbelievably fast and inexpensive computers, and our own intellectual abilities are indispensable tools for the future of structural science in general and food polysaccharides in particular.

Molecular modelling of the interaction between the catalytic site of pig pancreatic alpha-amylase and amylose fragments

A stereo chemical refinement of the crystalline complex between porcine pancreatic alpha-amylase and a pseudopentasaccharide from the amylostatin family has been performed through molecular mechanics calculations, using a set of parameters appropriate for protein and protein-carbohydrate interactions. The refinement provided a starting point for docking a maltopentaose moiety within the catalytic site, in the absence of water. A thorough exploration of the different orientations and conformations of maltopentaose established the sense of binding of the amylosic substrate in the amylase cleft. After optimising the geometry of the binding site, the conformations adopted by the four contiguous linkages could be rationalised by considering the environment, either hydrophobic or hydrophilic, of the different glucose moieties. Seemingly, details of the non-bonded interactions (hydrogen bonds, van der Waals and stacking interactions) that underlie this molecular recognition have been established. In particular, it was confirmed that the three acidic amino acids of the catalytic site (Asp197, Asp300 and Glu233) are close to their glucosidic target, and that there is no steric reason to propose an alteration of the 4C1 conformation of the glucose residue prior to hydrolysis. However, in the absence of water molecules, it is difficult to elucidate the details of the catalysis. Additional macroscopic information has been gained, such as the impossibility to fit a double-helical arrangement of amylose chains in the amylasic cleft. This explains why some native starches containing such motifs resist amylolytic enzymes. Tentative models involving longer amylosic chains have been elaborated, which extend our knowledge of the interaction and orientation of starch fragments in the vicinity of the hydrolytic sites.

Molecular modelling of the specific interactions involved in the amylose complexation by fatty acids

Comprehensive modelling of a fatty acid molecule inside a VH amylose helix is described. In a first step, the docking of an acetic acid molecule near the helix entry was performed. The low energy solutions were propagated by an iterative procedure involving the sequential addition of single CH2 groups up to a C12 fatty acid followed by energy minimizations. The main result is the superposition of the aliphatic and the helix axes. For the low-energy complexes, the mean plane of the aliphatic carbons has three potential orientations. In each, the aliphatic hydrogens point towards the less crowded regions near the glycosidic oxygens of the amylose. The close packing is due to the related symmetries of both the helix and aliphatic chain. In a second step, the relative roles of the aliphatic part and the polar group were studied separately. For the aliphatic chain, a map based on the two major internal parameters (translation and rotation) along the helix axis shows that the isolated docking solutions are related by a combination of a 60 degrees (360 degrees/6) rotation and a translation of p/6 (p = 0.804 nm corresponds to the pitch of Vhydrate amylose). The H5 glucopyranose atoms participate in close contacts and are responsible for steric conflicts in structures intermediate to the stable docking solutions. The four possible low-energy arrangements of the carboxylic group were added to the calculated amylose/aliphatic structures. Two stable conformations of the total fatty acid molecule were determined. For both stable solutions, the polar group is located near the entrance of the helix cavity.(ABSTRACT TRUNCATED AT 250 WORDS)

Simulations of the static and dynamic molecular conformations of xyloglucan. The role of the fucosylated sidechain in surface-specific sidechain folding

The hemicellulosic polysaccharide xyloglucan binds with a strong affinity to cellulosic cell wall microfibrils, the resulting heterogeneous network constituting up to 50% of the dry weight of the cell wall in dicotyledonous plants. To elucidate the molecular details of this interaction, we have performed theoretical potential energy calculations of the static and dynamic equilibrium conformations of xyloglucan using the GEGOP software. In particular, we have evaluated the preferred sidechain conformations of hexa-, octa-, deca- and heptadecasaccharide model fragments of xyloglucan for molecules with a cellulose-like, flat, glucan backbone, and a cellobiose-like, twisted, glucan backbone conformation. For the flat backbone conformation the determination of static equilibrium molecular conformations revealed a tendency for sidechains to fold onto one surface of the backbone, defined here as the H1S face, in the fucosylated region of the polymer. This folding produces a molecule that is sterically accessible on the opposite face of the backbone, the H4S face. Typically, this folding onto the H1S surface is significantly stabilized by favorable interactions between the fucosylated, trisaccharide sidechain and the backbone, with some stabilization from adjacent terminal xylosyl sidechains. In contrast, the trisaccharide sidechain folds onto the H4S face of xyloglucan fragments with a twisted backbone conformation. Preliminary NMR data on nonasaccharide fragments isolated from sycamore suspension-cultured cell walls are consistent with the hypothesis that the twisted conformation of xyloglucan represents the solution form of this molecule. Metropolis Monte Carlo (MMC) simulations were employed to assess sidechain flexibility of the heptadecasaccharide fragments. Simulations performed on the flat, rigid, backbone xyloglucan indicate that the trisaccharide sidechain is less mobile than the terminal xylosyl sidechains. MMC calculations on a fully relaxed molecule revealed a positive correlation between a specific trisaccharide sidechain orientation and the 'flatness' of the backbone glucosyl residues adjacent to this sidechain. These results suggest that the trisaccharide sidechain may play a role in the formation of nucleation sites that initiate the binding of these regions to cellulose. Based on these conformational preferences we suggest the following model for the binding of xyloglucan to cellulose. Nucleation of a binding site is initiated by the fucosylated, trisaccharide sidechain that flattens out an adjacent region of the xyloglucan backbone. Upon contacting a cellulose microfibril this region spreads by step-wise flattening of successive segments of the backbone. Self-association of xyloglucan molecules in solution may be prevented by the low frequency of formation of these nucleation sites and the geometry of the molecules in solution.