Vinh Tran

The double-helical nature of the crystalline part of A-starch.

A new three-dimensional structure of the crystalline part of A-starch is described in which the unit cell contains 12 glucose residues located in two left-handed, parallel-stranded double helices packed in a parallel fashion; four water molecules are located between these helices. Chains are crystallized in a monoclinic lattice with a = 2.124 nm, b = 1.172 nm, c = 1.069 nm and gamma = 123.5 degrees, the c axis being parallel to the helix axis. Systematic absences are consistent with the space group B2. The structure was derived from joint use of electron diffraction of single crystals, X-ray powder patterns decomposed into individual peaks and previously reported X-ray fibre diffraction data after adequate re-indexing. The repeating unit consists of a maltotriose moiety where the glucose residues have the 4C1 pyranose conformation and are alpha(1----4) linked. The conformation of the glycosidic linkage is characterized by torsion angles (phi, psi) which take the values (91.8, -153.2), (85.7, -145.3) and 91.8, -151.3); all the primary hydroxyl groups exist in a gauche-gauche conformation. There are no intramolecular hydrogen bonds. Within the double helix, interstrand stabilization is achieved without any steric conflict and through the occurrence of O(2)...O(6) type hydrogen bonds. The present structure is consistent with both physicochemical and biochemical aspects of the crystalline component of the cereal starch granules.

A lipid transfer protein binds to a receptor involved in the control of plant defence responses

Lipid transfer proteins (LTPs) and elicitins are both able to load and transfer lipidic molecules and share some structural and functional properties. While elicitins are known as elicitors of plant defence mechanisms, the biological function of LTP is still an enigma. We show that a wheat LTP1 binds with high affinity sites. Binding and in vivo competition experiments point out that these binding sites are common to LTP1 and elicitins and confirm that they are the biological receptors of elicitins. A mathematical analysis suggests that these receptors could be represented by an allosteric model corresponding to an oligomeric structure with four identical subunits.

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)

Structural features of fatty acid-amylose complexes

Abstract X-ray diffraction and Differential Scanning Calorimetry measurements were performed on highly crystalline complexes prepared from amyloses and fatty acids with different chain lengths. The complexes yielded very sharp V h -type diffraction diagrams except those prepared with the shortest amylose chains. The melting temperature of the complexes increased with increasing amylose chain length. In parallel, the inclusion of the fatty acid inside a 6 5 amylose helix, similar to that determined for the V h structure, was studied using molecular modelling. The aliphatic part of the fatty acid can be included in trans conformation. Six discrete positions per helix pitch were calculated. The polar group of the fatty acid cannot be included, due to both steric and electrostatic repulsions.

Geometric algorithms for the conformational analysis of long protein loops

The efficient filtering of unfeasible conformations would considerably benefit the exploration of the conformational space when searching for minimum energy structures or during molecular simulation. The most important conditions for filtering are the maintenance of molecular chain integrity and the avoidance of steric clashes. These conditions can be seen as geometric constraints on a molecular model. In this article, we discuss how techniques issued from recent research in robotics can be applied to this filtering. Two complementary techniques are presented: one for conformational sampling and another for computing conformational changes satisfying such geometric constraints. The main interest of the proposed techniques is their application to the structural analysis of long protein loops. First experimental results demonstrate the efficacy of the approach for studying the mobility of loop 7 in amylosucrase from Neisseria polysaccharea. The supposed motions of this 17‐residue loop would play an important role in the activity of this enzyme.

Inclusion/exclusion of fatty acids in amylose complexes as a function of the fatty acid chain length

Structural models are proposed for amylose-fatty acid complexes depending on the respective chain lengths of their constituents. The three studied fatty acids induce the Vh amylose crystalline type. However, in contrast to lauric and palmitic acids, caprylic acid is not present in crystals. On the basis of the relative amounts of amylose and fatty acid determined in complexes and previous results of molecular modelling, inclusion of lauric and palmitic acids inside the amylose helices is proposed; the acyl chains are included in crystalline areas and the carboxylic groups in amorphous areas. The absence of caprylic acid in crystals could be due to the solubility of this compound in the crystallization medium.

Data bank of three-dimensional structures of disaccharides, a tool to build 3-D structures of oligosaccharides

This work presents the first part of a database of conformations for all the disaccharide fragments that are found inN-glycans. The conformational study of the five disaccharides found in the oligo-mannose type are presented here. For each disaccharide, several possible conformations are described. A method is presented to obtain realistic models of oligosaccharides using molecular mechanic methods. Analysis of some possible conformations of the oligo-mannose type glycan Man6-GlcNAc2 is given as an illustration of the possibilities.

Towards a novel explanation of Pseudomonas cepacia lipase enantioselectivity via molecular modelling of the enantiomer trajectory into the active site

Abstract In the transesterification reaction between ( RS )-2-bromophenyl acetic acid ethyl ester and 1-octanol in n -octane, Pseudomonas cepacia lipase enantioselectivity towards the ( R )-isomer is 57. Two strategies are described to investigate the structural basis involved in this enzyme enantioselectivity. Molecular modelling of the tetrahedral intermediate mimicking the transition state enables the identification of two potentially productive substrate-binding modes for each enantiomer. However, the conformations obtained with the faster and slower-reacting enantiomers have equivalent potential energies and most of them possess the hydrogen bonds essential for catalysis. On this basis, it is not possible to distinguish the diastereomeric complexes. The second approach is original and consists in a simple but robust protocol of pseudomolecular dynamics simulations under constraints to map the probable trajectory of the enantiomers in the active site. Enzyme/substrate interaction energy is always found to be lower for the faster-reacting enantiomer, which satisfactorily corroborates the experimental results. Energy differences are attributed to specific interactions of these substrates with a network of hydrophobic residues lining the access path. Furthermore, mechanistic details suggest that the pivoting side chains of the hydrophobic residues act in a concerted step–tooth gear motion whose basic role is to select and guide the substrates towards the active site. With this type of lipase, such dynamic features could be the key explanation of this as yet unexplored enantiorecognition. For the slower-reacting enantiomer, it appears that the concerted motion of the side chains is perturbed when the substrate passes through a bottleneck formed by Val266 and Leu17. The enantioselectivity of mutant Val266Leu with a more bulky side chain at this position supports our assumption: by narrowing the bottleneck, the enantioselectivity was considerably enhanced as much as up to 200.

Amylose chain behavior in an interacting context. III. Complete occupancy of the AMY2 barley α-amylase cleft and comparison with biochemical data

In the first two papers of this series, the tools necessary to evaluate substrate ring deformations were developed, and then the modeling of short amylose fragments (maltotriose and maltopentaose) inside the catalytic site of barley alpha-amylase was performed. In this third paper, this docking has been extended to the whole catalytic cleft. A systematic approach to extend the substrate was used on the reducing side from the previous enzyme/pentasaccharide complex. However, due to the lack of an obvious subsite at the nonreducing side, an alternate protocol has been chosen that incorporates biochemical information on the enzyme and features on the substrate shape as well. As a net result, ten subsites have been located consistent with the distribution of Ajandouz et al. (E. H. Ajandouz, J. Abe, B. Svensson, and G. Marchis-Mouren, Biochimica Biophysica Acta, 1992, Vol. 1159, pp. 193-202) and corresponding binding energies were estimated. Among them, two extreme subsites (-6) and (+4), with stacking residues Y104 and Y211, respectively, have strong affinities with glucose rings added to the substrate. No other deformation has been found for the new glucose rings added to the substrate; therefore, only ring A of the DP 10 fragment has a flexible form when interacting with the inner stacking residues Y51. Global conservation of the helical shape of the substrate can be postulated in spite of its significant distortion at subsite (-1).

Configurational statistics of single chains of α-linked glucans

Abstract Unperturbed chain conformations are evaluated assuming separable chain configuration energies. Spatial chain propagations are constructed assuming an equiprobable occurrence of conformational states within topographically selected portions of the allowed energy space. Random coil dimensions, along with spatial representations of some single chains of α-linked glucans, such as amylose, pseudo-nigerose, nigeran and linear dextran are reported. Significant architectural differences are observed for these different α-linked glucan chains, since disordered random-coil as well as persistent pseudo-helical character, either cyclic or linear, are found, depending on the type of glycosidic linkage.