Molecular flexibility of citrus pectins by combined sedimentation and viscosity analysis

The flexibility/rigidity of pectins plays an important part in their structure-function relationship and therefore on their commercial applications in the food and biomedical industries. Earlier studies based on sedimentation analysis in the ultracentrifuge have focused on molecular weight distributions and qualitative and semi-quantitative descriptions based on power law and Wales-van Holde treatments of conformation in terms of "extended" conformations [Harding, S. E., Berth, G., Ball, A., Mitchell, J.R., & Garcìa de la Torre, J. (1991). The molecular weight distribution and conformation of citrus pectins in solution studied by hydrodynamics. Carbohydrate Polymers, 168, 1-15; Morris, G. A., Foster, T. J., & Harding, S.E. (2000). The effect of degree of esterification on the hydrodynamic properties of citrus pectin. Food Hydrocolloids, 14, 227-235]. In the present study, four pectins of low degree of esterification 17-27% and one of high degree of esterification (70%) were characterised in aqueous solution (0.1 M NaCl) in terms of intrinsic viscosity [η], sedimentation coefficient (s°20,w) and weight average molar mass (Mw). Solution conformation/flexibility was estimated qualitatively using the conformation zoning method [Pavlov, G.M., Rowe, A.J., & Harding, S.E. (1997). Conformation zoning of large molecules using the analytical ultracentrifuge. Trends in Analytical Chemistry, 16, 401-405] and quantitatively (persistence length Lp) using the traditional Bohdanecky and Yamakawa-Fujii relations combined together by minimisation of a target function. Sedimentation conformation zoning showed an extended coil (Type C) conformation and persistence lengths all within the range Lp=10-13 nm (for a fixed mass per unit length)

Coil-helix transition of polypeptide at water-lipid interface

We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an $\alpha$-helix conformation. The polypeptide is assumed to be adsorbed to the interface between a polar and a non-polar environment such as realized by water and the lipid bilayer of a membrane. The interfacial coil-helix transformation is the first stage in the folding process of helical membrane proteins. Depending on the values of model parameters, the conformation changes as a crossover, a discontinuous transition, or a continuous transition with helicity in the role of order parameter. Our model is constructed as a system of statistically interacting quasiparticles that are activated from the helix pseudo-vacuum. The particles represent links between adjacent residues in coil conformation that form a self-avoiding random walk in two dimensions. Explicit results are presented for helicity, entropy, heat capacity, and the average numbers and sizes of both coil and helix segments.Comment: 22 pages, 12 figures, accepted for publication by JSTA

Limited proteolysis in the investigation of beta2-microglobulin amyloidogenic and fibrillar states.

Amyloid fibrils of patients treated with regular haemodialysis essentially consists of β2-microglobulin (β2-m) and its truncated species ΔN6β2-m lacking six residues at the amino terminus. The truncated fragment shows a higher propensity to self-aggregate and constitutes an excellent candidate for the analysis of a protein in the amyloidogenic conformation. The surface topology and the conformational analysis of native β2-m and the truncated ΔN6β2-m species both in the soluble and in the fibrillar forms were investigated by the limited proteolysis/mass spectrometry strategy. The conformation in solution of a further truncated mutant ΔN3β2-m lacking three residues at the N-terminus was also examined. This approach appeared particularly suited to investigate the regions that are solvent-exposed, or flexible enough to be accessible to protein-protein interactions and to describe the conformation of transient intermediates. Moreover, proteolysis experiments can also be tailored to investigate amyloid fibrils by discriminating the protein regions constituting the unaccessible core of the fibrils and those still flexible and exposed to the solvent. Although native β2-m and ΔN3β2-m shared essentially the same conformation, significative structural differences exist between the native and the ΔN6β2-m proteins in solution with major differences located at the end moiety of strand V and subsequent loop with strand VI and at both the N- and C-termini of the proteins. On the contrary, an identical distribution of preferential proteolytic sites was observed in both proteins in the fibrillar state, which was nearly superimposible to that observed for the soluble form of ΔN6β2-m. These data revealed that synthetic fibrils essentially consists of an unaccessible core comprising residues 20-87 of the β2-m protein with exposed and flexible N- and C-terminal ends. Moreover, proteolytic cleavages observed in vitro at Lys 6 and Lys 19 reproduce specific cleavages that have to take place in vivo to generate the truncated forms of β2-m occurring in natural fibrils. On the basis of these results, a molecular mechanism for fibril formation has been propose

"Wet-to-Dry" Conformational Transition of Polymer Layers Grafted to Nanoparticles in Nanocomposite

The present communication reports the first direct measurement of the conformation of a polymer corona grafted around silica nano-particles dispersed inside a nanocomposite, a matrix of the same polymer. This measurement constitutes an experimental breakthrough based on a refined combination of chemical synthesis, which permits to match the contribution of the neutron silica signal inside the composite, and the use of complementary scattering methods SANS and SAXS to extract the grafted polymer layer form factor from the inter-particles silica structure factor. The modelization of the signal of the grafted polymer on nanoparticles inside the matrix and the direct comparison with the form factor of the same particles in solution show a clear-cut change of the polymer conformation from bulk to the nanocomposite: a transition from a stretched and swollen form in solution to a Gaussian conformation in the matrix followed with a compression of a factor two of the grafted corona. In the probed range, increasing the interactions between the grafted particles (by increasing the particle volume fraction) or between the grafted and the free matrix chains (decreasing the grafted-free chain length ratio) does not influence the amplitude of the grafted brush compression. This is the first direct observation of the wet-to-dry conformational transition theoretically expected to minimize the free energy of swelling of grafted chains in interaction with free matrix chains, illustrating the competition between the mixing entropy of grafted and free chains, and the elastic deformation of the grafted chains. In addition to the experimental validation of the theoretical prediction, this result constitutes a new insight for the nderstanding of the general problem of dispersion of nanoparticles inside a polymer matrix for the design of new nanocomposites materials

Asymmetric Electrophilic alpha-Amidoalkylation, VII1): Generation, Crystal Structure, and Trapping Reactions of a Chiral 6,7-Dimethoxy-1,2,3,4-tetrahydroisoquinoline Derived N-Acyliminium Ion

The camphanic acid amide 4 has efficiently been oxidized with triphenylcarbenium tetrafluoroborate (3) to yield the chiral N-acyliminium ion 1. Trapping reactions of 1 with the silyl nucleophiles 7a-c and 10a-f proceeded with stereoselective bond formation, affording the diastereomers (R)-8/(S)-9a-c and (R)-11/(S)-12a-f, respectively, with diastereoselectivities of up to 93.9/6.1. The amido ketones (R)-8/(S)-9a-c were employed in the synthesis of the secondary amines (R)-16a-c, (S)-16a and for the preparation of (-)-homolaudanosine (R)-18. By X-ray crystallography the conformation of 1 in the crystal lattice was established and the preferred conformation of 1 in solution was elucidated by NOE experiments. Finally, the addition reaction of 7a to the iminium ion 21 derived from menthyl carbamate 20 was investigated, which reaction, however, proceeded only with insignificant asymmetric induction

Quantum effective potential, electron transport and conformons in biopolymers

In the Kirchhoff model of a biopolymer, conformation dynamics can be described in terms of solitary waves, for certain special cross-section asymmetries. Applying this to the problem of electron transport, we show that the quantum effective potential arising due to the bends and twists of the polymer enables us to formalize and quantify the concept of a {\it conformon} that has been hypothesized in biology. Its connection to the soliton solution of the cubic nonlinear Schr\"{o}dinger equation emerges in a natural fashion.Comment: to appear in J. Phys.

CLP-based protein fragment assembly

The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a database of known protein structures that clusters and classifies the fragments according to similarity and frequency. The problem of assembling fragments into a complete conformation is mapped to a constraint solving problem and solved using CLP. The constraint-based model uses a medium discretization degree Ca-side chain centroid protein model that offers efficiency and a good approximation for space filling. The approach adapts existing energy models to the protein representation used and applies a large neighboring search strategy. The results shows the feasibility and efficiency of the method. The declarative nature of the solution allows to include future extensions, e.g., different size fragments for better accuracy.Comment: special issue dedicated to ICLP 201