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See detailIn silico predictions of 3D structures of linear and cyclic peptides with natural and non-proteinogenic residues.
Beaufays, Jérôme ULg; Lins, Laurence ULg; Thomas, Annick ULg et al

in Journal of Peptide Science : An Official Publication of the European Peptide Society (2012), 18(1), 17-24

We extended the use of Peplook, an in silico procedure for the prediction of three-dimensional (3D) models of linear peptides to the prediction of 3D models of cyclic peptides and thanks to the ab initio ... [more ▼]

We extended the use of Peplook, an in silico procedure for the prediction of three-dimensional (3D) models of linear peptides to the prediction of 3D models of cyclic peptides and thanks to the ab initio calculation procedure, to the calculation of peptides with non-proteinogenic amino acids. Indeed, such peptides cannot be predicted by homology or threading. We compare the calculated models with NMR and X-ray models and for the cyclic peptides, with models predicted by other in silico procedures (Pep-Fold and I-Tasser). For cyclic peptides, on a set of 38 peptides, average root mean square deviation of backbone atoms (BB-RMSD) was 3.8 and 4.1 A for Peplook and Pep-Fold, respectively. The best results are obtained with I-Tasser (2.5 A) although evaluations were biased by the fact that the resolved Protein Data Bank models could be used as template by the server. Peplook and Pep-Fold give similar results, better for short (up to 20 residues) than for longer peptides. For peptides with non-proteinogenic residues, performances of Peplook are sound with an average BB-RMSD of 3.6 A for 'non-natural peptides' and 3.4 A for peptides combining non-proteinogenic residues and cyclic structure. These results open interesting possibilities for the design of peptidic drugs. Copyright (c) 2011 European Peptide Society and John Wiley & Sons, Ltd. [less ▲]

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See detailModeling of non-covalent complexes of the cell-penetrating peptide CADY and its siRNA cargo.
Crowet, Jean-Marc ULg; Lins, Laurence ULg; Deshayes, Sebastien et al

in Biochimica et Biophysica Acta (2012)

CADY is a cell-penetrating peptide spontaneously making non-covalent complexes with siRNAs in water. Neither the structure of CADY nor that of the complexes is resolved. We have calculated and analyzed 3D ... [more ▼]

CADY is a cell-penetrating peptide spontaneously making non-covalent complexes with siRNAs in water. Neither the structure of CADY nor that of the complexes is resolved. We have calculated and analyzed 3D models of CADY and of the non-covalent CADY-siRNA complexes in order to understand their formation and stabilization. Data from the ab initio calculations and molecular dynamics support that, in agreement with the experimental data, CADY is a polymorphic peptide partly helical. Taking into consideration the polymorphism of CADY, we calculated and compared several complexes with peptide/siRNA ratios of up to 40. Four complexes were run by using molecular dynamics. The initial binding of CADYs is essentially due to the electrostatic interactions of the arginines with siRNA phosphates. Due to a repetitive arginine motif (XLWR(K)) in CADY and to the numerous phosphate moieties in the siRNA, CADYs can adopt multiple positions at the siRNA surface leading to numerous possibilities of complexes. Nevertheless, several complex properties are common: an average of 14+/-1 CADYs is required to saturate a siRNA as compared to the 12+/-2 CADYs experimentally described. The 40 CADYs/siRNA that is the optimal ratio for vector stability always corresponds to two layers of CADYs per siRNA. When siRNA is covered by the first layer of CADYs, the peptides still bind despite the electrostatic repulsion. The peptide cage is stabilized by hydrophobic CADY-CADY contacts thanks to CADY polymorphism. The analysis demonstrates that the hydrophobicity, the presence of several positive charges and the disorder of CADY are mandatory to make stable the CADY-siRNA complexes. [less ▲]

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See detailStandardized evaluation of protein stability.
Thomas, Annick ULg; Joris, Bernard ULg; Brasseur, Robert ULg

in Biochimica et Biophysica Acta (2010)

We compare Mean Force Potential values of a large series of PDB models of proteins and peptides and find that either as monomers or polymers, proteins longer than 200-250 residues have equivalent MFP ... [more ▼]

We compare Mean Force Potential values of a large series of PDB models of proteins and peptides and find that either as monomers or polymers, proteins longer than 200-250 residues have equivalent MFP values that are averaged to -65+/-3kcal/aa. This value is named the standard or stability value. The standard value is reached irrespective of sequences and 3D folds. Peptides are too short to follow the rule and frequently exist as populations of conformers; one exception are peptides in amyloid fibrils. Fibrils surpass the standard value in accordance with their uppermost stability. In parallel, we calculate median MFP values of amino acids in stably folded PDB models of proteins: median values vary from -25 for Gly to -115kcal/aa for Trp. These median values are used to score primary sequences of proteins: all sequences converge to a mean value of -63.5+/-2.5kcal/aa i.e. only 1.5kcal less than the folded model standard. Sequences from unfolded proteins have lower values. This supports the conclusion that sequences carry in an important message and more specifically that diversity of amino acids in sequences is mandatory for stability. We also use the median amino acid MFP to score residue stability in 3D folds. This demonstrates that 3D folds are compromises between fragments of high and fragments of low scores and that functional residues are often, but not always in the extreme score values. The approach opens to possibilities of evaluating any 3D model, of detecting functional residues and should help in conducting mutation assays. [less ▲]

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See detailRealistic modeling approaches of structure-function properties of CPPs in non-covalent complexes.
Thomas, Annick ULg; Lins, Laurence ULg; Divita, G. et al

in Biochimica et Biophysica Acta (2010)

Transfers of cargoes into cells by means of carrier peptides are multi-steps biological phenomenon the mechanisms of which are unclear. We here discuss bases of realistic in silico molecular modeling ... [more ▼]

Transfers of cargoes into cells by means of carrier peptides are multi-steps biological phenomenon the mechanisms of which are unclear. We here discuss bases of realistic in silico molecular modeling approaches of the formation of non-covalent complexes considering CPPs and cargo diversities. [less ▲]

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See detailCholesterol interaction with proteins that partition into membrane domains: an overview.
Epand, Richard M; Thomas, Annick ULg; Brasseur, Robert ULg et al

in Sub Cellular Biochemistry (2010), 51

Biological membranes are complex structures composed largely of proteins and lipids. These components have very different structural and physical properties and consequently they do not form a single ... [more ▼]

Biological membranes are complex structures composed largely of proteins and lipids. These components have very different structural and physical properties and consequently they do not form a single homogeneous mixture. Rather components of the mixture are more enriched in some regions than in others. This can be demonstrated with simple lipid mixtures that spontaneously segregate components so as to form different lipid phases that are immiscible with one another. The segregation of molecular components of biological membranes also involves proteins. One driving force that would promote the segregation of membrane components is the preferential interaction between a protein and certain lipid components. Among the varied lipid components of mammalian membranes, the structure and physical properties of cholesterol is quite different from that of other major membrane lipids. It would therefore be expected that in many cases proteins would have very different energies of interaction with cholesterol vs. those of other membrane lipids. This would be sufficient to cause segregation of components in membranes. The factors that facilitate the interaction of proteins with cholesterol are varied and are not yet completely understood. However, there are certain groups that are present in some proteins that facilitate interaction of the protein with cholesterol. These groups include saturated acyl chains of lipidated proteins, as well as certain amino acid sequences. Although there is some understanding as to why these particular groups favour interaction with cholesterol, our knowledge of these molecular features is not sufficiently developed to allow for the design of agents that will modify such binding. [less ▲]

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See detailInsight into the cellular uptake mechanism of a secondary amphipathic cell penetrating peptide for siRNA delivery.
Konate, K.; Crombez, L.; Deshayes, S. et al

in Biochemistry (2010)

Delivery of siRNA remains a major limitation to their clinical application and several technologies have been proposed to improve their cellular uptake. We recently described a peptide-based nanoparticle ... [more ▼]

Delivery of siRNA remains a major limitation to their clinical application and several technologies have been proposed to improve their cellular uptake. We recently described a peptide-based nanoparticle system for efficient delivery of siRNA into primary cell lines: CADY. CADY is a secondary amphipathic peptide that forms stable complexes with siRNA and improves their cellular uptake independently of the endosomal pathway. In the present work, we have combined molecular modelling, spectroscopy and membrane interaction approaches, in order to gain further insight into CADY/siRNA particle mechanism of interaction with biological membrane. We demonstrate that CADY forms stable complexes with siRNA and binds phospholipids tightly, mainly through electrostatic interactions. Binding to siRNA or phospholipids triggers a conformational transition of CADY from an unfolded state to an -helical structure, thereby stabilizing CADY/siRNA complexes and improving their interactions with cell membranes. Therefore, we propose that CADY cellular membrane interaction is driven by its structural polymorphism which enables stabilization of both electrostatic and hydrophobic contacts with surface membrane proteoglycan and phospholipids. [less ▲]

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See detailStudy of thermomyces ianuginosa lipase in the presence of tributyrylglycerol and water
Santini, Sébastien; Crowet, Jean-Marc ULg; Thomas, Annick ULg et al

in Biophysical Journal (2009), 96(12), 4814-4825

The Thermomyces lanuginosa lipase has been extensively studied in industrial and biotechnological research because of its potential for triacylglycerol transformation. This protein is known to catalyze ... [more ▼]

The Thermomyces lanuginosa lipase has been extensively studied in industrial and biotechnological research because of its potential for triacylglycerol transformation. This protein is known to catalyze both hydrolysis at high water contents and transesterification in quasi-anhydrous conditions. Here, we investigated the Thermomyces lanuginosa lipase structure in solution in the presence of a tributyrin aggregate using 30 ns molecular-dynamics simulations. The water content of the active-site groove was modified between the runs to focus on the protein-water molecule interactions and their implications for protein structure and protein-lipid interactions. The simulations confirmed the high plasticity of the lid fragment and showed that lipid molecules also bind to a secondary pocket beside the lid. Together, these results strongly suggest that the lid plays a role in the anchoring of the protein to the aggregate. The simulations also revealed the existence of a polar channel that connects the active-site groove to the outside solvent. At the inner extremity of this channel, a tyrosine makes hydrogen bonds with residues interacting with the catalytic triad. This system could function as a pipe (polar channel) controlled by a valve (the tyrosine) that could regulate the water content of the active site. [less ▲]

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See detailPepLook: An innovative in silico tool for determination of structure, polymorphism and stability of peptides
Thomas, Annick ULg; Deshayes, Sebastien; Decaffmeyer, Marc et al

in Advances in Experimental Medicine and Biology (2009), 611

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See detailInteresterification of rapeseed oil with anhydrous milk fat and its stearin fraction
Aguedo, Mario ULg; Giet, Jean-Michel ULg; Hanon, Emilien ULg et al

Poster (2009)

Rapeseed oil (RO) (a choice source of unsaturation-rich residues) was used in the present study to enrich anhydrous milk fat (AMF) with unsaturated C18 fatty acids (FA) (oleic, linoleic and linolenic ... [more ▼]

Rapeseed oil (RO) (a choice source of unsaturation-rich residues) was used in the present study to enrich anhydrous milk fat (AMF) with unsaturated C18 fatty acids (FA) (oleic, linoleic and linolenic acids). Comparatively, one “harder” fraction of AMF underwent the same reaction. The physico-chemical properties modifications induced by the reaction were followed. The compositional changes are reported in this first part and the consequent physical modifications are presented in a second part. [less ▲]

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See detailInteresterification of rapeseed oil with anhydrous milk fat and its stearin fraction
Giet, Jean-Michel ULg; Aguedo, Mario ULg; Hanon, Emilien ULg et al

Poster (2009)

The compositional changes occurring during the lipase-catalysed interesterification of AMF/rapeseed oil (RO) and AMF stearin fraction (AMFSF)/RO blends were described in the first part of this study. In ... [more ▼]

The compositional changes occurring during the lipase-catalysed interesterification of AMF/rapeseed oil (RO) and AMF stearin fraction (AMFSF)/RO blends were described in the first part of this study. In the present and second part are reported the resulting changes in physical properties, especially the melting behaviour through solid fat content (SFC), dropping point (DP) and fusion profiles by differential scanning calorimetry (DSC). [less ▲]

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See detailEnrichment of Anhydrous Milk Fat in Polyunsatured Fatty Acid Residues
Aguedo, Mario ULg; Hanon, Emilien ULg; Danthine, Sabine ULg et al

Poster (2009)

Lipozyme TL IM was used in a solvent-free batch, microaqueous system for enzymatic interesterification of anhydrous milkfat (AMF) with linseed oil (LO) in binary blends and with rapeseed oil (RO) in one ... [more ▼]

Lipozyme TL IM was used in a solvent-free batch, microaqueous system for enzymatic interesterification of anhydrous milkfat (AMF) with linseed oil (LO) in binary blends and with rapeseed oil (RO) in one ternary blend. [less ▲]

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See detailComputational Study Of Colipase Interaction With Lipid Droplets And Bile Salt Micelles
Kerfelec, Brigitte; Allouche, Maya; Colin, Damien et al

in Proteins-Structure Function and Bioinformatics (2008), 73(4), 828-38

Colipase is a key element in the lipase-catalyzed hydrolysis of dietary lipids. Although devoid of enzymatic activity, colipase promotes the pancreatic lipase activity in physiological intestinal ... [more ▼]

Colipase is a key element in the lipase-catalyzed hydrolysis of dietary lipids. Although devoid of enzymatic activity, colipase promotes the pancreatic lipase activity in physiological intestinal conditions by anchoring the enzyme at the surface of lipid droplets. Analysis of structures of NMR colipase models and simulations of their interactions with various lipid aggregates, lipid droplet, and bile salt micelle, were carried out to determine and to map the lipid binding sites on colipase. We show that the micelle and the oil droplet bind to the same side of colipase 3D structure, mainly the hydrophobic fingers. Moreover, it appears that, although colipase has a single direction of interaction with a lipid interface, it does not bind in a specific way but rather oscillates between different positions. Indeed, different NMR models of colipase insert different fragments of sequence in the interface, either simultaneously or independently. This supports the idea that colipase finger plasticity may be crucial to adapt the lipase activity to different lipid aggregates. [less ▲]

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See detailPeptides As Drugs: Myth Or Reality?
Decaffmeyer, Marc ULg; Thomas, Annick ULg; Brasseur, Robert ULg

in Biotechnologie, Agronomie, Société et Environnement = Biotechnology, Agronomy, Society and Environment [=BASE] (2008), 12(1),

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See detailRelationships between the orientation and the structural properties of peptides and their membrane interactions.
Lins, Laurence ULg; Decaffmeyer, Marc ULg; Thomas, Annick ULg et al

in Biochimica et biophysica acta (2008), 1778(7-8), 1537-44

Physical properties of membranes, such as fluidity, charge or curvature influence their function. Proteins and peptides can modulate those properties and conversely, the lipids can affect the activity and ... [more ▼]

Physical properties of membranes, such as fluidity, charge or curvature influence their function. Proteins and peptides can modulate those properties and conversely, the lipids can affect the activity and/or the structure of the former. Tilted peptides are short hydrophobic protein fragments characterized by an asymmetric distribution of their hydrophobic residues when helical. They were detected in viral fusion proteins and in proteins involved in different biological processes that need membrane destabilization. Those peptides and non lamellar lipids such as PE or PA appear to cooperate in the lipid destabilization process by enhancing the formation of negatively-curved domains. Such highly bent lipidic structures could favour the formation of the viral fusion pore intermediates or that of toroidal pores. Structural flexibility appears as another crucial property for the interaction of peptides with membranes. Computational analysis on another kind of lipid-interacting peptides, i.e. cell penetrating peptides (CPP) suggests that peptides being conformationally polymorphic should be more prone to traverse the bilayer. Future investigations on the structural intrinsic properties of tilted peptides and the influence of CPP on the bilayer organization using the techniques described in this chapter should help to further understand the molecular determinants of the peptide/lipid inter-relationships. [less ▲]

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See detailHydrophobic Substitutions In The First Residue Of The Crac Segment Of The Gp41 Protein Of Hiv
Vishwanathan, Sa.; Thomas, Annick ULg; Brasseur, Robert ULg et al

in Biochemistry (2008), 47(1), 124-30

We investigated the peptides N-acetyl-AWYIK-amide and N-acetyl-VWYIK-amide corresponding to single amino acid substitutions in LWYIK, a segment found in the gp41 protein of HIV and believed to play a role ... [more ▼]

We investigated the peptides N-acetyl-AWYIK-amide and N-acetyl-VWYIK-amide corresponding to single amino acid substitutions in LWYIK, a segment found in the gp41 protein of HIV and believed to play a role in sequestering this protein to a cholesterol-rich domain in the membrane. The effects of these peptides on the thermotropic phase transitions of 1-stearoyl-2-oleoylphosphatidylcholine (SOPC) and mixtures of SOPC and cholesterol were intermediate between that having the wild-type sequence (LWYIK) and another (IWYIK), the least active peptide previously studied. This correlated with results from studies of single mutations in the gp41 protein of HIV-1, in which L679 of the LWYIK segment is replaced with either A or V, measuring the capability of TZM-BL HeLa-based HIV-1 indicator cells to form syncytia. The peptides were also comparatively analyzed in silico. All together, the results suggest that the mode of interaction of this region of gp41 with the polar heads of membrane lipids contributes to its cholesterol selectivity and that this is somehow related to the biological activity of the viral glycoprotein. [less ▲]

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See detailDetermination Of The Topology Of The Hydrophobic Segment Of Mammalian Diacylglycerol Kinase Epsilon In A Cell Membrane And Its Relationship To Predictions From Modeling
Decaffmeyer, Marc ULg; Shulga, Yv.; Dicu, Ao. et al

in Journal of Molecular Biology (2008), 383(4), 797-809

The epsilon isoform of diacylglycerol kinase (DGKepsilon) is unique among mammalian DGKs in having a segment of hydrophobic amino acids comprising approximately residues 20 to 41. Several algorithms ... [more ▼]

The epsilon isoform of diacylglycerol kinase (DGKepsilon) is unique among mammalian DGKs in having a segment of hydrophobic amino acids comprising approximately residues 20 to 41. Several algorithms predict this segment to be a transmembrane (TM) helix. Using PepLook, we have performed an in silico analysis of the conformational preference of the segment in a hydrophobic environment comprising residues 18 to 42 of DGKepsilon. We find that there are two distinct groups of stable conformations, one corresponding to a straight helix that would traverse the membrane and the second corresponding to a bent helix that would enter and leave the same side of the membrane. Furthermore, the calculations predict that substituting the Pro32 residue in the hydrophobic segment with an Ala will cause the hydrophobic segment to favor a TM orientation. We have expressed the P32A mutant of DGKepsilon, with a FLAG tag (an N-terminal 3xFLAG epitope tag) at the amino terminus, in COS-7 cells. We find that this mutation causes a large reduction in both k(cat) and K(m) while maintaining k(cat)/K(m) constant. Specificity of the P32A mutant for substrates with polyunsaturated acyl chains is retained. The P32A mutant also has higher affinity for membranes since it is more difficult to extract from the membrane with high salt concentration or high pH compared with the wild-type DGKepsilon. We also evaluated the topology of the proteins with confocal immunofluorescence microscopy using NIH 3T3 cells. We find that the FLAG tag at the amino terminus of the wild-type enzyme is not reactive with antibodies unless the cell membrane is permeabilized with detergent. We also demonstrate that at least a fraction of the wild-type DGKepsilon is present in the plasma membrane and that comparable amounts of the wild-type and P32A mutant proteins are in the plasma membrane fraction. This indicates that in these cells the hydrophobic segment of the wild-type DGKepsilon is not TM but takes up a bent conformation. In contrast, the FLAG tag at the amino terminus of the P32A mutant is exposed to antibody both before and after membrane permeabilization. This modeling approach thus provides an explanation, not provided by simple predictive algorithms, for the observed topology of this protein in cell membranes. The work also demonstrates that the wild-type DGKepsilon is a monotopic protein. [less ▲]

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See detailStructural Polymorphism Of Two Cpp: An Important Parameter Of Activity
Deshayes, S.; Decaffmeyer, Marc ULg; Brasseur, Robert ULg et al

in Biochimica et Biophysica Acta-Biomembranes (2008), 1778(5), 1197-205

Despite numerous investigations, the important structural features of Cell Penetrating Peptides (CPPs) remain unclear as demonstrated by the difficulties encountered in designing new molecules. In this ... [more ▼]

Despite numerous investigations, the important structural features of Cell Penetrating Peptides (CPPs) remain unclear as demonstrated by the difficulties encountered in designing new molecules. In this study, we focused our interest on Penetratin and Transportan and several of their variants. Penetratin W48F and Penetratin W48F/W56F exhibit a reduced and a complete lack of cellular uptake, respectively; TP07 and TP10 present a similar cellular uptake as Transportan and TP08, TP13 and TP15 display no or weak internalization capacity. We applied the algorithmic method named PepLook to analyze the peptide polymorphism. The study reveals common conformational characteristics for the CPPs and their permeable variants: they all are polymorphic. Negative, non permeable, mutants share the opposite feature since they are monomorphic. Finally, we support the hypothesis that structural polymorphism may be crucial since it provides peptides with the possibility of adapting their conformation to medium hydrophobicity and or to partner diversity. [less ▲]

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See detailLarge Changes In The Crac Segment Of Gp41 Of Hiv Do Not Destroy Fusion Activity If The Segment Interacts With Cholesterol
Vishwanathan, Sa.; Thomas, Annick ULg; Brasseur, Robert ULg et al

in Biochemistry (2008), 47(45),

The membrane-proximal external region (MPER) of the gp41 fusion protein of HIV is highly conserved among isolates of this virus and is considered a target for vaccine development. This region also appears ... [more ▼]

The membrane-proximal external region (MPER) of the gp41 fusion protein of HIV is highly conserved among isolates of this virus and is considered a target for vaccine development. This region also appears to play a role in membrane fusion as well as localization of the virus to cholesterol-rich domains in membranes. The carboxyl terminus of MPER has the sequence LWYIK and appears to have an important role in cholesterol interactions. We have tested how amino acid substitutions that would affect the conformational flexibility of this segment could alter its interaction with cholesterol. We studied a family of peptides (all peptides as N-acetyl-peptide amides) with P, G, or A substituting for W and I of the LWYIK sequence. The peptide having the greatest effect on cholesterol distribution in membranes was the most flexible one, LGYGK. The corresponding mutation in gp41 resulted in a protein retaining 72% of the fusion activity of the wild-type protein. Two other peptides were synthesized, also containing two Gly residues, GWGIK and LWGIG, and did not have the ability to sequester cholesterol as efficiently as LGYGK did. Making the corresponding mutants of gp41 showed that these other two double Gly substitutions resulted in proteins that were much less fusogenic, although they were equally well expressed at the cell surface. The study demonstrates that drastic changes can be made in the LWYIK segment with the retention of a significant fraction of the fusogenic activity, as long as the mutant proteins interact with cholesterol. [less ▲]

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See detailEnrichment of anhydrous milk fat in polyunsatured fatty acid residues from linseed and rapeseed oil through enzymatic interesterification
Aguedo, Mario ULg; Hanon, Emilien ULg; Danthine, Sabine ULg et al

Poster (2007)

The interesterification, or ester exchange, between two fats leads to the rearrangement of acyl moieties in both. The use of a sn-1,3-specific lipase confines the exchange of fatty acid residues to the sn ... [more ▼]

The interesterification, or ester exchange, between two fats leads to the rearrangement of acyl moieties in both. The use of a sn-1,3-specific lipase confines the exchange of fatty acid residues to the sn-1 and sn-3 positions of triacylglycerides (TAG), generating products with characteristics that cannot be obtained through a chemical process or a blending. Such reactions require mild conditions with no solvent needed and they yield no unhealthful trans fatty acids, justifying the stepped-up interest of enzymatic interesterification for the production of margarines and other food fats. The aim of this work was to use enzymatic interesterification to enrich anhydrous milk fat (AMF) with unsaturated fatty acid C18 residues from linseed oil (LO) and eventually from rapeseed oil (RO) through some binary blends and one ternary blend. For that, the 1,3-specific lipase from Thermomyces lanuginosa (Lipozyme TL IM) was used in solvent-free batch and micro-aqueous reactions and fat blends with different mass ratios were tested. The evolution of TAG profiles, of interesterification degre (ID) and of free fatty acids (FFA), was followed along the reactions. Determination of dropping points (DP) and solid fat contents (SFC) enabled a rheological characterization of the products. The end products were also characterized for their oxidative stability and their textural properties. [less ▲]

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