Native-like {beta}-hairpin structure in an isolated fragment from ferredoxin: NMR and CD studies of solvent effects on the N-terminal 20 residues

The conformational properties of protein fragments have beenwidely studied as models of the earliest initiation events inprotein folding. While native-like -helices and ß-turnshave been identified, less is known about the factors that underlyß-sheet formation, in particular ß-hairpins,where considerably greater long-range order is required. TheN-terminal 20 residue sequence of native ferredoxin I (fromthe blue-green alga Aphanothece sacrum ) forms a ß-hairpinin the native structure and has been studied in isolation byNMR and CD spectroscopy. Local native-like interactions aloneare unable to stabilize significantly a folded conformationof the 20-residue fragment in purely aqueous solution. However,we show that the addition of low levels of organic co-solventspromotes formation of native-like ß-hairpin structure.The results suggest an intrinsic propensity of the peptide toform a native-like ß-hairpin structure, and that theorganic co-solvent acts in lieu of the stabilizing influenceof tertiary interactions (probably hydrophobic contacts) whichoccur in the folding of the complete ferredoxin sequence. Thestructure of the isolated hairpin, including the native-likeregister of interstrand hydrogen bonding interactions, appearsto be determined entirely by the amino acid sequence. The solventconditions employed have enabled this intrinsic property tobe established.     

The {alpha}/{beta} hydrolase fold

We have identified a new protein fold—the /ßhydrolase fold—that is common to several hydrolytic enzymesof widely differing phylogenetic origin and catalytic function.The core of each enzyme is similar: an /ß sheet, notbarrel, of eight ß-sheets connected by -helices. Theseenzymes have diverged from a common ancestor so as to preservethe arrangement of the catalytic residues, not the binding site.They all have a catalytic triad, the elements of which are borneon loops which are the best-conserved structural features inthe fold. Only the histidine in the nucleophile-histidine-acidcatalytic triad is completely conserved, with the nucleophileand acid loops accommodating more than one type of amino acid.The unique topological and sequence arrangement of the triadresidues produces a catalytic triad which is, in a sense, amirror-image of the serine protease catalytic triad. There arenow four groups of enzymes which contain catalytic triads andwhich are related by convergent evolution towards a stable,useful active site: the eukaryotic serine proteases, the cysteineproteases, subtilisins and the /ß hydrolase fold enzymes.     

Functional diversity of the phosphoglucomutase superfamily: structural implications

Three-dimensional structural models of three members of thephosphoglucomutase (PGM) superfamily, parafusin, phosphoglucomutase-relatedprotein and sarcoplasmic reticulum phosphoglucomutase, wereconstructed by homology modeling based on the known crystalstructure of rabbit muscle phosphoglucomutase. Parafusin, phosphoglucomutase-relatedprotein and sarcoplasmic reticulum phosphoglucomutase each have50% or more identity with rabbit muscle phosphoglucomutase atthe amino acid level and all are reported to exhibit no or minorphosphoglucomutase activity. There are four major insertionsand two deletions in the parafusin sequence relative to PGM,all of which are located in surface-exposed loops connectingsecondary structural elements. The remaining amino acid substitutionsare distributed throughout the sequence and are not predictedto alter the polypeptide fold. Parafusin contains a putativeprotein kinase C site located on a surface loop in domain IIthat is not present in the homologs. Although the general domainstructure and the active site of rabbit muscle phosphoglucomutaseare preserved in the model of phosphoglucomutase-related protein,a major structural difference is likely to occur in domain 1due to the absence of 55 amino acid residues in PGM-RP. Thisdeletion predicts the loss of three -helices and one ß-strandfrom an anti-parallel ß-sheet in this domain as comparedwith the rabbit muscle phosphoglucomutase.     

{beta}-sheet folding of fragment (16-36) of bovine pancreatic trypsin inhibitor as predicted by Monte Carlo simulated annealing

A tertiary structure prediction is described using Monte Carlosimulated annealing for the peptide fragment corresponding toresidues 16–36 of bovine pancreatic trypsin inhibitor(BPTI). The simulation starts with randomly chosen initial conformationsand is performed without imposing experimental constraints usingenergy functions given for generic interatomic interactions.Out of 20 simulation trials, seven conformations show a sheet-likestructure—two strands connected by a turn—althoughthis sheet-like structure is not as rigid as that observed innative BPTI. It is also shown that these conformations are mostlylooped and exhibit a native- like right-handed twist. Unlikethe case with the C-peptide of RNase A, no conspicuous -helicalstructure is found in any of the final conformations obtainedin the simulation. However, the lowest-energy conformation doesnot resemble exactly the native structure. This indicates thatthe rigid ß-sheet conformation of native BPTI merelycorresponds to a local minimum of the energy function if thefragment with residues 16–36 is isolated from the nativeprotein. A statistical analysis of all 20 final conformationssuggests that the tendency for the peptide segments to formextended ß-strands is strong for those with residues18–24, and moderate for those with residues 30–35.The segment of residues 25–29 does not tend to form anydefinite structure. In native BPTI, the former segments areinvolved in the ß-sheet and the latter in the turn.A folding scenario is also speculated from this analysis.     

Aspartic acid 50 and tyrosine 108 are essential for receptor binding and cytotoxic activity of tumour necrosis factor beta (lymphotoxin)

Single amino acid substitutions were generated in predictedhydrophilic loop regions of the human tumour necrosis factorbeta (TNF-ß) molecule, and the mutant proteins wereexpressed in Escherichia coli and purified. Mutants with singleamino acid changes at either of two distinct loop regions, atpositions aspartic acid 50 or tyrosine 108, were found to havegreatly reduced receptor binding and cytotoxic activity. Thesetwo regions in TNF-ß correspond to known loop regionswhere mutations also result in loss of biological activity ofTNF–, a related cytokine which shares the same cellularreceptors with TNF-ß. The two distinct loops at positions31-34 and 84-89 in the known three-dimensional structure ofTNF- (equivalent to positions 46–50 and 105–110respectively in TNF-ß), lie on opposite sides of theTNF- monomer. When the TNF-a monomer forms a trimer, the twoloops, each from a different subunit of the trimer, come togetherand lie in a cleft between adjacent subunits. Together, thesefindings suggest that a TNF receptor binds to a cleft betweensubunits via surface loops at amino acid residues 31–34and 84–89 in TNF–, and similarly via surface loopsincluding amino acids aspartic acid 50 and tyrosine 108 in TNF–ß.     

Model structures and action of interleukin 1 and its antagonist

A comparison has been made between the homology and hydrophobkityprofiles of six interleukin amino add sequences and that ofthe human interleukin 1ß (IL-lß) for whicha crystal structure exists. The resulting sequence alignmentwas used to build model structures for the sequences for threeIL-l, two IL-1ß and an interleukin receptor antagonist.Analysis of these structures demonstrates that the interleukinmolecule has a strong electric dipole which is generated bythe topological position of the amino acids in the sequence.Electrostatic surface calculations implicate a particular residues(Lysl45) as being fundamental to interleukin activity and thissupports site-directed mutation evidence that this residue isrequired for activity.     

Protein modification from mutational analysis of an autologous peptide fragment

In the -complementation of ß-galactosidase an N-terminalpeptide fragment (-peptide) of the wild-type enzyme interactswith a defective ß-galactosidase enzyme to restorecapacity for subunit assembly and activity. We have used previouslya random mutagenesis and screening approach to identify a pentapeptideresidue tract in the -peptide that was highly tolerant of residuesubstitution, with some mutations conferring improved function.This tract is of clear importance for -peptide function butis apparently dispensible in the intact parental enzyme. Toinvestigate this further, we selected tract mutations and placedthem into intact ß-galactosidase, at the correspondingN-terminal position as in the -peptide. We then tested whethersuch specific tract sequences conferred properties to the wholeenzyme which could be predicted from the behaviour of the defectiveenzyme complemented with the corresponding mutant -peptide.This was shown for mutations which positively or negativelyaffected enzyme stability. Additionally, a subset of mutationswhich affected complementation efficiency in vivo were predictedto affect the formation of higher-order structures in the intactprotein, and this was observed experimentally. Mutations whichdecreased peptide complementation dramatically decreased thelevel of formation of multimers in the intact protein and amutation which increased peptide complementation produced markedenhancement of multimer formation in a protein with a preexistingimpairment in higher-order structure formation. Such subtleeffects are difficult to detect directly in the whole proteinby randomization/selection approaches, but in the complementingpeptide the role of the residues within the pentapeptide tractis effectively amplified. Identification of residue tracts exhibitingfunctional tolerance to amino acid substitution in an activepeptide fragment can thus be combined with transferral of potentiallyuseful mutant peptide sequences back into the intact protein.Manipulation of a complementation system in this manner affordsa sensitive approach towards targeted improvement of proteins.     

Cloning of rabbit interleukin-1{beta}: differential evolution of IL-1{alpha} and IL-1{beta} proteins

We have cloned the rabbit IL-1ß cDNA, which encodesa 268 amino acid precursor similar in length to other sequencedIL-1 precursors. Comparison of all published IL-1 and IL-1ßsequences respectively indicates that the IL-1 gene family isevolving faster than the IL-1ß family, and that thetwo genes diverged –270 million years ago. Surprisingly,there are differences in the regions preferentially conservedwithin the two families. The IL-1 family is most conserved atthe amino terminus whereas the IL-1ß family is mostconserved in the carboxy-terminal half. This is despite thefact that the carboxy-terminal half encodes the active portionof both molecules and would be expected to adopt a similar ß-sheetstructure in IL-1 as in the published X-ray structure of matureIL-1ß. These findings suggest that differences inthe function and properties of the IL-1 and IL-1ßprecursor molecules may have been conserved. These differencesmay therefore provide an explanation for the existence of twoIL-1 molecules.     

Family of G protein {alpha} chains: amphipathic analysis and predicted structure of functional domains

The G proteins transduce hormonal and other signals into regulationof enzymes such as adenylyl cyclase and retinal cGMP phosphodiesterase.Each G protein contains an subunit that binds and hydrolyzesguanine nucleotides and interacts with ß subunitsand specific receptor and effector proteins. Amphipathic andsecondary structure analysis of the primary sequences of fivedifferent chains (bovine _s, _t1 and _t2, mouse _i, and rat _o)predicted the secondary structure of a composite chain (_avg).The chains contain four short regions of sequence homologousto regions in the GDP binding domain of bacterial elongationfactor Tu (EF-Tu). Similarities between the predicted secondarystructures of these regions in _avg and the known secondary structureof EF-Tu allowed us to construct a three-dimensional model ofthe GDP binding domain of _avg. Identification of the GDP bindingdomain of _avg defined three additional domains in the compositepolypeptide. The first includes the amino terminal 41 residuesof _avg, with a predicted am phipathic helical structure; thisdomain may control binding of the chains to the ßcomplex. The second domain, containing predicted ßstrands and helices, several of which are strongly amphipathic,probably contains sequences responsible for interaction of chains with effector enzymes. The predicted structure of thethird domain, containing the carhoxy terminal 100 amino acids,is predominantly ß sheet with an amphipathic helixat the carboxy terminus. We propose that this domain is reponsiblefor receptor binding. Our model should help direct further experimentsinto the structure and function of the G protein chain.     

Permuteins of interleukin 1{beta}--a simplified approach for the construction of permutated proteins having new termini

A technique for the rapid and simple generation of permutatedversions of the interleukin-1ß (IL-1ß) geneis described. In this method, the human IL-1ß cDNAis twice amplified by the polymerase chain reaction (PCR) andthe resulting DNA fragments are ligated in tandem. Between thetwo genes, the DNA sequence encodes a short four amino acidloop to link the native N- and C-terminal ends of the IL-1ßprotein. By using PCR amplification from this starting template,a new version of the IL-1ß cDNA was obtained thatencodes a permutated form of the IL-1ß protein wherethe new N- and C-terminal amino acids correspond to residues65 and 64 of the native IL-1ß sequence, respectively.The name ‘permutein’ is proposed to describe proteinsgenerated by this technology. The molecular profile (IL-1 receptorbinding, biologic activity and solution properties) of the IL-1permutein produced by this technology, permutein 65/64, is shownto be identical to that of native IL-1ß The approachshould be useful to define further the structural features ofthis protein that are important for its function.     

Expression of the synthetic gene of an artificial DDT-binding polypeptide in Escherichia coli

This paper reports the expression of an artificial functionalpolypeptide in bacteria. The gene of a designed 24-residue DDT-bindingpolypeptide (DBP) was inserted between the BamHI and PstI cleavagesites of plasmid pUR291. The hybrid plasmid, pUR291-DBP, wascloned in Escherichia coli JM109. After induction by isopropyl-ß-D-thiogalactopyranosidea fusion protein was expressed in which DBP was linked to theCOOH-termiuus of ß-galactosidase. DBP, which is stableto trypsin, was obtained by tryptic digestion of the fusionprotein and subsequent fractionation of the tryptic peptidesby reversed-phase h.p.l.c. Recombinant and chemically synthesizedDBP showed identical chromatographic properties, amino acidcomposition, and chymotryptic digestion patterns. Both the ß-galactosidase-DBPfusion and isolated recombinant DBP bound DDT. The fusion proteinwas 25 times as potent as the designed 24-residue DBP in activatinga cytochrome P-450 model system using equimolar catalytic amountsof the two proteins.     

The cystine knot of a squash-type protease inhibitor as a structural scaffold for Escherichia coli cell surface display of conformationally constrained peptides

The Ecballium elaterium trypsin inhibitor II (EETI-II), a memberof the squash family of protease inhibitors, is composed of28 amino acid residues and is a potent inhibitor of trypsin.Its compact structure is defined by a triple-stranded antiparallelß-sheet, which is held together by three intramoleculardisulfide bonds forming a cystine knot. In order to explorethe potential of the EETI-II peptide to serve as a structuralscaffold for the presentation of randomized oligopeptides, weconstructed two EETI-II derivatives, where the six-residue inhibitorloop was replaced by a 13-residue epitope of Sendai virus L-proteinand by a 17-residue epitope from human bone Gla-protein. EETI-IIand derived variants were produced via fusion to maltose bindingprotein MalE. By secretion of the fusion into the periplasmicspace, fully oxidized and correctly folded EETI-II was obtainedin high yield. EETI-II and derived variants could be presentedon the Escherichia coli outer membrane by fusion to truncatedLpp'–OmpA', which comprises the first nine residues ofmature lipoprotein plus the membrane spanning ß-strandfrom residues 46–66 of OmpA protein. Gene expression wasunder control of the strong and tightly regulated tetA promoter/operator.Cell viability was found to be drastically reduced by high levelexpression of Lpp'–OmpA'–EETI-II fusion protein.To restore cell viability, net accumulation of fusion proteinin the outer membrane was reduced to a tolerable level by introductionof an amber codon at position 9 of the lpp' sequence and utilizingan amber suppressor strain as expression host. Cells expressingEETI-II variants containing an epitope were shown to be surfacelabeled with the respective monoclonal antibody by indirectimmunofluorescence corroborating the cell surface exposure ofthe epitope sequences embedded in the EETI-II cystine knot scaffold.Cells displaying a particular epitope sequence could be enriched10⁷-fold by combining magnetic cell sorting with fluorescence-activatedcell sorting. These results demonstrate that E.coli cell surfacedisplay of conformationally constrained peptides tethered tothe EETI-II cystine knot scaffold has the potential to becomean effective technique for the rapid isolation of small peptidemolecules from combinatorial libraries that bind with high affinityto acceptor molecules.     

Studies of the pore-forming domain of a voltage-gated potassium channel protein

Recent mutagenesis studies nave identified a stretch of aminoacid residues which form the ion-selective pore of the voltage-gatedpotassium channel. It has been suggested that this sequenceof amino acids forms a ß-barrel structure making upthe structure of the ion-selective pore [Hartman,H.A., Kirsch,G.E.,DreweJ.A., Taglialatela.M., Joho.R.H. and Brown,A.M. (1991)Science, 251, 942–944; YeUen.G., Jurman,M.E., Abramson,T.and MacKinnon,R. (1991) Science, 251, 939–942; Yool,AJ.and Schwarz.T.L. (1991) Nature, 349, 700–704]. We havesynthesized a polypeptide corresponding to this amino add sequence(residues 431–449 of the ShA potassium channel from Drosophila).A tetrameric version of this sequence was also synthesized byUnking together four of these peptldes onto a branching lysinecore. Fourier transform infrared (FT-LR) and circular dichroism(CD) spectroscopy have been used to investigate the structureof these peptides after their reconstitution into lyso phos-phatidylcholinemicelles and lipid bilayers composed of dimyristoyl phosphatidyfcholineand dimyristoyl phosphatidyl-glycerol. The spectroscopic studiesshow that these peptides are predominantly a-helical in theselipid environments. When Incorporated into planar lipid bilayersboth peptides induce ion channel activity. Molecular modellingstudies based upon the propensity of these peptides to forman -helical secondary structure in a hydrophobfc environmentare described. These results are discussed in the light of recentmutagenesis and binding studies of the Drosophila Shaker potassiumion channel protein     

Solution structure and dynamics of a serpin reactive site loop using interleukin 1 as a presentation scaffold

Human interleukin-1ß (IL1ß) was used as a presentationscaffold for the characterization of the reactive site loop(RSL) of the serpin 1-antitrypsin (A1AT), the physiologicalinhibitor of leukocyte elastase. A chimeric protein was generatedby replacement of residues 50–53 of IL1ß, correspondingto an exposed reverse turn in IL1ß, with the 10-residueP5-P5' sequence EAIPMSIPPE from A1AT. The chimera (antitrypsin-interleukin,AT-IL) inhibits elastase specifically and also binds the IL1ßreceptor. Multinuclear NMR characterization of AT-IL establishedthat, with the exception of the inserted sequence, the structureof the IL1ß scaffold is preserved in the chimera. Thestructure of the inserted RSL was analyzed relative to thatof the isolated 10-residue RSL peptide, which was shown to beessentially disordered in solution. The chimeric RSL was alsofound to be solvent exposed and conformationally mobile in comparisonwith the IL1ß scaffold, and there was no evidence of persistinginteractions with the scaffold outside of the N- and C-terminallinkages. However, AT-IL exhibits sigificant differences inchemical shift and NOE patterns relative to the isolated RSLthat are consistent with local features of non-random structure.The proximity of these features to the P1-P1' residues suggeststhat they may be responsible for the inhibitory activity ofthe chimera.     

Structural and functional domains in human tumour necrosis factors

Human tumour necrosis factors (hTNFs) and ß are relatedpleiotropic cytokines which share many activities and competewith each other for binding to two receptor components on manycell types. Although structural and biological data indicatethat the active form of hTNF- may be a symmetrical trimer, themanner in which hTNFs interact with their receptors to triggera myriad of cell type-dependent responses is not clear. A combinationof chemical modification, epitope mapping and site-directedmutagenesis approaches suggest that at least four distinct peptidesequences are Important for the biological activity of hTNF-.In particular, certain peptide sequences between amino acidpositions 11 and 35 in hTNF- appear to be critical for receptorbinding and triggering biological responses. The recent cloningof the two hTNF-/ß receptors opens the way for precisemapping of the functional domains in hTNFs     

Functionally essential, invariant glutamate near the C-terminus of strand {beta}5 in various ({alpha}/{beta})8-barrel enzymes as a possible indicator of their evolutionary relatedness

Twelve different (/ß)₈-barrel enzymes belonging tothree structurally distinct families were found to contain,near the C-terminus of their strand ß5, a conservedinvariant glutamic acid residue that plays an important functionalrole in each of these enzymes. The search was based on the ideathat a conserved sequence region of an (/ß)₈-barrelenzyme should be more or less conserved also in the equivalentpart of the structure of the other enzymes with this foldingmotif owing to their mutual evolutionary relatedness. For thispurpose, the sequence region around the well conserved fifthß-strand of a-amylase containing catalytic glutamate(Glu230, Aspergillus oryzae -amylase numbering), was used asthe sequence-structural template. The isolated sequence stretchesof the 12 (/ß)₈-barrels are discussed from both thesequence-structural and the evolutionary point of view, theinvariant glutamate residue being proposed to be a joining featureof the studied group of enzymes remaining from their ancestral(/ß)₈-barrel     

Detection of secondary structure elements in proteins by hydrophobic cluster analysis

Hydrophobic cluster analysis (HCA) is a protein sequence comparisonmethod based on -helical representations of the sequences wherethe size, shape and orientation of the clusters of hydrophobicresidues are primarily compared. The effectiveness of HCA hasbeen suggested to originate from its potential ability to focuson the residues forming the hydrophobic core of globular proteins.We have addressed the robustness of the bidimensional representationused for HCA in its ability to detect the regular secondarystructure elements of proteins. Various parameters have beenstudied such as those governing cluster size and limits, thehydrophobic residues constituting the clusters as well as thepotential shift of the cluster positions with respect to theposition of the regular secondary structure elements. The followingresults have been found to support the -helical bidimensionalrepresentation used in HCA: (i) there is a positive correlation(clearly above background noise) between the hydrophobic clustersand the regular secondary structure elements in proteins; (ii)the hydrophobic clusters are centred on the regular secondarystructure elements; (iii) the pitch of the helical representationwhich gives the best correspondence is that of an -helix. Thecorrespondence between hydrophobic clusters and regular secondarystructure elements suggests a way to implement variable gappenalties during the automatic alignment of protein sequences.     

Biosynthesis of winter flounder antifreeze proprotein in E.coli

A semisynthetic winter flounder antifreeze proprotein (proAFP)coding region was constructed and inserted into a lacZ expressionvector. ProAFP was produced from the vector in Escherichia colias a C-terminal fusion to the first 289 amino acids of ß-galactosidase(ß-gal). The proAFP and ß-gal domains ofthe ß-gal–proAFP fusion protein were separatedby the recognition signal for the blood coagulation protease,factor X_a. Upon induction with isopropylthio-ß-D-galactosidethe fusion protein accumulated to levels of 15% of the totalprotein. The ß-gal–proAFP fusion protein waspartially purified by differential centrifugation, but requiredsolubilization prior to factor X_a digestion. The solubilizedfusion protein was efficiently and correctly cleaved by factorX_a, after which the proAFP was purified by gel permeation. BacterialproAFP was indistinguishable from natural proAFP by the criteriaof antifreeze activity, amino-terminal sequence (15 cycles),reverse-phase HPLC and SDS–polyacrylamide gel electrophoresis.Circular dichroism measurements showed that proAFP is a compositeof random coil and -helical secondary structure, with an -helicalcontent of 44% at 0°C. It seems probable that the C-terminalregion of proAFP, which corresponds to the mature AFP protein,is mainly -helical, and that the N-terminal pro-segment is randomcoiled.     

Main-chain complementarity in protein-protein recognition

We present a statistical analysis of protein structures basedon interatomic C_a distances. The overall distance distributionsreflect in detail the contents of sequence-specific substructuresmaintained by local interactions (such as -helixes) and longerrange interactions (such as disulfide bridges and ß-sheets).We also show that a volume scaling of the distances makes distancedistributions for protein chains of different length superimposable.Distance distributions were also calculated specifically foramino acids separated by a given number of residues. Specificfeatures in these distributions are visible for sequence separationsof up to 20 amino acid residues. A simple representation, whichpreserves most of the information in the distance distributions,was obtained using six parameters only. The parameters giverise to canonical distance intervals and when predicting coarse-graineddistance constraints by methods such as data-driven artificialneural networks, these should preferably be selected from theseintervals. We discuss the use of the six parameters for determiningor reconstructing 3-D protein structures.     

Molecular modeling of the amyloid-{beta}-peptide using the homology to a fragment of triosephosphate isomerase that forms amyloid in vitro

The main component of the amyloid senile plaques found in Alzheimer'sbrain is the amyloid-ß-peptide (Aß), a proteolyticproduct of a membrane precursor protein. Previous structuralstudies have found different conformations for the Aßpeptide depending on the solvent and pH used. In general, theyhave suggested an -helix conformation at the N-terminal domainand a ß-sheet conformation for the C-terminal domain.The structure of the complete Aß peptide (residues 1–40)solved by NMR has revealed that only helical structure is presentin Aß. However, this result cannot explain the large ß-sheetAß aggregates known to form amyloid under physiologicalconditions. Therefore, we investigated the structure of Aßby molecular modeling based on extensive homology using theSmith and Waterman algorithm implemented in the MPsrch program(Blitz server). The results showed a mean value of 23% identitywith selected sequences. Since these values do not allow a clearhomology to be established with a reference structure in orderto perform molecular modeling studies, we searched for detailedhomology. A 28% identity with an /ß segment of a triosephosphateisomerase (TIM) from Culex tarralis with an unsolved three-dimensionalstructure was obtained. Then, multiple sequence alignment wasperformed considering Aß, TIM from C.tarralis and anotherfive TIM sequences with known three-dimensional structures.We found a TIM segment with secondary structure elements inagreement with previous experimental data for Aß. Moreover,when a synthetic peptide from this TIM segment was studied invitro, it was able to aggregate and to form amyloid fibrils,as established by Congo red binding and electron microscopy.The Aß model obtained was optimized by molecular dynamicsconsidering ionizable side chains in order to simulate Aßin a neutral pH environment. We report here the structural implicationsof this study.