Clustering and Cooperative Dynamics in Reactive MixturesDisparate fluids can evolve into structurally arrestedstates, either of glass or gel type, with <strong>di</strong>fferentvariables serving as a control parameter [1]. Weconcentrate on the idea that clusters of correlatedparticles are at the basis of glass formation an<strong>di</strong>nvestigate how the dynamics and clustering are, infact, intimately related [2, 3].Experimental stu<strong>di</strong>es provi<strong>di</strong>ng evidence for aquantitative connection of this type are generallyprevented by the absence of <strong>di</strong>rect access to relevantcluster properties in real systems. We have exploitedparticle clustering that occurs by stepwiseaggregation in a two-component reactive mixture(DGEBA-DETA N e:N a). Step polymerization is a selforganizationprocess able to generate permanentmolecular clusters similar in shape to the transientones observed in cooperativity stu<strong>di</strong>es. While theirgeometry and mass <strong>di</strong>stribution depends on anumber of factors, their average size x n (i.e., theaverage number of monomers per molecule) turnsout to be only dependent on the functionality (i.e.,reactive groups per molecule) of the reagents andthe number of bonds created, accor<strong>di</strong>ng tox n(α)=1/(1-f α), where α is the chemical conversion,and f=2N e/(N e+N a) denotes the average functionalityof the system. Thus, knowing f for a given mixtureand measuring α by <strong>di</strong>fferential scanning calorimetry,enabled us to calculate the average size x n ofmolecular clusters making up the system at any timeof reaction. x n <strong>di</strong>splays critical behavior at α=1/f.The structural dynamics of our reactive system wasmonitored throughout reaction by VH depolarizedphoton correlation spectroscopy, probing opticalanisotropy fluctuations, which arrest at the glasstransition. Instead, the technique is blind to theformation of a gel phase. The structural relaxationtime τ exhibits a strongly nonlinear dependence onα. Figure 1, showing logτ versus x n for <strong>di</strong>fferentreactions, reveals how the x n and the τ data,independently determined, relate to each other. Wefind that the x n dependence of τ is expressedremarkably well by an exponential law, that is,τ ∝ exp(Bx n). This means that the relaxation time<strong>di</strong>verges, determining a structurally arrested glassstate, when the average size of particle clustersbecomes infinite.The Adam-Gibbs model provides a convenientframework for interpreting our fin<strong>di</strong>ng. One canargue that a monomer involved in a rearrangementis likely to take its bonded monomers along, so thatthe average number of particles in the system thatcooperate to move grows proportionally to x n. Thus,an exponential variation of τ with x n would beexpected, as we find to be the case.In conclusion, our data reveal the cluster propertyinvolved in the glasslike arrest and its quantitativelink with the structural relaxation time. We find thatincreasing the average size of clusters of bondedparticles causes the dynamics to slowdownprogressively in such a way that, <strong>di</strong>fferently fromgelation, an arrested glass state forms (τ→∞) whenx n <strong>di</strong>verges. The behavior of x n correlates to the sizeof the ‘cooperatively rearranging regions’ postulatedby the Adam-Gibbs model for glass forming liquids.These results have two implications. First, they bringout a major <strong>di</strong>fference between the glass andgelation transitions in terms of the cluster propertywhich is relevant to the transition [2]: a glass resultswhen the average number of particles in a cluster(x n) tends to infinity; by contrast, the gelationtransition is known to occur when the weightaveragecluster size (x w) <strong>di</strong>verges due to theformation of the first particle network of macroscopicsize. Second, our fin<strong>di</strong>ngs suggest that the steppolymerization process generates clusters that,although they are of a non-transient nature, behavemuch like dynamical heterogeneities observed insupercooled liquids [3]. Their size, in particular,identifies a growing, <strong>di</strong>verging lengthscale associatedwith the cooperative dynamics of the system.2N e:N a1 10:35:25:2.804:310:9-1N a/N e0.2 0.4 0.6 0.8 1.0-21.00.9-3α 00.80.7-40.62 3 4 5 6 7 8 9 10xFig.1. Semilogarithmic plot n of the structuralrelaxation time τ, vs the average size x n of clustersgrown by polymerization, for five DGEBA-DETA N e:N acompositions as in<strong>di</strong>cated. The data follow straightlines for more than five decades in τ. In the frame ofthe Adam-Gibbs model, an exponential variation of τwith x n, in a process at constant temperature,supports a <strong>di</strong>rect relationship between x n and the sizeof the CRRs. In the inset: Dependence on the molarratio N a/N e between the reagents, of the values α 0 atwhich the τ data (<strong>di</strong>rectly analyzed as a function of α)tend to <strong>di</strong>verge. They match the expected variationof 1/f=[1+(N a/N e)]/2 (solid line).log 10τ(s)References[1] S. Corezzi, D. Fioretto, P. Rolla, Nature 420, 653(2002)[2] S. Corezzi, L. Palmieri, J.M. Kenny, D. Fioretto, J.Phys.: Condens. Matter 17, S3557 (2005)[3] S. Corezzi, D. Fioretto, J.M. Kenny, Phys. Rev.Lett. 94, 065702 (2005)Authors:S. Corezzi (a), D. Fioretto (b), and J.M. Kenny (c)(a) CRS-SOFT and <strong>Dipartimento</strong> <strong>di</strong> <strong>Fisica</strong>, Università<strong>di</strong> Roma La <strong>Sapienza</strong>, Roma (Italy); (b) CRS-SOFTand <strong>Dipartimento</strong> <strong>di</strong> <strong>Fisica</strong>, Università <strong>di</strong> Perugia,Perugia (Italy); (c) Materials Engineering Center,Università <strong>di</strong> Perugia, Terni (Italy)89SOFT Scientific <strong>Report</strong> 2004-06
Scientific <strong>Report</strong> – Self Assembly, Clustering, Structural arrestRole of metal ions in protein aggregation processesAmyloidosis is a family of pathologies caused by thetransition of endogenous proteins and peptides fromthe physiological globular configuration to apathological fibrillar state. The term amyloidosisdescribes a heterogeneous group of <strong>di</strong>seases (morethan 20), which are characterized by extra-cellulardeposition of fibrillar material. Among them, theAlzheimer’s <strong>di</strong>sease (AD) is a progressive anddevastating neurodegenerative pathology affectingan important fraction of the aged population in thedeveloped world. AD is characterized by memory<strong>di</strong>sorders, degradation of the personality and otherbehavioural abnormalities correlated to the loss ofneurons from cortex and hippocampus. These eventsare accompanied by peculiar morphologicalmanifestations like formation of senile plaques in thebrain, amyloidosis of brain vessels and intraneuronaldeposits of amyloid fibrils. The majorcomponent of the AD amyloid plaques are the β-amyloid peptides (Aβ). It has been observed thatplaques contain large amounts of transition metalslike Cu, Fe and Zn (the last one being the mostabundant). Their role is not yet fully understood, butit has been conjectured to be crucial in thepathological effects of AD. X-ray absorptionspectroscopy (XAS) can be profitably used forstructural stu<strong>di</strong>es on biological material [1-3], as thetechnique can be employed for samples in any stateof aggregation, in particular for proteins in solution,thus allowing investigations in physiologicalcon<strong>di</strong>tions. Owing to its chemical selectivity andsensitivity to the local atomic arrangement aroundthe absorber, one can get a clear-cut identification ofthe amino acid residues primarily bound to themetal. XAS has been used to investigate the localstructure around the ion in samples of Aβ-peptidescomplexed with Cu 2+ or Zn 2+ . Our data show<strong>di</strong>fferent metal bin<strong>di</strong>ng site structures in β-amyloidpeptides accor<strong>di</strong>ng to whether they are complexedwith Cu 2+ or Zn 2+ ions. While the geometry aroundcopper is stably consistent with an intra-peptidebin<strong>di</strong>ng with three metal-coor<strong>di</strong>nated Histi<strong>di</strong>neresidues, the zinc coor<strong>di</strong>nation mode depends onspecific solution con<strong>di</strong>tions. In particular, <strong>di</strong>fferentsample preparations are seen to lead to <strong>di</strong>fferentgeometries around the absorber that are compatiblewith either an intra- or an inter-peptide coor<strong>di</strong>nationmode (fig. 1). This result reinforces the hypothesisthat assigns <strong>di</strong>fferent physiological roles to the twometals, with Zn favoring peptide aggregation and, asa consequence, plaque formation. The human priona) b) c)Fig. 1: Schematic illustration of the structures of(Cu–Aβ) 1 (panel a), (Zn–Aβ) 1 (panel b) and (Zn–Aβ) 2(panel c), as they emerge from the fit to the data.Only metal–Histi<strong>di</strong>ne bonds are explicitly shown. TheAβ-peptide backbone is drawn as a shoe string (fromRef. [3])protein binds Cu 2+ ions in the octarepeat domain ofthe N-terminal tail up to full occupancy at pH=7.4.Recent experiments show that the HGGG octarepeatsub-domain is responsible for hol<strong>di</strong>ng the metalbound in a square planar configuration. On thenumerical side [4-6], we have approached a similarproblem which has to do with cellular prion protein(PrP c ). PrP c is a cell surface glycoprotein that isconsidered a key molecule for the understan<strong>di</strong>ng ofthe development of a group of neuro-degenerative<strong>di</strong>seases, generically referred to as “prion <strong>di</strong>seases”.Prion <strong>di</strong>seases are characterized by theconformational transition of the native,predominantly α-helical, PrP c , into a pathogenic,mostlyβ-sheet,conformer called scrapie,PrP Sc .The human prion proteinbinds Cu 2+ ions in theoctarepeat domain of theN-terminal tail up to fulloccupancy at pH=7.4.Recent experiments showthat the HGGG octarepeatsub-domain is responsible for hol<strong>di</strong>ng the metalbound in a square planar configuration. By using firstprinciple ab initio molecular dynamics simulations ofthe Car-Parrinello type, we have investigated thecoor<strong>di</strong>nation of Cu to the bin<strong>di</strong>ng sites of the prionprotein octarepeat region [7]. Simulations arecarried out for the complexes Cu(HGGGW)(wat),Cu(HGGG) and [Cu(HGGG)] 2. While the presence ofa Trp residue and a water molecule does not affectthe nature of the Cu coor<strong>di</strong>nation, high stability ofthe bond between Cu and the amide nitrogen ofdeprotonated Gly’s is confirmed in all cases. For themore interesting [Cu(HGGG)] 2 complex adynamically entangled arrangement of the twodomains with exchange of amide nitrogen bondsbetween the two Cu centers emerges (fig. 2), whichis consistent with the short Cu-Cu <strong>di</strong>stance observe<strong>di</strong>n experiments at full Cu occupancy.Fig. 2: Structure of the [Cu(HG − G − G)] 2 systemobtained in the (spin-restricted simulation) atT=300 K and at t=0.86 ps (from Ref. [7])References[1] S.Morante, et al., J. Biol. Chem. 279, 11753(2004).[2] M.Benfatto, et al., Biophys. Chem. 110, 191(2004).[3] F.Stellato, et al., Eur. Biophys. J. 35(4), 340(2006).[4] G. La Penna, et al., Int. J. Mod. Phys. C 15, 205(2004).[5] G.La Penna, et al., J. Chem. Phys. 121, 10725(2004).[6] S.Morante, et al., J. Chem. Phys. 125. 034101(2006)AuthorsF. Guerrieri (a, c), V. Minicozzi (a), S. Morante (a, b, c),G. C. Rossi (a, c), F. Stellato (a, c)(a) Dip. <strong>di</strong> <strong>Fisica</strong>, Univ. <strong>di</strong> Roma Tor Vergata, Roma II(b) CRS SOFT-INFM-CNR, Roma, Italy(c) INFN, Sez. <strong>di</strong> Roma Tor VergataSOFT Scientific <strong>Report</strong> 2004-0690
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