Role of water around biomolecules and surfactantsIn solution the mutual interactions between solutesand solvents define all the conformation anddynamical properties, as well as the deviation of thesolvent from its pure state. Our work is devoted tothe analysis of these interactions, both withexperiments and Molecular Dynamics simulations, inaqueous solutions of biopolymers and surfactants.Network of vicinal water around C 12E 6 surfactant.We analysed the solute-water interactions in proteinsbelonging to organisms living at ambienttemperature, named mesophiles, or extremetemperatures, even excee<strong>di</strong>ng the boilingtemperature of water, named thermophiles. Up tonow a satisfactory explanation on the origins ofadaptation at extreme con<strong>di</strong>tions is still lacking. Therelated scenario depends on many independentfactors, the amino aci<strong>di</strong>c primary sequence, thetypes of amino acids exposed to the solvent, i.e. thesecondary and tertiary structure, the morphologyand energetics of the interfacial region. Wesimulated the thermal response of two proteinshaving a high homology in the primary structure, theG-domain of the Elongation Factor of Escherichia coli(mesophilic) and Thermus thermophilus (moderatelythermophilic) with denaturation temperatures<strong>di</strong>ffering by about 15 K. Our stu<strong>di</strong>es showed thatunfol<strong>di</strong>ng in the mesophile is preceded by anenhanced exchange of interfacial water moleculeswith the bulk, accompanied by concomitantabsorption of heat by hydrophilic aminoacids [1].Pertaining the comparative study of mesophilic andthermophilic counterparts, and notwithstan<strong>di</strong>ng thesame hydrophobic/hydrophilic composition, the moststriking result regards the high efficiency of thethermophile in adsorbing water molecules, inparticular at high temperature and the largerhydrophilic character of the thermophile [2]. Thedata support the notion that water is an ambivalentelement, destabilizing proteins due to its efficiency inhydrogen bon<strong>di</strong>ng and acting as a bio-protectantwith respect to thermal or mechanical stress. Asuggestive interpretation is that the strategydeveloped by thermophilic species to defend againsttemperature and, in<strong>di</strong>rectly, water floo<strong>di</strong>ng theprotein core, is to allow for a small, but significantportion of water molecules to partially penetrate theprotein-water interface.Solutions of non-ionic surfactants were investigatedby looking at the molar volumetry andcompressibility as a function of temperature andconcentration. The results allowed the determinationof the hydration state and its temperaturedependence [3]. The visco-elastic response wasrevealed at high concentration and an extracontribution to the compressibility at lowconcentration, probably due to water exchange [4].To understand the microscopic origin of suchbehaviour we performed Molecular DynamicSimulation on C 12E 6 spherical micelle. The resultsin<strong>di</strong>cated that: 1) dehydration occurs mainly on theoil core exposed surface [5]; 2) water moleculesaround the oil core form H-bound clusters whose sizeand <strong>di</strong>stribution change with temperature; 3) in thisregion the water cluster have the largest size [6].The <strong>di</strong>ffusion of water close to biological materialsdoes not grow linearly in time, as expected by thebrownian motion. The onset of spatial and temporalcorrelations, arising from the heterogeneity of theexposed, is usually invoked to explain thisphenomenon. Our simulations of water confined by amodel membrane showed that the dynamics can befairly well described by a simple brownian model withan effective <strong>di</strong>ffusion coefficient [7]. Longitu<strong>di</strong>nal<strong>di</strong>ffusion follows a standard behavior whereas theeffect of confinement manifests itself in mixing thelongitu<strong>di</strong>nal and transversal dynamics. The essenceof the process has been captured by our simplifiedapproach which covers a considerably large timeinterval.References[1] S. Melchionna, G. Briganti, P. Londei, P.Cammarano, Phys.Rev.Lett., 92, 158101 (2004).[2] S.Melchionna, R.Sinibal<strong>di</strong>, G.Briganti, Biophys. J.90, 4204 (2004).[3] G. Briganti, M. Maccarini, G. D’Arrigo Journal ofPhysical Chemistry B,108, 4039 (2004).[4] G. D’Arrigo, G. Briganti, M. Maccarini, Journal ofPhysical Chemistry B,110, 4612 (2006).[5] F. Sterpone, C. Pierleoni, G. Briganti, M. Marchi,Langmuir 20, 4311 (2004).[6] F. Sterpone, C. Pierleoni, G. Briganti, M. Marchi,Journal of Physical Chemistry B,110, 18254 (2006).[7] M. Sega, R. Vallauri, S. Melchionna, Phys. Rev. E72, 041201 (2005).Authors:S. Melchionna (a), G. Briganti (a), P. Londei (b), P.Cammarano (b), R.Sinibal<strong>di</strong> (c), M. Sega (d), R.Vallauri (d), C. Pierleoni (e), F. Sterpone (f), M.Marchi (g), M. Maccarini (h), G. D’Arrigo (i).(a) CRS-SOFT, Department of Physics, University “La<strong>Sapienza</strong>” (Rome, Italy), (b) Department of Me<strong>di</strong>calBiochemical and Biological Me<strong>di</strong>cine, University “La<strong>Sapienza</strong>” (Rome, Italy), (c) Department of AppliedScience, “Politecnico delle Marche” (Ancona, Italy),(d) Department of Physics, University of Trento(Italy), (e) Department of Physics, University ofL’Aquila (Italy), (f) Department of Chemistry,University of Texas (USA) (g) Centre d’etudes Saclay(France), (h) Institut fϋr physikalische chemie(Heidelberg, Germany), (i) Department of Energetic,University “La <strong>Sapienza</strong>” (Rome, Italy)91SOFT Scientific <strong>Report</strong> 2004-06
Scientific <strong>Report</strong> – Self Assembly, Clustering, Structural arrestMulti-Scale Simulations of Macromolecular SystemsMathematical modelling and computer simulation ofmacromolecular and biological systems is in a stageof burgeoning progress. Such systems raisenonetheless a great challenge to computationalscientists, mostly on account of the wide and<strong>di</strong>sparate range of spatio-temporal scales involved intheir dynamical evolution. Typically both problemsinvolve space and time-scale separation calling formulti-scale modelling and proper theoreticalmethodologies derived from statistical mechanics.We tackle the problem with two <strong>di</strong>stinct strategies. Afirst approach, typically applied to colloidal andbiological polymers, is based on a multi-scaleseparation between degrees of freedom, namelyheavy solutes in presence of a light surroun<strong>di</strong>ngsolvent. The solvent hydrodynamics is treated at thelevel of the lattice Boltzmann method while thesolutes are treated by means of Molecular Dynamics.The connection between the two descriptions isestablished by introducing thermal noise in theframework of fluctuating hydrodynamics and by amomentum balance technique [1]. Alternatively, wehave developed a numerical scheme to <strong>di</strong>rectly solvethe time-dependent Fokker-Planck equation in orderto account for the liquid state of the solvent at thelevel of the collision operators [2]. Our secondstrategy focuses on rare events and complex freeenergylandscapes. The goal here is to reduce thetemporal <strong>di</strong>versity (restriction of internal modes,spectrum compression, and similar techniques) andartificially induce the process under study (the socalledrare event) in order to investigate itsspontaneous evolution. The two approachesdeveloped in our group are the so-called Blue MoonEnsemble [3] and Mass Rescaling [4] which eitherintroduce a constraint to explore the veryunprobable regions of phase space or alter thevisiting frequency of the low probability regions.Our laboratory is specialized in large-scale simulationof complex systems by developing innovativeFig.1: Transition path of Alanine <strong>di</strong>peptide inducedby enhanced conformational sampling.numerical techniques. In the past years we havedeveloped an open-source simulation platformnamed DLPROTEIN which allows for parallel andcross-platform simulation of complex macromolecularsystems [5]. The inclusion of multi-scalemethods into the package is currently in progress.Hydration states is a major actor in stabilizingproteins in aqueous environments. A particularlyinteresting class of proteins are the thermophilicones, which, in contrast to the mesophilic variants,present a smaller heat capacity upon unfol<strong>di</strong>ng. Inout stu<strong>di</strong>es we have found that the water-exposedsurface area is larger for the thermophile, probablydue to a peculiar corrugation of the exposed surfaceof this species with a larger number of intramolecular hydrogen bonds, stronger electrostaticinteractions and a flatter free energy landscape. Thiswork suggest that the specific hydration stateenhances macromolecular fluctuations but, at thesame time, increases thermal stability [6].Biomolecules embedded in sugar matrices canovercome adverse con<strong>di</strong>tions such as dehydrationand/or high temperatures. Among sugars, trehalosehas been found the most effective protectant.Notwithstan<strong>di</strong>ng the large attention devoted, thetrehalose peculiarity is still poorly understood.Experiments show how the size and the hydrogenbon<strong>di</strong>ng capability of <strong>di</strong>fferent saccharides affectprotein dynamics and the protein-matrix coupling ina subtle way. MD simulations have been performedon carboxy myoglobin/water/saccharide (trehalose,sucrose, maltose, glucose) systems. Atomicfluctuations, heme pocket structures, protein-solventhydrogen bon<strong>di</strong>ng have been analyzed and compared[7]. Results suggest the action of saccharides be dueto protein-water-sugar interactions via the presenceof interfacial structures containing excess water withrespect to the bulk, and few sugar molecules boundto protein via single hydrogen bonds,in agreementwith the "preferential hydration model".References[1] M. Fyta, S. Melchionna, S. Succi, E. Kaxiras, inpreparation.[2] S. Melchionna, S. Succi, J.-P. Hansen, Intl. J.Mod. Phys. (2006), in press.[3] E.A.Carter, G.Ciccotti, J.T.Hynes, R. Kapral,Chem.Phys.Lett. 156, 472 (1989).[4] S.Melchionna, Phys.Rev.E 62, 8762 (2000).[5] http://www.sissa.it/cm/DLPROTEIN.[6] S. Melchionna, G. Briganti, R. Sinibal<strong>di</strong>, Biophys.J. (2006) in press.[7] G. Cottone, S. Giuffrida, G. Ciccotti, L. Cordone,Proteins 59, 291 (2005).AuthorsS. Melchionna, G. CiccottiSOFT-INFM, <strong>Dipartimento</strong> <strong>di</strong> <strong>Fisica</strong>, Università <strong>di</strong>Roma La <strong>Sapienza</strong>.SOFT Scientific <strong>Report</strong> 2004-0692
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