A course of coordinated sciences: The structure of matter

1976

The role of water in hemoglobin function and stability

1993

Effects of electric charges on hydrophobic forces. II.

2000

We study by molecular-dynamics simulations the effect of electric charges of either sign on hydrophobic interactions and on the dynamics of hydration water, using explicit water and very simplified solutes. Results show that the presence of a charged solute can disrupt the "hydrophobic contact bond" between two apolar solutes nearby, by forcing them towards a different configuration. As a consequence of different structural changes of the solvent caused by charges of opposite sign, the effect is markedly charge-sign-dependent. Analogous weaker effects appear to be induced by the presence of one additional apolar element. The dynamics of hydration water around each solute is also seen to be …

Physical Origin and Biological Significance of Solvent Induced Forces

1994

The notion of solvent-induced forces (SIFs), as distinct from solute-solute forces acting through the solvent, is illustrated in terms of: i) the microscopic space-and time-resolved view provided by Molecular Dynamics Simulations; ii) the standard statistical-mechanical formulation, and iii) the inherent structures of water. It is shown that the origin of SIFs is in the non-additivity of the effects of solute-perturbation on the H-bond network in the solvent. This nonadditivity does not require non-additivity of water-water and solute-water interaction potentials. Two experimental studies, illustrating different aspects of SIFs are discussed in detail. One is the case of Human Adult Hemoglo…

Demixing and polymerization in systems of anisotropic globular particles: A molecular dynamics simulation study

1991

We report a first set of results of Molecular Dynamics simulations of phase separation in a two-dimensional system of identical particles bearing attachment sites at their surface. Morphology of regions of aggregation so obtained appear similar to images of biologically self-assembled structures. Also, they evidence the relevance of the region of thermodynamic instability and of the presence and range of interaction of specific attachment sites. Particles of our system are apt to represent indifferently, though grossly, globular proteins or rigid cells, bearing specific and fixed adhesion sites at their surface. Results illustrate some basic aspects of the origin of the morphology of extend…

Experimental studies of the rheological behavior of a demixing biopolymeric sol

1995

Experimental data are presented concerning a large transient viscosity surge occurring in the course of spinodal demixing of agarose aqueous solutions. The study includes the effects of water perturbation by minor proportions of compatible cosolutes. Three observations are noteworthy. One concerns an upward or downward shift of the spinodal temperature, caused by cosolutes, which agrees with their expected modulation of solvent-induced forces. The second concerns the time of appearance of the viscosity surge. This is observed to follow a critical law, with an exponent independent of polymer concentration and solvent perturbation. The third concerns the inverse-power-law dependence of the vi…

A molecular dynamics study of large-scale reversible aggregation of anisotropic particles

1992

We report findings of 1000 ps molecular dynamics simulations of a bidimensional system of 4050 Lennard–Jones particles with electric dipoles, undergoing spinodal separation. This simple system is used to model the reversible aggregation of building blocks bearing specific and fixed adhesion sites at their surface. Aggregation regions so obtained resemble images of self-assembled biological structures. Statistical analyses of these regions evidence the interplay of thermodynamic instability and of interaction range between the attachment sites. They also illustrate some basic aspects of the morphogenesis of extended biomolecular/cellular structures, self-organized from initially homogeneous …

Effect of T-R conformational change on sickle-cell hemoglobin interactions and aggregation

2004

We compare the role of a conformational switch and that of a point mutation in the thermodynamic stability of a protein solution and in the consequent propensity toward aggregation. We study sickle-cell hemoglobin (HbS), the beta6 Glu-Val point mutant of adult human hemoglobin (HbA), in its R (CO-liganded) conformation, and compare its aggregation properties to those of both HbS and HbA in their T (unliganded) conformation. Static and dynamic light scattering measurements performed for various hemoglobin concentrations showed critical divergences with mean field exponents as temperature was increased. This allowed determining spinodal data points T(S)(c) by extrapolation. These points were …

Anomalies in the temperature dependence of the 1.2-? absorption of liquid water

1975

The weakly absorbed 1.2-μ combination band of water was accurately studied as a function of temperature, in both its profile and first derivative, to obtain information on the bulk properties of liquid water. Arrhenius plots of integrated component intensity ratios showed well aligned experimental points, except for a neatly defined break occurring in the 30 to 40°C temperature interval for pure water A similar break, shifted by some 18°C towards lower temperature, was found in the case of 1M NaClO4 aqueous solutions. The breaks are tentatively assumed to result from abrupt though subtle changes involving low-frequency modes. This tentative, assumption appears independent of specific models…

Protein aggregation/crystallization and minor structural changes: universal versus specific aspects.

2007

AbstractProtein association covers wide interests in biophysics, protein science, and biotechnologies, and it is often viewed as governed by conformation details. More recently, the existence of a universal physical principle governing aggregation/crystallization processes has been suggested by a series of experiments and shown to be linked to the universal scaling properties of concentration fluctuations occurring in the proximity of a phase transition (spinodal demixing in the specific case). Such properties have provided a quantitative basis for capturing kinetic association data on a universal master curve, ruled by the normalized distance of the state of the system from its instability…

Irreversible formation of intermediate BSA oligomers requires and induces conformational changes.

2004

Understanding the relation between protein conformational changes and aggregation, and the physical mechanisms leading to such processes, is of primary importance, due to its direct relation to a vast class of severe pathologies. Growing evidence also suggests that oligomeric intermediates, which may occur early in the aggregation pathway, can be themselves pathogenic. The possible cytotoxicity of oligomers of non-disease-associated proteins adds generality to such suggestion and to the interest of studies of oligomer formation. Here we study the early stages of aggregation of Bovine Serum Albumin (BSA), a non pathogenic protein which has proved to be a useful model system. Dynamic light sc…

Multiple interactions between molecular and supramolecular ordering

1999

We report studies of the interplay among processes of molecular conformational changes, spinodal demixing of the solution, and molecular crosslinking involved in the physical gelation of a biopolysaccharide-water system. Multiple interactions and kinetic competition among these processes were studied under largely different absolute and relative values of their individual rates by appropriate choices of the quenching temperature at constant polymer concentration. Quenching temperature strongly affects the rate of growth but not the final value of the fractal dimension of the gel. Kinetic competition plays a central role in determining the final conformation of individual molecules and the s…

Low-temperature optical absorption of nickel fluosilicate crystals

1964

Abstract The vibronic absorption spectrum of the Ni++ ion in an electric field of trigonal (nearly cubic) symmetry at temperatures down to 4°K is reported and analysed in terms of ligand field and vibronic theory. The positions, widths, shapes and strengths of the bands are satisfactorily explained, together with their associated fine structures. In particular, the complex structure of the red band is well explained in detail as a consequence of the mutual perturbation of the 1E and 3T4 levels, which strongly modifies the vibronic coupling and results in two fairly narrow bands, each showing resolved vibrational structure, superposed on a broad band. A Trees correction term, αL(L+1), helps …

Lysozyme crystallization rates controlled by anomalous fluctuations

2005

Abstract Nucleation of protein aggregates and crystals is a process activated by statistical fluctuations of concentration. Nucleation rates may change by several orders of magnitude upon apparently minor changes in the multidimensional space of parameters (temperature, pH, protein concentration, salt type and concentrations, additives). We use available data on hen egg lysozyme crystal induction times in different solution conditions. We measure by static and dynamic light scattering the amplitudes and lifetimes of anomalously ample and long-lived fluctuations occurring in proximity of the liquid–liquid demixing region of the given lysozyme solutions. This allows determining the related sp…

Micro- and mesoscopic process interactions in protein coagulation

2000

It has recently been recognized that pathological protein coagulation is responsible for lethal pathologies as diverse as amyloidosis, Alzheimer and TSE. Understanding the coagulation mechanisms is therefore stirring great interest. In previous studies we have shown that on profoundly different systems coagulation is the result of a strong interaction between two processes on different length scales (mesoscopic and microscopic). Here we report experiments on bovine serum albumin (BSA) showing that the overall mechanism is the result of at least 3 distinct and strongly intertwined processes, on both length scales: molecular conformational changes, solution demixing and intermolecular crossli…

Spinodal demixing, percolation and gelation of biostructural polymers

1990

We present a variety of new experiments which concern the self-assembly of a polymeric network from homogeneous solutions of Agarose, a representative biostructural polysaccharide used for previous studies at our laboratories. They allow deriving a semi-quantitative phase diagram in the T, C plane. The diagram includes both the spinodal and gelation lines. Below a value of about 2% w/v, concentration is not sufficient for direct gelation; however, quenching of the sol from high temperatures to below the spinodal line initiates the spinodal demixing. The latter generates two sets of regions having respectively, higher- and lower-than-average polymer concentrations. In the higher-concentratio…

Spontaneous symmetry-breaking pathways: time-resolved study of agarose gelation

1996

Abstract Extensive time-resolved studies of self-assembly of agarose gels, performed with the use of a variety of techniques allowed identification of the initial break of symmetry and the actual path leading to self-assembly at concentrations well below the random percolation threshold. The overall process is seen to occur through the following sequence: (i) break of symmetry in the sol, causing the spontaneous generation of mesoscopic polymer-rich and solvent-rich regions; (ii) percolation, or nearly percolation [see (iv) below], of polymer-rich regions through the sample, still in the sol state; (iii) start of polymer cross-linking within polymer-rich regions; (iv) progress of cross-link…

Collective properties of hydration: long range and specificity of hydrophobic interactions

1997

We report results of molecular dynamics (MD) simulations of composite model solutes in explicit molecular water solvent, eliciting novel aspects of the recently demonstrated, strong many-body character of hydration. Our solutes consist of identical apolar (hydrophobic) elements in fixed configurations. Results show that the many-body character of PMF is sufficiently strong to cause 1) a remarkable extension of the range of hydrophobic interactions between pairs of solute elements, up to distances large enough to rule out pairwise interactions of any type, and 2) a SIF that drives one of the hydrophobic solute elements toward the solvent rather than away from it. These findings complement re…

Solvent-induced free energy landscape and solute-solvent dynamic coupling in a multielement solute

1999

AbstractMolecular dynamics simulations using a simple multielement model solute with internal degrees of freedom and accounting for solvent-induced interactions to all orders in explicit water are reported. The potential energy landscape of the solute is flat in vacuo. However, the sole untruncated solvent-induced interactions between apolar (hydrophobic) and charged elements generate a rich landscape of potential of mean force exhibiting typical features of protein landscapes. Despite the simplicity of our solute, the depth of minima in this landscape is not far in size from free energies that stabilize protein conformations. Dynamical coupling between configurational switching of the syst…

Protein crystallization: universal thermodynamic vs. specific effects of PEG

2008

The interest of nucleation of protein crystals and aggregates (including oligomerization) spans from basic physics theory all the way to biophysics, nanophysics, clinical sciences, biotechnologies, food technologies and polymer–solvent interactions. Understanding nucleation within a theoretical framework capable of providing quantitative predictions and control of nucleation rates, or even the very occurrence of crystallization, is a long-sought goal of remarkable relevance to each of the above fields. A large amount of work has been aimed at such goal, but success has been so far rather limited. Work at our laboratory has more recently highlighted a direct link between nucleation rates and…

Physics and biophysics of solvent induced forces: hydrophobic interactions and context-dependent hydration

1998

Solvent induced forces (SIFs) among solutes derive from solvent structural modification due to solutes, and consequent thermodynamic drive towards minimization of related free energy costs. The role of SIFs in biomolecular conformation and function is appreciated by observing that typical SIF values fall within the 20–200 pN interval, and that proteins are stable by only a few kcal mol–1 (1 kcal mol–1 corresponds to 70 pN A). Here we study SIFs, in systems of increasing complexity, using Molecular Dynamics (MD) simulations which give time- and space-resolved details on the biologically significant scale of single protein residues and sidechains. Of particular biological relevance among our …

Cooperative onset of a different state of water in the presence of macromolecules.

1973

Interacting processes in protein coagulation

1999

A strong interest is currently focused on protein self-association and deposit. This usually involves conformational changes of the entire protein or of a fragment. It can occur even at low concentrations and is responsible for pathologies such as systemic amyloidosis, Alzheimer's and Prion diseases, and other neurodegenerative pathologies. Readily available proteins, exhibiting at low concentration self-association properties related to conformational changes, offer very convenient model systems capable of providing insight into this class of problems. Here we report experiments on bovine serum albumin, showing that the process of conformational change of this protein towards an intermedia…

Time scale of protein aggregation dictated by liquid-liquid demixing

2003

The growing impact of protein aggregation pathologies, together with the current high need for extensive information on protein structures are focusing much interest on the physics underlying the nucleation and growth of protein aggregates and crystals. Sickle Cell Hemoglobin (HbS), a point-mutant form of normal human Hemoglobin (HbA), is the first recognized and best-studied case of pathologically aggregating protein. Here we reanalyze kinetic data on nucleation of deoxy-HbS aggregates by referring them to the (concentration-dependent) temperature Ts characterizing the occurrence of the phase transition of liquid-liquid demixing (LLD) of the solution. In this way, and by appropriate scalin…

Contributory presentations/posters

1999

Biomolecular-solvent stereodynamic coupling probed by deuteration.

1983

Thermodynamic interpretation of experiments with isotopically perturbed solvent supports the view that solvent stereodynamics is directly relevant to thermodynamic stability of biomolecules. According with the current understanding of the structure of the aqueous solvent, in any stereodynamic configuration of the latter, connectivity pathways are identifiable for their topologic and order properties. Perturbing the solvent by isotopic substitution or, e.g., by addition of co-solvents, can therefore be viewed as reinforcing or otherwise perturbing these topologic structures. This microscopic model readily visualizes thermodynamic interpretation. In conclusion, the topologic stereodynamic str…

Behaviour of Interacting Protons: The Average-Mass Approach to its Study and its Possible Biological Relevance

1973

Among all other kinds of ions occurring in the solid, liquid and living states of matter, positive hydrogen ions (which we shall henceforth call protons for brevity) are singled out by their exceptionally small mass. This is the reason for their specific property of tunnelling through potential barriers, which in turn is responsible for such properties as hydrogen bonding. This is also responsible for the unique properties exhibited in many cases by (sub)systems of interacting protons. Examples are the intriguing properties of liquid water and ice [1]; the para-ferroelectric transition in hydrogen-bonded ferroelectrics [2]; the cooperative transitions in ammonium salts [3] and in hexamine h…

I.R. Experimental studies of dynamical aspects of water structure: Effects of HD substitution and of small solutes

1980

Abstract Results on i.r. absorption spectra of H2O, D2O and electrolytic solutions and their thermal modifications are presented. From the data, some parameters can be obtained which are suitable for a description of dynamical aspects of water structure. Solute induced changes of these parameters provide a quantitative, although phenomenologic description of the water-solute interaction.

Enthalpic and entropic contributions of water molecules to the functional T → R transition of human hemoglobin in solution

1992

Generalized solvent-mediated forces contribute to free energy at the functional T → R transition of human hemoglobin A (HbA). Their contribution is here sorted out quantitatively in both its enthalpic and entropic parts, along with the average number of water molecules involved. The latter (about 75 waters in average) must be considered together with HbA as one statistically defined functional unit for oxygen transport. Their configurations are expected to undergo frequent structural rearrangements. Lifetimes of statistically relevant configurations do not need to (although, of course, they may) exceed by more than a factor 5 the normal H-bond lifetimes of the pure solvent. Compared to the …