On the form of growing strings

Patterns and forms adopted by Nature, such as the shape of living cells, the geometry of shells and the branched structure of plants, are often the result of simple dynamical paradigms. Here we show that a growing self-interacting string attached to a tracking origin, modeled to resemble nascent polypeptides in vivo, develops helical structures which are more pronounced at the growing end. We also show that the dynamic growth ensemble shares several features of an equilibrium ensemble in which the growing end of the polymer is under an effective stretching force. A statistical analysis of native states of proteins shows that the signature of this non-equilibrium phenomenon has been fixed by evolution at the C-terminus, the growing end of a nascent protein. These findings suggest that a generic non-equilibrium growth process might have provided an additional evolutionary advantage for nascent proteins by favoring the preferential selection of helical structures.Comment: 4 pages, 3 figures. Accepted for publication in Phys. Rev. Let

Critical Casimir effect in films for generic non-symmetry-breaking boundary conditions

Systems described by an O(n) symmetrical $\phi^4$ Hamiltonian are considered in a $d$-dimensional film geometry at their bulk critical points. A detailed renormalization-group (RG) study of the critical Casimir forces induced between the film's boundary planes by thermal fluctuations is presented for the case where the O(n) symmetry remains unbroken by the surfaces. The boundary planes are assumed to cause short-ranged disturbances of the interactions that can be modelled by standard surface contributions $\propto \bm{\phi}^2$ corresponding to subcritical or critical enhancement of the surface interactions. This translates into mesoscopic boundary conditions of the generic symmetry-preserving Robin type $\partial_n\bm{\phi}=\mathring{c}_j\bm{\phi}$. RG-improved perturbation theory and Abel-Plana techniques are used to compute the $L$-dependent part $f_{\mathrm{res}}$ of the reduced excess free energy per film area $A\to\infty$ to two-loop order. When $d<4$, it takes the scaling form $f_{\mathrm{res}}\approx D(c_1L^{\Phi/\nu},c_2L^{\Phi/\nu})/L^{d-1}$ as $L\to\infty$, where $c_i$ are scaling fields associated with the surface-enhancement variables $\mathring{c}_i$, while $\Phi$ is a standard surface crossover exponent. The scaling function $D(\mathsf{c}_1,\mathsf{c}_2)$ and its analogue $\mathcal{D}(\mathsf{c}_1,\mathsf{c}_2)$ for the Casimir force are determined via expansion in $\epsilon=4-d$ and extrapolated to $d=3$ dimensions. In the special case $\mathsf{c}_1=\mathsf{c}_2=0$, the expansion becomes fractional. Consistency with the known fractional expansions of D(0,0) and $\mathcal{D}(0,0)$ to order $\epsilon^{3/2}$ is achieved by appropriate reorganisation of RG-improved perturbation theory. For appropriate choices of $c_1$ and $c_2$, the Casimir forces can have either sign. Furthermore, crossovers from attraction to repulsion and vice versa may occur as $L$ increases.Comment: Latex source file, 40 pages, 9 figure

Lack of self-averaging in neutral evolution of proteins

We simulate neutral evolution of proteins imposing conservation of the thermodynamic stability of the native state in the framework of an effective model of folding thermodynamics. This procedure generates evolutionary trajectories in sequence space which share two universal features for all of the examined proteins. First, the number of neutral mutations fluctuates broadly from one sequence to another, leading to a non-Poissonian substitution process. Second, the number of neutral mutations displays strong correlations along the trajectory, thus causing the breakdown of self-averaging of the resulting evolutionary substitution process.Comment: 4 pages, 2 figure

In-cell NMR characterization of the secondary structure populations of a disordered conformation of α-Synuclein within E. coli cells

α-Synuclein is a small protein strongly implicated in the pathogenesis of Parkinson’s disease and related neurodegenerative disorders. We report here the use of in-cell NMR spectroscopy to observe directly the structure and dynamics of this protein within E. coli cells. To improve the accuracy in the measurement of backbone chemical shifts within crowded in-cell NMR spectra, we have developed a deconvolution method to reduce inhomogeneous line broadening within cellular samples. The resulting chemical shift values were then used to evaluate the distribution of secondary structure populations which, in the absence of stable tertiary contacts, are a most effective way to describe the conformational fluctuations of disordered proteins. The results indicate that, at least within the bacterial cytosol, α-synuclein populates a highly dynamic state that, despite the highly crowded environment, has the same characteristics as the disordered monomeric form observed in aqueous solution

Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric aggregates

The presence of oligomeric aggregates, which is often observed during the process of amyloid formation, has recently attracted much attention since it has been associated with neurodegenerative conditions such as Alzheimer's and Parkinson's diseases. We provide a description of a sequence-indepedent mechanism by which polypeptide chains aggregate by forming metastable oligomeric intermediate states prior to converting into fibrillar structures. Our results illustrate how the formation of ordered arrays of hydrogen bonds drives the formation of beta-sheets within the disordered oligomeric aggregates that form early under the effect of hydrophobic forces. Initially individual beta-sheets form with random orientations, which subsequently tend to align into protofilaments as their lengths increases. Our results suggest that amyloid aggregation represents an example of the Ostwald step rule of first order phase transitions by showing that ordered cross-beta structures emerge preferentially from disordered compact dynamical intermediate assemblies.Comment: 14 pages, 4 figure

Disordered Flat Phase and Phase Diagram for Restricted Solid on Solid Models of Fcc(110) Surfaces

We discuss the results of a study of restricted solid-on-solid models for fcc (110) surfaces. These models are simple modifications of the exactly solvable BCSOS model, and are able to describe a $(2\times 1)$ missing-row reconstructed surface as well as an unreconstructed surface. They are studied in two different ways. The first is by mapping the problem onto a quantum spin-1/2 one-dimensional hamiltonian of the Heisenberg type, with competing $S^z_iS^z_j$ couplings. The second is by standard Monte Carlo simulations. We find phase diagrams with the following features, which we believe to be quite generic: (i) two flat, ordered phases (unreconstructed and missing-row reconstructed); a rough, disordered phase; an intermediate disordered flat (DF) phase, characterized by monoatomic steps, whose physics is shown to be akin to that of a dimer spin state. (ii) a transition line from the $(2\times 1)$ reconstructed phase to the DF phase showing exponents which appear to be close, within our numerical accuracy, to the 2D-Ising universality class. (iii) a critical (preroughening) line with variable exponents, separating the unreconstructed phase from the DF phase. Possible signatures and order parameters of the DF phase are investigated.Comment: Revtex (22 pages) + 15 figures (uuencoded file

Modeling study on the validity of a possibly simplified representation of proteins

The folding characteristics of sequences reduced with a possibly simplified representation of five types of residues are shown to be similar to their original ones with the natural set of residues (20 types or 20 letters). The reduced sequences have a good foldability and fold to the same native structure of their optimized original ones. A large ground state gap for the native structure shows the thermodynamic stability of the reduced sequences. The general validity of such a five-letter reduction is further studied via the correlation between the reduced sequences and the original ones. As a comparison, a reduction with two letters is found not to reproduce the native structure of the original sequences due to its homopolymeric features.Comment: 6 pages with 4 figure

Metastability of native proteins and the phenomenon of amyloid formation

An experimental determination of the thermodynamic stabilities of a series of amyloid fibrils reveals that this structural form is likely to be the most stable one that protein molecules can adopt even under physiological conditions. This result challenges the conventional assumption that functional forms of proteins correspond to the global minima in their free energy surfaces and suggests that living systems are conformationally as well as chemically metastable. © 2011 American Chemical Society

Nucleation phenomena in protein folding: The modulating role of protein sequence

For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation mechanism for protein folding whose basic premise is the idea that after completion of a specific set of contacts forming the so-called folding nucleus the native state is achieved promptly. Here we propose a methodology to identify folding nuclei in small lattice polymers and apply it to the study of protein molecules with chain length N=48. To investigate the extent to which protein topology is a robust determinant of the nucleation mechanism we compare the nucleation scenario of a native-centric model with that of a sequence specific model sharing the same native fold. To evaluate the impact of the sequence's finner details in the nucleation mechanism we consider the folding of two non- homologous sequences. We conclude that in a sequence-specific model the folding nucleus is, to some extent, formed by the most stable contacts in the protein and that the less stable linkages in the folding nucleus are solely determined by the fold's topology. We have also found that independently of protein sequence the folding nucleus performs the same `topological' function. This unifying feature of the nucleation mechanism results from the residues forming the folding nucleus being distributed along the protein chain in a similar and well-defined manner that is determined by the fold's topological features.Comment: 10 Figures. J. Physics: Condensed Matter (to appear