Warm and Cold Denaturation in the Phase Diagram of a Protein Lattice Model

Studying the properties of the solvent around proteins, we propose a much more sophisticated model of solvation than temperature-independent pairwise interactions between monomers, as is used commonly in lattice representations. We applied our model of solvation to a 16-monomer chain constrained on a two-dimensional lattice. We compute a phase diagram function of the temperature and a solvent parameter which is related to the pH of the solution. It exhibits a native state in which the chain coalesces into a unique compact conformation as well as a denatured state. Under certain solvation conditions, both warm and cold denaturations occur between the native and the denatured states. A good agreement is found with the data obtained from calorimetric experiments, thereby validating the proposed model.Comment: 7 pages, 2 figure

Inferring the diameter of a biopolymer from its stretching response

We investigate the stretching response of a thick polymer model by means of extensive stochastic simulations. The computational results are synthesized in an analytic expression that characterizes how the force versus elongation curve depends on the polymer structural parameters: its thickness and granularity (spacing of the monomers). The expression is used to analyze experimental data for the stretching of various different types of biopolymers: polypeptides, polysaccharides, and nucleic acids. Besides recovering elastic parameters (such as the persistence length) that are consistent with those obtained from standard entropic models, the approach allows us to extract viable estimates for the polymers diameter and granularity. This shows that the basic structural polymer features have such a profound impact on the elastic behavior that they can be recovered with the sole input of stretching measurements

Assembly and structural analysis of a covalently closed nano-scale DNA cage

The inherent properties of DNA as a stable polymer with unique affinity for partner molecules determined by the specific Watson–Crick base pairing makes it an ideal component in self-assembling structures. This has been exploited for decades in the design of a variety of artificial substrates for investigations of DNA-interacting enzymes. More recently, strategies for synthesis of more complex two-dimensional (2D) and 3D DNA structures have emerged. However, the building of such structures is still in progress and more experiences from different research groups and different fields of expertise are necessary before complex DNA structures can be routinely designed for the use in basal science and/or biotechnology. Here we present the design, construction and structural analysis of a covalently closed and stable 3D DNA structure with the connectivity of an octahedron, as defined by the double-stranded DNA helices that assembles from eight oligonucleotides with a yield of ∼30%. As demonstrated by Small Angle X-ray Scattering and cryo-Transmission Electron Microscopy analyses the eight-stranded DNA structure has a central cavity larger than the apertures in the surrounding DNA lattice and can be described as a nano-scale DNA cage, Hence, in theory it could hold proteins or other bio-molecules to enable their investigation in certain harmful environments or even allow their organization into higher order structures

Solvent Effects on Ionization Potentials of Guanine Runs and Chemically Modified Guanine in Duplex DNA: Effect of Electrostatic Interaction and Its Reduction due to Solvent

We examined the ionization potential (IP) corresponding to the free energy of a hole on duplex DNA by semiempirical molecular orbital theory with a continuum solvent model. As for the contiguous guanines (a guanine run), we found that the IP in the gas phase significantly decreases with the increasing number of nucleotide pairs of the guanine run, whereas the IP in water (OP, oxidation potential) only slightly does. The latter result is consistent with the experimental result for DNA oligomers in water. This decrease in the IP is mainly due to the attractive electrostatic interaction between the hole and a nucleotide pair in the duplex DNA. This interaction is reduced in water, which results in the small decrease in the IP in water. This mechanism explains the discrepancy between the experimental result and the previous computational results obtained by neglecting the solvent. As for the chemically modified guanine, the previous work showed that the removal of some solvent (water) molecules due to the attachment of a neutral functional group to a guanine in a duplex DNA stabilizes the hole on the guanine. One might naively have expected the opposite case, since a polar solvent usually stabilizes ions. This mechanism also explains this unexpected stabilization of a hole as follows. When some water molecules are removed, the attractive electrostatic interaction stabilizing the hole increases, and thus, the hole is stabilized. In order to design the hole energetics by a chemical modification of DNA, this mechanism has to be taken into account and can be used. 1

Diffusion de la lumière par des suspensions de noir de carbone

Nous montrons qu’il est possible (l’utiliser la technique de la diffusion de la lumière pour étudier des suspensions de noir de carbone. Certaines modifications de la théorie de la diffusion de la lumière par des solutions de macromolécules permettent d’interpréter les résultats expérimentaux et de déterminer la masse moléculaire moyenne des agrégats de noir ainsi que leur dimension. Nous confrontons nos résultats avec ceux obtenus par viscosité, sédimentation et microscopie électronique

N° 18. — Étude par diffusion de la lumière de suspensions de noir de carbone

L’étude critique des diagrammes de ZIMM relatifs à des suspensions de noir de carbone (du type HAF) dans des solvants d’indices de réfraction différents, étudiés pour deux longueurs d’onde de la lumière incidente, nous permet de construire les courbes P-1(θ).Nous soulignons l'importance de diverses corrections à apporter à la méthode d’extrapolation habituelle.Nous déterminons ainsi plus correctement les valeurs des rayons de giration et des masses moléculaires des chaînes de noir de carbone étudiés

Diffusion de la lumière par des batonnets anisotropes orientés dans un champ électrique

Nous avons déterminé lus expressions des composantes Vv, Hv, Hh de l'intensité de la lumière diffusée par des solutions de bâtonnets anisotropes (virus de la mosaïque du tabac) orientés par un champ électrique horizontal ou vertical. Ces résultats, nouveaux, nous permettent par simplification des relations obtenues de retrouver les expressions relatives aux bâtonnets isotropes orientés.Nos mesures nous permettent de déterminer le coefficient d'orientation et surtout la valeur absolue et le signe de l'anisotropie optique des particules en solution, sans avoir recours à l'étude de l'effet KERR. L'effet de la fréquence du champ électrique d'orientation a également été étudié. L'accord entre les résultats théoriques et expérimentaux est très satisfaisant

N° 19. — Étude par diffusion de la lumière de suspensions de noir de carbone

L’étude de la dépolarisation de la lumière diffusée par des suspensions de noir de carbone du type HAF, en fonction de l’indice du solvant et de la longueur d’onde utilisée, nous amène à interpréter ce phénomène de dépolarisation comme étant dû à l’anisotropie de macroforme des agrégats de noir de carbone.Nous déterminons ainsi la valeur de la différence des polarisabilités principales en fonction de la masse moléculaire des chaînes de noir de carbone, ainsi que l’ellipticité des ellipsoïdes optiquement équivalents aux agrégats de noir de carbone

Hydration effects in a lattice model of protein folding

The problem of protein folding is approached by introducing explicit solvent effects on a lattice model of chains composed of hydrophobic and polar units. The free energy and entropy of the chain hydration are defined using different values for the contact energy between units. Results obtained from an exhaustive exploration, on a 2D lattice, of the complete set of conformations and possible sequences of 10 unit chains, show that hydration decreases the degeneracy of the ground state of certain sequences, thus allowing a better selection between the specific sequences which present a low free energy and compact structures