Spontaneous Structure Formation Research Articles

Folding propensities of peptide fragments of myoglobin

Myoglobin has been studied extensively as a paradigm for protein folding. As part of an ongoing study of potential folding initiation sites in myoglobin, we have synthetized a series of peptides covering the entire sequence of sperm whale myoglobin. We report here on the conformation preferences of a series of peptides that cover the region from the A helix to the FG turn. Structural propensities were determined using circular dichroism and nuclear magnetic resonance spectroscopy in aqueous solution, trifluoroethanol, and methanol. Peptides corresponding to helical regions in the native protein, namely the B, C, D, and E helices, populate the alpha region of (phi, psi) space in water solution but show no measurable helix formation except in the presence of trifluoroethanol. The F-helix sequence has a much lower propensity to populate helical conformations even in TFE. Despite several attempts, we were not successful in synthesizing a peptide corresponding to the A-helix region that was soluble in water. A peptide termed the AB domain was constructed spanning the A- and B-helix sequences. The AB domain is not soluble in water, but shows extensive helix formation throughout the peptide when dissolved in methanol, with a break in the helix at a site close to the A-B helix junction in the intact folded myoglobin protein. With the exception of one local preference for a turn conformation stabilized by hydrophobic interactions, the peptides corresponding to turns in the folded protein do not measurably populate beta-turn conformations in water, and the addition of trifluoroethanol does not enhance the formation of either helical or turn structure. In contrast to the series of peptides described here, either studies of peptides from the GH region of myoglobin show a marked tendency to populate helical structures (H), nascent helical structures (G), or turn conformations (GH peptide) in water solution. This region, together with the A-helix and part of the B-helix, has been shown to participate in an early folding intermediate. The complete analysis of conformational properties of isolated myoglobin peptides supports the hypothesis that spontaneous secondary structure formation in local regions of the polypeptide may play an important role in the initiation of protein folding.

Capillaries in alginate gel as an example of dissipative structure formation

Abstract Capillaries of uniform diameter (8–300 μm) are formed in a gel growing during diffusion of Me 2+ metal ions into a sol of Na alginate. The alginate chains are cross-linked by the metal ions. The transition from sol to gel is limited by diffusion and occurs in a propagating front. Our investigations provide evidence that the dissipative process of structure formation in this front is caused by friction between the contracting alginate chains and the surrounding solution, leading to a pattern of hydrodynamic flow similar to Rayleigh-Benard convection. This flow pattern is mapped on the growing gel and leads to a structure of parallel capillaries filled with aqueous solution. We present a reduced mathematical model describing the onset of a spontaneous structure formation. The model includes the hydrodynamics of the system formulated by a Navier-Stokes equation. In this equation the frictional force between the contracting alginate chains and the solution plays the role of an external force. A second basic equation describes the binding of alginate molecules to the gel front. The model shows that pattern formation occurs above a critical value of the contraction velocity. This critical value and the spacing of the resulting pattern depend on a number of parameters such as viscosity, chain density, thickness of the contraction zone, friction coefficient between contracting chains and surrounding solution, diffusion constant of alginate and concentration of the sol.

Transverse Pattern Formation in Optical Parametric Oscillators

Abstract The transverse pattern formation in singly and doubly resonant optical parametric oscillators (OPOs) is investigated. The study is based on the derivation and analysis of the amplitude equation for these two cases of OPOs. It is shown that the amplitude equation of a singly resonant OPO (the complex Ginzburg-Landau equation) is similar to that of a class A laser. The doubly resonant OPO is described by a Swift-Hohenberg equation analogous to the amplitude equation obtained recently in the optical bistability. The spontaneous structure formation of OPOs is also demonstrated numerically.

Spontaneous structure formation in driven systems with two species: Exact solutions in a mean-field theory.

A stochastic lattice gas of particles, subject to an excluded volume constraint and to a uniform external driving field, is investigated. Using a mean-field theory for a system with equal number of oppositely charged particles, exact results are obtained. Focusing on the current-vs-density plot, we propose an explanation for the discontinuous transition found in earlier simulations. A critical value of the drive, below which this transition becomes continuous, is found. These results are supported by a bifurcation analysis, leading to an equation of motion for the amplitude of the soft mode.

Folding and association of oligomeric enzymes

The spontaneous structure formation of oligomeric enzymes consists of the consecutive ‘folding’ and association of the constituent polypeptide chains. Whether catalytic function is an intrinsic property of the folded monomers may be determined using kinetic reconstitution experiments. It is shown that full activity requires association; the correct assembly of subunits depends on their proper folding. The native structure is determined as the kinetically accessible state of lowest free energy.

Selforganisation as a result of effective nonlocality

A one-component quasilinear kinetic system with nonlocal spatial coupling is considered. The long-range inhibition effect combined with a short-range activation is shown to provide a possibility of spontaneous dissipative structure formation. The effective nonlocality can be due to diffusion of an intermediate.

Folding and association of oligomeric enzymes.

The spontaneous structure formation of oligomeric enzymes consists of the consecutive 'folding' and association of the constituent polypeptide chains. Whether catalytic function is an intrinsic property of the folded monomers may be determined using kinetic reconstitution experiments. It is shown that full activity requires association; the correct assembly of subunits depends on their proper folding. The native structure is determined as the kinetically accessible state of lowest free energy.

Dynamic Molecular Organization in Vesicles and Membranes

AbstractThe physico chemical properties of lipid layers and membranes which are of special interest in connection with processes in organized molecular assemblies are summarized. In particular the basic physical principles governing structure formation in lipid/protein/water systems are discussed. As a first step towards structure formation the self association of lipids in water is discussed. It is then shown that 2‐dimensional lipid mixtures possess an intrinsic tendency towards lateral structure (domain) formation which originates in differences in symmetry of the possible polymorphic states of lipid layers. Evidence is provided that the lateral structure formation is greately enforced by incorporation of macromolecules into lipid layers, while in membranes containing charged lipids, domain formation may also be triggered by electrostatic binding of water soluble proteins. ‐The origins of the spontaneous structure formation in lipid/protein systems are (1) cooperative lipid protein interaction which is caused by lipid‐mediated elastic long range forces, (2) the capacity of proteins to select specific lipids in lipid alloys either by electrostatic forces or by a steric‐elastic effect. Finally, it is shown that (domain) structure formation is a very fast process, which, in the presence of charged lipids, may be accompanied by pronounced hysteresis effects. The close analogies between the physical properties of lipid mixtures and metal alloy are discussed.