PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 9408943

Evolution of model proteins on a foldability landscape.

S Govindarajan·R A Goldstein
View original source ↗Export metadata ↓

Abstract

We model the evolution of simple lattice proteins as a random walk in a fitness landscape, where the fitness represents the ability of the protein to fold. At higher selective pressure, the evolutionary trajectories are confined to neutral networks where the native structure is conserved and the dynamics are non self-averaging and nonexponential. The optimizability of the corresponding native structure has a strong effect on the size of these neutral networks and thus on the nature of the evolutionary process.

Explore related subjects

BiopolymersEvolution, MolecularMathematical ComputingModels, MolecularProtein ConformationProtein FoldingProteinsJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

S Govindarajan, R A Goldstein. 1997. Evolution of model proteins on a foldability landscape.. https://doi.org/10.1002/(sici)1097-0134(199712)29%3A4%3C461%3A%3Aaid-prot6%3E3.0.co%3B2-b

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2007

Negative compressibility and nonequivalence of two statistical ensembles in the escape transition of a polymer chain.

An end-tethered polymer chain compressed between two pistons undergoes an abrupt transition from a confined coil state to an inhomogeneous flowerlike conformation partially escaped from the gap. This phase transition is first order in the thermodynamic limit of infinitely long chains. A rigorous analytical theory is presented for a Gaussian chain in two ensembles: (a) the H-ensemble, in which the distance H between the pistons plays the role of the independent control parameter, and (b) the conjugate f-ensemble, in which the external compression force f is the independent parameter. Details about the metastable chain configurations are analyzed by introducing the Landau free energy as a function of the chain stretching order parameter. The binodal and spinodal lines, as well as the barrier heights between the stable and metastable states in the free energy landscape, are presented in both ensembles. In the loop region for the average force with dependence on the distance H (i.e., in the H-ensemble) a negative compressibility exists, whereas in the f-ensemble the average distance as a function of the force is strictly monotonic. The average fraction of imprisoned segments and the lateral force, taken as functions of the distance H or the average H, respectively, have different behaviors in the two ensembles. These results demonstrate a clear counterexample of a main principle of statistical mechanics, stating that all ensembles are equivalent in the thermodynamic limit. The authors show that the negative compressibility in the escape transition is a purely equilibrium result and analyze in detail the origin of the nonequivalence of the ensembles. It is argued that it should be possible to employ the escape transition and its anomalous behavior in macroscopically homogeneous, but microscopically inhomogeneous, materials.

Biopolymers↗
PubMed2007

Rheology of a reversible supramolecular polymer studied by comparison of the effects of temperature and chain stoppers.

The rheology of a reversible supramolecular polymer is studied by comparing the effects of an increase in temperature and the addition of chain stoppers. The dependence of the zero-shear viscosity and the terminal relaxation time on temperature is exponential, and the activation energy for viscous flow can be calculated. Above a critical stopper fraction, power laws describe the stopper dependence of the viscosity and relaxation time. A simple model for the effect of the addition of chain stoppers on the average degree of polymerization adequately describes the results. A comparison of flow curves at several temperatures and stopper fractions reveals considerable differences between solutions with the same zero-shear viscosity. These are mainly associated with differences in the terminal relaxation time. A mechanism of shear-induced alignment and subsequent elongation of chains is proposed, with which the experimental results are consistent.

Biopolymers↗
PubMed2007

Preparation and characterization of water/oil and water/oil/water emulsions containing biopolymer-gelled water droplets.

The purpose of this study was to create water-in-oil (W/O) and water-in-oil-in-water (W/O/W) emulsions containing gelled internal water droplets. Twenty weight percent W/O emulsions stabilized by a nonionic surfactant (6.4 wt % polyglycerol polyricinoleate, PGPR) were prepared that contained either 0 or 15 wt % whey protein isolate (WPI) in the aqueous phase, with the WPI-containing emulsions being either unheated or heated (80 degrees C for 20 min) to gel the protein. Optical microscopy and sedimentation tests did not indicate any significant changes in droplet characteristics of the W/O emulsions depending on WPI content (0 or 15%), shearing (0-7 min at constant shear), thermal processing (30-90 degrees C for 30 min), or storage at room temperature (up to 3 weeks). W/O/W emulsions were produced by homogenizing the W/O emulsions with an aqueous Tween 20 solution using either a membrane homogenizer (MH) or a high-pressure valve homogenizer (HPVH). For the MH the mean oil droplet size decreased with increasing number of passes, whereas for the HPVH it decreased with increasing number of passes and increasing homogenization pressure. The HPVH produced smaller droplets than the MH, but the MH produced a narrower particle size distribution. All W/O/W emulsions had a high retention of water droplets (>95%) within the larger oil droplets after homogenization. This study shows that W/O/W emulsions containing oil droplets with gelled water droplets inside can be produced by using MH or HPVH.

Biopolymers↗