Effective interactions cannot replace solvent effects in a lattice model of proteins.

G Salvi; P De Los Rios

doi:10.1103/physrevlett.91.258102

Home/Archive/PubMed

PubMed · 14754161

Effective interactions cannot replace solvent effects in a lattice model of proteins.

G Salvi·P De Los Rios

View original source ↗Export metadata ↓

Abstract

Protein folding and protein design are among the most challenging problems of the past ten years in biophysics and molecular biology. For a given protein, it is possible to extract, from existing protein databases, a set of specific (i.e., belonging to the investigated protein) effective amino-acid (AA) interactions able to stabilize the native state. On the other hand, attempts to find global effective AA interactions, which would be able to stabilize all proteins at once, failed. Using a simple lattice model where the solvent degrees of freedom are (semi)explicitly taken into account, we show that the absence of global effective AA interactions is due to the solvent and that on this lattice model the solvent effects cannot be reproduced by amino-acid effective interactions.

Explore related subjects

Hydrophobic and Hydrophilic Interactions Models, Chemical Protein Folding Proteins Journal Article Research Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

G Salvi, P De Los Rios. 2003-12-16. Effective interactions cannot replace solvent effects in a lattice model of proteins.. https://doi.org/10.1103/physrevlett.91.258102

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

KEEP EXPLORING

Related citations

PubMed2007

Rheological properties of a telechelic associative polymer in the presence of alpha- and methylated beta-cyclodextrins.

The viscosity of hydrophobic ethoxylated urethane (HEUR) solution decreased in the presence of alpha-CD or m-beta-CD; however their interactions were quite different. When the alpha-CD/hydrophobe molar ratio exceeded 5.0, the viscosity was close to that of a PEO solution of similar molecular weight. Oscillatory shear indicated that the mechanically active chains in HEUR solution decreased with the addition of alpha-CD. This agreed with the hypothesis that alpha-CD formed an inclusion complex with the hydrophobic moiety of the HEUR polymer, thereby destroying the transient hydrophobic associative network. The viscosity/temperature relationship of the alpha-CD/HEUR system (for HEUR with 70% of the PEO chains capped at both ends) did not obey the Arrhenius relationship for alpha-CD/hydrophobe molar ratio in the range 0.8-5.0. The low shear viscosity increased with increasing temperature at molar ratio of 1.0, and this was attributed to the competitive complexation of the alpha-CD/hydrophobe and the alpha-CD/PEO chain. Increasing temperature favored alpha-CD/PEO complexation. Comparison between the behavior of alpha-CD/HEUR and m-beta-CD/HEUR resulting from the different binding characteristics was discussed.

Hydrophobic and Hydrophilic Interactions↗

PubMed2007

Liquid matrix deposition on conductive hydrophobic surfaces for tuning and quantitation in UV-MALDI mass spectrometry.

With its highly fluctuating ion production matrix-assisted laser desorption/ionization (MALDI) poses many practical challenges for its application in mass spectrometry. Instrument tuning and quantitative ion abundance measurements using ion signal alone depend on a stable ion beam. Liquid MALDI matrices have been shown to be a promising alternative to the commonly used solid matrices. Their application in areas where a stable ion current is essential has been discussed but only limited data have been provided to demonstrate their practical use and advantages in the formation of stable MALDI ion beams. In this article we present experimental data showing high MALDI ion beam stability over more than two orders of magnitude at high analytical sensitivity (low femtomole amount prepared) for quantitative peptide abundance measurements and instrument tuning in a MALDI Q-TOF mass spectrometer. Samples were deposited on an inexpensive conductive hydrophobic surface and shrunk to droplets <10 nL in size. By using a sample droplet <10 nL it was possible to acquire data from a single irradiated spot for roughly 10,000 shots with little variation in ion signal intensity at a laser repetition rate of 5-20 Hz.

Hydrophobic and Hydrophilic Interactions↗

PubMed2007

Effects of lengthscales and attractions on the collapse of hydrophobic polymers in water.

We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on folding. Hydrophobic polymers display parabolic, protein-like, temperature-dependent free energy of unfolding. Folded states of small attractive polymers are marginally stable at 300 K and can be unfolded by heating or cooling. Increasing the lengthscale or decreasing the polymer-water attractions stabilizes folded states significantly, the former dominated by the hydration contribution. That hydration contribution can be described by the surface tension model, DeltaG = gamma(T)DeltaA, where the surface tension, gamma, is lengthscale-dependent and decreases monotonically with temperature. The resulting variation of the hydration entropy with polymer lengthscale is consistent with theoretical predictions of Huang and Chandler [Huang DM, Chandler D (2000) Proc Natl Acad Sci USA 97:] that explain the blurring of entropy convergence observed in protein folding thermodynamics. Analysis of water structure shows that the polymer-water hydrophobic interface is soft and weakly dewetted, and is characterized by enhanced interfacial density fluctuations. Formation of this interface, which induces polymer folding, is strongly opposed by enthalpy and favored by entropy, similar to the vapor-liquid interface.

Hydrophobic and Hydrophilic Interactions↗