TITLE

Kinetics of proteinlike models: The energy landscape factors that determine folding

AUTHOR(S)
Betancourt, Marcos R.; Onuchic, José Nelson
PUB. DATE
July 1995
SOURCE
Journal of Chemical Physics;7/8/1995, Vol. 103 Issue 2, p773
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
The factors responsible for fast folding and stable 2D lattice proteins are studied by Monte Carlo kinetic simulations and by full enumeration. For weak effective coupling between residues ( i.e., high temperatures) the folding time is mainly controlled by the free energy gradient. When this coupling is strong, entrapment in local minima plays a major role. The energy gap separating the native state from the remaining conformations shows some correlation to the folding and unfolding times for a variety of sequences. These concepts are related to the ratio Tf/Tg proposed by Bryngelson and Wolynes. One source of local minima are strong, non-native (hindering) contacts. An exclusive increase in hindering contacts shows a strong correlation between the energy gap and the folding/unfolding times. Other local minima results from several native contacts that, if formed prematurely, interfere with the formation of others. To study these factors, we use a semispecific model characterized by attractive interactions between similar residues. A procedure to design stabler sequences with smoother landscapes is discussed. By comparing this model to the hydrophobic HP model, we show how higher potential heterogeneity can be used to improve folding. © 1995 American Institute of Physics.
ACCESSION #
7624144

 

Related Articles

  • Single- and two-particle energy gaps across the disorder-driven superconductor-insulator transition. Bouadim, Karim; Loh, Yen Lee; Randeria, Mohit; Trivedi, Nandini // Nature Physics;Nov2011, Vol. 7 Issue 11, p884 

    The competition between superconductivity and localization raises profound questions in condensed-matter physics. In spite of decades of research, the mechanism of the superconductor-insulator transition and the nature of the insulator are not understood. We use quantum Monte Carlo simulations...

  • Librational modes of ice I. Severson, Mark W.; Devlin, J. Paul; Buch, Victoria // Journal of Chemical Physics;8/22/2003, Vol. 119 Issue 8, p4449 

    A joint spectroscopic–computational study was carried out of molecular librations in ice. The measured Fourier transform infrared spectra included H[sub 2]O and HDO isolated in D[sub 2]O ice and D[sub 2]O and HDO isolated in H[sub 2]O ice. Isotopic isolation greatly simplifies the...

  • Fast and accurate prediction of protein side-chain conformations. Liang, Shide; Zheng, Dandan; Zhang, Chi; Standley, Daron M. // Bioinformatics;Oct2011, Vol. 27 Issue 20, p2913 

    Summary: We developed a fast and accurate side-chain modeling program [Optimized Side Chain Atomic eneRgy (OSCAR)-star] based on orientation-dependent energy functions and a rigid rotamer model. The average computing time was 18 s per protein for 218 test proteins with higher prediction accuracy...

  • Monte Carlo study of the early growth stages of 3C-SiC on misoriented <11-20> and <1-100> 6H-SiC substrates. Camarda, M.; Magna, A. La; Via, F. La // Materials Science Forum;2014, Vol. 778-780, p238 

    In this paper we used three dimensional kinetic Monte Carlo simulations on super-lattices to study the hetero-polytypical growth of cubic silicon carbide polytype (3C-SiC) on hexagonal 6H-SiC substrates with miscuts towards the <11-20> and <1-100> directions. We analyze the grown film for...

  • Insulator to metal transition in fluid deuterium. Hood, Randolph Q.; Galli, Giulia // Journal of Chemical Physics;3/22/2004, Vol. 120 Issue 12, p5691 

    We have investigated the insulator to metal transition in fluid deuterium using first principles simulations. Both density functional and quantum Monte Carlo calculations indicate that the electronic energy gap of the liquid vanishes at about ninefold compression and 3000 K. At these conditions...

  • Equilibrium density of states and thermodynamic properties of a model glass former. Calvo, Florent; Bogdan, Tetyana V.; de Souza, Vanessa K.; Wales, David J. // Journal of Chemical Physics;7/28/2007, Vol. 127 Issue 4, p044508 

    This paper presents an analysis of the thermodynamics of a model glass former. We have performed equilibrium sampling of a popular binary Lennard-Jones model, employing parallel tempering Monte Carlo to cover the crystalline, amorphous, and liquid regions of configuration space. Disconnectivity...

  • Steady state and transient electron transport properties of bulk dilute GaNxAs1-x. Naylor, Daniel R.; Dyson, Angela; Ridley, Brian K. // Journal of Applied Physics;Mar2012, Vol. 111 Issue 5, p053703 

    Two valley ensemble Monte Carlo simulations have been performed to investigate the electronic transport properties of bulk GaNxAs1-x alloys where the nitrogen concentration x ≤ 0.02 (2%). We have investigated these properties using two separate approaches, 1) through simulation of GaAs...

  • Importance of the correct Fermi energy on the calculation of defect formation energies in semiconductors. West, D.; Sun, Y. Y.; Zhang, S. B. // Applied Physics Letters;8/20/2012, Vol. 101 Issue 8, p082105 

    Density functional theory (DFT) is a major theoretical tool for the study of defects in semiconductors. However, the results suffer from the often too-small DFT band gap. The calculation of defect formation energy (ΔH) using more sophisticated DFT+GW and hybrid functional methods, however,...

  • Indirect-to-direct band gap transition in relaxed and strained Ge1-x-ySixSny ternary alloys. Attiaoui, Anis; Moutanabbir, Oussama // Journal of Applied Physics;2014, Vol. 116 Issue 6, p063712-1 

    Sn-containing group IV semiconductors create the possibility to independently control strain and band gap thus providing a wealth of opportunities to develop an entirely new class of low dimensional systems, heterostructures, and silicon-compatible electronic and optoelectronic devices. With...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics