✦ LIBER ✦

Folding funnels: The key to robust protein structure prediction

✍ Scribed by Corey Hardin; Michael P. Eastwood; Michael Prentiss; Z. Luthey-Schulten; Peter G. Wolynes

Publisher: John Wiley and Sons
Year: 2001
Tongue: English
Weight: 998 KB
Volume: 23
Category: Article
ISSN: 0192-8651
DOI: 10.1002/jcc.1162

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

Natural proteins fold because their free energy landscapes are funneled to their native states. The degree to which a model energy function for protein structure prediction can avoid the multiple minima problem and reliably yield at least low‐resolution predictions is also dependent on the topography of the energy landscape. We show that the degree of funneling can be quantitatively expressed in terms of a few averaged properties of the landscape. This allows us to optimize simplified energy functions for protein structure prediction even in the absence of homology information. Here we outline the optimization procedure in the context of associative memory energy functions originally introduced for tertiary structure recognition and demonstrate that even partially funneled landscapes lead to qualitatively correct, low‐resolution predictions. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 138–146, 2002

📜 SIMILAR VOLUMES

Prediction of protein structure: The pro

Prediction of protein structure: The problem of fold multiplicity

✍ Andrei L. Lomize; Irina D. Pogozheva; Henry I. Mosberg 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 154 KB 👁 2 views

Three-dimensional (3D) models of four CASP3 targets were calculated using a simple modeling procedure that includes prediction of regular secondary structure, analysis of possible ␤-sheet topologies, assembly of amphiphilic helices and ␤-sheets to bury their nonpolar surfaces, and adjustment of side

Use of quantitative structure-property r

Use of quantitative structure-property relationships to predict the folding ability of model proteins

✍ Aaron R. Dinner; Sung-Sau So; Martin Karplus 📂 Article 📅 1998 🏛 John Wiley and Sons 🌐 English ⚖ 461 KB 👁 2 views

We investigate the folding of a 125-bead heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice. Detailed study of a few sequences revealed a folding mechanism consisting of a rapid collapse followed by a slow search for a stable core that served as the transition

Structure prediction and fold recognitio

Structure prediction and fold recognition for the ferrochelatase family of proteins

✍ M. Hansson; S.P. Gough; S.S. Brody 📂 Article 📅 1997 🏛 John Wiley and Sons 🌐 English ⚖ 214 KB 👁 2 views

An alpha/beta barrel is predicted for the three-dimensional (3D) structure of Bacillus subtilis ferrochelatase. To arrive at this structure, the THREADER program was used to find possible homologous 3D structures and to predict the secondary structure for the ferrochelatase sequence. The secondary s

Predicting the equilibrium protein foldi

Predicting the equilibrium protein folding pathway: Structure-based analysis of staphylococcal nuclease

✍ Vincent J. Hilser; Ernesto Freire 📂 Article 📅 1997 🏛 John Wiley and Sons 🌐 English ⚖ 203 KB 👁 2 views

The equilibrium folding pathway of staphylococcal nuclease (SNase) has been approximated using a statistical thermodynamic formalism that utilizes the highresolution structure of the native state as a template to generate a large ensemble of partially folded states. Close to 400,000 different states

Predicted structure and fold recognition

Predicted structure and fold recognition for the glutamyl tRNA reductase family of proteins

✍ S.S. Brody; S.P. Gough; C.G. Kannangara 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 556 KB

The conserved residues of glutamyl tRNA reductase (GTR) from Hordeum vulgare (GTRhorvu) were found from an alignment/pile-up of 24 homologous sequences found using BLAST searches. A multiple alignment of sequences was used to obtain a prediction of the secondary structure of the GTR's. This secondar

The Key to Solving the Protein-Folding P

The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State

✍ Wilfred F. van Gunsteren; Roland Bürgi; Christine Peter; Xavier Daura 📂 Article 📅 2001 🏛 John Wiley and Sons 🌐 English ⚖ 299 KB 👁 2 views