Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils

DOI10.1016/J.JTBI.2011.02.012MaRDI QIDQ1783477zbMATH OpenOpenAlexWikidataFDO

Authors Jiapu Zhang, Jie Sun, Changzhi Wu

Publication date 21 September 2018

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1012.2504

zbMATH Keywords

molecular modelinghybrid computational algorithmsoptimizing molecular structures

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Software, source code, etc. for problems pertaining to biology (92-04)

Abstract: X-ray crystallography is a powerful tool to determine the protein 3D structure. However, it is time-consuming and expensive, and not all proteins can be successfully crystallized, particularly for membrane proteins. Although nuclear magnetic resonance (NMR) spectroscopy is indeed a very powerful tool in determining the 3D structures of membrane proteins, it is also time-consuming and costly. To the best of the authors' knowledge, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins due to the noncrystalline and insoluble nature of the amyloid fibril, although many experimental studies have shown that this region has amyloid fibril forming properties and plays an important role in prion diseases. In view of this, the present study is devoted to address this problem from computational approaches such as global energy optimization, simulated annealing, and structural bioinformatics. The optimal atomic-resolution structures of prion AGAAAAGA amyloid fibils reported in this paper have a value to the scientific community in its drive to find treatments for prion diseases.

Recommendations

• A novel canonical dual computational approach for prion AGAAAAGA amyloid fibril molecular modeling
• Studies on the structural stability of rabbit prion probed by molecular dynamics simulations of its wild-type and mutants
• Molecular dynamics simulations of the full-length prion protein
• Mathematical aspects of protein structure determination with NMR orientational restraints
• Extended Abstract: Structure Determination of Symmetric Protein Complexes by a Complete Search of Symmetry Configuration Space Using NMR Distance Restraints

Cites work

• scientific article; zbMATH DE number 3577030 (Why is no real title available?)
• scientific article; zbMATH DE number 852532 (Why is no real title available?)
• A hybrid descent method for global optimization
• A multivariate partition approach to optimization problems
• A parallel build-up algorithm for global energy minimizations of molecular clusters using effective energy simulated annealing
• An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation
• Comparative analysis of the cutting angle and simulated annealing methods in global optimization
• Continuous subdifferential approximations and their applications
• Discrete gradient method: Derivative-free method for nonsmooth optimization
• Equivalent formulations and necessary optimality conditions for the Lennard-Jones problem
• Finding the nearest point in A polytope
• GLOBAL CONVERGENCE OF A SPECIAL CASE OF THE DAI–YUAN FAMILY WITHOUT LINE SEARCH
• GLOBAL CONVERGENCE OF SHORTEST-RESIDUAL FAMILY OF CONJUGATE GRADIENT METHODS WITHOUT LINE SEARCH
• Global convergence of conjugate gradient methods without line search
• Global optima of Lennard-Jones clusters
• Improvement on the Northby algorithm for molecular conformation: Better solutions
• Molecular conformation on the CM-5 by parallel two-level simulated annealing
• Optimization and nonsmooth analysis
• Optimization by simulated annealing
• Optimization methods for computing global minima of nonconvex potential energy functions
• Predicting protein structural classes with pseudo amino acid composition: an approach using geometric moments of cellular automaton image
• Quasidifferentiability and related topics. Dedicated to Prof. Franco Giannessi on his 65th birthday and to Prof. Diethard Pallaschke on his 60th birthday
• Soliton/exciton transport in proteins
• Some remarks on protein attribute prediction and pseudo amino acid composition
• Studies on the structural stability of rabbit prion probed by molecular dynamics simulations of its wild-type and mutants
• The optimal geometry of Lennard-Jones clusters: 148-309

Cited in

(1)

• A novel canonical dual computational approach for prion AGAAAAGA amyloid fibril molecular modeling

Describes a project that uses

Uses Software

• GPCR-CA

This page was built for publication: Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q1783477)