Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils
From MaRDI portal
Publication:1783477
DOI10.1016/J.JTBI.2011.02.012zbMATH Open1397.92549arXiv1012.2504OpenAlexW2075506718WikidataQ43581078 ScholiaQ43581078MaRDI QIDQ1783477FDOQ1783477
Authors: Jiapu Zhang, Jie Sun, Changzhi Wu 
Publication date: 21 September 2018
Published in: Journal of Theoretical Biology (Search for Journal in Brave)
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.
Full work available at URL: https://arxiv.org/abs/1012.2504
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
Protein sequences, DNA sequences (92D20) Software, source code, etc. for problems pertaining to biology (92-04)
Cites Work
- Discrete gradient method: Derivative-free method for nonsmooth optimization
- Optimization by simulated annealing
- Optimization and nonsmooth analysis
- Title not available (Why is that?)
- A multivariate partition approach to optimization problems
- Continuous subdifferential approximations and their applications
- Title not available (Why is that?)
- Some remarks on protein attribute prediction and pseudo amino acid composition
- Finding the nearest point in A polytope
- Global optima of Lennard-Jones clusters
- Predicting protein structural classes with pseudo amino acid composition: an approach using geometric moments of cellular automaton image
- Soliton/exciton transport in proteins
- Quasidifferentiability and related topics. Dedicated to Prof. Franco Giannessi on his 65th birthday and to Prof. Diethard Pallaschke on his 60th birthday
- A hybrid descent method for global optimization
- Global convergence of conjugate gradient methods without line search
- Optimization methods for computing global minima of nonconvex potential energy functions
- A parallel build-up algorithm for global energy minimizations of molecular clusters using effective energy simulated annealing
- Equivalent formulations and necessary optimality conditions for the Lennard-Jones problem
- GLOBAL CONVERGENCE OF SHORTEST-RESIDUAL FAMILY OF CONJUGATE GRADIENT METHODS WITHOUT LINE SEARCH
- The optimal geometry of Lennard-Jones clusters: 148-309
- Molecular conformation on the CM-5 by parallel two-level simulated annealing
- Improvement on the Northby algorithm for molecular conformation: Better solutions
- An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation
- Studies on the structural stability of rabbit prion probed by molecular dynamics simulations of its wild-type and mutants
- GLOBAL CONVERGENCE OF A SPECIAL CASE OF THE DAI–YUAN FAMILY WITHOUT LINE SEARCH
- Comparative analysis of the cutting angle and simulated annealing methods in global optimization
Cited In (1)
Uses Software
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)
