Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils

Zhang, Jiapu; Sun, Jie; Wu, Changzhi

doi:10.1016/j.jtbi.2011.02.012

Cited by 12 publications

(12 citation statements)

References 99 publications

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“…on R n (where n = 3N) is an optimization problem min x∈R n f (x), (1.3) which is a well-known and challenging test problem for global optimization (see http://www-wales.ch.cam.ac.uk/CCD.html and its recent references such as [10,11,12,13,14]). It is very hard for global optimization to directly solve Eq.…”

Section: )mentioning

confidence: 99%

“…We set σ 1 = 10 −4 , σ 2 = 0.1 ∼ 0.9, m 1 = 3 ∼ 7, take the initial solution x 0 =(-0.067, 5.274, 7.860; -1.119, 1.311, 13.564) and calculate its gradient g 0 =(-69.7747, 140.135, 365.852, which is a positive definite matrix with eigenvalues (1085.02, 372.093, 341.157, 230.049, 61.2695, 61.2695). Then Algorithm 1 hybridized with simulated annealing global optimal search (in order to bring local optimal solutions to jump out of local traps, replacing the discrete gradient local optimal search method in Algorithm 1 of [14] by the Algorithm 1 of this paper) is executed and the optimal solution ( The initial structure of Model 1 illuminated in Figure 6(a)∼6(b) is not the optimal structure with the lowest total potential energy. The initial structure also has no hydrogen atoms (so no hydrogen bonds existed) and water molecules added.…”

Section: New Molecular Modeling Homology Modelmentioning

confidence: 99%

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The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils

Zhang¹,

Hou²,

Wang³

et al. 2012

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<p> Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein); theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method—an improved LBFGS Quasi-Newtonian mathematical optimization method—to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field. </p>

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Section: )mentioning

confidence: 99%

Section: New Molecular Modeling Homology Modelmentioning

confidence: 99%

The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils

Zhang¹,

Hou²,

Wang³

et al. 2012

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“…Solving the ten MDGPs in the above section by any Optimization Solver (which will remove the bad vdW/HB contacts) [9][10][11][12][13][14][15][16] and then refining all the models by the Optimization program of Amber 11 [9,17]. At last we got the optimized prion 113-120 GAAAAGA amyloid fibril models, which are illuminated in Figures 8-14.…”

Section: Resultsmentioning

confidence: 99%

The Sensor Network in Molecular Structures of PrP(113-120) AGAAAAGA Amyloid Fibrils

Zhang¹

2014

J Comput Sci Syst Biol

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The problem of locating sensors in telecommunication networks is a distance geometry problem (DGP). In such a case, the positions of some sensors are known (which are called anchors) and some of the distances between sensors (which can or cannot be anchors) are known. The DGP is to locate the positions of all the sensors. Molecular DGP (MDGP) looks sensors as atoms and their telecommunication network as a molecule for the determination of its three-dimensional (3D) structure. This Chapter defines some sensor networks for determining molecular structures of PrP(113-120) AGAAAAGA amyloid fibrils, which are unstable, noncrystalline, insoluble and hard to be determined in NMR or X-ray experimental laboratories. The amyloid fibril structure is the common structure associated with some 20 neurodegenerative amyloid diseases (including Parkinson's, Alzheimer's, Huntington's, and Prions'), and other diseases such as Type II diabetes, etc. The sensor networks established in this Chapter will benefit the study of 3D molecular structures of all these diseases and will be useful in the research areas such as structural materials, computer-aided or structure-based drug design, and the computational theory of molecular dynamics, and quantum mechanics/molecular mechanics.

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“…2.1.2. Hybrid method of discrete gradient with simulated annealing Zhang et al (2011aZhang et al ( , 2011d) used 3FVA.pdb as the pdb template to build two MM-Models (Figs. 11~12 in (Zhang et al, 2011a)).…”

Section: Molecular Structures Of Prion Agaaaaga Amyloid Fibrilsmentioning

confidence: 99%

Recent Advances in Crystallography

Benedict¹

2012

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Dr Jason Benedict received his B.S. in Chemistry from Arizona State University in 2001. He completed his Ph.D. in Chemistry at the University of Washington in the laboratory of Professor Bart Kahr in 2007. His graduate work involved the optical characterization of anisotropic media including dyed crystals, spherulites, and poled polymers. He was a postdoctoral researcher with Professor Philip Coppens at the University at Buffalo from 2008-2011 developing time-resolved X-ray diffraction techniques as well as synthesizing and characterizing functionalized semiconductor nanoparticles. In 2011, Dr Benedict joined the Department of Chemistry at the University at Buffalo as an Assistant Professor where he is developing new 'in-house' time-resolved X-ray diffraction, imaging, and spectroscopic techniques and synthesizing novel molecular nanomaterials for a variety of materials science applications. ContentsPreface XI Section History of Crystallography 1Chapter Histories of Crystallography by Shafranovskii and Schuh 3 PrefaceThe advent of X-ray diffraction in the early twentieth century transformed crystallography from an area of scientific inquiry largely limited to physics, mineralogy, and mathematics, to a highly interdisciplinary field which now includes nearly all life and physical sciences as well as materials science and engineering. The atomic resolution structural information which is now routinely afforded by the combination of X-ray diffraction and crystallography is indispensable for the characterization of many modern materials, the interpretation of their function, and when applicable the rational improvement of their properties. Brighter X-ray sources and improved computing resources drive the evolution of new techniques for the characterization of increasingly exotic materials.This book is a collection of works showcasing some of the most recent developments in the field of crystallography. The history of a scientific field seldom accompanies a field's most recent technical advances between the same two covers. This collection, however, commences with a search for the elusive single narrative of the history of crystallography. Kahr and Shtukenberg introduce the reader to the numerous works which have attempted to describe the evolution of the study of crystals. Ultimately, the authors conclude that the independent narratives of Ilarion Ilarionovich Shafronovskii and Curtis Schuh provide the most comprehensive accounts of the history of crystallography to date and are 'unlikely to be surpassed for a very long time.' X Preface contribution of this section authored by Paradies and coworkers employs a wide variety of experimental techniques including X-ray scattering and diffraction as well as electron microscopy and diffraction on nanocrystals and crystalline colloids of Lipid A-diphosphate to unravel the structure of this biologically important molecule.Crystals as functional materials drives the field of crystal engineering which seeks to create solid-state structures with targeted physical and chemical pr...

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Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils

Cited by 12 publications

References 99 publications

The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils

The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils

The Sensor Network in Molecular Structures of PrP(113-120) AGAAAAGA Amyloid Fibrils

Recent Advances in Crystallography

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