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Literature DB >> 10354416

Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing.

Abstract

A method is proposed to restore ab initio low resolution shape and internal structure of chaotically oriented particles (e.g., biological macromolecules in solution) from isotropic scattering. A multiphase model of a particle built from densely packed dummy atoms is characterized by a configuration vector assigning the atom to a specific phase or to the solvent. Simulated annealing is employed to find a configuration that fits the data while minimizing the interfacial area. Application of the method is illustrated by the restoration of a ribosome-like model structure and more realistically by the determination of the shape of several proteins from experimental x-ray scattering data.

Entities: Disease

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Year: 1999 PMID： 10354416 PMCID： PMC1300260 DOI： 10.1016/S0006-3495(99)77443-6

Source DB: PubMed Journal: Biophys J ISSN： 0006-3495 Impact factor: 4.033

22 in total

1. The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA.

Authors: V Ramakrishnan; S W White
Journal: Nature Date: 1992-08-27 Impact factor: 49.962

2. Pentameric and decameric structures in solution of serum amyloid P component by X-ray and neutron scattering and molecular modelling analyses.

Authors: A W Ashton; M K Boehm; J R Gallimore; M B Pepys; S J Perkins
Journal: J Mol Biol Date: 1997-09-26 Impact factor: 5.469

3. Structural basis of asymmetry in the human immunodeficiency virus type 1 reverse transcriptase heterodimer.

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Journal: Proc Natl Acad Sci U S A Date: 1994-07-19 Impact factor: 11.205

4. Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit: ribosomal protein S8 from Bacillus stearothermophilus at 1.9 A resolution.

Authors: C Davies; V Ramakrishnan; S W White
Journal: Structure Date: 1996-09-15 Impact factor: 5.006

5. Solution structure of the ribosomal RNA binding protein S15 from Thermus thermophilus.

Authors: H Berglund; A Rak; A Serganov; M Garber; T Härd
Journal: Nat Struct Biol Date: 1997-01

6. A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli.

Authors: M S Capel; D M Engelman; B R Freeborn; M Kjeldgaard; J A Langer; V Ramakrishnan; D G Schindler; D K Schneider; B P Schoenborn; I Y Sillers
Journal: Science Date: 1987-12-04 Impact factor: 47.728

7. The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation.

Authors: M Kjeldgaard; P Nissen; S Thirup; J Nyborg
Journal: Structure Date: 1993-09-15 Impact factor: 5.006

8. Structures of calmodulin and a functional myosin light chain kinase in the activated complex: a neutron scattering study.

Authors: J K Krueger; G A Olah; S E Rokop; G Zhi; J T Stull; J Trewhella
Journal: Biochemistry Date: 1997-05-20 Impact factor: 3.162

9. A model of the quaternary structure of the Escherichia coli F1 ATPase from X-ray solution scattering and evidence for structural changes in the delta subunit during ATP hydrolysis.

Authors: D I Svergun; I Aldag; T Sieck; K Altendorf; M H Koch; D J Kane; M B Kozin; G Grüber
Journal: Biophys J Date: 1998-11 Impact factor: 4.033

10. Inter-protein distances within the large subunit from Escherichia coli ribosomes.

Authors: R P May; V Nowotny; P Nowotny; H Voss; K H Nierhaus
Journal: EMBO J Date: 1992-01 Impact factor: 11.598

807 in total

1. Determination of domain structure of proteins from X-ray solution scattering.

Authors: D I Svergun; M V Petoukhov; M H Koch
Journal: Biophys J Date: 2001-06 Impact factor: 4.033

2. Modeling the hydration of proteins: prediction of structural and hydrodynamic parameters from X-ray diffraction and scattering data.

Authors: Helmut Durchschlag; Peter Zipper
Journal: Eur Biophys J Date: 2003-04-25 Impact factor: 1.733

3. Macromolecular docking restrained by a small angle X-ray scattering profile.

Authors: Dina Schneidman-Duhovny; Michal Hammel; Andrej Sali
Journal: J Struct Biol Date: 2010-10-12 Impact factor: 2.867

4. Determination of the topological shape of integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria in the detergent solution by small-angle X-ray scattering.

Authors: Xinguo Hong; Yu-Xiang Weng; Ming Li
Journal: Biophys J Date: 2004-02 Impact factor: 4.033

5. 19 A solution structure of the filarial nematode immunomodulatory protein, ES-62.

Authors: Claire J Ackerman; Margaret M Harnett; William Harnett; Sharon M Kelly; Dmitri I Svergun; Olwyn Byron
Journal: Biophys J Date: 2003-01 Impact factor: 4.033

6. Detection of ligand- and solvent-induced shape alterations of cell-growth-regulatory human lectin galectin-1 in solution by small angle neutron and x-ray scattering.

Authors: Lizhong He; Sabine André; Hans-Christian Siebert; Heike Helmholz; Bernd Niemeyer; Hans-Joachim Gabius
Journal: Biophys J Date: 2003-07 Impact factor: 4.033

7. Avoiding steric congestion in dendrimer growth through proportionate branching: a twist on da Vinci's rule of tree branching.

Authors: Xuyi Yue; Marc B Taraban; Laura L Hyland; Yihua Bruce Yu
Journal: J Org Chem Date: 2012-10-10 Impact factor: 4.354