Literature DB >> 29377013

Ab initio electron density determination directly from solution scattering data.

Thomas D Grant1,2.   

Abstract

Using a novel iterative structure factor retrieval algorithm, here I show that electron density can be directly calculated from solution scattering data without modeling. The algorithm was validated with experimental data from 12 different biological macromolecules. This approach avoids many of the assumptions limiting the resolution and accuracy of modeling algorithms by explicitly calculating electron density. This algorithm can be applied to a wide variety of molecular systems.

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Year:  2018        PMID: 29377013     DOI: 10.1038/nmeth.4581

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  18 in total

1.  Resolution measurement in structures derived from single particles.

Authors:  N Grigorieff
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-10

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

Authors:  D I Svergun
Journal:  Biophys J       Date:  1999-06       Impact factor: 4.033

3.  Atomic resolution imaging of a carbon nanotube from diffraction intensities.

Authors:  J M Zuo; I Vartanyants; M Gao; R Zhang; L A Nagahara
Journal:  Science       Date:  2003-05-30       Impact factor: 47.728

4.  UCSF Chimera--a visualization system for exploratory research and analysis.

Authors:  Eric F Pettersen; Thomas D Goddard; Conrad C Huang; Gregory S Couch; Daniel M Greenblatt; Elaine C Meng; Thomas E Ferrin
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

Review 5.  X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.

Authors:  Christopher D Putnam; Michal Hammel; Greg L Hura; John A Tainer
Journal:  Q Rev Biophys       Date:  2007-08       Impact factor: 5.318

6.  Reconstruction of an object from the modulus of its Fourier transform.

Authors:  J R Fienup
Journal:  Opt Lett       Date:  1978-07-01       Impact factor: 3.776

7.  Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm.

Authors:  P Chacón; F Morán; J F Díaz; E Pantos; J M Andreu
Journal:  Biophys J       Date:  1998-06       Impact factor: 4.033

8.  Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography.

Authors:  Jesús G Galaz-Montoya; Corey W Hecksel; Philip R Baldwin; Eryu Wang; Scott C Weaver; Michael F Schmid; Steven J Ludtke; Wah Chiu
Journal:  J Struct Biol       Date:  2016-03-22       Impact factor: 2.867

9.  Conventions and workflows for using Situs.

Authors:  Willy Wriggers
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-03-16

10.  Endophilin-A1 BAR domain interaction with arachidonyl CoA.

Authors:  Maxim V Petoukhov; Winfried Weissenhorn; Dmitri I Svergun
Journal:  Front Mol Biosci       Date:  2014-10-28
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  45 in total

1.  Inhibition, crystal structures, and in-solution oligomeric structure of aldehyde dehydrogenase 9A1.

Authors:  Jesse W Wyatt; David A Korasick; Insaf A Qureshi; Ashley C Campbell; Kent S Gates; John J Tanner
Journal:  Arch Biochem Biophys       Date:  2020-07-24       Impact factor: 4.013

2.  D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures.

Authors:  Avi Ginsburg; Tal Ben-Nun; Roi Asor; Asaf Shemesh; Lea Fink; Roee Tekoah; Yehonatan Levartovsky; Daniel Khaykelson; Raviv Dharan; Amos Fellig; Uri Raviv
Journal:  J Appl Crystallogr       Date:  2019-02-01       Impact factor: 3.304

3.  SASBDB: Towards an automatically curated and validated repository for biological scattering data.

Authors:  Alexey G Kikhney; Clemente R Borges; Dmitry S Molodenskiy; Cy M Jeffries; Dmitri I Svergun
Journal:  Protein Sci       Date:  2019-10-11       Impact factor: 6.725

4.  Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data.

Authors:  Darren J Hsu; Denis Leshchev; Irina Kosheleva; Kevin L Kohlstedt; Lin X Chen
Journal:  J Chem Phys       Date:  2020-05-29       Impact factor: 3.488

5.  Structural basis of peptidoglycan endopeptidase regulation.

Authors:  Jung-Ho Shin; Alan G Sulpizio; Aaron Kelley; Laura Alvarez; Shannon G Murphy; Lixin Fan; Felipe Cava; Yuxin Mao; Mark A Saper; Tobias Dörr
Journal:  Proc Natl Acad Sci U S A       Date:  2020-05-11       Impact factor: 11.205

6.  Structural Adaptation in Its Orphan Domain Engenders Betaglycan with an Alternate Mode of Growth Factor Binding Relative to Endoglin.

Authors:  Sun Kyung Kim; Matthew J Whitley; Troy C Krzysiak; Cynthia S Hinck; Alexander B Taylor; Christian Zwieb; Chang-Hyeock Byeon; Xiaohong Zhou; Valentín Mendoza; Fernando López-Casillas; William Furey; Andrew P Hinck
Journal:  Structure       Date:  2019-07-18       Impact factor: 5.006

7.  Molecular Architecture of the Inositol Phosphatase Siw14.

Authors:  Tyler J Florio; Ravi K Lokareddy; Richard E Gillilan; Gino Cingolani
Journal:  Biochemistry       Date:  2019-01-03       Impact factor: 3.162

8.  Perturbation of the interactions of calmodulin with GRK5 using a natural product chemical probe.

Authors:  Tyler S Beyett; Amy E Fraley; Emily Labudde; Dhabaleswar Patra; Ryan C Coleman; Akito Eguchi; Alisa Glukhova; Qiuyan Chen; Robert M Williams; Walter J Koch; David H Sherman; John J G Tesmer
Journal:  Proc Natl Acad Sci U S A       Date:  2019-07-23       Impact factor: 11.205

9.  Large-scale conformational rearrangement of the α5-helix of Gα subunits in complex with the guanine nucleotide exchange factor Ric8A.

Authors:  Dhiraj Srivastava; Nikolai O Artemyev
Journal:  J Biol Chem       Date:  2019-10-17       Impact factor: 5.157

10.  Unfolding bovine α-lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations.

Authors:  Darren J Hsu; Denis Leshchev; Irina Kosheleva; Kevin L Kohlstedt; Lin X Chen
Journal:  J Chem Phys       Date:  2021-03-14       Impact factor: 3.488

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