Literature DB >> 28805795

M3: an integrative framework for structure determination of molecular machines.

Ezgi Karaca1, João P G L M Rodrigues2, Andrea Graziadei1, Alexandre M J J Bonvin2, Teresa Carlomagno1,3,4.   

Abstract

We present a broadly applicable, user-friendly protocol that incorporates sparse and hybrid experimental data to calculate quasi-atomic-resolution structures of molecular machines. The protocol uses the HADDOCK framework, accounts for extensive structural rearrangements both at the domain and atomic levels and accepts input from all structural and biochemical experiments whose data can be translated into interatomic distances and/or molecular shapes.

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Year:  2017        PMID: 28805795     DOI: 10.1038/nmeth.4392

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


  38 in total

1.  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 2.  The system-resonance approach in modeling genetic structures.

Authors:  Sergey V Petoukhov
Journal:  Biosystems       Date:  2015-11-03       Impact factor: 1.973

3.  Structures of complete RNA polymerase II and its subcomplex, Rpb4/7.

Authors:  Karim-Jean Armache; Simone Mitterweger; Anton Meinhart; Patrick Cramer
Journal:  J Biol Chem       Date:  2004-12-09       Impact factor: 5.157

4.  The structure of the box C/D enzyme reveals regulation of RNA methylation.

Authors:  Audrone Lapinaite; Bernd Simon; Lars Skjaerven; Magdalena Rakwalska-Bange; Frank Gabel; Teresa Carlomagno
Journal:  Nature       Date:  2013-10-13       Impact factor: 49.962

5.  Conserved architecture of the core RNA polymerase II initiation complex.

Authors:  Wolfgang Mühlbacher; Sarah Sainsbury; Matthias Hemann; Merle Hantsche; Simon Neyer; Franz Herzog; Patrick Cramer
Journal:  Nat Commun       Date:  2014-07-10       Impact factor: 14.919

6.  Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2.

Authors:  M Nilges; A M Gronenborn; A T Brünger; G M Clore
Journal:  Protein Eng       Date:  1988-04

7.  Analyzing RNA-protein crosslinking sites in unlabeled ribonucleoprotein complexes by mass spectrometry.

Authors:  Henning Urlaub; Eva Kühn-Hölsken; Reinhard Lührmann
Journal:  Methods Mol Biol       Date:  2008

8.  The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

Authors:  G C P van Zundert; J P G L M Rodrigues; M Trellet; C Schmitz; P L Kastritis; E Karaca; A S J Melquiond; M van Dijk; S J de Vries; A M J J Bonvin
Journal:  J Mol Biol       Date:  2015-09-26       Impact factor: 5.469

9.  Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.

Authors:  Marc van Dijk; Alexandre M J J Bonvin
Journal:  Nucleic Acids Res       Date:  2010-05-13       Impact factor: 16.971

10.  LEGO-NMR spectroscopy: a method to visualize individual subunits in large heteromeric complexes.

Authors:  Markus Mund; Jan H Overbeck; Janina Ullmann; Remco Sprangers
Journal:  Angew Chem Int Ed Engl       Date:  2013-08-14       Impact factor: 15.336

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  10 in total

1.  High-density chemical cross-linking for modeling protein interactions.

Authors:  Julian Mintseris; Steven P Gygi
Journal:  Proc Natl Acad Sci U S A       Date:  2019-12-17       Impact factor: 11.205

Review 2.  Chemical shift-based methods in NMR structure determination.

Authors:  Santrupti Nerli; Andrew C McShan; Nikolaos G Sgourakis
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2018-03-11       Impact factor: 9.795

Review 3.  Integrative structural modeling of macromolecular complexes using Assembline.

Authors:  Vasileios Rantos; Kai Karius; Jan Kosinski
Journal:  Nat Protoc       Date:  2021-11-29       Impact factor: 13.491

Review 4.  Recent advances in RNA structurome.

Authors:  Bingbing Xu; Yanda Zhu; Changchang Cao; Hao Chen; Qiongli Jin; Guangnan Li; Junfeng Ma; Siwy Ling Yang; Jieyu Zhao; Jianghui Zhu; Yiliang Ding; Xianyang Fang; Yongfeng Jin; Chun Kit Kwok; Aiming Ren; Yue Wan; Zhiye Wang; Yuanchao Xue; Huakun Zhang; Qiangfeng Cliff Zhang; Yu Zhou
Journal:  Sci China Life Sci       Date:  2022-06-14       Impact factor: 10.372

5.  The guide sRNA sequence determines the activity level of box C/D RNPs.

Authors:  Andrea Graziadei; Frank Gabel; John Kirkpatrick; Teresa Carlomagno
Journal:  Elife       Date:  2020-03-23       Impact factor: 8.140

Review 6.  Computational modeling of RNA 3D structure based on experimental data.

Authors:  Almudena Ponce-Salvatierra; Katarzyna Merdas; Chandran Nithin; Pritha Ghosh; Sunandan Mukherjee; Janusz M Bujnicki
Journal:  Biosci Rep       Date:  2019-02-08       Impact factor: 3.840

Review 7.  Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes.

Authors:  Chandran Nithin; Pritha Ghosh; Janusz M Bujnicki
Journal:  Genes (Basel)       Date:  2018-08-25       Impact factor: 4.096

8.  High-resolution small RNA structures from exact nuclear Overhauser enhancement measurements without additional restraints.

Authors:  Parker J Nichols; Morkos A Henen; Alexandra Born; Dean Strotz; Peter Güntert; Beat Vögeli
Journal:  Commun Biol       Date:  2018-06-07

9.  Histone chaperone exploits intrinsic disorder to switch acetylation specificity.

Authors:  Nataliya Danilenko; Lukas Lercher; John Kirkpatrick; Frank Gabel; Luca Codutti; Teresa Carlomagno
Journal:  Nat Commun       Date:  2019-08-06       Impact factor: 14.919

Review 10.  Modeling the Dynamics of Protein-Protein Interfaces, How and Why?

Authors:  Ezgi Karaca; Chantal Prévost; Sophie Sacquin-Mora
Journal:  Molecules       Date:  2022-03-11       Impact factor: 4.411

  10 in total

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