Literature DB >> 25825836

Integrative, dynamic structural biology at atomic resolution--it's about time.

Henry van den Bedem1, James S Fraser2.   

Abstract

Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and other techniques are helping us realize the dream of seeing--in atomic detail--how different parts of biomolecules shift between functional substates using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution.

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Year:  2015        PMID: 25825836      PMCID: PMC4457290          DOI: 10.1038/nmeth.3324

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


  106 in total

1.  Inferential structure determination.

Authors:  Wolfgang Rieping; Michael Habeck; Michael Nilges
Journal:  Science       Date:  2005-07-08       Impact factor: 47.728

2.  Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics.

Authors:  P Gros; W F van Gunsteren; W G Hol
Journal:  Science       Date:  1990-09-07       Impact factor: 47.728

3.  Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion.

Authors:  Paul Schanda; Matthias Huber; Jérôme Boisbouvier; Beat H Meier; Matthias Ernst
Journal:  Angew Chem Int Ed Engl       Date:  2011-09-14       Impact factor: 15.336

4.  Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics.

Authors:  Mats Linder; Adam Johannes Johansson; Tjelvar S G Olsson; John Liebeschuetz; Tore Brinck
Journal:  J Comput Aided Mol Des       Date:  2012-09-16       Impact factor: 3.686

5.  Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge.

Authors:  F Aboul-ela; J Karn; G Varani
Journal:  Nucleic Acids Res       Date:  1996-10-15       Impact factor: 16.971

6.  Modeling conformational ensembles of slow functional motions in Pin1-WW.

Authors:  Faruck Morcos; Santanu Chatterjee; Christopher L McClendon; Paul R Brenner; Roberto López-Rendón; John Zintsmaster; Maria Ercsey-Ravasz; Christopher R Sweet; Matthew P Jacobson; Jeffrey W Peng; Jesús A Izaguirre
Journal:  PLoS Comput Biol       Date:  2010-12-02       Impact factor: 4.475

7.  The spatial architecture of protein function and adaptation.

Authors:  Richard N McLaughlin; Frank J Poelwijk; Arjun Raman; Walraj S Gosal; Rama Ranganathan
Journal:  Nature       Date:  2012-10-07       Impact factor: 49.962

8.  Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR.

Authors:  Daniel A Keedy; Henry van den Bedem; David A Sivak; Gregory A Petsko; Dagmar Ringe; Mark A Wilson; James S Fraser
Journal:  Structure       Date:  2014-05-29       Impact factor: 5.006

9.  Improving the accuracy of macromolecular structure refinement at 7 Å resolution.

Authors:  Axel T Brunger; Paul D Adams; Petra Fromme; Raimund Fromme; Michael Levitt; Gunnar F Schröder
Journal:  Structure       Date:  2012-06-06       Impact factor: 5.006

10.  Site-resolved measurement of microsecond-to-millisecond conformational-exchange processes in proteins by solid-state NMR spectroscopy.

Authors:  Martin Tollinger; Astrid C Sivertsen; Beat H Meier; Matthias Ernst; Paul Schanda
Journal:  J Am Chem Soc       Date:  2012-08-28       Impact factor: 15.419

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  87 in total

1.  Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.

Authors:  Rei Matsuoka; Atsushi Shimada; Yasuaki Komuro; Yuji Sugita; Daisuke Kohda
Journal:  Protein Sci       Date:  2016-01-13       Impact factor: 6.725

2.  Classic Analysis of Biopolymer Dynamics Is Model Free.

Authors:  R Bryn Fenwick; H Jane Dyson
Journal:  Biophys J       Date:  2016-01-05       Impact factor: 4.033

3.  The Exact NOE as an Alternative in Ensemble Structure Determination.

Authors:  Beat Vögeli; Simon Olsson; Peter Güntert; Roland Riek
Journal:  Biophys J       Date:  2016-01-05       Impact factor: 4.033

4.  Tau-ism: The Yin and Yang of Microtubule Sliding, Detachment, and Rupture.

Authors:  Henry van den Bedem; Ellen Kuhl
Journal:  Biophys J       Date:  2015-12-01       Impact factor: 4.033

5.  Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series.

Authors:  Clare-Louise Towse; Jiri Vymetal; Jiri Vondrasek; Valerie Daggett
Journal:  Biophys J       Date:  2016-01-19       Impact factor: 4.033

Review 6.  Expanding the Range of Protein Function at the Far End of the Order-Structure Continuum.

Authors:  Virginia M Burger; Diego O Nolasco; Collin M Stultz
Journal:  J Biol Chem       Date:  2016-02-05       Impact factor: 5.157

7.  Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.

Authors:  Petra Rovó; Colin A Smith; Diego Gauto; Bert L de Groot; Paul Schanda; Rasmus Linser
Journal:  J Am Chem Soc       Date:  2019-01-08       Impact factor: 15.419

8.  The dynamic conformational landscape of the protein methyltransferase SETD8.

Authors:  Shi Chen; Rafal P Wiewiora; Fanwang Meng; Nicolas Babault; Anqi Ma; Wenyu Yu; Kun Qian; Hao Hu; Hua Zou; Junyi Wang; Shijie Fan; Gil Blum; Fabio Pittella-Silva; Kyle A Beauchamp; Wolfram Tempel; Hualiang Jiang; Kaixian Chen; Robert J Skene; Yujun George Zheng; Peter J Brown; Jian Jin; Cheng Luo; John D Chodera; Minkui Luo
Journal:  Elife       Date:  2019-05-13       Impact factor: 8.140

Review 9.  Serial Femtosecond Crystallography of G Protein-Coupled Receptors.

Authors:  Benjamin Stauch; Vadim Cherezov
Journal:  Annu Rev Biophys       Date:  2018-03-15       Impact factor: 12.981

10.  qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.

Authors:  Gydo C P van Zundert; Brandi M Hudson; Saulo H P de Oliveira; Daniel A Keedy; Rasmus Fonseca; Amelie Heliou; Pooja Suresh; Kenneth Borrelli; Tyler Day; James S Fraser; Henry van den Bedem
Journal:  J Med Chem       Date:  2018-12-06       Impact factor: 7.446

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