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Literature DB >> 19223165

The structural dynamics of macromolecular processes.

Daniel Russel¹, Keren Lasker, Jeremy Phillips, Dina Schneidman-Duhovny, Javier A Velázquez-Muriel, Andrej Sali.

Abstract

Dynamic processes involving macromolecular complexes are essential to cell function. These processes take place over a wide variety of length scales from nanometers to micrometers, and over time scales from nanoseconds to minutes. As a result, information from a variety of different experimental and computational approaches is required. We review the relevant sources of information and introduce a framework for integrating the data to produce representations of dynamic processes.

Entities: Chemical Disease Gene Mutation Species

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Year: 2009 PMID： 19223165 PMCID： PMC2774249 DOI： 10.1016/j.ceb.2009.01.022

Source DB: PubMed Journal: Curr Opin Cell Biol ISSN： 0955-0674 Impact factor: 8.382

113 in total

1. Systematic derivation of coarse-grained fluctuating hydrodynamic equations for many Brownian particles under nonequilibrium conditions.

Authors: Takenobu Nakamura; Shin-ichi Sasa
Journal: Phys Rev E Stat Nonlin Soft Matter Phys Date: 2006-09-08

Review 2. Kinesin motor mechanics: binding, stepping, tracking, gating, and limping.

Authors: Steven M Block
Journal: Biophys J Date: 2007-02-26 Impact factor: 4.033

3. Determining the stoichiometry of protein heterocomplexes in living cells with fluorescence fluctuation spectroscopy.

Authors: Yan Chen; Joachim D Müller
Journal: Proc Natl Acad Sci U S A Date: 2007-02-16 Impact factor: 11.205

4. Small-angle X-ray scattering from RNA, proteins, and protein complexes.

Authors: Jan Lipfert; Sebastian Doniach
Journal: Annu Rev Biophys Biomol Struct Date: 2007

5. Generation, comparison, and merging of pathways between protein conformations: gating in K-channels.

Authors: Angela Enosh; Barak Raveh; Ora Furman-Schueler; Dan Halperin; Nir Ben-Tal
Journal: Biophys J Date: 2008-07-11 Impact factor: 4.033

Review 6. Advances in single-molecule fluorescence methods for molecular biology.

Authors: Chirlmin Joo; Hamza Balci; Yuji Ishitsuka; Chittanon Buranachai; Taekjip Ha
Journal: Annu Rev Biochem Date: 2008 Impact factor: 23.643

7. Autonomy and robustness of translocation through the nuclear pore complex: a single-molecule study.

Authors: Thomas Dange; David Grünwald; Antje Grünwald; Reiner Peters; Ulrich Kubitscheck
Journal: J Cell Biol Date: 2008-09-29 Impact factor: 10.539

8. Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly.

Authors: Tadepalli Adilakshmi; Deepti L Bellur; Sarah A Woodson
Journal: Nature Date: 2008-09-10 Impact factor: 49.962

9. Artificial nanopores that mimic the transport selectivity of the nuclear pore complex.

Authors: Tijana Jovanovic-Talisman; Jaclyn Tetenbaum-Novatt; Anna Sophia McKenney; Anton Zilman; Reiner Peters; Michael P Rout; Brian T Chait
Journal: Nature Date: 2008-12-21 Impact factor: 49.962

10. Diffusional channeling in the sulfate-activating complex: combined continuum modeling and coarse-grained brownian dynamics studies.

Authors: Yuhui Cheng; Chia-En A Chang; Zeyun Yu; Yongjie Zhang; Meihao Sun; Thomas S Leyh; Michael J Holst; J Andrew McCammon
Journal: Biophys J Date: 2008-08-08 Impact factor: 4.033

22 in total

1. Toward an integrated structural model of the 26S proteasome.

Authors: Friedrich Förster; Keren Lasker; Stephan Nickell; Andrej Sali; Wolfgang Baumeister
Journal: Mol Cell Proteomics Date: 2010-05-13 Impact factor: 5.911

2. Recombination-induced tag exchange to track old and new proteins.

Authors: Kitty F Verzijlbergen; Victoria Menendez-Benito; Tibor van Welsem; Sjoerd J van Deventer; Derek L Lindstrom; Huib Ovaa; Jacques Neefjes; Daniel E Gottschling; Fred van Leeuwen
Journal: Proc Natl Acad Sci U S A Date: 2009-12-14 Impact factor: 11.205

The structural dynamics of macromolecular processes.

1. Systematic derivation of coarse-grained fluctuating hydrodynamic equations for many Brownian particles under nonequilibrium conditions.

Review 2. Kinesin motor mechanics: binding, stepping, tracking, gating, and limping.

3. Determining the stoichiometry of protein heterocomplexes in living cells with fluorescence fluctuation spectroscopy.

4. Small-angle X-ray scattering from RNA, proteins, and protein complexes.

5. Generation, comparison, and merging of pathways between protein conformations: gating in K-channels.

Review 6. Advances in single-molecule fluorescence methods for molecular biology.

7. Autonomy and robustness of translocation through the nuclear pore complex: a single-molecule study.

8. Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly.

9. Artificial nanopores that mimic the transport selectivity of the nuclear pore complex.

10. Diffusional channeling in the sulfate-activating complex: combined continuum modeling and coarse-grained brownian dynamics studies.

1. Toward an integrated structural model of the 26S proteasome.

2. Recombination-induced tag exchange to track old and new proteins.

Review 3. Mass spectrometry: come of age for structural and dynamical biology.

Review 4. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

5. Integrative structure modeling with the Integrative Modeling Platform.

6. Probing the Dissociation of Protein Complexes by Means of Gas-Phase H/D Exchange Mass Spectrometry.

7. Dynamic active-site protection by the M. tuberculosis protein tyrosine phosphatase PtpB lid domain.

8. MSCALE: A General Utility for Multiscale Modeling.

9. Multiscale dynamics of macromolecules using normal mode Langevin.

10. Collective motions and specific effectors: a statistical mechanics perspective on biological regulation.