Publication date: Available online 17 April 2017 Source:Methods in Enzymology
Author(s): Matthew K. Thompson, Aaron C. Ehlinger, Walter J. Chazin
Multiprotein machines drive virtually all primary cellular processes. Modular multidomain proteins are widely distributed within these dynamic complexes because they provide the flexibility needed to remodel structure as well as rapidly assemble and disassemble components of the machinery. Understanding the functional dynamics of modular multidomain proteins is a major challenge confronting structural biology today because their structure is not fixed in time. Small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy have proven particularly useful for the analysis of the structural dynamics of modular multidomain proteins because they provide highly complementary information for characterizing the architectural landscape accessible to these proteins. SAXS provides a global snapshot of all architectural space sampled by a molecule in solution. Furthermore, SAXS is sensitive to conformational changes, organization and oligomeric states of protein assemblies, and the existence of flexibility between globular domains in multiprotein complexes. The power of NMR to characterize dynamics provides uniquely complementary information to the global snapshot of the architectural ensemble provided by SAXS because it can directly measure domain motion. In particular, NMR parameters can be used to define the diffusion of domains within modular multidomain proteins, connecting the amplitude of interdomain motion to the architectural ensemble derived from SAXS. Our laboratory has been studying the roles of modular multidomain proteins involved in human DNA replication using SAXS and NMR. Here, we present the procedure for acquiring and analyzing SAXS and NMR data, using DNA primase and replication protein A as examples.
A functional NMR for membrane proteins: dynamics, ligand binding, and allosteric modulation
A functional NMR for membrane proteins: dynamics, ligand binding, and allosteric modulation
Abstract
By nature of conducting ions, transporting substrates and transducing signals, membrane channels, transporters and receptors are expected to exhibit intrinsic conformational dynamics. It is therefore of great interest and importance to understand the various properties of conformational dynamics acquired by these proteins, for example, the relative population of states, exchange rate, conformations of multiple states, and how small molecule ligands modulate the conformational exchange....
nmrlearner
Journal club
0
03-29-2016 04:59 PM
[NMR paper] Tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies.
Tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies.
Tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies.
Biochim Biophys Acta. 2014 Nov 22;
Authors: Kim JH, Bothe JR, Reid Alderson T, Markley JL
Abstract
Proteins containing iron-sulfur (Fe-S) clusters arose early in evolution and are essential to life. Organisms have...
nmrlearner
Journal club
0
12-03-2014 04:05 PM
Tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies
Tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies
Publication date: Available online 22 November 2014
Source:Biochimica et Biophysica Acta (BBA) - Molecular Cell Research</br>
Author(s): Jin Hae Kim , Jameson R. Bothe , T. Reid Alderson , John L. Markley</br>
Proteins containing iron-sulfur (Fe-S) clusters arose early in evolution and are essential to life. Organisms have evolved machinery consisting of specialized proteins that operate together to assemble...
nmrlearner
Journal club
0
11-22-2014 01:48 PM
[NMR paper] NMR approaches for structural analysis of multidomain proteins and complexes in solution.
NMR approaches for structural analysis of multidomain proteins and complexes in solution.
Related Articles NMR approaches for structural analysis of multidomain proteins and complexes in solution.
Prog Nucl Magn Reson Spectrosc. 2014 Jul;80C:26-63
Authors: Göbl C, Madl T, Simon B, Sattler M
Abstract
NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about...
nmrlearner
Journal club
0
06-14-2014 03:41 PM
NMR approaches for structural analysis of multidomain proteins and complexes in solution
NMR approaches for structural analysis of multidomain proteins and complexes in solution
Publication date: Available online 23 May 2014
Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br>
Author(s): Christoph Göbl , Tobias Madl , Bernd Simon , Michael Sattler</br>
NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue...
nmrlearner
Journal club
0
05-23-2014 03:21 PM
TransientElectrostatic Interactions Dominate theConformational Equilibrium Sampled by Multidomain Splicing FactorU2AF65: A Combined NMR and SAXS Study
TransientElectrostatic Interactions Dominate theConformational Equilibrium Sampled by Multidomain Splicing FactorU2AF65: A Combined NMR and SAXS Study
Jie-rong Huang, Lisa R. Warner, Carolina Sanchez, Frank Gabel, Tobias Madl, Cameron D. Mackereth, Michael Sattler and Martin Blackledge
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja502030n/aop/images/medium/ja-2014-02030n_0009.gif
Journal of the American Chemical Society
DOI: 10.1021/ja502030n
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
nmrlearner
Journal club
0
04-30-2014 02:03 AM
[NMR paper] Functional dynamics of cell surface membrane proteins
Functional dynamics of cell surface membrane proteins
Publication date: Available online 22 November 2013
Source:Journal of Magnetic Resonance</br>
Author(s): Noritaka Nishida , Masanori Osawa , Koh Takeuchi , Shunsuke Imai , Pavlos Stampoulis , Yutaka Kofuku , Takumi Ueda , Ichio Shimada</br>
Cell surface receptors are integral membrane proteins that receive external stimuli, and transmit signals across plasma membranes. In the conventional view of receptor activation, ligand binding to the extracellular side of the receptor induces conformational changes,...
nmrlearner
Journal club
0
11-23-2013 04:05 AM
Functional dynamics of proteins revealed by solution NMR
Functional dynamics of proteins revealed by solution NMR
October 2012
Publication year: 2012
Source:Current Opinion in Structural Biology, Volume 22, Issue 5</br>
</br>
Solution NMR spectroscopy can analyze the dynamics of proteins on a wide range of timescales, from picoseconds to even days, in a site-specific manner, and thus its results are complementary to the detailed but largely static structural information obtained by X-ray crystallography. We review recent progresses in a variety of NMR techniques, including relaxation dispersion and paramagnetic relaxation...
Analysis of Functional Dynamics of Modular Multidomain Proteins by SAXS and NMR
Linear Mode
