PCS-based structure determination of proteinā??protein complexes
Abstract A simple and fast nuclear magnetic resonance method for docking proteins using pseudo-contact shift (PCS) and 1HN/15N chemical shift perturbation is presented. PCS is induced by a paramagnetic lanthanide ion that is attached to a target protein using a lanthanide binding peptide tag anchored at two points. PCS provides long-range (~40 Ć?) distance and angular restraints between the lanthanide ion and the observed nuclei, while the 1HN/15N chemical shift perturbation data provide loose contact-surface information. The usefulness of this method was demonstrated through the structure determination of the p62 PB1-PB1 complex, which forms a front-to-back 20 kDa homo-oligomer. As p62 PB1 does not intrinsically bind metal ions, the lanthanide binding peptide tag was attached to one subunit of the dimer at two anchoring points. Each monomer was treated as a rigid body and was docked based on the backbone PCS and backbone chemical shift perturbation data. Unlike NOE-based structural determination, this method only requires resonance assignments of the backbone 1HN/15N signals and the PCS data obtained from several sets of two-dimensional 15N-heteronuclear single quantum coherence spectra, thus facilitating rapid structure determination of the proteinā??protein complex.
Content Type Journal Article
DOI 10.1007/s10858-010-9401-4
Authors
Tomohide Saio, Hokkaido University Graduate School of Life Science Sapporo 001-0021 Japan
Masashi Yokochi, Hokkaido University Graduate School of Pharmaceutical Sciences Sapporo 001-0021 Japan
Hiroyuki Kumeta, Hokkaido University Graduate School of Pharmaceutical Sciences Sapporo 001-0021 Japan
Fuyuhiko Inagaki, Hokkaido University Graduate School of Pharmaceutical Sciences Sapporo 001-0021 Japan
Fast methionine-based solution structure determination of calcium-calmodulin complexes
Fast methionine-based solution structure determination of calcium-calmodulin complexes
Abstract Here we present a novel NMR method for the structure determination of calcium-calmodulin (Ca2+-CaM)-peptide complexes from a limited set of experimental restraints. A comparison of solved CaM-peptide structures reveals invariability in CaMā??s backbone conformation and a structural plasticity in CaMā??s domain orientation enabled by a flexible linker. Knowing this, the collection and analysis of an extensive set of NOESY spectra is redundant. Although RDCs can define CaM domain orientation in...
nmrlearner
Journal club
0
03-03-2011 02:06 AM
Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy.
Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy.
Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy.
Prog Nucl Magn Reson Spectrosc. 2011 Feb;58(1-2):1-61
Authors: Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FH
nmrlearner
Journal club
0
01-19-2011 11:18 AM
[NMR paper] Structure determination of protein/RNA complexes by NMR.
Structure determination of protein/RNA complexes by NMR.
Related Articles Structure determination of protein/RNA complexes by NMR.
Methods Enzymol. 2005;394:525-45
Authors: Wu H, Finger LD, Feigon J
Structure determination of protein?RNA complexes in solution provides unique insights into factors that are involved in protein/RNA recognition. Here, we review the methodology used in our laboratory to overcome the challenges of protein?RNA structure determination by nuclear magnetic resonance (NMR). We use as two examples complexes recently...
nmrlearner
Journal club
0
11-24-2010 11:14 PM
[NMR paper] Structure determination of protein complexes by NMR.
Structure determination of protein complexes by NMR.
Related Articles Structure determination of protein complexes by NMR.
Methods Mol Biol. 2004;278:255-88
Authors: Nietlispach D, Mott HR, Stott KM, Nielsen PR, Thiru A, Laue ED
This chapter describes nuclear magnetic resonance (NMR) methods that can be used to determine the structures of protein complexes. Many of these techniques are also applicable to other systems (e.g., protein-nucleic acid complexes). In the first section, we discuss methodologies for optimizing the sample conditions for...
nmrlearner
Journal club
0
11-24-2010 09:25 PM
[NMR paper] Structure prediction of protein complexes by an NMR-based protein docking algorithm.
Structure prediction of protein complexes by an NMR-based protein docking algorithm.
Related Articles Structure prediction of protein complexes by an NMR-based protein docking algorithm.
J Biomol NMR. 2001 May;20(1):15-21
Authors: Kohlbache O, Burchardt A, Moll A, Hildebrandt A, Bayer P, Lenhof HP
Protein docking algorithms can be used to study the driving forces and reaction mechanisms of docking processes. They are also able to speed up the lengthy process of experimental structure elucidation of protein complexes by proposing potential...
nmrlearner
Journal club
0
11-19-2010 08:32 PM
[NMR paper] NMR structure determination of proteins and protein complexes larger than 20 kDa.
NMR structure determination of proteins and protein complexes larger than 20 kDa.
Related Articles NMR structure determination of proteins and protein complexes larger than 20 kDa.
Curr Opin Chem Biol. 1998 Oct;2(5):564-70
Authors: Clore GM, Gronenborn AM
Recent advances in multidimensional nuclear magnetic resonance methodology to obtain 1H, 15N and 13C resonance assignments, interproton distance and torsion angle restraints, and restraints that characterize long-range order, coupled with new methods of structure refinement and novel methods...
nmrlearner
Journal club
0
11-17-2010 11:15 PM
Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy
Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy
Publication year: 2010
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 6 October 2010</br>
Cyril, Dominguez , Mario, Schubert , Olivier, Duss , Sapna, Ravindranathan , Frédéric H.-T., Allain</br>
More...
nmrlearner
Journal club
0
10-07-2010 02:32 PM
Structure Determination of Protein Complexes by NMR
Structure Determination of Protein Complexes by NMR
D. Nietlispach, H.R. Mott, K.M. Stott, P.R. Nielsen, A. Thiru & E.D. Laue
The Department of Biochemistry, University of Cambridge
Introduction
As the structures of more proteins and domains are solved by structural genomics projects, the future of structural biology will be oriented more toward the study of macromolecular complexes. Since so many biological processes are mediated by interactions between proteins, it is important to study them at a molecular level. The study of protein-protein interactions also has applications in a...
PCS-based structure determination of proteinā??protein complexes
Linear Mode
