Abstract Many biomolecular interactions proceed via a short-lived encounter state, consisting of multiple, lowly-populated species invisible to most experimental techniques. Recent development of paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance (NMR) spectroscopy has allowed to directly visualize such transient intermediates in a number of protein-protein and protein-DNA complexes. Here we present an analysis of the recently published PRE NMR data for a protein complex of yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP). First, we describe a simple, general method to map out the spatial and temporal distributions of binding geometries constituting the Cc-CcP encounter state. We show that the spatiotemporal mapping provides a reliable estimate of the experimental coverage and, at higher coverage levels, allows to delineate the conformational space sampled by the minor species. To further refine the encounter state, we performed PRE-based ensemble simulations. The generated solutions reproduce well the experimental data and lie within the allowed regions of the encounter maps, confirming the validity of the mapping approach. The refined encounter ensembles are distributed predominantly in a region encompassing the dominant form of the complex, providing experimental proof for the results of classical theoretical simulations.
Content Type Journal Article
DOI 10.1007/s10858-010-9452-6
Authors
Alexander N. Volkov, Department of Molecular and Cellular Interactions, VIB, Pleinlaan 2, 1050 Brussels, Belgium
Marcellus Ubbink, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
Nico A. J. van Nuland, Department of Molecular and Cellular Interactions, VIB, Pleinlaan 2, 1050 Brussels, Belgium
Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy.
Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy.
Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy.
Biochemistry. 2011 Sep 26;
Authors: Wang Q, Zhuravleva A, Gierasch LM
Abstract
Biology relies on functional interplay of proteins in the crowded and heterogeneous environment inside cells, and functional protein interactions are often weak and transient. Thus, methods are needed that preserve these interactions...
nmrlearner
Journal club
0
09-30-2011 06:00 AM
Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy.
Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy.
Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy.
Biochemistry. 2011 Sep 26;
Authors: Wang Q, Zhuravleva A, Gierasch LM
Abstract
Biology relies on functional interplay of proteins in the crowded and heterogeneous environment inside cells, and functional protein interactions are often weak and transient. Thus, methods are needed that preserve these...
nmrlearner
Journal club
0
09-30-2011 05:59 AM
Solid-state NMR spectroscopy on complex biomolecules.
Solid-state NMR spectroscopy on complex biomolecules.
Solid-state NMR spectroscopy on complex biomolecules.
Angew Chem Int Ed Engl. 2010 Nov 2;49(45):8346-57
Authors: Renault M, Cukkemane A, Baldus M
Biomolecular applications of NMR spectroscopy are often merely associated with soluble molecules or magnetic resonance imaging. However, since the late 1970s, solid-state NMR (ssNMR) spectroscopy has demonstrated its ability to provide atomic-level insight into complex biomolecular systems ranging from lipid bilayers to complex biomaterials. In the...
nmrlearner
Journal club
0
02-15-2011 07:17 PM
[NMR paper] NMR analysis of the transient complex between membrane photosystem I and soluble cyto
NMR analysis of the transient complex between membrane photosystem I and soluble cytochrome c6.
Related Articles NMR analysis of the transient complex between membrane photosystem I and soluble cytochrome c6.
J Biol Chem. 2005 Mar 4;280(9):7925-31
Authors: Díaz-Moreno I, Díaz-Quintana A, Molina-Heredia FP, Nieto PM, Hansson O, De la Rosa MA, Karlsson BG
A structural analysis of the surface areas of cytochrome c(6), responsible for the transient interaction with photosystem I, was performed by NMR transverse relaxation-optimized spectroscopy....
nmrlearner
Journal club
0
11-24-2010 10:03 PM
[NMR paper] Fast mapping of protein-protein interfaces by NMR spectroscopy.
Fast mapping of protein-protein interfaces by NMR spectroscopy.
Related Articles Fast mapping of protein-protein interfaces by NMR spectroscopy.
J Am Chem Soc. 2003 Nov 26;125(47):14250-1
Authors: Reese ML, Dötsch V
Identifying the interface of protein complexes can represent a difficult task in structural biology. Here, we report a method for the fast mapping of interfaces of protein complexes by NMR without the need for the assignments of the proteins involved.
nmrlearner
Journal club
0
11-24-2010 09:16 PM
[NMR paper] Transient protein interactions studied by NMR spectroscopy: the case of cytochrome C
Transient protein interactions studied by NMR spectroscopy: the case of cytochrome C and adrenodoxin.
Related Articles Transient protein interactions studied by NMR spectroscopy: the case of cytochrome C and adrenodoxin.
Biochemistry. 2003 Jun 17;42(23):7068-76
Authors: Worrall JA, Reinle W, Bernhardt R, Ubbink M
The interaction between yeast iso-1-cytochrome c (C102T) and two forms of bovine adrenodoxin, the wild type and a truncated form comprising residues 4-108, has been investigated using a combination of one- and two-dimensional...
nmrlearner
Journal club
0
11-24-2010 09:01 PM
Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy.
Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy.
Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy.
J Biomol NMR. 2010 Nov 4;
Authors: Volkov AN, Ubbink M, van Nuland NA
Many biomolecular interactions proceed via a short-lived encounter state, consisting of multiple, lowly-populated species invisible to most experimental techniques. Recent development of paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance (NMR) spectroscopy has allowed to directly visualize such...
nmrlearner
Journal club
0
11-05-2010 10:01 AM
[NMR paper] Mapping hydration water molecules in the HIV-1 protease/DMP323 complex in solution by
Mapping hydration water molecules in the HIV-1 protease/DMP323 complex in solution by NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Mapping hydration water molecules in the HIV-1 protease/DMP323 complex in solution by NMR spectroscopy.
Biochemistry. 1996 Oct 1;35(39):12694-704
Authors: Wang YX, Freedberg DI, Grzesiek S, Torchia DA, Wingfield PT, Kaufman JD, Stahl SJ, Chang CH, Hodge CN
A tetrahedrally hydrogen-bonded structural water molecule, water 301, is seen in...
Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy
Linear Mode
