ArticleJournal of biomolecular NMR2010
Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy.
Article in Journal of biomolecular NMR, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 54 citations in OpenAlex.
- Probing Biomolecular Interactions with Paramagnetic Nuclear Magnetic Resonance Spectroscopy.Chembiochem : a European journal of chemical biology · 2025Review
- HECT domain interaction with ubiquitin binding sites on Tsg101-UEV controls HIV-1 egress, maturation, and infectivity.The Journal of biological chemistry · 2023Article
- Solution Structure of a Lanthanide-binding DNA Aptamer Determined Using High Quality pseudocontact shift restraints.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Efficient Encounter Complex Formation and Electron Transfer to Cytochrome c Peroxidase with an Additional, Distant Electrostatic Binding Site.Angewandte Chemie (International ed. in English) · 2020Article
- NMR Analysis of Apo Glutamine-Binding Protein Exposes Challenges in the Study of Interdomain Dynamics.Angewandte Chemie (International ed. in English) · 2019Article
- MCMap-A Computational Tool for Mapping Energy Landscapes of Transient Protein-Protein Interactions.ACS omega · 2018Article
- Identification of primary and secondary UBA footprints on the surface of ubiquitin in cell-mimicking crowded solution.FEBS letters · 2017Article
- A New Method for Determining Structure Ensemble: Application to a RNA Binding Di-Domain Protein.Biophysical journal · 2016Article
- Weak self-association of cytochrome c peroxidase molecules observed by paramagnetic NMR.Journal of biomolecular NMR · 2016Article
- Effects of membrane mimetics on cytochrome P450-cytochrome b5 interactions characterized by NMR spectroscopy.The Journal of biological chemistry · 2015Article
- The low-affinity complex of cytochrome c and its peroxidase.Nature communications · 2015Article
- Control of cyclic photoinitiated electron transfer between cytochrome c peroxidase (W191F) and cytochrome c by formation of dynamic binary and ternary complexes.Biochemistry · 2015Article
- Visualizing transient dark states by NMR spectroscopy.Quarterly reviews of biophysics · 2015Article
- Electrostatic interactions in the binding pathway of a transient protein complex studied by NMR and isothermal titration calorimetry.The Journal of biological chemistry · 2014Article
- Examining weak protein-protein interactions in start codon recognition via NMR spectroscopy.The FEBS journal · 2014Review
- The IR-¹⁵N-HSQC-AP experiment: a new tool for NMR spectroscopy of paramagnetic molecules.Journal of biomolecular NMR · 2014Article
- Recovering a representative conformational ensemble from underdetermined macromolecular structural data.Journal of the American Chemical Society · 2013Article
- NMR-based conformational ensembles explain pH-gated opening and closing of OmpG channel.Journal of the American Chemical Society · 2013Article
- A model of the membrane-bound cytochrome b5-cytochrome P450 complex from NMR and mutagenesis data.The Journal of biological chemistry · 2013Article
- Solution NMR study of the yeast cytochrome c peroxidase: cytochrome c interaction.Journal of biomolecular NMR · 2013Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.