ArticleStructure (London, England : 1993)2011
Optimal mutation sites for PRE data collection and membrane protein structure prediction.
Article in Structure (London, England : 1993), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 25 citations in OpenAlex.
- How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations.Computational and structural biotechnology journal · 2021Review
- The PRE-Derived NMR Model of the 38.8-kDa Tri-Domain IsdH Protein from Staphylococcus aureus Suggests That It Adaptively Recognizes Human Hemoglobin.Journal of molecular biology · 2016Article
- GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome.Structure (London, England : 1993) · 2015Article
- Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA).Journal of biomolecular NMR · 2015Article
- Computational modeling of membrane proteins.Proteins · 2015Review
- NMR-based conformational ensembles explain pH-gated opening and closing of OmpG channel.Journal of the American Chemical Society · 2013Article
- Advances in NMR structures of integral membrane proteins.Current opinion in structural biology · 2013Review
- The quiet renaissance of protein nuclear magnetic resonance.Biochemistry · 2013Review
- Identification and removal of nitroxide spin label contaminant: impact on PRE studies of α-helical membrane proteins in detergent.Protein science : a publication of the Protein Society · 2012Article
- BCL::Fold--de novo prediction of complex and large protein topologies by assembly of secondary structure elements.PloS one · 2012Article
- Multi-dimensional NMR without coherence transfer: minimizing losses in large systems.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2011Article
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
Nuclear magnetic resonance paramagnetic relaxation enhancement (PRE) measures long-range distances to isotopically labeled residues, providing useful constraints for protein structure prediction. The method usually requires labor-intensive conjugation of nitroxide labels to multiple locations on the protein, one at a time. Here a computational procedure, based on protein sequence and simple secondary structure models, is presented to facilitate optimal placement of a minimum number of labels needed to determine the correct topology of a helical transmembrane protein. Tests on DsbB (four helices) using just one label lead to correct topology predictions in four of five cases, with the predicted structures <6 Å to the native structure. Benchmark results using simulated PRE data show that we can generally predict the correct topology for five and six to seven helices using two and three labels, respectively, with an average success rate of 76% and structures of similar precision. The results show promise in facilitating experimentally constrained structure prediction of membrane proteins.
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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.