ArticleProtein science : a publication of the Protein Society2011
Measuring rapid hydrogen exchange in the homodimeric 36 kDa HIV-1 integrase catalytic core domain.
Article in Protein science : a publication of the Protein Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed.
- A low-complexity linker as a driver of intra- and intermolecular interactions in DNAJB chaperones.Nature communications · 2025Article
- Exploring Residue-Level Interactions between the Biofilm-Driving R2ab Protein and Polystyrene Nanoparticles.Langmuir : the ACS journal of surfaces and colloids · 2024Article
- Exploring the Residue-Level Interactions between the R2ab Protein and Polystyrene Nanoparticles.bioRxiv : the preprint server for biology · 2023Article
- SARS-CoV-2 omicron variants harbor spike protein mutations responsible for their attenuated fusogenic phenotype.Communications biology · 2023Article
- Real-time Exchange of the Lipid-bound Intermediate and Post-fusion States of the HIV-1 gp41 Ectodomain.Journal of molecular biology · 2022Article
- High-Resolution Hydrogen-Deuterium Protection Factors from Sparse Mass Spectrometry Data Validated by Nuclear Magnetic Resonance Measurements.Journal of the American Society for Mass Spectrometry · 2022Article
- Native state fluctuations in a peroxiredoxin active site match motions needed for catalysis.Structure (London, England : 1993) · 2022Article
- Transient lipid-bound states of spike protein heptad repeats provide insights into SARS-CoV-2 membrane fusion.Science advances · 2021Article
- Hydrogen-exchange kinetics studied through analysis of self-decoupling of nuclear magnetic resonance.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2020Article
- Protein Interactions with Nanoparticle Surfaces: Highlighting Solution NMR Techniques.Israel journal of chemistry · 2019Article
- Remarkable Rigidity of the Single α-Helical Domain of Myosin-VI As Revealed by NMR Spectroscopy.Journal of the American Chemical Society · 2019Article
- Equilibrium folding dynamics of meACP in water, heavy water, and low concentration of urea.Scientific reports · 2017Article
- Monitoring Hydrogen Exchange During Protein Folding by Fast Pressure Jump NMR Spectroscopy.Journal of the American Chemical Society · 2017Article
- Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis.Journal of chemical information and modeling · 2015Article
- Mechanisms of amyloid formation revealed by solution NMR.Progress in nuclear magnetic resonance spectroscopy · 2015Review
- Investigation of signal transduction routes within the sensor/transducer protein BlaR1 of Staphylococcus aureus.Biochemistry · 2015Article
- Visualizing transient dark states by NMR spectroscopy.Quarterly reviews of biophysics · 2015Article
- The influenza hemagglutinin fusion domain is an amphipathic helical hairpin that functions by inducing membrane curvature.The Journal of biological chemistry · 2015Article
- Measuring hydrogen exchange in proteins by selective water saturation in (1)H- (15)N SOFAST/BEST-type experiments: advantages and limitations.Journal of biomolecular NMR · 2014Article
- Measuring hydrogen exchange rates in invisible protein excited states.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
Measurements of rapid hydrogen exchange (HX) of water with protein amide sites contain valuable information on protein structure and function, but current NMR methods for measuring HX rates are limited in their applicability to large protein systems. An alternate method for measuring rapid HX is presented that is well-suited for larger proteins, and we apply the method to the deuterated, homodimeric 36 kDa HIV-1 integrase catalytic core domain (CCD). Using long mixing times for water-amide magnetization exchange at multiple pH values, HX rates spanning more than four orders of magnitude were measured, as well as NOE cross-relaxation rates to nearby exchangeable protons. HX protection factors for the CCD are found to be large (>10(4)) for residues along the dimer interface, but much smaller in many other regions. Notably, the catalytic helix (residues 152-167) exhibits low HX protection at both ends, indicative of fraying at both termini as opposed to just the N-terminal end, as originally thought. Residues in the LEDGF/p75 binding pocket also show marginal stability, with protection factors in the 10-100 range (∼1.4-2.7 kcal/mol). Additionally, elevated NOE cross-relaxation rates are identified and, as expected, correspond to proximity of the amide proton to a rapidly exchanging proton, typically from an OH side chain. Indirect NOE transfer between H(2) O and the amide proton of I141, a residue in the partially disordered active site of the enzyme, suggests its proximity to the side chain of S147, an interaction seen in the DNA-bound form for a homologous integrase.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.