ArticlePLoS biology2011
Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis.
Article in PLoS biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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
17 citing papers in PubMed, 43 citations in OpenAlex.
- Rational Design of Ligands with Optimized Residence Time.ACS pharmacology & translational science · 2025Article
- Disorder-to-order active site capping regulates the rate-limiting step of the inositol pathway.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Cloning and functional characterization of the peptide deformylase encoding gene EuPDF1B from Eucommia ulmoides Oliv.Scientific reports · 2024Article
- Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam.Nature communications · 2023Article
- System-wide analyses reveal essential roles of N-terminal protein modification in bacterial membrane integrity.iScience · 2022Article
- Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches.The journal of physical chemistry. B · 2021Article
- Total synthesis of (±)-fumimycin and analogues for biological evaluation as peptide deformylase inhibitors.Tetrahedron · 2019Article
- Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism.Acta crystallographica. Section D, Structural biology · 2018Article
- The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation.Scientific reports · 2017Article
- A unique peptide deformylase platform to rationally design and challenge novel active compounds.Scientific reports · 2016Article
- Quality control of mitochondrial protein synthesis is required for membrane integrity and cell fitness.The Journal of cell biology · 2015Article
- An ordered water channel in Staphylococcus aureus FabI: unraveling the mechanism of substrate recognition and reduction.Biochemistry · 2015Article
- A structural and energetic model for the slow-onset inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA.ACS chemical biology · 2014Article
- Structural basis for the recognition of mycolic acid precursors by KasA, a condensing enzyme and drug target from Mycobacterium tuberculosis.The Journal of biological chemistry · 2013Article
- Experimental phasing using zinc anomalous scattering.Acta crystallographica. Section D, Biological crystallography · 2012Article
- Avibactam is a covalent, reversible, non-β-lactam β-lactamase inhibitor.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Co-factor binding confers substrate specificity to xylose reductase from Debaryomyces hansenii.PloS one · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally "zipped up" by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A "movie" that reconstructs this entire process can be further extrapolated to catalysis.
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.