ArticleArchives of biochemistry and biophysics2015
The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans.
Article in Archives of biochemistry and biophysics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 16 citations in OpenAlex.
- Conformational Heterogeneity of Pro-Pro Containing 23-Membered Ring Conopeptides by NMR.ACS omega · 2025Article
- ProlineJournal of the American Chemical Society · 2025Article
- Cis-trans isomerization of peptoid residues in the collagen triple-helix.Nature communications · 2023Article
- Review
- How phosphorylation impacts intrinsically disordered proteins and their function.Essays in biochemistry · 2022Article
- An Unbound Proline-Rich Signaling Peptide Frequently SamplesFrontiers in molecular biosciences · 2021Article
- A Proline-Based Tectons and Supramolecular Synthons for Drug Design 2.0: A Case Study of ACEI.Pharmaceuticals (Basel, Switzerland) · 2020Article
- Implementation of adaptive integration method for free energy calculations in molecular systems.PeerJ. Computer science · 2020Article
- Initiation of prolyl cis-trans isomerisation in the CDR-H3 loop of an antibody in response to antigen binding.Scientific reports · 2017Article
- Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The cis and trans conformations of the Xaa-Pro (Xaa: any amino acid) peptide bond are thermodynamically stable while other peptide bonds strongly prefer trans. The effect of proline cis-trans isomerization on protein binding has not been thoroughly investigated. In this study, computer simulations were used to calculate the absolute binding affinity for a p53 peptide (residues 17-29) to MDM2 for both cis and trans isomers of the p53 proline in position 27. Results show that the cis isomer of p53(17-29) binds more weakly to MDM2 than the trans isomer, and that this is primarily due to the difference in the free energy cost associated with the loss of conformational entropy of p53(17-29) when it binds to MDM2. The population of cis p53(17-29) was estimated to be 0.8% of the total population in the bound state. The stronger binding of trans p53(17-29) to MDM2 compared to cis may leave a minimal level of p53 available to respond to cellular stress. This study demonstrates that it is feasible to estimate the absolute binding affinity for an intrinsically disordered protein fragment binding to an ordered protein that are in good agreement with experimental results.
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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.