ArticleJournal of chemical information and modeling2023
Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations.
Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 24 citations in OpenAlex.
- Beyond the structure-function paradigm: A comprehensive review of intrinsically disordered proteins.Biochemistry and biophysics reports · 2026Review
- Allosteric Protein Chemical Shift Perturbations are Ubiquitous.bioRxiv : the preprint server for biology · 2026Article
- Loop Plasticity Drives Paralog-Specific Recognition in BET ET Domains.Journal of chemical information and modeling · 2026Article
- How Well Do Molecular Dynamics Force Fields Model Peptides: A Systematic Benchmark across Diverse Folding Behaviors.The journal of physical chemistry. B · 2026Article
- Ensemble Sensitivity to Chemical Modifications in Free and Bound Macrocyclic Peptides.The journal of physical chemistry. B · 2026Article
- Efficient exploration of peptide libraries using active learning with AlphaFold-based screening.bioRxiv : the preprint server for biology · 2026Article
- Beyond Classical Force Fields: Physics-Driven Assessment of the Grappa Machine-Learned Force Field on the FoldBind Dataset.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Plant-Based Protein Bioinks with Transglutaminase Crosslinking: 3D Printability and Molecular Insights from NMR and Synchrotron-FTIR.Foods (Basel, Switzerland) · 2026Article
- Structural details of helix-mediated multimerization of the conserved region of TDP-43 C-terminal domain.Nature communications · 2025Article
- Loop Plasticity Drives Paralog-Specific Recognition in BET ET Domains.bioRxiv : the preprint server for biology · 2025Article
- PERRC: Protease Engineering with Reactant Residence Time Control.ACS synthetic biology · 2025Article
- MELD in Action: Harnessing Data to Accelerate Molecular Dynamics.Journal of chemical information and modeling · 2025Review
- Structural information in therapeutic peptides: Emerging applications in biomedicine.FEBS open bio · 2025Review
- Integrative Modeling of Protein-Polypeptide Complexes by Bayesian Model Selection using AlphaFold and NMR Chemical Shift Perturbation Data.bioRxiv : the preprint server for biology · 2024Article
- Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices.Journal of chemical theory and computation · 2024Article
- A Computational Pipeline for Accurate Prioritization of Protein-Protein Binding Candidates in High-Throughput Protein Libraries.Angewandte Chemie (International ed. in English) · 2024Article
- Sifting Through the Noise: A Computational Pipeline for Accurate Prioritization of Protein-Protein Binding Candidates in High-Throughput Protein Libraries.bioRxiv : the preprint server for biology · 2024Article
- Assessing a computational pipeline to identify binding motifs to theFrontiers in chemistry · 2023Article
- AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.Frontiers in molecular biosciences · 2022Article
- Towards rational computational peptide design.Frontiers in bioinformatics · 2022Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
Abstract
Intrinsically disordered regions of proteins often mediate important protein-protein interactions. However, the folding-upon-binding nature of many polypeptide-protein interactions limits the ability of modeling tools to predict the three-dimensional structures of such complexes. To address this problem, we have taken a tandem approach combining NMR chemical shift data and molecular simulations to determine the structures of peptide-protein complexes. Here, we use the MELD (Modeling Employing Limited Data) technique applied to polypeptide complexes formed with the extraterminal domain (ET) of bromo and extraterminal domain (BET) proteins, which exhibit a high degree of binding plasticity. This system is particularly challenging as the binding process includes allosteric changes across the ET receptor upon binding, and the polypeptide binding partners can adopt different conformations (e.g., helices and hairpins) in the complex. In a blind study, the new approach successfully modeled bound-state conformations and binding poses, using only protein receptor backbone chemical shift data, in excellent agreement with experimentally determined structures for moderately tight (
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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.