ArticleScience advances2017
Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations.
Article in Science advances, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- ZnJournal of the American Chemical Society · 2025Article
- Protein Secondary Structure Patterns in Short-Range Cross-Link Atlas.Angewandte Chemie (International ed. in English) · 2025Article
- Cross-Interaction with Amyloid-β Drives Pathogenic Structural Transformation within the Amyloidogenic Core Region of TDP-43.ACS chemical neuroscience · 2025Article
- Computational exploration of the self-aggregation mechanisms of phenol-soluble modulins β1 and β2 in Staphylococcus aureus biofilms.Colloids and surfaces. B, Biointerfaces · 2025Article
- Computational insights into the aggregation mechanism of human calcitonin.International journal of biological macromolecules · 2025Article
- Characterization of the KRas G12D-inhibitor interactions by differential HDX-MS and molecular dynamics simulations.Computational and structural biotechnology journal · 2025Article
- Filling in missing puzzle pieces in protein structural biology with cross-linking mass spectrometry.QRB discovery · 2025Review
- Computational insights into the aggregation mechanism and amyloidogenic core of aortic amyloid medin polypeptide.Colloids and surfaces. B, Biointerfaces · 2024Article
- Cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure.Nature communications · 2024Article
- Computational Investigation of Coaggregation and Cross-Seeding between Aβ and hIAPP Underpinning the Cross-Talk in Alzheimer's Disease and Type 2 Diabetes.Journal of chemical information and modeling · 2024Article
- Molecular Insights into the Effects of F16L and F19L Substitutions on the Conformation and Aggregation Dynamics of Human Calcitonin.Journal of chemical information and modeling · 2024Article
- Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures.Journal of chemical information and modeling · 2024Article
- Computational insights into the cross-talk between medin and Aβ: implications for age-related vascular risk factors in Alzheimer's disease.Briefings in bioinformatics · 2024Article
- Deciphering the influence of Y12L and N17H substitutions on the conformation and oligomerization of human calcitonin.Soft matter · 2024Article
- Unveiling Medin Folding and Dimerization Dynamics and Conformations via Atomistic Discrete Molecular Dynamics Simulations.Journal of chemical information and modeling · 2023Article
- Direct Observation of Seeded Conformational Conversion of hIAPPJournal of chemical information and modeling · 2023Article
- Determination of Protein Monoclonal-Antibody Epitopes by a Combination of Structural Proteomics Methods.Journal of proteome research · 2023Article
- Dissecting the Self-assembly Dynamics of Imperfect Repeats in α-Synuclein.Journal of chemical information and modeling · 2023Article
- SEVI Inhibits Aβ Amyloid Aggregation by Capping the β-Sheet Elongation Edges.Journal of chemical information and modeling · 2023Article
- Determining the gas-phase structures of α-helical peptides from shape, microsolvation, and intramolecular distance data.Nature communications · 2023Article
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Authors and funding
5 authors.
Funding
Abstract
We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein-models for α helix-rich and β sheet-rich proteins, respectively-and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data. Our approach is readily applicable to other proteins with unknown structures.
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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.