ArticleJournal of the American Chemical Society2015
Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles.
Article in Journal of the American Chemical Society, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 28 citations in OpenAlex.
- Catalytic architecture and cyclase-mediated dimerization of a newly identified class III-c lanthipeptide synthetase.Protein science : a publication of the Protein Society · 2026Article
- Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus.Proceedings of UrgentHPC 2021 : the Third International Workshop on HPC for Urgent Decision Making · 2021Article
- Scalable molecular dynamics on CPU and GPU architectures with NAMD.The Journal of chemical physics · 2020Article
- Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials.Journal of chemical information and modeling · 2020Article
- Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons.Journal of structural biology · 2018Article
- Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Phosphate-phosphate oligomerization drives higher order co-assemblies with stacks of cyanostar macrocycles.Chemical science · 2018Article
- CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments.The journal of physical chemistry. B · 2017Article
- Macrocyclic shape-persistency of cyclo[6]aramide results in enhanced multipoint recognition for the highly efficient template-directed synthesis of rotaxanes.Chemical science · 2017Article
- Crystal Structure and Conformational Change Mechanism of a Bacterial Nramp-Family Divalent Metal Transporter.Structure (London, England : 1993) · 2016Article
- Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.eLife · 2016Article
- Advances in the molecular dynamics flexible fitting method for cryo-EM modeling.Methods (San Diego, Calif.) · 2016Article
- Flexibility Coexists with Shape-Persistence in Cyanostar Macrocycles.Journal of the American Chemical Society · 2016Article
- The crystalline sponge method updated.IUCrJ · 2016Article
- Creating molecular macrocycles for anion recognition.Beilstein journal of organic chemistry · 2016Review
- Oxatub[4]arene: a smart macrocyclic receptor with multiple interconvertible cavities.Chemical science · 2015Article
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9 authors at 2 institutions in 1 country.
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Abstract
Crystal structure determination has long provided insight into structure and bonding of small molecules. When those same small molecules are designed to come together in multimolecular assemblies, such as in coordination cages, supramolecular architectures and organic-based frameworks, their crystallographic characteristics closely resemble biological macromolecules. This resemblance suggests that biomacromolecular refinement approaches be used for structure determination of abiological molecular complexes that arise in an aggregate state. Following this suggestion we investigated the crystal structure of a pentagonal macrocycle, cyanostar, by means of biological structure analysis methods and compared results to traditional small molecule methods. Cyanostar presents difficulties seen in supramolecular crystallography including whole molecule disorder and highly flexible solvent molecules sitting in macrocyclic and intermolecule void spaces. We used the force-field assisted refinement method, molecular dynamics flexible fitting algorithm for X-ray crystallography (xMDFF), along with tools from the macromolecular structure determination suite PHENIX. We found that a standard implementation of PHENIX, namely one without xMDFF, either fails to produce a solution by molecular replacement alone or produces an inaccurate structure when using generic geometry restraints, even at a very high diffraction data resolution of 0.84 Å. The problems disappear when taking advantage of xMDFF, which applies an optimized force field to realign molecular models during phasing by providing accurate restraints. The structure determination for this model system shows excellent agreement with the small-molecule methods. Therefore, the joint xMDFF-PHENIX refinement protocol provides a new strategy that uses macromolecule methods for structure determination of small molecules and their assemblies.
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