ArticleJournal of the American Chemical Society2007
Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.
Article in Journal of the American Chemical Society, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- NMR in the Age of Modern Biomedical Research and Drug Discovery.Journal of molecular biology · 2025Review
- An integrated approach of NMR experiments and MD simulations visualizes structural dynamics of a cyclic multi-domain protein.Protein science : a publication of the Protein Society · 2023Article
- Mutational and Environmental Effects on the Dynamic Conformational Distributions of Lys48-Linked Ubiquitin Chains.International journal of molecular sciences · 2023Article
- Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints.Biophysical reviews · 2022Review
- Cryo-EM density map fitting driven in-silico structure of human soluble guanylate cyclase (hsGC) reveals functional aspects of inter-domain cross talk upon NO binding.Journal of molecular graphics & modelling · 2019Article
- Diubiquitin-Based NMR Analysis: Interactions Between Lys6-Linked diUb and UBA Domain of UBXN1.Frontiers in chemistry · 2019Article
- Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers.PLoS computational biology · 2018Article
- Structural insights into pro-aggregation effects of C. elegans CRAM-1 and its human ortholog SERF2.Scientific reports · 2018Article
- Probing the Binding Modes of a Multidomain Protein to Lipid-based Nanoparticles by Relaxation-based NMR.The journal of physical chemistry letters · 2017Article
- Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities.Protein science : a publication of the Protein Society · 2016Article
- PolyUbiquitin chain linkage topology selects the functions from the underlying binding landscape.PLoS computational biology · 2014Article
- Deriving quantitative dynamics information for proteins and RNAs using ROTDIF with a graphical user interface.Journal of biomolecular NMR · 2013Article
- Equivalence between Euler angle conventions for the description of tensorial interactions in liquid NMR: application to different software programs.Journal of biomolecular NMR · 2013Review
- Determining interdomain structure and dynamics of a retroviral capsid protein in the presence of oligomerization: implication for structural transition in capsid assembly.Biochemistry · 2013Article
- Structural and biochemical studies of the open state of Lys48-linked diubiquitin.Biochimica et biophysica acta · 2012Article
- Integrative structural modeling with small angle X-ray scattering profiles.BMC structural biology · 2012Review
- Water proton spin saturation affects measured protein backbone 15N spin relaxation rates.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2011Article
- Fast approximations of the rotational diffusion tensor and their application to structural assembly of molecular complexes.Proteins · 2011Article
- Impact of 15N R2/R1 relaxation restraints on molecular size, shape, and bond vector orientation for NMR protein structure determination with sparse distance restraints.Journal of the American Chemical Society · 2011Article
- NMR studies on domain diffusion and alignment in modular GB1 repeats.Biophysical journal · 2010Article
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2 authors.
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Abstract
We present a simple and robust approach that uses the overall rotational diffusion tensor as a structural constraint for domain positioning in multidomain proteins and protein-protein complexes. This method offers the possibility to use NMR relaxation data for detailed structure characterization of such systems provided the structures of individual domains are available. The proposed approach extends the concept of using long-range information contained in the overall rotational diffusion tensor. In contrast to the existing approaches, we use both the principal axes and principal values of protein's rotational diffusion tensor to determine not only the orientation but also the relative positioning of the individual domains in a protein. This is achieved by finding the domain arrangement in a molecule that provides the best possible agreement with all components of the overall rotational diffusion tensor derived from experimental data. The accuracy of the proposed approach is demonstrated for two protein systems with known domain arrangement and parameters of the overall tumbling: the HIV-1 protease homodimer and Maltose Binding Protein. The accuracy of the method and its sensitivity to domain positioning are also tested using computer-generated data for three protein complexes, for which the experimental diffusion tensors are not available. In addition, the proposed method is applied here to determine, for the first time, the structure of both open and closed conformations of a Lys48-linked diubiquitin chain, where domain motions render impossible accurate structure determination by other methods. The proposed method opens new avenues for improving structure characterization of proteins in solution.
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