ArticleBiophysical journal2004
Molecular mechanism of domain swapping in proteins: an analysis of slower motions.
Article in Biophysical journal, 2004. 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, 47 citations in OpenAlex.
- Functional implication of the homotrimeric multidomain vacuolar sorting receptor 1 (VSR1) from Arabidopsis thaliana.Scientific reports · 2024Article
- Revealing Allosteric Mechanism of Amino Acid Binding Proteins from Open to Closed State.Molecules (Basel, Switzerland) · 2023Article
- Testing the length limit of loop grafting in a helical repeat protein.Current research in structural biology · 2021Article
- Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering.Chembiochem : a European journal of chemical biology · 2020Article
- Exploring the Roles of Proline in Three-Dimensional Domain Swapping from Structure Analysis and Molecular Dynamics Simulations.The protein journal · 2018Article
- Domain Motions and Functionally-Key Residues of L-Alanine Dehydrogenase Revealed by an Elastic Network Model.International journal of molecular sciences · 2015Article
- Models to Approximate the Motions of Protein Loops.Journal of chemical theory and computation · 2010Article
- REACH coarse-grained normal mode analysis of protein dimer interaction dynamics.Biophysical journal · 2009Article
- Protein acrobatics in pairs--dimerization via domain swapping.Current opinion in structural biology · 2009Review
- Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit.The Journal of chemical physics · 2008Article
- REACH coarse-grained biomolecular simulation: transferability between different protein structural classes.Biophysical journal · 2008Article
- Protein unfolding behavior studied by elastic network model.Biophysical journal · 2008Article
- Predicting the order in which contacts are broken during single molecule protein stretching experiments.Proteins · 2008Article
- Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian.Biophysical journal · 2007Article
- Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations.Biophysical journal · 2007Article
- Analysis of domain movements in glutamine-binding protein with simple models.Biophysical journal · 2007Article
- Packing regularities in biological structures relate to their dynamics.Methods in molecular biology (Clifton, N.J.) · 2007Article
- Loop motions of triosephosphate isomerase observed with elastic networks.Biochemistry · 2006Article
- The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models.Journal of chemical theory and computation · 2006Article
- Structure of peptide sex pheromone receptor PrgX and PrgX/pheromone complexes and regulation of conjugation in Enterococcus faecalis.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Domain swapping is a structural phenomenon that plays an important role in the mechanism of oligomerization of some proteins. The monomer units in the oligomeric structure become entangled with each other. Here we investigate the mechanism of domain swapping in diphtheria toxin and the structural criteria required for it to occur by analyzing the slower modes of motion with elastic network models, Gaussian network model and anisotropic network model. We take diphtheria toxin as a representative of this class of domain-swapped proteins and show that the domain, which is being swapped in the dimeric state, rotates and twists, in going from the "open" to the "closed" state, about a hinge axis that passes through the middle of the loop extending between two domains. A combination of the intra- and intermolecular contacts of the dimer is almost equivalent to that of the monomer, which shows that the relative orientations of the residues in both forms are almost identical. This is also reflected in the calculated B-factors when compared with the experimentally determined B-factors in x-ray crystal structures. The slowest modes of both the monomer and dimer show a common hinge centered on residue 387. The differences in distances between the monomer and the dimer also shows the hinge at nearly the same location (residue 381). Finally, the first three dominant modes of anisotropic network model together shows a twisting motion about the hinge centered on residue 387. We further identify the location of hinges for a set of another 12 domain swapped proteins and give the quantitative measures of the motions of the swapped domains toward their "closed" state, i.e., the overlap and correlation between vectors.
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