Three-dimensional domain swapping in the protein structure space

2012 ◽  
Vol 80 (6) ◽  
pp. 1610-1619 ◽  
Author(s):  
Yongqi Huang ◽  
Huaiqing Cao ◽  
Zhirong Liu
Keyword(s):  
Protein Structure ◽  
Three Dimensional ◽  
Domain Swapping ◽  
Structure Space ◽  
Dimensional Domain ◽  
Protein Structure Space

scholarly journals Interactions Crucial for Three-Dimensional Domain Swapping in the HP-RNase Variant PM8

2011 ◽  
Vol 101 (2) ◽  
pp. 459-467 ◽  
Author(s):  
Pere Tubert ◽  
Douglas V. Laurents ◽  
Marc Ribó ◽  
Marta Bruix ◽  
Maria Vilanova ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Domain Swapping ◽  
Dimensional Domain

scholarly journals The Unfolding Story of Three-Dimensional Domain Swapping

Structure ◽  
2003 ◽  
Vol 11 (3) ◽  
pp. 243-251 ◽  
Author(s):  
Frederic Rousseau ◽  
Joost W.H. Schymkowitz ◽  
Laura S. Itzhaki
Keyword(s):  
Three Dimensional ◽  
Domain Swapping ◽  
Dimensional Domain

scholarly journals Evidences for the unfolding mechanism of three-dimensional domain swapping

2013 ◽  
Vol 22 (3) ◽  
pp. 280-286 ◽  
Author(s):  
Zhirong Liu ◽  
Yongqi Huang
Keyword(s):  
Three Dimensional ◽  
Domain Swapping ◽  
Dimensional Domain

scholarly journals Human FoxP Transcription Factors as Tractable Models of the Evolution and Functional Outcomes of Three-Dimensional Domain Swapping

2021 ◽  
Vol 22 (19) ◽  
pp. 10296
Author(s):  
Pablo Villalobos ◽  
César A. Ramírez-Sarmiento ◽  
Jorge Babul ◽  
Exequiel Medina
Keyword(s):  
Transcription Factors ◽  
Dissociation Constants ◽  
Functional Characterization ◽  
Three Dimensional ◽  
Domain Swapping ◽  
Evolutionary Strategies ◽  
Protein Oligomerization ◽  
Biophysical Parameters ◽  
Physiological Conditions ◽  
Dimensional Domain

The association of two or more proteins to adopt a quaternary complex is one of the most widespread mechanisms by which protein function is modulated. In this scenario, three-dimensional domain swapping (3D-DS) constitutes one plausible pathway for the evolution of protein oligomerization that exploits readily available intramolecular contacts to be established in an intermolecular fashion. However, analysis of the oligomerization kinetics and thermodynamics of most extant 3D-DS proteins shows its dependence on protein unfolding, obscuring the elucidation of the emergence of 3D-DS during evolution, its occurrence under physiological conditions, and its biological relevance. Here, we describe the human FoxP subfamily of transcription factors as a feasible model to study the evolution of 3D-DS, due to their significantly faster dissociation and dimerization kinetics and lower dissociation constants in comparison to most 3D-DS models. Through the biophysical and functional characterization of FoxP proteins, relevant structural aspects highlighting the evolutionary adaptations of these proteins to enable efficient 3D-DS have been ascertained. Most biophysical studies on FoxP suggest that the dynamics of the polypeptide chain are crucial to decrease the energy barrier of 3D-DS, enabling its fast oligomerization under physiological conditions. Moreover, comparison of biophysical parameters between human FoxP proteins in the context of their minute sequence differences suggests differential evolutionary strategies to favor homoassociation and presages the possibility of heteroassociations, with direct impacts in their gene regulation function.

scholarly journals Short paths in protein structure space originate in graph structure

2009 ◽  
Vol 106 (51) ◽  
pp. E137-E137 ◽  
Author(s):  
M. Zimmermann ◽  
F. Towfic ◽  
R. L. Jernigan ◽  
A. Kloczkowski
Keyword(s):  
Protein Structure ◽  
Graph Structure ◽  
Structure Space ◽  
Protein Structure Space

Three-dimensional domain swapping and supramolecular protein assembly: insights from the X-ray structure of a dimeric swapped variant of human pancreatic RNase

2013 ◽  
Vol 69 (10) ◽  
pp. 2116-2123 ◽  
Author(s):  
Andrea Pica ◽  
Antonello Merlino ◽  
Alexander K. Buell ◽  
Tuomas P. J. Knowles ◽  
Elio Pizzo ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Supramolecular Assembly ◽  
Domain Swapping ◽  
Crystallographic Axis ◽  
Force Microscopy ◽  
Atomic Force ◽  
Pancreatic Rnase ◽  
Quaternary Structures ◽  
New Evidence ◽  
Dimensional Domain

The deletion of five residues in the loop connecting the N-terminal helix to the core of monomeric human pancreatic ribonuclease leads to the formation of an enzymatically active domain-swapped dimer (desHP). The crystal structure of desHP reveals the generation of an intriguing fibril-like aggregate of desHP molecules that extends along theccrystallographic axis. Dimers are formed by three-dimensional domain swapping. Tetramers are formed by the aggregation of swapped dimers with slightly different quaternary structures. The tetramers interact in such a way as to form an infinite rod-like structure that propagates throughout the crystal. The observed supramolecular assembly captured in the crystal predicts that desHP fibrils could form in solution; this has been confirmed by atomic force microscopy. These results provide new evidence that three-dimensional domain swapping can be a mechanism for the formation of elaborate large assemblies in which the protein, apart from the swapping, retains its original fold.

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