Efficient Relaxation of Protein–Protein Interfaces by Discrete Molecular Dynamics Simulations

2012 ◽  
Vol 9 (2) ◽  
pp. 1222-1229 ◽  
Author(s):  
Agusti Emperador ◽  
Albert Solernou ◽  
Pedro Sfriso ◽  
Carles Pons ◽  
Josep Lluis Gelpi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Protein Interfaces ◽  
Discrete Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals Mechanistic and Structural Insights on the IL-15 System through Molecular Dynamics Simulations

Molecules ◽  
2019 ◽  
Vol 24 (18) ◽  
pp. 3261
Author(s):  
Sousa ◽  
Laurent ◽  
Quéméner ◽  
Mortier ◽  
Questel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Features ◽  
Cellular Functions ◽  
Α Subunit ◽  
X Ray Crystallography ◽  
Receptor Complexes ◽  
Protein Interfaces ◽  
Dynamics Simulations ◽  
Comparison Of The Results

Interleukin 15 (IL-15), a four-helix bundle cytokine, is involved in a plethora of different cellular functions and, particularly, plays a key role in the development and activation of immune responses. IL-15 forms receptor complexes by binding with IL-2Rβ- and common γ(γc)-signaling subunits, which are shared with other members of the cytokines family (IL-2 for IL-2Rβ- and all other γc- cytokines for γc). The specificity of IL-15 is brought by the non-signaling α-subunit, IL-15Rα. Here we present the results of molecular dynamics simulations carried out on four relevant forms of IL-15: its monomer, IL-15 interacting individually with IL-15Rα (IL-15/IL-15Rα), with IL-2Rβ/γc subunits (IL-15/IL-2Rβ/γc) or with its three receptors simultaneously (IL-15/IL-15Rα/IL-2Rβ/γc). Through the analyses of the various trajectories, new insights on the structural features of the interfaces are highlighted, according to the considered form. The comparison of the results with the experimental data, available from X-ray crystallography, allows, in particular, the rationalization of the importance of IL-15 key residues (e.g. Asp8, Lys10, Glu64). Furthermore, the pivotal role of water molecules in the stabilization of the various protein-protein interfaces and their H-bonds networks are underlined for each of the considered complexes.

scholarly journals Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

2017 ◽  
Vol 3 (7) ◽  
pp. e1700479 ◽  
Author(s):  
Nicholas I. Brodie ◽  
Konstantin I. Popov ◽  
Evgeniy V. Petrotchenko ◽  
Nikolay V. Dokholyan ◽  
Christoph H. Borchers
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Short Distance ◽  
Protein Structures ◽  
Cross Linking ◽  
Discrete Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals Structure of prion β‐oligomers as determined by short‐distance crosslinking constraint‐guided discrete molecular dynamics simulations

PROTEOMICS ◽  
2021 ◽  
pp. 2000298
Author(s):  
Jason J. Serpa ◽  
Konstantin I. Popov ◽  
Evgeniy V. Petrotchenko ◽  
Nikolay V. Dokholyan ◽  
Christoph H. Borchers
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Short Distance ◽  
Discrete Molecular Dynamics ◽  
Dynamics Simulations

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations

2012 ◽  
Vol 8 (11) ◽  
pp. 4707-4718 ◽  
Author(s):  
Pedro Sfriso ◽  
Agusti Emperador ◽  
Laura Orellana ◽  
Adam Hospital ◽  
Josep Lluis Gelpí ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Transition ◽  
Discrete Molecular Dynamics ◽  
Transition Pathways ◽  
Dynamics Simulations
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