Low‐Resolution Molecular Dynamics Simulations of the 30S Ribosomal Subunit

2006 ◽  
Vol 5 (4) ◽  
pp. 1248-1263 ◽  
Author(s):  
Qizhi Cui ◽  
Robert K.‐Z. Tan ◽  
Stephen C. Harvey ◽  
David A. Case
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ribosomal Subunit ◽  
Low Resolution ◽  
Dynamics Simulations

scholarly journals Improving the Reconstruction of Low-Resolution CryoEM Map using Enhanced Molecular Dynamics Simulations

2019 ◽  
Vol 116 (3) ◽  
pp. 61a
Author(s):  
Cesar A. Lopez ◽  
Mark Swift ◽  
Xiao-Ping Xu ◽  
Dorit Hanein ◽  
Niels Volkmann ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Low Resolution ◽  
Dynamics Simulations

scholarly journals Integrity of the P-site is probed during maturation of the 60S ribosomal subunit

2012 ◽  
Vol 197 (6) ◽  
pp. 747-759 ◽  
Author(s):  
Cyril Bussiere ◽  
Yaser Hashem ◽  
Sucheta Arora ◽  
Joachim Frank ◽  
Arlen W. Johnson
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ribonucleic Acid ◽  
Ribosomal Subunit ◽  
Elongation Factor ◽  
Molecular Signaling ◽  
Conformation Change ◽  
Guanosine Triphosphatase ◽  
Dynamics Simulations ◽  
Late Maturation

Eukaryotic ribosomes are preassembled in the nucleus and mature in the cytoplasm. Release of the antiassociation factor Tif6 by the translocase-like guanosine triphosphatase Efl1 is a critical late maturation step. In this paper, we show that a loop of Rpl10 that embraces the P-site transfer ribonucleic acid was required for release of Tif6, 90 Å away. Mutations in this P-site loop blocked 60S maturation but were suppressed by mutations in Tif6 or Efl1. Molecular dynamics simulations of the mutant Efl1 proteins suggest that they promote a conformation change in Efl1 equivalent to changes that elongation factor G and eEF2 undergo during translocation. These results identify molecular signaling from the P-site to Tif6 via Efl1, suggesting that the integrity of the P-site is interrogated during maturation. We propose that Efl1 promotes a functional check of the integrity of the 60S subunit before its first round of translation.

scholarly journals Low-Resolution Models for the Interaction Dynamics of Coated Gold Nanoparticles with β2-microglobulin

2019 ◽  
Vol 20 (16) ◽  
pp. 3866 ◽  
Author(s):  
Giorgia Brancolini ◽  
Hender Lopez ◽  
Stefano Corni ◽  
Valentina Tozzini
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Computational Cost ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Low Resolution ◽  
Β2 Microglobulin ◽  
Coating Roughness ◽  
Gold Nps ◽  
Dynamics Simulations

A large number of low-resolution models have been proposed in the last decades to reduce the computational cost of molecular dynamics simulations for bio-nano systems, such as those involving the interactions of proteins with functionalized nanoparticles (NPs). For the proteins, “minimalist” models at the one-bead-per residue (Cα-based) level and with implicit solvent are well established. For the gold NPs, widely explored for biotechnological applications, mesoscale (MS) models treating the NP core with a single spheroidal object are commonly proposed. In this representation, the surface details (coating, roughness, etc.) are lost. These, however, and the specificity of the functionalization, have been shown to have fundamental roles for the interaction with proteins. We presented a mixed-resolution coarse-grained (CG) model for gold NPs in which the surface chemistry is reintroduced as superficial smaller beads. We compared molecular dynamics simulations of the amyloid β2-microglobulin represented at the minimalist level interacting with NPs represented with this model or at the MS level. Our finding highlights the importance of describing the surface of the NP at a finer level as the chemical-physical properties of the surface of the NP are crucial to correctly understand the protein-nanoparticle association.

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