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RecA filament and RecBCD reconstructed from David Goodsell's E. coli painting (Courtesy of David Goodsell, TSRI, The Machinery of Life, Springer Ed. 2009):

RecABCD

 

A first attempt of a bacterial replisome 3D model made with Graphite-LifeExplorer.  It contains: one hexameric DnaB helicase in complex with the DnaG primase, two copies of the DNA Polymerase III (the alpha-subunit) close to a beta-clamp, eight SSB proteins. The gamma-complex has not been included yet. One HU protein bends the DNA on the right:

Replisome

 

Ambient occlusion is one of the meaningful and insigthful ways providing a better perception not only of the protein shape but of the relative position of the components within the scene during the interactive navigation. In Graphite-LifeExplorer ambient occlusion is real-time like in the QuteMol software. These two renderings are obtained in Graphite-LifeExplorer with and without AO:

AO_1.png 

AO_2.png

 

Complicated shapes can be created in a fast and easy manner:

DNAcreation_1.pngDNAcreation_2

 

Bacterial repair protein MutL in an extended state, attached to the endonuclease MutH, and set back in its DNA environment. According to Goodsell (PMID: 21445900) the spacing between DNA strands in the E. coli nucleoid is about 6.4 nm and is reproduced hereafter. About genome organization in E. coli, the DNA is condensed into a compact structure called the nucleoid and is organized into macrodomains (See Espeli et al, 2008: PMID:18410497). However  the fine spatial organization of the DNA inside a macrodomain is still highly debated:

MutL_surrounding_1.png

 

3D model of a bacterial polyribosomal organization observed from in vitro translation by Brandt and coworkers (PMID:19167328). The 30S subunit is in dark grey, the 50S is in light grey with residues in red at the surface delineating the nascent peptide tunnel exit. The mRNA transcript (in orange) is sequestred on the inside, the tRNA entrance sites are accessible, and the nascent protein chain exits face the cytosol. In such arrangement the distance between nascent chains on adjacent ribosomes is maximized, thereby reducing the probability of intermolecular interactions thatwould give rise to aggregation and misfolding:

polysome2.png

 

When a bacteria like E. coli divides, the DNA transporter FtsK is responsible of the correct distribution of the genetic material into the daughter cells by pulling the chromosome at a speed of 5 Kbp per second. Here is represented the motor part of FtsK made of the assembling of 6 domains connected to the membrane by a long unstructured linker. FtsK is thus rather fixed at the septal region of the cell (Source Crozat et al, 2010 PMID: 20379135; Dubarry and Barre, 2010 PMID: 20033058):

FtsK_AO_smoothed.PNG

 

The complex comprising MutS (in pink), MutL (in yellow) and MutH (in cyan) is a key intermediate in the DNA mismatch repair (Winkler et al, 2011 PMID: 21454657). In E. coli, MutS recruits MutL and together, by recruiting MutH, signal to MutH and other proteins to start the repair process:

SLH_openconformation

 

The same illustration with a cartoon effect:

SLH_openconformation_cartoon

 

The same scene imported by Ludovic Autin and Adam Gardner (Scripps) in Cinema4D thanks the ePMV plugin. An Inverse Kinematic chain has been applied onto the linkers:

  SLH_linklers with bones

 

Wrapping of DNA around histones made with Graphite-LifeExplorer (PDB code 1KX5). Real-time ambient occlusion is used:

Nucleosome_AO

The same image (for artistic purpose) with a metallic texture applied on the surface of DNA:

Nucleosome_texture

 

Bacterial division machinery visualized in LifeExplorer (Vendeville et al, FEMS Microbiology Reviews, Vol 35, Issue 2, March 2011):

Septosome

 

Bacterial repair protein MutL in an "extended state" created with Graphite-LifeExplorer. The Nter and Cter domains are connected by two 40 nm long linkers (Source: Ahrends et al, Nucleic Acids Research, 2006, Vol.34, N°10; http://www.uniprot.org/uniprot/P23367). 

MutL

 

Graphite-LifeExplorer can be used to model mRNA inside a ribosome and between adjacent ribosomes:

Ribosome

 

Cluster of 2 single-strand DNA binding proteins (SSB35 binding mode) created with Graphite-LifeExplorer:

SSB

 

Holliday junction 3CRX extended with Graphite-LifeExplorer:

HollidayJunction_Image1

 

A brief overview of DNA modeling with Graphite-LifeExplorer:

 

 

This video shows two nucleosomes connected by double-stranded DNA:

 

 

This video shows 28,000 bp of dsDNA visualized with levels of detail in  Graphite-LifeExplorer:

 

 

This video shows a 3D model of the cell-division machinery:

 

 

Our model of the E.coli divisome made the cover of MolMic:

Cover MolMic

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