Two Structures of a λ Cro Variant Highlight Dimer Flexibility but Disfavor Major Dimer Distortions upon Specific Binding of Cognate DNA

Hall, Branwen M.; Roberts, S.A.; Héroux, A.; Cordes, Matthew

doi:10.1016/j.jmb.2007.10.082

Cited by 13 publications

(23 citation statements)

References 33 publications

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“…45,46 For wild-type λ Cro and the triply mutated variant (PSQ), untagged versions were also generated, and the proteins were expressed and purified according to a previously described procedure. 47 …”

Section: Mutagenesis and Protein Purificationmentioning

confidence: 99%

Reengineering Cro Protein Functional Specificity with an Evolutionary Code

Hall

Vaughn

Begaye

et al. 2011

Journal of Molecular Biology

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Section: Mutagenesis and Protein Purificationmentioning

confidence: 99%

Reengineering Cro Protein Functional Specificity with an Evolutionary Code

Hall

Vaughn

Begaye

et al. 2011

Journal of Molecular Biology

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“…Using HHpred and the Conserved Domains Database (CDD) of NCBI (74), it was found that the products of gene 29 of J-1, which is transcribed leftward, and of gene 31 (gene 27 in PL-1), which is transcribed rightward, have maximal homology to CI and Cro proteins of lambda (75,76). It is plausible that this organization corresponds to the synteny found in other lambda-like phages where CI is coded from right to left and Cro in the opposite direction.…”

Section: Resultsmentioning

confidence: 99%

Exposing the Secrets of Two Well-Known Lactobacillus casei Phages, J-1 and PL-1, by Genomic and Structural Analysis

Dieterle

Bowman

Batthyány

et al. 2014

Appl Environ Microbiol

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c Bacteriophage J-1 was isolated in 1965 from an abnormal fermentation of Yakult using Lactobacillus casei strain Shirota, and a related phage, PL-1, was subsequently recovered from a strain resistant to J-1. Complete genome sequencing shows that J-1 and PL-1 are almost identical, but PL-1 has a deletion of 1.9 kbp relative to J-1, resulting in the loss of four predicted gene products involved in immunity regulation. The structural proteins were identified by mass spectrometry analysis. Similarly to phage A2, two capsid proteins are generated by a translational frameshift and undergo proteolytic processing. The structure of gene product 16 (gp16), a putative tail protein, was modeled based on the crystal structure of baseplate distal tail proteins (Dit) that form the baseplate hub in other Siphoviridae. However, two regions of the C terminus of gp16 could not be modeled using this template. The first region accounts for the differences between J-1 and PL-1 gp16 and showed sequence similarity to carbohydratebinding modules (CBMs). J-1 and PL-1 GFP-gp16 fusions bind specifically to Lactobacillus casei/paracasei cells, and the addition of L-rhamnose inhibits binding. J-1 gp16 exhibited a higher affinity than PL-1 gp16 for cell walls of L. casei ATCC 27139 in phage adsorption inhibition assays, in agreement with differential adsorption kinetics observed for both phages in this strain. The data presented here provide insights into how Lactobacillus phages interact with their hosts at the first steps of infection.

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“…Variation among the Cro crystal structures ranges from an apo closed [50] to a DNA-bound open [51] global conformation. Two new open-like X-ray structures were recently solved in the absence of DNA [52], bringing into question its dominant solution form and DNA-binding mechanism. To address these issues, REMD simulation was performed to elucidate the conformational space available to the protein in solution [31].…”

Section: Examples Of Network Visualization To Analyze MD Trajectoriesmentioning

confidence: 99%

Network visualization of conformational sampling during molecular dynamics simulation

Ahlstrom¹,

Baker²,

Ehrlich³

et al. 2013

Journal of Molecular Graphics and Modelling

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Effective data reduction methods are necessary for uncovering the inherent conformational relationships present in large molecular dynamics (MD) trajectories. Clustering algorithms provide a means to interpret the conformational sampling of molecules during simulation by grouping trajectory snapshots into a few subgroups, or clusters, but the relationships between the individual clusters may not be readily understood. Here we show that network analysis can be used to visualize the dominant conformational states explored during simulation as well as the connectivity between them, providing a more coherent description of conformational space than traditional clustering techniques alone. We compare the results of network visualization against 11 clustering algorithms and principal component conformer plots. Several MD simulations of proteins undergoing different conformational changes demonstrate the effectiveness of networks in reaching functional conclusions.

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Two Structures of a λ Cro Variant Highlight Dimer Flexibility but Disfavor Major Dimer Distortions upon Specific Binding of Cognate DNA

Cited by 13 publications

References 33 publications

Reengineering Cro Protein Functional Specificity with an Evolutionary Code

Reengineering Cro Protein Functional Specificity with an Evolutionary Code

Exposing the Secrets of Two Well-Known Lactobacillus casei Phages, J-1 and PL-1, by Genomic and Structural Analysis

Network visualization of conformational sampling during molecular dynamics simulation

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