Automatic generation of protein structure cartoons with Pro-origami

Stivala, Alex; Wybrow, Michael; Wirth, Anthony; Whisstock, James C.; Stuckey, Peter J.

doi:10.1093/bioinformatics/btr575

Cited by 175 publications

(108 citation statements)

References 16 publications

Supporting

Mentioning

107

Contrasting

Unclassified

Order By: Relevance

“…Both PyMOL and VMD (46,47) were used for structure visualization and image generation. The protein topology graph was generated by Proorigami, available online (48).…”

Section: Methodsmentioning

confidence: 99%

A Recombinant Fungal Chitin Deacetylase Produces Fully Defined Chitosan Oligomers with Novel Patterns of Acetylation

Naqvi

Cord‐Landwehr

Singh

et al. 2016

Appl Environ Microbiol

View full text Add to dashboard Cite

Partially acetylated chitosan oligosaccharides (paCOS) are potent biologics with many potential applications, and their bioactivities are believed to be dependent on their structure, i.e., their degrees of polymerization and acetylation, as well as their pattern of acetylation. However, paCOS generated via chemical N-acetylation or de-N-acetylation of GlcN or GlcNAc oligomers, respectively, typically display random patterns of acetylation, making it difficult to control and predict their bioactivities. In contrast, paCOS produced from chitin deacetylases (CDAs) acting on chitin oligomer substrates may have specific patterns of acetylation, as shown for some bacterial CDAs. However, compared to what we know about bacterial CDAs, we know little about the ability of fungal CDAs to produce defined paCOS with known patterns of acetylation. Therefore, we optimized the expression of a chitin deacetylase from the fungus Puccinia graminis f. sp. tritici in Escherichia coli. The best yield of functional enzyme was obtained as a fusion protein with the maltose-binding protein (MBP) secreted into the periplasmic space of the bacterial host. We characterized the MBP fusion protein from P. graminis (PgtCDA) and tested its activity on different chitinous substrates. Mass spectrometric sequencing of the products obtained by enzymatic deacetylation of chitin oligomers, i.e., tetramers to hexamers, revealed that PgtCDA generated paCOS with specific acetylation patterns of A-A-D-D, A-A-D-D-D, and A-A-D-D-D-D, respectively (A, GlcNAc; D, GlcN), indicating that PgtCDA cannot deacetylate the two GlcNAc units closest to the oligomer's nonreducing end. This unique property of PgtCDA significantly expands the so far very limited library of well-defined paCOS available to test their bioactivities for a wide variety of potential applications. IMPORTANCEWe successfully achieved heterologous expression of a fungal chitin deacetylase gene from the basidiomycete Puccinia graminis f. sp. tritici in the periplasm of E. coli as a fusion protein with the maltose-binding protein; this strategy allows the production of these difficult-to-express enzymes in sufficient quantities for them to be characterized and optimized through protein engineering. Here, the recombinant enzyme was used to produce partially acetylated chitosan oligosaccharides from chitin oligomers, whereby the pronounced regioselectivity of the enzyme led to the production of defined products with novel patterns of acetylation. This approach widens the scope for both the production and functional analysis of chitosan oligomers and thus will eventually allow the detailed molecular structure-function relationships of biologically active chitosans to be studied, which is essential for developing applications for these functional biopolymers for a circular bioeconomy, e.g., in agriculture, medicine, cosmetics, and food sciences.

show abstract

“…Both PyMOL and VMD (46,47) were used for structure visualization and image generation. The protein topology graph was generated by Proorigami, available online (48).…”

Section: Methodsmentioning

confidence: 99%

A Recombinant Fungal Chitin Deacetylase Produces Fully Defined Chitosan Oligomers with Novel Patterns of Acetylation

Naqvi

Cord‐Landwehr

Singh

et al. 2016

Appl Environ Microbiol

View full text Add to dashboard Cite

show abstract

“…The figure was generated using LigPlotϩ (68). E, topology diagrams of Rv1636 apo (left) and MSMEG_3811/ cAMP (right), generated with TopDraw and Pro-Origami (67,69). Cylinders represent ␣-helices, and arrows correspond to ␤-strands.…”

Section: Significant Fraction Of Cytosolic Camp Is Bound To Protein-mentioning

confidence: 99%

A Universal Stress Protein (USP) in Mycobacteria Binds cAMP

Banerjee

Adolph

Gopalakrishnapai

et al. 2015

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background: Mycobacteria utilize cAMP for regulating transcription and protein acetylation. Results: We identify and structurally characterize a universal stress protein as an abundant and specific cAMP-binding protein. Conclusion:The USP domain is a novel cAMP-binding module. Significance: Certain members of the universal stress protein family serve to sequester cAMP, acting as sinks to regulate the availability of cAMP for downstream effectors.

show abstract

“…9C and D) (PDB accession numbers 1I3C, 1K66, 1K68, and 4ZYL) (25)(26)(27) and is distinct from the three other known RR homo (25). Topology diagrams were generated using the Pro-origami system (55). dimerization modes (28).…”

Section: Rtbrrmentioning

confidence: 99%

Arm-in-Arm Response Regulator Dimers Promote Intermolecular Signal Transduction

et al. 2016

View full text Add to dashboard Cite

Bacteriophytochrome photoreceptors (BphPs) and their cognate response regulators make up two-component signal transduction systems which direct bacteria to mount phenotypic responses to changes in environmental light quality. Most of these systems utilize single-domain response regulators to transduce signals through unknown pathways and mechanisms. Here we describe the photocycle and autophosphorylation kinetics of RtBphP1, a red light-regulated histidine kinase from the desert bacterium Ramlibacter tataouinensis. RtBphP1 undergoes red to far-red photoconversion with rapid thermal reversion to the dark state. RtBphP1 is autophosphorylated in the dark; this activity is inhibited under red light. The RtBphP1 cognate response regulator, the R. tataouinensis bacteriophytochrome response regulator (RtBRR), and a homolog, AtBRR from Agrobacterium tumefaciens, crystallize unexpectedly as arm-in-arm dimers, reliant on a conserved hydrophobic motif, hFWAhL (where h is a hydrophobic M, V, L, or I residue). RtBRR and AtBRR dimerize distinctly from four structurally characterized phytochrome response regulators found in photosynthetic organisms and from all other receiver domain homodimers in the Protein Data Bank. A unique cacodylate-zinc-histidine tag metal organic framework yielded single-wavelength anomalous diffraction phases and may be of general interest. Examination of the effect of the BRR stoichiometry on signal transduction showed that phosphorylated RtBRR is accumulated more efficiently than the engineered monomeric RtBRR (RtBRR mon ) in phosphotransfer reactions. Thus, we conclude that arm-in-arm dimers are a relevant signaling intermediate in this class of two-component regulatory systems. IMPORTANCEBphP histidine kinases and their cognate response regulators comprise widespread red light-sensing two-component systems. Much work on BphPs has focused on structural understanding of light sensing and on enhancing the natural infrared fluorescence of these proteins, rather than on signal transduction or the resultant phenotypes. To begin to address this knowledge gap, we solved the crystal structures of two single-domain response regulators encoded by a region immediately downstream of that encoding BphPs. We observed a previously unknown arm-in-arm dimer linkage. Monomerization via deletion of the C-terminal dimerization motif had an inhibitory effect on net response regulator phosphorylation, underlining the importance of these unusual dimers for signal transduction. Bacteria utilize two-component systems (TCSs) to monitor and respond to diverse signals in the environment, including the spectrum and intensity of visible (Vis) light. Light of a specific wavelength can control directed responses, as in the case of phototaxis (1, 2), or can control generalized stress responses (3). Bacteriophytochrome photoreceptors (BphPs) are soluble cytoplasmic red light-sensing modules, often histidine kinases (HKs), encoded by a region adjacent to a single-domain response regulator (SDRR) to which phosphate is transfe...

show abstract

Automatic generation of protein structure cartoons with Pro-origami

Abstract: a.stivala@pgrad.unimelb.edu.au; pjs@csse.unimelb.edu.au.

Cited by 175 publications

References 16 publications

A Recombinant Fungal Chitin Deacetylase Produces Fully Defined Chitosan Oligomers with Novel Patterns of Acetylation

A Recombinant Fungal Chitin Deacetylase Produces Fully Defined Chitosan Oligomers with Novel Patterns of Acetylation

A Universal Stress Protein (USP) in Mycobacteria Binds cAMP

Arm-in-Arm Response Regulator Dimers Promote Intermolecular Signal Transduction

Contact Info

Product

Resources

About