Phylogenetic and Structural Analysis of Chemokine Binding Proteins

We used Clustal-W in Megalign Pro (DNAStar version 12.3.1, DNAStar Inc.), to construct CKBP sequence alignments and generate a sequence-similarity based phylogenetic tree which was exported to FigTree (version 1.4.2, http://tree.bio.ed.ac.uk/software/figtree/). Glycosylation sites were predicted using NetNGlyc1.0 (http://www.cbs.dtu.dk/services/NetNGlyc/) and NetOGlyc4.0 (http://www.cbs.dtu.dk/services/NetOGlyc/)^{59 (link)}. Molecular weight and isoelectric point (pI) of proteins were calculated at ExPASy(http://web.expasy.org/compute_pi/). We used MUSCLE in Megalign Pro to construct chemokine sequence alignments and sequence-similarity based phylogenetic trees. Homology modelling was performed using MODELLER^{60 (link)}, within PYMOD2.0^{61 (link)}, using the evasin 1: CCL3 structure 3FPU^{26 (link)} as template. Disulfide bonds were identified using using the Protein Interaction Calculator^{62 (link)}.

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Alenazi Y., Singh K., Davies G., Eaton J.R., Elders P., Kawamura A, & Bhattacharya S. (2018). Genetically engineered two-warhead evasins provide a method to achieve precision targeting of disease-relevant chemokine subsets. Scientific Reports, 8, 6333.

Publication 2018

Megalign Pro

Ccl3 Chemokine Disulfide Glycosylation Muscle Protein Sequence alignments Tree

Corresponding Organization :

Other organizations : University of Oxford

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Variable analysis

independent variables

Clustal-W in Megalign Pro (DNAStar version 12.3.1, DNAStar Inc.) to construct CKBP sequence alignments
NetNGlyc1.0 and NetOGlyc4.0 to predict glycosylation sites
MUSCLE in Megalign Pro to construct chemokine sequence alignments and sequence-similarity based phylogenetic trees
MODELLER within PYMOD2.0 to perform homology modelling using the evasin 1: CCL3 structure 3FPU as template

dependent variables

Sequence-similarity based phylogenetic tree
Glycosylation sites
Molecular weight and isoelectric point (pI) of proteins
Homology model

control variables

FigTree (version 1.4.2) to export the phylogenetic tree
ExPASy to calculate molecular weight and isoelectric point (pI) of proteins
Protein Interaction Calculator to identify disulfide bonds

controls

No positive or negative controls are explicitly mentioned.

Annotations

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