Decoding the vital segments in human ATP-dependent RNA helicase

Journal of Genetic Engineering and Biotechnology

Sai

Kamjula

et al. 2020

Self Cite

Background To achieve a high yield of terpenoid-based therapeutics, 1-deoxy-d-xylulose-5-phosphate (DXP) pathway has been significantly exploited for the production of downstream enzymes. The DXP synthase (DXS) enzyme, the initiator of this pathway, is pivotal for the convergence of carbon flux, and is computationally studied well for the industrially utilized generally regarded as safe (GRAS) bacterium Bacillus subtilis to decode its vital regions for aiding the construction of a functionally improved mutant library. Results For the 546 sequence dataset of DXS sequences, a representative set of 108 sequences is created, and it shows a significant evolutionary divergence across different species clubbed into 37 clades, whereas three clades are observed for the 76 sequence dataset of Bacillus subtilis. The DXS enzyme, sharing a statistically significant homology to transketolase, is shown to be evolutionarily too distant. By the mutual information-based co-evolutionary network and hotspot analysis, the most crucial loci within the active site are deciphered. The 650-residue representative structure displays a complete conservation of 114 loci, and only two co-evolving residues ASP154 and ILE371 are found to be the conserved ones. Lastly, P318D is predicted to be the top-ranked mutation causing the increase in the thermodynamic stability of 6OUW. Conclusion The study excavates the vital functional, phylogenetic, and conserved residues across the active site of the DXS protein, the key rate-limiting controller of the entire pathway. It would aid to computationally understand the evolutionary landscape of this industrially useful enzyme and would allow us to widen its substrate repertoire to increase the enzymatic yield of unnatural molecules for in vivo and in vitro applications.

Section: Crucial Residues For Functional Mutagenesis and Directed Evomentioning

confidence: 99%

Excavating the functionally crucial active-site residues of the DXS protein of Bacillus subtilis by exploring its closest homologues

Journal of Genetic Engineering and Biotechnology

Sai

Kamjula

et al. 2020

Self Cite

“…Topological detail of a protein provides valuable resource for the routinely deployed lifescience studies including the annotation of disulphide connectivity pattern [1,2], functional annotation [3][4][5] , molecular docking and cross-talk based studies [6,7], enzyme design [8,9] and drug development [10]. For technical and resource limitations, the structure determination methodologies have failed to bridge the ever-increasing sequence-structure gap of the protein sequences [11], and have started deploying the predicted models for building more accurate solutions [12].…”

Section: Introductionmentioning

confidence: 99%

Probabilistic divergence of a template-based modelling methodology from the ideal protocol

2021

J Mol Model

Protein structural information is essential for the detailed mapping of a functional protein network. For a higher modelling accuracy and quicker implementation, template based algorithms have been extensively deployed and redefined. The methods only assess the predicted structure against its native state/template, and do not estimate the accuracy for each modelling step. A divergence measure is postulated to estimate the modelling accuracy against its theoretical optimal benchmark. By freezing the domain boundaries, the divergence measures are predicted for the most crucial steps of a modelling algorithm. To precisely refine the score using weighting constants , big data analysis could further be deployed.

“…An evolutionary relationship is usually drawn to screen the sequence/functional similarity among the protein sequences (Chan 1989; Kamjula et al 2020; Keeling et al 1998; Sharma et al 2018; T. Lanisňik Rizňer 2001). On the basis of mutual sequence similarity, the phylogenetic tree is constructed as the schematic depiction of the evolutionary connection between the species of different origins, and evolutionary distance/relatedness is assessed through several non-absolute scores including branch length, maximum likelihood score, and topology.…”

Section: Introductionmentioning

confidence: 99%

“…An evolutionary relationship is usually drawn to screen the sequence/functional similarit y among the protein sequences (Chan 1989;Kamjula et al 2020;Keeling et al 1998; nine different substitution matrices, viz. Dayhoff (Winona C. Barker 1978), JJT, BLOSUM62, WAG, PMB, DCMut (Kosiol and Goldman 2005), JTTDCmut (Kosiol and Goldman 2005),…”

Section: Introductionmentioning

confidence: 99%

Current strategic limitations of phylogenetic tools badly impact the inference of an evolutionary tree

Nasika

2021

Preprint

For drawing an evolutionary relationship among several protein sequences, the phylogenetic tree is usually constructed through maximum likelihood-based algorithms. To improve the accuracy of these methodologies, many parameters like bootstrap methods, correlation coefficient and residue-substitution models are presumably over-ranked to derive biologically credible relationships. Although the accuracy of protein sequence alignment and the substitution matrix are preliminary constraints to define the biological accuracy of the overlapped sequences/residues, the alignment is not iteratively optimized through the statistical testing of residue-substitution models. The study majorly highlights the potential pitfalls that significantly affect the accuracy of an evolutionary protocol. It emphasizes the need for a more accurate scrutiny of the entire phylogenetic methodology. The need of iterative optimizations is illustrated to construct a biologically credible and not mathematically optimal tree for a sequence dataset.