ProTSAV: A protein tertiary structure analysis and validation server

Aquaporins (AQPs) are of vital importance in the cellular transport system of all living organisms. In this study, genome-wide identification, distribution, and characterization of AQPs were determined in Arabidopsis lyrata, Capsella grandiflora, C. rubella, Eutrema salsugineum, Brassica rapa, B. oleracea, and B. napus (canola). Classification and phylogeny of AQPs revealed the loss of XIPs and NIP-IIIs in all species. Characterization of distinctive AQP features showed a high level of conservation in spacing between NPA-domains, and selectivity filters. Interestingly, TIP3s were found to be highly expressed in developing seeds, suggesting their role in seed desiccation. Analysis of available RNA-seq data obtained under biotic and abiotic stresses led to the identification of AQPs involved in stress tolerance mechanisms in canola. In addition, analysis of the effect of ploidy level, and resulting gene dose effect performed with the different combinations of Brassica A and C genomes revealed that more than 70% of AQPs expression were dose-independent, thereby supporting their role in stress alleviation. This first in-depth characterization of Brassicaceae AQPs highlights transport mechanisms and related physiological processes that could be exploited in breeding programs of stress-tolerant cultivars.

show abstract

“…ProTSAV was used for quality assessment of the 3D structures 33 . (http://www.scfbio-iitd.res.in/software/proteomics/protsavzip.jsp)…”

Section: Methodsmentioning

confidence: 99%

Analysis of aquaporins in Brassicaceae species reveals high-level of conservation and dynamic role against biotic and abiotic stress in canola

Sonah

Deshmukh

Labbé

et al. 2017

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Single-model methods use evolutionary information (Kalman & Ben-Tal, 2010), statistical potentials, physics-based potentials and combinations of different features (Benkert et al, 2011;Singh et al, 2016;Liu et al, 2016) obtained from only one model to evaluate the model quality (Wallner & Elofsson, 2003).…”

Section: Single-model Methodsmentioning

confidence: 99%

An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences

Das

Sillitoe

et al. 2017

Acta Crystallogr D Struct Biol

View full text Add to dashboard Cite

Computational modelling of proteins has been a major catalyst in structural biology. Bioinformatics groups have exploited the repositories of known structures to predict high-quality structural models with high efficiency at low cost. This article provides an overview of comparative modelling, reviews recent developments and describes resources dedicated to large-scale comparative modelling of genome sequences. The value of subclustering protein domain superfamilies to guide the template-selection process is investigated. Some recent cases in which structural modelling has aided experimental work to determine very large macromolecular complexes are also cited.

show abstract

“…Further, quality of models was assessed using NIH‐SAVES and ProTsav server. ProTsav is a meta‐server combined eight individual servers (DDFIRE, ERRAT, NACCESS, PROSA, PROCHECK, VERIFY 3D, MOLPROBITY and D2N) and assigns a cumulative score on a scale of 0–1. Any structure with a ProTsav score ≤ 0.4 is considered acceptable.…”

Section: Resultsmentioning

confidence: 99%

“…The shortlisted models were further subjected to structural refinement using 3D refine server (http://sysbio.rnet.missouri.edu/3Drefine/) and Galaxy WEB server (http://galaxy.seoklab.org/). The resultant high‐quality models were used for further analysis …”

Section: Methodsmentioning

confidence: 99%

Understanding the mechanism of copurification of “difficult to remove” host cell proteins in rituximab biosimilar products

Singh

Mishra

Yadav

et al. 2019

Biotechnology Progress

Self Cite

View full text Add to dashboard Cite

Host cell proteins (HCPs) are considered a critical quality attribute and are linked to safety and efficacy of biotherapeutic products. Researchers have identified 10 HCPs in Chinese hamster ovary (CHO) that exhibit common characteristics of product association, coelution, and age‐dependent expression and therefore are “difficult to remove” during downstream purification. These include cathepsin D, clusterin, galectin‐3‐binding protein, G‐protein coupled receptor 56, lipoprotein lipase, metalloproteinase inhibitor, nidogen‐1 secreted protein acidic and rich in cysteine (SPARC), sulfated glycoprotein, and insulin‐like growth factor‐2 RNA‐binding protein. While the levels of HCPs in the investigated biosimilars were within the acceptable range of <100 ppm, certain “difficult to remove” HCPs were found in the biosimilar samples. This article aims to elucidate the underlying interactions between these “difficult to remove” HCPs and the mAb product. Surface study of rituximab exhibited unstable discontinuous patches of residues on the protein surface that have high propensity to get buried and lower the solvent exposed area. The higher order structure and the receptor binding were not affected, except for one of the biosimilars, owing to extremely low‐HCP levels in its final drug product. Finally, based on the combined experimental and computational data from this study, a probable mechanism of retention for the 10 HCPs is proposed. The results presented here can guide downstream process design or avenues for protein engineering during product discovery to achieve more effective removal of the impurities.

show abstract

ProTSAV: A protein tertiary structure analysis and validation server

Cited by 68 publications

References 69 publications

Analysis of aquaporins in Brassicaceae species reveals high-level of conservation and dynamic role against biotic and abiotic stress in canola

Analysis of aquaporins in Brassicaceae species reveals high-level of conservation and dynamic role against biotic and abiotic stress in canola

An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences

Understanding the mechanism of copurification of “difficult to remove” host cell proteins in rituximab biosimilar products

Contact Info

Product

Resources

About