Of capsid structure and stability: The partnership between charged residues of E-loop and P-domain of the bacteriophage P22 coat protein

Asija, Kunica; Teschke, Carolyn M.

doi:10.1016/j.virol.2019.05.021

Cited by 6 publications

(10 citation statements)

References 56 publications

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“…The cell pellets were resuspended in 20 mM sodium phosphate (pH 7.6) containing 20 mM MgCl 2 and frozen at −20 °C. The pellet was processed as described previously, and the procapsids were loaded onto a 150-mL Sephacryl S1000 column (GE Healthcare, Chicago, IL, USA) equilibrated in 20 mM sodium phosphate (pH 7.6) at a flow rate of 0.20 mL/min at 4 °C [ 41 ]. The procapsid-containing fractions were pooled, pelleted by ultracentrifugation at 206,000× g for 40 min at 4 °C, and resuspended overnight (O/N) at 4 °C in 20 mM sodium phosphate (pH 7.6).…”

Section: Methodsmentioning

confidence: 99%

“…The cells were simultaneously induced with anhydrotetracycline (5 µg/L) and infected with 1 -amE5 13 -amH101 phages (the 13amber mutation prevents cell lysis) at an MOI of 5. The infected cultures were grown for an additional 4 h then harvested by centrifugation at 7900× g in a Sorvall SLC-6000 rotor for 15 min at 4 • C. The cell pellets were resuspended in 20 mM sodium phosphate (pH 7.6) containing 20 mM MgCl 2 and frozen at −20 • C. The pellet was processed as described previously, and the procapsids were loaded onto a 150-mL Sephacryl S1000 column (GE Healthcare, Chicago, IL, USA) equilibrated in 20 mM sodium phosphate (pH 7.6) at a flow rate of 0.20 mL/min at 4 • C [41]. The procapsid-containing fractions were pooled, pelleted by ultracentrifugation at 206,000× g for 40 min at 4 • C, and resuspended overnight (O/N) at 4 • C in 20 mM sodium phosphate (pH 7.6).…”

Section: In Vivo Production Of Procapsidsmentioning

confidence: 99%

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Tryptophan Residues Are Critical for Portal Protein Assembly and Incorporation in Bacteriophage P22

Woodbury

Motwani

Leroux

et al. 2022

Viruses

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The oligomerization and incorporation of the bacteriophage P22 portal protein complex into procapsids (PCs) depends upon an interaction with scaffolding protein, but the region of the portal protein that interacts with scaffolding protein has not been defined. In herpes simplex virus 1 (HSV-1), conserved tryptophan residues located in the wing domain are required for portal-scaffolding protein interactions. In this study, tryptophan residues (W) present at positions 41, 44, 207 and 211 within the wing domain of the bacteriophage P22 portal protein were mutated to both conserved and non-conserved amino acids. Substitutions at each of these positions were shown to impair portal function in vivo, resulting in a lethal phenotype by complementation. The alanine substitutions caused the most severe defects and were thus further characterized. An analysis of infected cell lysates for the W to A mutants revealed that all the portal protein variants except W211A, which has a temperature-sensitive incorporation defect, were successfully recruited into procapsids. By charge detection mass spectrometry, all W to A mutant portal proteins were shown to form stable dodecameric rings except the variant W41A, which dissociated readily to monomers. Together, these results suggest that for P22 conserved tryptophan, residues in the wing domain of the portal protein play key roles in portal protein oligomerization and incorporation into procapsids, ultimately affecting the functionality of the portal protein at specific stages of virus assembly.

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Section: Methodsmentioning

confidence: 99%

Section: In Vivo Production Of Procapsidsmentioning

confidence: 99%

Tryptophan Residues Are Critical for Portal Protein Assembly and Incorporation in Bacteriophage P22

Woodbury

Motwani

Leroux

et al. 2022

Viruses

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“…Gly and Ala were discovered in 50-residues, which were necessary for the inclusion of the M13 filamentous bacteriophage coat (Roth et al, 2002[ 50 ]). Furthermore, Ala substitution at Glu52, Glu59, and Glu72 in the coat protein E-loop enhanced the stability of procapsids and virions of bacteriophages P22 (Asija and Teschke, 2019[ 3 ]). According to these results, PVPs favored amino acids with high alpha-helix propensity and hydrophobic side index.…”

Section: Characterization Of Phage Virion Proteinsmentioning

confidence: 99%

Large-scale comparative review and assessment of computational methods for phage virion proteins identification

Kabir

Nantasenamat

Kanthawong

et al. 2022

EXCLI Journal; 21:Doc11; ISSN 1611-2156

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Phage virion proteins (PVPs) are effective at recognizing and binding to host cell receptors while having no deleterious effects on human or animal cells. Understanding their functional mechanisms is regarded as a critical goal that will aid in rational antibacterial drug discovery and development. Although high-throughput experimental methods for identifying PVPs are considered the gold standard for exploring crucial PVP features, these procedures are frequently time-consuming and labor-intensive. Thusfar, more than ten sequence-based predictors have been established for the in silico identification of PVPs in conjunction with traditional experimental approaches. As a result, a revised and more thorough assessment is extremely desirable. With this purpose in mind, we first conduct a thorough survey and evaluation of a vast array of 13 state-of-the-art PVP predictors. Among these PVP predictors, they can be classified into three groups according to the types of machine learning (ML) algorithms employed (i.e. traditional ML-based methods, ensemble-based methods and deep learning-based methods). Subsequently, we explored which factors are important for building more accurate and stable predictors and this included training/independent datasets, feature encoding algorithms, feature selection methods, core algorithms, performance evaluation metrics/strategies and web servers. Finally, we provide insights and future perspectives for the design and development of new and more effective computational approaches for the detection and characterization of PVPs.

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“…In this section, the PVPred-SCM method was exploited to analyze the crucial physicochemical properties (PCPs) of PVPs. Previously, many studies have reported that the biochemical and biophysical properties such as side-chain [45], alpha-helix propensity [46,47], and hydrophobicity [48] affect the biological activities of PVPs. To analyze the important characteristics of PVPs, Pearson correlation coefficient (R) between the propensity scores of amino acids and the PCPs in the AA index were used to identify informative PCPs that were useful in the analysis of PVPs.…”

Section: Analysis Of Pvps Using Informative Physicochemical Propertiesmentioning

confidence: 99%

“…It could be noted that the substitution of Glu with Ala increased the stability of procapsids and virions of bacteriophages. Although electrostatic repulsion could cause destabilization between the E-loop residue and spine helix, hydrophobic interaction could relieve this effect by balancing the repulsive electrostatic interactions [48]. As noticed in Table 8, the ranks of propensity scores (PS, hydrophobicity index) for Glu and Ala were (18,19) and (1,5), respectively, while the propensity scores of charged amino acid side chains of Lys, Glu, His, Arg, and Asp were ranked at 20, 19, 18, 17, and 12, respectively.…”

Section: Analysis Of Pvps Using Informative Physicochemical Propertiesmentioning

confidence: 99%

PVPred-SCM: Improved Prediction and Analysis of Phage Virion Proteins Using a Scoring Card Method

Charoenkwan

Kanthawong

Schaduangrat

et al. 2020

Cells

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Although, existing methods have been successful in predicting phage (or bacteriophage) virion proteins (PVPs) using various types of protein features and complex classifiers, such as support vector machine and naïve Bayes, these two methods do not allow interpretability. However, the characterization and analysis of PVPs might be of great significance to understanding the molecular mechanisms of bacteriophage genetics and the development of antibacterial drugs. Hence, we herein proposed a novel method (PVPred-SCM) based on the scoring card method (SCM) in conjunction with dipeptide composition to identify and characterize PVPs. In PVPred-SCM, the propensity scores of 400 dipeptides were calculated using the statistical discrimination approach. Rigorous independent validation test showed that PVPred-SCM utilizing only dipeptide composition yielded an accuracy of 77.56%, indicating that PVPred-SCM performed well relative to the state-of-the-art method utilizing a number of protein features. Furthermore, the propensity scores of dipeptides were used to provide insights into the biochemical and biophysical properties of PVPs. Upon comparison, it was found that PVPred-SCM was superior to the existing methods considering its simplicity, interpretability, and implementation. Finally, in an effort to facilitate high-throughput prediction of PVPs, we provided a user-friendly web-server for identifying the likelihood of whether or not these sequences are PVPs. It is anticipated that PVPred-SCM will become a useful tool or at least a complementary existing method for predicting and analyzing PVPs.

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Of capsid structure and stability: The partnership between charged residues of E-loop and P-domain of the bacteriophage P22 coat protein

Cited by 6 publications

References 56 publications

Tryptophan Residues Are Critical for Portal Protein Assembly and Incorporation in Bacteriophage P22

Tryptophan Residues Are Critical for Portal Protein Assembly and Incorporation in Bacteriophage P22

Large-scale comparative review and assessment of computational methods for phage virion proteins identification

PVPred-SCM: Improved Prediction and Analysis of Phage Virion Proteins Using a Scoring Card Method

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