Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2
Two photoactivatable near infrared fluorescent proteins (NIR FPs) named “PAiRFP1” and “PAiRFP2” are formed by directed molecular evolution from Agp2, a bathy bacteriophytochrome of <i>Agrobacterium tumefaciens</i> C58. There are 15 and 24 amino acid substitutions in the structure of PAiR...
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MDPI AG
2020-09-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/10/9/1286 |
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| author | Faez Iqbal Khan Fakhrul Hassan Razique Anwer Feng Juan Dakun Lai |
| author_facet | Faez Iqbal Khan Fakhrul Hassan Razique Anwer Feng Juan Dakun Lai |
| author_sort | Faez Iqbal Khan |
| collection | DOAJ |
| description | Two photoactivatable near infrared fluorescent proteins (NIR FPs) named “PAiRFP1” and “PAiRFP2” are formed by directed molecular evolution from Agp2, a bathy bacteriophytochrome of <i>Agrobacterium tumefaciens</i> C58. There are 15 and 24 amino acid substitutions in the structure of PAiRFP1 and PAiRFP2, respectively. A comprehensive molecular exploration of these bacteriophytochrome photoreceptors (BphPs) are required to understand the structure dynamics. In this study, the NIR fluorescence emission spectra for PAiRFP1 were recorded upon repeated excitation and the fluorescence intensity of PAiRFP1 tends to increase as the irradiation time was prolonged. We also predicted that mutations Q168L, V244F, and A480V in Agp2 will enhance the molecular stability and flexibility. During molecular dynamics (MD) simulations, the average root mean square deviations of Agp2, PAiRFP1, and PAiRFP2 were found to be 0.40, 0.49, and 0.48 nm, respectively. The structure of PAiRFP1 and PAiRFP2 were more deviated than Agp2 from its native conformation and the hydrophobic regions that were buried in PAiRFP1 and PAiRFP2 core exposed to solvent molecules. The eigenvalues and the trace of covariance matrix were found to be high for PAiRFP1 (597.90 nm<sup>2</sup>) and PAiRFP2 (726.74 nm<sup>2</sup>) when compared with Agp2 (535.79 nm<sup>2</sup>). It was also found that PAiRFP1 has more sharp Gibbs free energy global minima than Agp2 and PAiRFP2. This comparative analysis will help to gain deeper understanding on the structural changes during the evolution of photoactivatable NIR FPs. Further work can be carried out by combining PCR-based directed mutagenesis and spectroscopic methods to provide strategies for the rational designing of these PAiRFPs. |
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| series | Biomolecules |
| spelling | doaj.art-6e331f28fbf248a4bc1a0963dd3f5cef2023-11-20T12:50:04ZengMDPI AGBiomolecules2218-273X2020-09-01109128610.3390/biom10091286Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2Faez Iqbal Khan0Fakhrul Hassan1Razique Anwer2Feng Juan3Dakun Lai4School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, ChinaSchool of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, ChinaDepartment of Pathology, College of Medicine, Imam Mohammad ibn Saud Islamic University (IMSIU), Riyadh 13317, Saudi ArabiaSchool of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, ChinaSchool of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 610054, ChinaTwo photoactivatable near infrared fluorescent proteins (NIR FPs) named “PAiRFP1” and “PAiRFP2” are formed by directed molecular evolution from Agp2, a bathy bacteriophytochrome of <i>Agrobacterium tumefaciens</i> C58. There are 15 and 24 amino acid substitutions in the structure of PAiRFP1 and PAiRFP2, respectively. A comprehensive molecular exploration of these bacteriophytochrome photoreceptors (BphPs) are required to understand the structure dynamics. In this study, the NIR fluorescence emission spectra for PAiRFP1 were recorded upon repeated excitation and the fluorescence intensity of PAiRFP1 tends to increase as the irradiation time was prolonged. We also predicted that mutations Q168L, V244F, and A480V in Agp2 will enhance the molecular stability and flexibility. During molecular dynamics (MD) simulations, the average root mean square deviations of Agp2, PAiRFP1, and PAiRFP2 were found to be 0.40, 0.49, and 0.48 nm, respectively. The structure of PAiRFP1 and PAiRFP2 were more deviated than Agp2 from its native conformation and the hydrophobic regions that were buried in PAiRFP1 and PAiRFP2 core exposed to solvent molecules. The eigenvalues and the trace of covariance matrix were found to be high for PAiRFP1 (597.90 nm<sup>2</sup>) and PAiRFP2 (726.74 nm<sup>2</sup>) when compared with Agp2 (535.79 nm<sup>2</sup>). It was also found that PAiRFP1 has more sharp Gibbs free energy global minima than Agp2 and PAiRFP2. This comparative analysis will help to gain deeper understanding on the structural changes during the evolution of photoactivatable NIR FPs. Further work can be carried out by combining PCR-based directed mutagenesis and spectroscopic methods to provide strategies for the rational designing of these PAiRFPs.https://www.mdpi.com/2218-273X/10/9/1286Agp2PAiRFP1PAiRFP2protein folding and stabilitymolecular dynamics simulation |
| spellingShingle | Faez Iqbal Khan Fakhrul Hassan Razique Anwer Feng Juan Dakun Lai Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2 Biomolecules Agp2 PAiRFP1 PAiRFP2 protein folding and stability molecular dynamics simulation |
| title | Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2 |
| title_full | Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2 |
| title_fullStr | Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2 |
| title_full_unstemmed | Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2 |
| title_short | Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2 |
| title_sort | comparative analysis of bacteriophytochrome agp2 and its engineered photoactivatable nir fluorescent proteins pairfp1 and pairfp2 |
| topic | Agp2 PAiRFP1 PAiRFP2 protein folding and stability molecular dynamics simulation |
| url | https://www.mdpi.com/2218-273X/10/9/1286 |
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