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Supplementary Data for "Molecular characterization of PhiKo endolysin of Thermus thermophilus HB27 bacteriophage phiKo and its cryptic lytic peptide RAP-29" by Szadkowska M, Kocot AM, Sowik D, Wyrzykowski D, Jankowska E, Kozlowski LP, Makowska J, Plotka M

Version 3.0

Kozlowski, Lukasz P., 2023, "Supplementary Data for "Molecular characterization of PhiKo endolysin of Thermus thermophilus HB27 bacteriophage phiKo and its cryptic lytic peptide RAP-29" by Szadkowska M, Kocot AM, Sowik D, Wyrzykowski D, Jankowska E, Kozlowski LP, Makowska J, Plotka M", https://doi.org/10.18150/8ZXKT8, RepOD, V3

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Description

Bioinformatics results related to the article "Molecular characterization of PhiKo endolysin of Thermus thermophilus HB27 bacteriophage phiKo and its cryptic lytic peptide RAP-29"

Sequence:

>AYJ74695.1 lysozyme [Thermus phage phiKo]

MNWIEFWRSKKPTWRHRPVDPAYIVLHHTAGPVDQAPQAIWDYHVKVRGWPHGGYHFLVYHDGTVVKMLPLSAQPICVGEYNHLAICIALVGNFVGGYPPEWNERAPGWKSLAWLVRELRKHDSGLRLRLVRHKDLRPTKCPGTVTWEEALVRGGVPQEQVETLKVAGVIA


>RAP-29 - phiKo derived potent antimicrobial peptide (105-133 aa)

RAPGWKSLAWLVRELRKHDSGLRLRLVRH


Models are done by:

1) Phyre2 (intensive mode)

./models/phyre2/final.casp.pdb


2) hhsearch+modeller (modelled on all templates) - quite poor model

./models/modeller_2483784.pdb


3) AlphaFold2 (colab over pdb70)

./models/PhiKo_f9d15.result.af2


4) deepfold (https://zhanggroup.org/DeepFold/) - quite poor model

./models/DeepFold/model1_DeepFold.pdb


5) omegafold

./models/omegafold/phiKo.pdb


6) RGN2 - unexpectly, quite poor model

./models/RGN2/phiKo_729bd0_prediction_RGN2.pdb


7) RoseTTAFold (run online)

./models/rosseta


8) ESMFold --> the best model

./models/ESMFold/ptm0.912_r3_default.ESMFold.pdb


Additionally, from one of the templates (Ts2631 PDB:6SU5) Zn i PO4 had been taken to complement the catalytic center


.

├── figure1_alignment.gb

├── models

│  ├── all_models_aligned.pdf

│  ├── all_models_aligned.tif

│  ├── all_models_aligned_Zn_added.py

│  ├── all_models_aligned_Zn_added.pyc

│  ├── DeepFold

│  ├── ESMFold

│  ├── Fig_S1a.png

│  ├── Fig_S1a_ray.png

│  ├── Fig_S1b.png

│  ├── Fig_S1b_ray.png

│  ├── Fig_S1.png

│  ├── Fig_S2a.png

│  ├── Fig_S2.png

│  ├── modeller_2483784.pdb

│  ├── model_with_black105-133.tif

│  ├── model_with_black140.tif

│  ├── omegafold

│  ├── phiKo_all.mp4

│  ├── phiKo_catalitic_center_closeup_T7_Ts2631.py

│  ├── phiKo_catalitic_center_plus_K140.py

│  ├── phiKo_catalitic_center_plus_K140.pyc

│  ├── phiKo_catalitic_center.py

│  ├── phiKo_catalytic_center_all.mp4

│  ├── phiKo_catalytic_center_all.pdf

│  ├── phiKo_catalytic_center_all.tif

│  ├── phiKo_catalytic_center_plus_K140.webm

│  ├── phiKo_catalytic_center.tif

│  ├── PhiKo_f9d15.result.af2

│  ├── phiKo_main_model_with_ligands_all_models.py

│  ├── phiKo_main_model_with_ligands_all_models.pyc

│  ├── phiKo_main_model_with_ligands_all_models_v2.py

│  ├── phiKo_main_model_with_ligands.pdb

│  ├── phiKo_main_model_with_ligands.py

│  ├── phiKo_main_model_with_ligands.tif

│  ├── phiKo.mp4

│  ├── phiKo_vs_T7.mp4

│  ├── phiKo_vs_T7.pdf

│  ├── phiKo_vs_T7.py

│  ├── phiKo_vs_T7.pyc

│  ├── phiKo_vs_T7.tif

│  ├── phiKo_vs_T7_Ts2631_ph2119.png

│  ├── phiKo_vs_T7_Ts2631_ph2119.py

│  ├── phiKo_vs_Ts2631.mp4

│  ├── phiKo_vs_Ts2631.py

│  ├── phiKo_vs_Ts2631.pyc

│  ├── phiKo_vs_Ts2631.tif

│  ├── phyre2

│  ├── RGN2

│  └── rosseta

├── phiKo.fas

├── RAP-29.fas

└── README.txt


Files *.py are UCSF Chimera viewer sessions storing superposition of

multiple models, homolog proteins, catalytic center zoom in, etc.

Subject
Chemistry; Computer and Information Science; Medicine, Health and Life Sciences
Keyword

biochemistry, bioinformatics, phage, endolysin, bacteriophage, Thermus thermophilus, enzyme, lysin, thermostable enzyme

Related Publication

Molecular characterization of PhiKo endolysin of Thermus thermophilus HB27 bacteriophage phiKo and its cryptic lytic peptide RAP-29 :

CC0 Creative Commons Zero 1.0 CC0 Creative Commons Zero 1.0

1 File
phiKo.zip
ZIP Archive - 162.4 MB - Nov 28, 2023 - 5 Downloads
MD5: fed3f1485ddc1b3162674806b5ed2ec4
License: CC0 Creative Commons Zero 1.0
Bioinformatics results related to the article "Molecular characterization of PhiKo endolysin of Thermus thermophilus HB27 bacteriophage phiKo and its cryptic lytic peptide RAP-29"
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