Proteopedia - User contributions [en]

User:David Bogle/Sandbox 2

2025-04-22T20:38:03Z

David Bogle:

== Scenes == <StructureSection>

<scene name='10/1076054/Iccg_disulfide_bridge/4'>Disulfide Bridge white</scene>

<scene name='10/1076054/Iccg_disulfide_bridge/6'>Disulfide Bridge blue</scene>

<scene name='10/1076054/Thermostability_wild_type/5'>D238 and S283</scene>

== Text ==

Main Article<ref name="main">PMID:32269349</ref>

PET Recycling<ref name="recycle">Babaei, M., Jalilian, M., & Shahbaz, K. (2024). Chemical recycling of Polyethylene terephthalate: A mini-review. Journal of Environmental Chemical Engineering, 12(3), 112507. [https://doi.org/10.1016/j.jece.2024.112507. DOI: 10.1016/j.jece.2024.112507]</ref>

LCC identification <ref name="LCC">PMID:22194294</ref>

Engineering PET Hydrolases <ref name="Hydrolases">Jayasekara, S. K., Joni, H. D., Jayantha, B., Dissanayake, L., Mandrell, C., Sinharage, M. M. S., Molitor, R., Jayasekara, T., Sivakumar, P., & Jayakody, L. N. (2023). Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET. Computational and structural biotechnology journal, 21, 3513–3521. [https://doi.org/10.1016/j.csbj.2023.06.004 DOI: 10.1016/j.csbj.2023.06.004]</ref>

PET Mechanism <ref name="mechanism">Han, X., Liu, W., Huang, J. W., et al. (2017). Structural insight into catalytic mechanism of PET hydrolase. Nature Communications, 8, 2106. https://doi.org/10.1038/s41467-017-02255-z.Heredia-Guerrero, J. A., Heredia, A., García-Segura, R., & Benítez, J. J. (2009). Synthesis and characterization of a plant cutin mimetic polymer. Polymer, 50(24), 5633–5637. [https://doi.org/10.1016/j.polymer.2009.10.018 DOI: 10.1016/j.polymer.2009.10.018]</ref>

Biodegradation of PET <ref name="biodegradation">Hiraga, K., Taniguchi, I., Yoshida, S., Kimura, Y., & Oda, K. (2019). Biodegradation of waste PET: A sustainable solution for dealing with plastic pollution. EMBO Reports, 20(11), e49365. https://doi.org/10.15252/embr.201949365. [Published correction appears in EMBO Reports, 21(2), e49826. [https://doi.org/10.15252/embr.201949826. DOI: 10.15252/embr.201949826]</ref>

Mechanism of PET Degradation <ref name="breakdown">PMID:29374183</ref>

PET Degradation by TF <ref name="TF">PMID:24728714</ref>

Dr.K <ref name="substrate">A binding model of the substrate 2-HE(MHET)3 in wild-type LLC (4eb0.pdb) was constructed and refined to mimic the 3D structure illustrated in Figure 2 of reference “1”. The software Maestro (Schrödinger, Inc; version 14.2.118) was used to construct the initial binding structure, followed by energy minimization in the context of the rigid protein that had previously been processed to add/refine all hydrogen atoms. The ligand model was then used without further modification to identify and illustrate the cited active-site residues.</ref>

<ref group="xtra">PMID:15068885</ref>

== References ==

<references />

===Additional Literature and Resources===
<references group="xtra"/>

====PDB Files====
PDB Files

Wild Type LCC: [https://www.rcsb.org/structure/4EB0 4EB0]
Mutant ICCG: [https://www.rcsb.org/structure/6THT 6THT]

User:David Bogle/Sandbox 2

2025-04-22T20:36:43Z

David Bogle:

== Scenes == <StructureSection>

<scene name='10/1076054/Iccg_disulfide_bridge/4'>Disulfide Bridge white</scene>

<scene name='10/1076054/Iccg_disulfide_bridge/6'>Disulfide Bridge blue</scene>

<scene name='10/1076054/Thermostability_wild_type/5'>D238 and S283</scene>

== Text ==

Main Article<ref name="main">PMID:32269349</ref>

PET Recycling<ref name="recycle">Babaei, M., Jalilian, M., & Shahbaz, K. (2024). Chemical recycling of Polyethylene terephthalate: A mini-review. Journal of Environmental Chemical Engineering, 12(3), 112507. [https://doi.org/10.1016/j.jece.2024.112507. DOI: 10.1016/j.jece.2024.112507]</ref>

LCC identification <ref name="LCC">PMID:22194294</ref>

Engineering PET Hydrolases <ref name="Hydrolases">Jayasekara, S. K., Joni, H. D., Jayantha, B., Dissanayake, L., Mandrell, C., Sinharage, M. M. S., Molitor, R., Jayasekara, T., Sivakumar, P., & Jayakody, L. N. (2023). Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET. Computational and structural biotechnology journal, 21, 3513–3521. [https://doi.org/10.1016/j.csbj.2023.06.004 DOI: 10.1016/j.csbj.2023.06.004]</ref>

PET Mechanism <ref name="mechanism">Han, X., Liu, W., Huang, J. W., et al. (2017). Structural insight into catalytic mechanism of PET hydrolase. Nature Communications, 8, 2106. https://doi.org/10.1038/s41467-017-02255-z.Heredia-Guerrero, J. A., Heredia, A., García-Segura, R., & Benítez, J. J. (2009). Synthesis and characterization of a plant cutin mimetic polymer. Polymer, 50(24), 5633–5637. [https://doi.org/10.1016/j.polymer.2009.10.018 DOI: 10.1016/j.polymer.2009.10.018]</ref>

Biodegradation of PET <ref name="biodegradation">Hiraga, K., Taniguchi, I., Yoshida, S., Kimura, Y., & Oda, K. (2019). Biodegradation of waste PET: A sustainable solution for dealing with plastic pollution. EMBO Reports, 20(11), e49365. https://doi.org/10.15252/embr.201949365. [Published correction appears in EMBO Reports, 21(2), e49826. [https://doi.org/10.15252/embr.201949826. DOI: 10.15252/embr.201949826]</ref>

Mechanism of PET Degradation <ref name="breakdown">PMID:29374183</ref>

PET Degradation by TF <ref name="TF">PMID:24728714</ref>

Dr.K <ref name="substrate">A binding model of the substrate 2-HE(MHET)3 in wild-type LLC (4eb0.pdb) was constructed and refined to mimic the 3D structure illustrated in Figure 2 of reference “1”. The software Maestro (Schrödinger, Inc; version 14.2.118) was used to construct the initial binding structure, followed by energy minimization in the context of the rigid protein that had previously been processed to add/refine all hydrogen atoms. The ligand model was then used without further modification to identify and illustrate the cited active-site residues.</ref>

<ref group="xtra">PMID:15068885</ref>

== References ==

<references />

PDB Files

Wild Type LCC: [https://www.rcsb.org/structure/4EB0 4EB0]
Mutant ICCG: [https://www.rcsb.org/structure/6THT 6THT]

Additional Literature and Resources
<references group="xtra"/>

User:David Bogle/Sandbox 2

2025-04-22T20:29:36Z

David Bogle:

== Scenes == <StructureSection>

<scene name='10/1076054/Iccg_disulfide_bridge/4'>Disulfide Bridge white</scene>

<scene name='10/1076054/Iccg_disulfide_bridge/6'>Disulfide Bridge blue</scene>

<scene name='10/1076054/Thermostability_wild_type/5'>D238 and S283</scene>

== Text ==

Main Article<ref name="main">PMID:32269349</ref>

PET Recycling<ref name="recycle">Babaei, M., Jalilian, M., & Shahbaz, K. (2024). Chemical recycling of Polyethylene terephthalate: A mini-review. Journal of Environmental Chemical Engineering, 12(3), 112507. [https://doi.org/10.1016/j.jece.2024.112507. DOI: 10.1016/j.jece.2024.112507]</ref>

LCC identification <ref name="LCC">PMID:22194294</ref>

Engineering PET Hydrolases <ref name="Hydrolases">Jayasekara, S. K., Joni, H. D., Jayantha, B., Dissanayake, L., Mandrell, C., Sinharage, M. M. S., Molitor, R., Jayasekara, T., Sivakumar, P., & Jayakody, L. N. (2023). Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET. Computational and structural biotechnology journal, 21, 3513–3521. [https://doi.org/10.1016/j.csbj.2023.06.004 DOI: 10.1016/j.csbj.2023.06.004]</ref>

PET Mechanism <ref name="mechanism">Han, X., Liu, W., Huang, J. W., et al. (2017). Structural insight into catalytic mechanism of PET hydrolase. Nature Communications, 8, 2106. https://doi.org/10.1038/s41467-017-02255-z.Heredia-Guerrero, J. A., Heredia, A., García-Segura, R., & Benítez, J. J. (2009). Synthesis and characterization of a plant cutin mimetic polymer. Polymer, 50(24), 5633–5637. [https://doi.org/10.1016/j.polymer.2009.10.018 DOI: 10.1016/j.polymer.2009.10.018]</ref>

Biodegradation of PET <ref name="biodegradation">Hiraga, K., Taniguchi, I., Yoshida, S., Kimura, Y., & Oda, K. (2019). Biodegradation of waste PET: A sustainable solution for dealing with plastic pollution. EMBO Reports, 20(11), e49365. https://doi.org/10.15252/embr.201949365. [Published correction appears in EMBO Reports, 21(2), e49826. [https://doi.org/10.15252/embr.201949826. DOI: 10.15252/embr.201949826]</ref>

Mechanism of PET Degradation <ref name="breakdown">PMID:29374183</ref>

PET Degradation by TF <ref name="TF">PMID:24728714</ref>

Dr.K <ref name="substrate">A binding model of the substrate 2-HE(MHET)3 in wild-type LLC (4eb0.pdb) was constructed and refined to mimic the 3D structure illustrated in Figure 2 of reference “1”. The software Maestro (Schrödinger, Inc; version 14.2.118) was used to construct the initial binding structure, followed by energy minimization in the context of the rigid protein that had previously been processed to add/refine all hydrogen atoms. The ligand model was then used without further modification to identify and illustrate the cited active-site residues.</ref>

<ref group="xtra">PMID:15068885</ref>

== References ==

<references />

Additional Literature and Resources
<references group="xtra"/>

User:David Bogle/Sandbox 2

2025-04-22T20:27:01Z

David Bogle:

== Scenes == <StructureSection>

<scene name='10/1076054/Iccg_disulfide_bridge/4'>Disulfide Bridge white</scene>

<scene name='10/1076054/Iccg_disulfide_bridge/5'>Disulfide Bridge blue</scene>

<scene name='10/1076054/Thermostability_wild_type/4'>D238 and S283</scene>

== Text ==

Main Article<ref name="main">PMID:32269349</ref>

PET Recycling<ref name="recycle">Babaei, M., Jalilian, M., & Shahbaz, K. (2024). Chemical recycling of Polyethylene terephthalate: A mini-review. Journal of Environmental Chemical Engineering, 12(3), 112507. [https://doi.org/10.1016/j.jece.2024.112507. DOI: 10.1016/j.jece.2024.112507]</ref>

LCC identification <ref name="LCC">PMID:22194294</ref>

Engineering PET Hydrolases <ref name="Hydrolases">Jayasekara, S. K., Joni, H. D., Jayantha, B., Dissanayake, L., Mandrell, C., Sinharage, M. M. S., Molitor, R., Jayasekara, T., Sivakumar, P., & Jayakody, L. N. (2023). Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET. Computational and structural biotechnology journal, 21, 3513–3521. [https://doi.org/10.1016/j.csbj.2023.06.004 DOI: 10.1016/j.csbj.2023.06.004]</ref>

PET Mechanism <ref name="mechanism">Han, X., Liu, W., Huang, J. W., et al. (2017). Structural insight into catalytic mechanism of PET hydrolase. Nature Communications, 8, 2106. https://doi.org/10.1038/s41467-017-02255-z.Heredia-Guerrero, J. A., Heredia, A., García-Segura, R., & Benítez, J. J. (2009). Synthesis and characterization of a plant cutin mimetic polymer. Polymer, 50(24), 5633–5637. [https://doi.org/10.1016/j.polymer.2009.10.018 DOI: 10.1016/j.polymer.2009.10.018]</ref>

Biodegradation of PET <ref name="biodegradation">Hiraga, K., Taniguchi, I., Yoshida, S., Kimura, Y., & Oda, K. (2019). Biodegradation of waste PET: A sustainable solution for dealing with plastic pollution. EMBO Reports, 20(11), e49365. https://doi.org/10.15252/embr.201949365. [Published correction appears in EMBO Reports, 21(2), e49826. [https://doi.org/10.15252/embr.201949826. DOI: 10.15252/embr.201949826]</ref>

Mechanism of PET Degradation <ref name="breakdown">PMID:29374183</ref>

PET Degradation by TF <ref name="TF">PMID:24728714</ref>

Dr.K <ref name="substrate">A binding model of the substrate 2-HE(MHET)3 in wild-type LLC (4eb0.pdb) was constructed and refined to mimic the 3D structure illustrated in Figure 2 of reference “1”. The software Maestro (Schrödinger, Inc; version 14.2.118) was used to construct the initial binding structure, followed by energy minimization in the context of the rigid protein that had previously been processed to add/refine all hydrogen atoms. The ligand model was then used without further modification to identify and illustrate the cited active-site residues.</ref>

<ref group="xtra">PMID:15068885</ref>

== References ==

<references />

Additional Literature and Resources
<references group="xtra"/>

User:David Bogle/Sandbox 2

2025-04-22T20:18:21Z

David Bogle:

== Scenes == <StructureSection>

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>

== Text ==

Main Article<ref name="main">PMID:32269349</ref>

PET Recycling<ref name="recycle">Babaei, M., Jalilian, M., & Shahbaz, K. (2024). Chemical recycling of Polyethylene terephthalate: A mini-review. Journal of Environmental Chemical Engineering, 12(3), 112507. [https://doi.org/10.1016/j.jece.2024.112507. DOI: 10.1016/j.jece.2024.112507]</ref>

LCC identification <ref name="LCC">PMID:22194294</ref>

Engineering PET Hydrolases <ref name="Hydrolases">Jayasekara, S. K., Joni, H. D., Jayantha, B., Dissanayake, L., Mandrell, C., Sinharage, M. M. S., Molitor, R., Jayasekara, T., Sivakumar, P., & Jayakody, L. N. (2023). Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET. Computational and structural biotechnology journal, 21, 3513–3521. [https://doi.org/10.1016/j.csbj.2023.06.004 DOI: 10.1016/j.csbj.2023.06.004]</ref>

PET Mechanism <ref name="mechanism">Han, X., Liu, W., Huang, J. W., et al. (2017). Structural insight into catalytic mechanism of PET hydrolase. Nature Communications, 8, 2106. https://doi.org/10.1038/s41467-017-02255-z.Heredia-Guerrero, J. A., Heredia, A., García-Segura, R., & Benítez, J. J. (2009). Synthesis and characterization of a plant cutin mimetic polymer. Polymer, 50(24), 5633–5637. [https://doi.org/10.1016/j.polymer.2009.10.018 DOI: 10.1016/j.polymer.2009.10.018]</ref>

Biodegradation of PET <ref name="biodegradation">Hiraga, K., Taniguchi, I., Yoshida, S., Kimura, Y., & Oda, K. (2019). Biodegradation of waste PET: A sustainable solution for dealing with plastic pollution. EMBO Reports, 20(11), e49365. https://doi.org/10.15252/embr.201949365. [Published correction appears in EMBO Reports, 21(2), e49826. [https://doi.org/10.15252/embr.201949826. DOI: 10.15252/embr.201949826]</ref>

Mechanism of PET Degradation <ref name="breakdown">PMID:29374183</ref>

PET Degradation by TF <ref name="TF">PMID:24728714</ref>

Dr.K <ref name="substrate">A binding model of the substrate 2-HE(MHET)3 in wild-type LLC (4eb0.pdb) was constructed and refined to mimic the 3D structure illustrated in Figure 2 of reference “1”. The software Maestro (Schrödinger, Inc; version 14.2.118) was used to construct the initial binding structure, followed by energy minimization in the context of the rigid protein that had previously been processed to add/refine all hydrogen atoms. The ligand model was then used without further modification to identify and illustrate the cited active-site residues.</ref>

<ref group="xtra">PMID:15068885</ref>

== References ==

<references />

Additional Literature and Resources
<references group="xtra"/>

User:David Bogle/Sandbox 2

2025-04-22T18:45:06Z

David Bogle:

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>

== Text ==

Main Article<ref name="main">PMID:32269349</ref>

PET Recycling<ref name="recycle">Babaei, M., Jalilian, M., & Shahbaz, K. (2024). Chemical recycling of Polyethylene terephthalate: A mini-review. Journal of Environmental Chemical Engineering, 12(3), 112507. [https://doi.org/10.1016/j.jece.2024.112507. DOI: 10.1016/j.jece.2024.112507]</ref>

LCC identification <ref name="LCC">PMID:22194294</ref>

Engineering PET Hydrolases <ref name="Hydrolases">Jayasekara, S. K., Joni, H. D., Jayantha, B., Dissanayake, L., Mandrell, C., Sinharage, M. M. S., Molitor, R., Jayasekara, T., Sivakumar, P., & Jayakody, L. N. (2023). Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET. Computational and structural biotechnology journal, 21, 3513–3521. [https://doi.org/10.1016/j.csbj.2023.06.004 DOI: 10.1016/j.csbj.2023.06.004]</ref>

PET Mechanism <ref name="mechanism">Han, X., Liu, W., Huang, J. W., et al. (2017). Structural insight into catalytic mechanism of PET hydrolase. Nature Communications, 8, 2106. https://doi.org/10.1038/s41467-017-02255-z.Heredia-Guerrero, J. A., Heredia, A., García-Segura, R., & Benítez, J. J. (2009). Synthesis and characterization of a plant cutin mimetic polymer. Polymer, 50(24), 5633–5637. [https://doi.org/10.1016/j.polymer.2009.10.018 DOI: 10.1016/j.polymer.2009.10.018]</ref>

Biodegradation of PET <ref name="biodegradation">Hiraga, K., Taniguchi, I., Yoshida, S., Kimura, Y., & Oda, K. (2019). Biodegradation of waste PET: A sustainable solution for dealing with plastic pollution. EMBO Reports, 20(11), e49365. https://doi.org/10.15252/embr.201949365. [Published correction appears in EMBO Reports, 21(2), e49826. [https://doi.org/10.15252/embr.201949826. DOI: 10.15252/embr.201949826]</ref>

Mechanism of PET Degradation <ref name="breakdown">PMID:29374183</ref>

PET Degradation by TF <ref name="TF">PMID:24728714</ref>

Dr.K <ref name="substrate">A binding model of the substrate 2-HE(MHET)3 in wild-type LLC (4eb0.pdb) was constructed and refined to mimic the 3D structure illustrated in Figure 2 of reference “1”. The software Maestro (Schrödinger, Inc; version 14.2.118) was used to construct the initial binding structure, followed by energy minimization in the context of the rigid protein that had previously been processed to add/refine all hydrogen atoms. The ligand model was then used without further modification to identify and illustrate the cited active-site residues.</ref>

<ref group="xtra">PMID:15068885</ref>

== References ==

<references />

Additional Literature and Resources
<references group="xtra"/>

User:David Bogle/Sandbox 2

2025-04-22T18:44:53Z

David Bogle:

User:David Bogle/Sandbox 2

2025-04-22T18:43:00Z

David Bogle:

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>

== Text ==

Main Article<ref name="main">PMID:32269349</ref>

PET Recycling<ref name="recycle">Babaei, M., Jalilian, M., & Shahbaz, K. (2024). Chemical recycling of Polyethylene terephthalate: A mini-review. Journal of Environmental Chemical Engineering, 12(3), 112507. [https://doi.org/10.1016/j.jece.2024.112507. DOI: 10.1016/j.jece.2024.112507]</ref>

LCC identification <ref name="LCC">PMID:22194294</ref>

Engineering PET Hydrolases <ref name="Hydrolases">Jayasekara, S. K., Joni, H. D., Jayantha, B., Dissanayake, L., Mandrell, C., Sinharage, M. M. S., Molitor, R., Jayasekara, T., Sivakumar, P., & Jayakody, L. N. (2023). Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET. Computational and structural biotechnology journal, 21, 3513–3521. [https://doi.org/10.1016/j.csbj.2023.06.004 DOI: 10.1016/j.csbj.2023.06.004]</ref>

PET Mechanism <ref name="mechanism">Han, X., Liu, W., Huang, J. W., et al. (2017). Structural insight into catalytic mechanism of PET hydrolase. Nature Communications, 8, 2106. https://doi.org/10.1038/s41467-017-02255-z.Heredia-Guerrero, J. A., Heredia, A., García-Segura, R., & Benítez, J. J. (2009). Synthesis and characterization of a plant cutin mimetic polymer. Polymer, 50(24), 5633–5637. [https://doi.org/10.1016/j.polymer.2009.10.018 DOI: 10.1016/j.polymer.2009.10.018]</ref>

Biodegradation of PET <ref name="biodegradation">Hiraga, K., Taniguchi, I., Yoshida, S., Kimura, Y., & Oda, K. (2019). Biodegradation of waste PET: A sustainable solution for dealing with plastic pollution. EMBO Reports, 20(11), e49365. https://doi.org/10.15252/embr.201949365. [Published correction appears in EMBO Reports, 21(2), e49826. [https://doi.org/10.15252/embr.201949826. DOI: 10.15252/embr.201949826]</ref>

Mechanism of PET Degradation <ref name="breakdown">PMID:29374183</ref>

PET Degradation by TF <ref name="TF">PMID:24728714</ref>

Dr.K <ref name="substrate">A binding model of the substrate 2-HE(MHET)3 in wild-type LLC (4eb0.pdb) was constructed and refined to mimic the 3D structure illustrated in Figure 2 of reference “1”. The software Maestro (Schrödinger, Inc; version 14.2.118) was used to construct the initial binding structure, followed by energy minimization in the context of the rigid protein that had previously been processed to add/refine all hydrogen atoms. The ligand model was then used without further modification to identify and illustrate the cited active-site residues.</ref>

<ref group="xtra">PMID:15068885</ref>

== References ==

<references />

=Additional Literature and Resources=
<references group="xtra"/>

User:David Bogle/Sandbox 2

2025-04-22T18:42:00Z

David Bogle:

User:David Bogle/Sandbox 2

2025-04-22T18:38:09Z

David Bogle:

User:David Bogle/Sandbox 2

2025-04-22T18:25:10Z

David Bogle:

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>

== Text ==

Main Article<ref>PMID:32269349</ref>

PET Recycling<ref>Babaei, M., Jalilian, M., & Shahbaz, K. (2024). Chemical recycling of Polyethylene terephthalate: A mini-review. Journal of Environmental Chemical Engineering, 12(3), 112507. [https://doi.org/10.1016/j.jece.2024.112507. DOI: 10.1016/j.jece.2024.112507]</ref>

LCC identification <ref>PMID:22194294</ref>

Engineering PET Hydrolases <ref>Jayasekara, S. K., Joni, H. D., Jayantha, B., Dissanayake, L., Mandrell, C., Sinharage, M. M. S., Molitor, R., Jayasekara, T., Sivakumar, P., & Jayakody, L. N. (2023). Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET. Computational and structural biotechnology journal, 21, 3513–3521. [https://doi.org/10.1016/j.csbj.2023.06.004 DOI: 10.1016/j.csbj.2023.06.004]</ref>

PET Mechanism <ref>Han, X., Liu, W., Huang, J. W., et al. (2017). Structural insight into catalytic mechanism of PET hydrolase. Nature Communications, 8, 2106. https://doi.org/10.1038/s41467-017-02255-z.Heredia-Guerrero, J. A., Heredia, A., García-Segura, R., & Benítez, J. J. (2009). Synthesis and characterization of a plant cutin mimetic polymer. Polymer, 50(24), 5633–5637. [https://doi.org/10.1016/j.polymer.2009.10.018 DOI: 10.1016/j.polymer.2009.10.018]</ref>

Biodegradation of PET <ref>Hiraga, K., Taniguchi, I., Yoshida, S., Kimura, Y., & Oda, K. (2019). Biodegradation of waste PET: A sustainable solution for dealing with plastic pollution. EMBO Reports, 20(11), e49365. https://doi.org/10.15252/embr.201949365. [Published correction appears in EMBO Reports, 21(2), e49826. [https://doi.org/10.15252/embr.201949826. DOI: 10.15252/embr.201949826]</ref>

Mechanism of PET Degradation <ref>PMID:29374183</ref>

PET Degradation by TF <ref>PMID:24728714</ref>

Dr.K <ref>A binding model of the substrate 2-HE(MHET)3 in wild-type LLC (4eb0.pdb) was constructed and refined to mimic the 3D structure illustrated in Figure 2 of reference “1”. The software Maestro (Schrödinger, Inc; version 14.2.118) was used to construct the initial binding structure, followed by energy minimization in the context of the rigid protein that had previously been processed to add/refine all hydrogen atoms. The ligand model was then used without further modification to identify and illustrate the cited active-site residues.</ref>

== References ==

<references />

User:David Bogle/Sandbox 2

2025-04-15T20:03:05Z

David Bogle:

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>

== Text ==

Main Article<ref>PMID:32269349</ref>

PET Recycling<ref>Babaei, M., Jalilian, M., & Shahbaz, K. (2024). Chemical recycling of Polyethylene terephthalate: A mini-review. Journal of Environmental Chemical Engineering, 12(3), 112507. [https://doi.org/10.1016/j.jece.2024.112507. DOI: 10.1016/j.jece.2024.112507]</ref>

LCC identification <ref>PMID:22194294</ref>

Engineering PET Hydrolases <ref>Jayasekara, S. K., Joni, H. D., Jayantha, B., Dissanayake, L., Mandrell, C., Sinharage, M. M. S., Molitor, R., Jayasekara, T., Sivakumar, P., & Jayakody, L. N. (2023). Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET. Computational and structural biotechnology journal, 21, 3513–3521. [https://doi.org/10.1016/j.csbj.2023.06.004 DOI: 10.1016/j.csbj.2023.06.004]</ref>

PET Mechanism <ref>Han, X., Liu, W., Huang, J. W., et al. (2017). Structural insight into catalytic mechanism of PET hydrolase. Nature Communications, 8, 2106. https://doi.org/10.1038/s41467-017-02255-z.Heredia-Guerrero, J. A., Heredia, A., García-Segura, R., & Benítez, J. J. (2009). Synthesis and characterization of a plant cutin mimetic polymer. Polymer, 50(24), 5633–5637. [https://doi.org/10.1016/j.polymer.2009.10.018 DOI: 10.1016/j.polymer.2009.10.018]</ref>

Biodegradation of PET <ref>Hiraga, K., Taniguchi, I., Yoshida, S., Kimura, Y., & Oda, K. (2019). Biodegradation of waste PET: A sustainable solution for dealing with plastic pollution. EMBO Reports, 20(11), e49365. https://doi.org/10.15252/embr.201949365. [Published correction appears in EMBO Reports, 21(2), e49826. [https://doi.org/10.15252/embr.201949826. DOI: 10.15252/embr.201949826]</ref>

Mechanism of PET Degradation <ref>PMID:29374183</ref>

PET Degradation by TF <ref>PMID:24728714</ref>

== References ==

<references />

User:David Bogle/Sandbox 2

2025-04-15T20:02:15Z

David Bogle:

User:David Bogle/Sandbox 2

2025-04-15T20:01:42Z

David Bogle:

User:David Bogle/Sandbox 2

2025-04-15T20:00:49Z

David Bogle:

User:David Bogle/Sandbox 2

2025-04-15T19:54:08Z

David Bogle:

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>

== Text ==

Main Article<ref>PMID:32269349</ref>

PET Recycling<ref>DOI: 10.1016/j.jece.2024.112507</ref>

LCC identification <ref>PMID:22194294</ref>

Engineering PET Hydrolases <ref>DOI: 10.1016/j.csbj.2023.06.004</ref>

PET Mechanism <ref>DOI: 10.1016/j.polymer.2009.10.018</ref>

Biodegradation of PET <ref>DOI: 10.15252/embr.201949826</ref>

Mechanism of PET Degradation <ref>PMID:29374183</ref>

PET Degradation by TF <ref>PMID:24728714</ref>

== References ==

<references />

User:David Bogle/Sandbox 2

2025-04-15T19:53:45Z

David Bogle:

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>

== Text ==

Main Article<ref>PMID:32269349</ref>

PET Recycling<ref>DOI: 10.1016/j.jece.2024.112507</ref>

LCC identification <ref>PMID:22194294</ref>

Engineering PET Hydrolases <ref>DOI: 10.1016/j.csbj.2023.06.004</ref>

PET Mechanism <ref>DOI: 10.1016/j.polymer.2009.10.018</ref>

Biodegradation of PET <ref>DOI: 10.15252/embr.201949826</ref>

Mechanism of PET Degradation <ref>PMID:29374183</ref>

PET Degradation by TF <ref>DOI: 10.1007/s00253-014-5672-0</ref>

== References ==

<references />

User:David Bogle/Sandbox 2

2025-04-15T19:52:56Z

David Bogle:

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>

== Text ==

Main Article<ref>PMID:32269349</ref>

PET Recycling<ref>DOI: 10.1016/j.jece.2024.112507</ref>

LCC identification <ref>PMID:22194294</ref>

Engineering PET Hydrolases <ref>DOI: 10.1016/j.csbj.2023.06.004</ref>

PET Mechanism <ref>DOI: 10.1016/j.polymer.2009.10.018</ref>

Biodegradation of PET <ref>DOI: 10.15252/embr.201949826</ref>

Mechanism of PET Degradation <ref>DOI: 10.1038/s41467-018-02881-1</ref>

PET Degradation by TF <ref>DOI: 10.1007/s00253-014-5672-0</ref>

== References ==

<references />

User:David Bogle/Sandbox 2

2025-04-15T19:44:39Z

David Bogle:

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>

== Text ==

Main Article<ref>PMID:32269349</ref>

PET Recycling<ref>DOI: 10.1016/j.jece.2024.112507</ref>

LCC identification <ref>DOI: 10.1128/AEM.06725-11</ref>

Engineering PET Hydrolases <ref>DOI: 10.1016/j.csbj.2023.06.004</ref>

PET Mechanism <ref>DOI: 10.1016/j.polymer.2009.10.018</ref>

Biodegradation of PET <ref>DOI: 10.15252/embr.201949826</ref>

Mechanism of PET Degradation <ref>DOI: 10.1038/s41467-018-02881-1</ref>

PET Degradation by TF <ref>DOI: 10.1007/s00253-014-5672-0</ref>

== References ==

<references />

User:David Bogle/Sandbox 2

2025-04-15T19:42:09Z

David Bogle:

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>

== Text ==

Main Article<ref>DOI: 10.1038/s41586-020-2149-4</ref>

PET Recycling<ref>DOI: 10.1016/j.jece.2024.112507</ref>

LCC identification <ref>DOI: 10.1128/AEM.06725-11</ref>

Engineering PET Hydrolases <ref>DOI: 10.1016/j.csbj.2023.06.004</ref>

PET Mechanism <ref>DOI: 10.1016/j.polymer.2009.10.018</ref>

Biodegradation of PET <ref>DOI: 10.15252/embr.201949826</ref>

Mechanism of PET Degradation <ref>DOI: 10.1038/s41467-018-02881-1</ref>

PET Degradation by TF <ref>DOI: 10.1007/s00253-014-5672-0</ref>

== References ==

<references />

User:David Bogle/Sandbox 2

2025-04-15T19:29:55Z

David Bogle:

User:David Bogle/Sandbox 2

2025-04-15T19:21:13Z

David Bogle:

User:David Bogle/Sandbox 2

2025-04-15T19:18:50Z

David Bogle:

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>

== Text ==
<ref name="PET">{{Wikipedia|Polyethylene_terephthalate}}</ref>

One of the most commonly used plastics is a polymer called Polyethylene Terephthalate, also known as [https://en.wikipedia.org/wiki/Polyethylene_terephthalate PET]<ref name="PET">{{Wikipedia|Polyethylene_terephthalate}}</ref>. PET is commonly used to make plastic bottles or food containers due to its thermal stability, transparency, and impermeability to liquids and gases. Unfortunately, these properties that make it desirable also make it non-biodegradable, meaning that we must recycle PET to avoid polluting the environment with it. Traditional methods, such as melting and reforming the plastic, destroy the mechanical properties of PET, eliminating the ability to recycle it and necessitating a new strategy for recycling PET.

== References ==

<references />

User:David Bogle/Sandbox 2

2025-04-15T19:15:58Z

David Bogle:

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>

== Text ==
<ref name="PET">{{Wikipedia|Polyethylene_terephthalate}}</ref>

{{Wikipedia|Polyethylene_terephthalate}}

== References ==

<references />

User:David Bogle/Sandbox 2

2025-04-15T19:15:04Z

David Bogle:

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>

== Text ==
<ref name="PET">https://en.wikipedia.org/wiki/Polyethylene_terephthalate</ref>

{{Wikipedia|Polyethylene_terephthalate}}

== References ==

<references />

User:David Bogle/Sandbox 2

2025-04-15T19:06:02Z

David Bogle:

User:David Bogle/Sandbox 2

2025-04-14T03:49:28Z

David Bogle:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''David Bogle/Sandbox 2'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/3'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/3'>D238 and S283</scene>
== Images ==

== Text ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:David Bogle/Sandbox 2

2025-04-08T20:09:39Z

David Bogle:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''David Bogle/Sandbox 2'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Scenes ==

<scene name='10/1076054/Iccg_disulfide_bridge/2'>Disulfide Bridge</scene>
<scene name='10/1076054/Thermostability_wild_type/2'>D238 and S283</scene>
== Images ==

== Text ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

File:4eb0.pdb

2025-04-08T18:26:28Z

David Bogle:

File:ICCG sub.pdb

2025-04-01T19:12:52Z

David Bogle:

File:ICCG sep.pdb

2025-04-01T18:41:35Z

David Bogle:

File:ICCG substrate.pdb

2025-04-01T18:19:20Z

David Bogle:

User:David Bogle/Sandbox 2

2025-03-25T19:45:39Z

David Bogle:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''David Bogle/Sandbox 2'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Scenes ==
<scene name='10/1076054/Iccg_disulfide_bridge/1'>Disulfide Bridge</scene>

== Images ==

== Text ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:David Bogle/Sandbox 2

2025-03-25T19:44:35Z

David Bogle:

<scene name='10/1076054/Iccg_disulfide_bridge/1'>Disulfide Bridge</scene>==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''David Bogle/Sandbox 2'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:David Bogle

2025-03-25T19:38:01Z

David Bogle:

* Full Real Name: David Bogle

* Position: Student

* Institution (NO ABBREVIATIONS): Butler University

* City, State/Province, Country: Indianapolis, Indiana, United States

* Field of Expertise or Study: Biochemistry

*[[User:David Bogle/Sandbox 2]]

User:David Bogle/Sandbox1

2025-03-25T19:32:36Z

David Bogle:

<scene name='10/1076056/Iccg_disulfide_bridge/1'>Disulfide Bridge</scene>==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''David Bogle/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

File:ICCG.pdb

2025-03-25T19:23:12Z

David Bogle:

User:David Bogle/Sandbox1

2025-03-25T18:55:34Z

David Bogle: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''David Bogle/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

File:4EB0.pdb

2025-03-25T18:45:18Z

David Bogle:

User:David Bogle/Sandbox 2

2025-03-25T18:44:12Z

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''David Bogle/Sandbox 2'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User talk:David Bogle

2025-03-25T18:29:33Z

David Bogle: Replacing page with '*User:David Bogle/Sandbox 1'

*[[User:David Bogle/Sandbox 1]]