{"id":{"repo_id":"dundee","oai_identifier":"oai:discovery.dundee.ac.uk:studenttheses/39cd7ecc-d09b-4295-933e-725538437046"},"canonical_url":"https://search.dev.ndltd.org/etd/dundee/oai:discovery.dundee.ac.uk:studenttheses/39cd7ecc-d09b-4295-933e-725538437046","repository":{"repo_id":"dundee","name":"University of Dundee","base_url":"https://discovery.dundee.ac.uk/ws/oai"},"display":{"title":"The Development of Photo-crosslinkable Trapping Mutants as Tools to Investigate the Interactions of Protein Tyrosine Phosphatases","abstract":"Abnormalities in the coordinated activities of protein phosphatases (PPs) and
protein kinases (PKs) contribute to the development of many diseases.
Phosphatase of regenerating liver (PRL)-3 and Vaccinia H1-Related (VHR) are
two members of the protein tyrosine phosphatase (PTP) family shown to be
involved in cancer. PRL-3 is a member of the PRL phosphatases containing a
unique post-translationally modifiable prenylation CAAX motif at the carboxy
(C)- terminal end. There is an immense body of evidence to support a role for
PRL-3 in the development of various types of cancer and in progression to
metastasic disease. However, many questions are still pending, especially with
respect to the identity of physiological substrates, and interacting partners in
general, of PRL-3. VHR is a model for a group of atypical dual specificity
protein phosphatases (DUSPs) with a role in cell cycle progression. Only a few
of VHR’s physiological substrates have been reported to date and there are
very few studies addressing its regulation and physiological role(s).
Generally, in order to isolate and identify transient phosphatase-substrate
interactions, substrate-trapping mutants of PTPs are employed. Mutants which
can function as substrate traps have the ability to recognise and bind
substrates, yet they lack functionality of the key catalytic residues and cannot
efficiently process the hydrolysis of the substrate. However, it is acknowledged
that the efficiency of such standard substrate-trapping mutants of PTPs is low.
In this work, the expanded genetic code approach was applied to develop more
efficient substrate trapping variants of the PTPs by incorporating the photocross-linkable amino acid para-benzoylphenylalanine (pBPA). The concept was optimised for PRL-3 and VHR, and for both proteins, pBPA-containing variantswere expressed at excellent yields and were highly purified.
By utilizing the photo-cross-linkable F68pBPA variant of VHR, dimerisation of
VHR was detected in an in vitro ultraviolet (UV) exposure-mediated crosslinking
assay. VHR dimerisation was further demonstrated to be a potential
novel regulatory mechanism for VHR, having a negative effect on the catalytic
activity of the protein. A specific region in VHR known as the variable insert
segment was pinpointed as a region in the protein, which is either at the dimer
interface or heavily contributing to dimeric association. Furthermore, the
intrinsic ability of VHR to self-associate was also demonstrated by
complementary methods.
For PRL-3 it was demonstrated that its D72pBPA variant could recognise and
bind to lipids, with a stronger signal detected in the UV-exposed sample, and
without altering the lipid binding profile with respect to the native protein. Lastly, the potential of exploiting photo-cross-linkable variants of the PTPs was also demonstrated by incubating PRL-3 variants, with or without selectively
introduced pBPA, with mammalian cell lysates, followed by UV exposure.
Western blot analysis detected new bands corresponding to covalently crosslinked PRL-3-protein complexes. Future work in our laboratory will follow up on these newly identified interactions.","abstract_html":"Abnormalities in the coordinated activities of protein phosphatases (PPs) and<br/>protein kinases (PKs) contribute to the development of many diseases.<br/>Phosphatase of regenerating liver (PRL)-3 and Vaccinia H1-Related (VHR) are<br/>two members of the protein tyrosine phosphatase (PTP) family shown to be<br/>involved in cancer. PRL-3 is a member of the PRL phosphatases containing a<br/>unique post-translationally modifiable prenylation CAAX motif at the carboxy<br/>(C)- terminal end. There is an immense body of evidence to support a role for<br/>PRL-3 in the development of various types of cancer and in progression to<br/>metastasic disease. However, many questions are still pending, especially with<br/>respect to the identity of physiological substrates, and interacting partners in<br/>general, of PRL-3. VHR is a model for a group of atypical dual specificity<br/>protein phosphatases (DUSPs) with a role in cell cycle progression. Only a few<br/>of VHR’s physiological substrates have been reported to date and there are<br/>very few studies addressing its regulation and physiological role(s).<br/>Generally, in order to isolate and identify transient phosphatase-substrate<br/>interactions, substrate-trapping mutants of PTPs are employed. Mutants which<br/>can function as substrate traps have the ability to recognise and bind<br/>substrates, yet they lack functionality of the key catalytic residues and cannot<br/>efficiently process the hydrolysis of the substrate. However, it is acknowledged<br/>that the efficiency of such standard substrate-trapping mutants of PTPs is low.<br/>In this work, the expanded genetic code approach was applied to develop more<br/>efficient substrate trapping variants of the PTPs by incorporating the photocross-linkable amino acid para-benzoylphenylalanine (pBPA). The concept was optimised for PRL-3 and VHR, and for both proteins, pBPA-containing variantswere expressed at excellent yields and were highly purified.<br/>By utilizing the photo-cross-linkable F68pBPA variant of VHR, dimerisation of<br/>VHR was detected in an in vitro ultraviolet (UV) exposure-mediated crosslinking<br/>assay. VHR dimerisation was further demonstrated to be a potential<br/>novel regulatory mechanism for VHR, having a negative effect on the catalytic<br/>activity of the protein. A specific region in VHR known as the variable insert<br/>segment was pinpointed as a region in the protein, which is either at the dimer<br/>interface or heavily contributing to dimeric association. Furthermore, the<br/>intrinsic ability of VHR to self-associate was also demonstrated by<br/>complementary methods.<br/>For PRL-3 it was demonstrated that its D72pBPA variant could recognise and<br/>bind to lipids, with a stronger signal detected in the UV-exposed sample, and<br/>without altering the lipid binding profile with respect to the native protein. Lastly, the potential of exploiting photo-cross-linkable variants of the PTPs was also demonstrated by incubating PRL-3 variants, with or without selectively<br/>introduced pBPA, with mammalian cell lysates, followed by UV exposure.<br/>Western blot analysis detected new bands corresponding to covalently crosslinked PRL-3-protein complexes. Future work in our laboratory will follow up on these newly identified interactions.","abstract_has_math":false,"creators":["Pavic, Karolina"],"institution":"University of Dundee","degree_name":"Doctor of Philosophy","degree_level":"Doctoral Thesis","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Keyse, Stephen","Kohn, Maja","Krijgsveld , Jeroen","Lemke, Edward"],"committee_chairs":[],"committee_members":[],"year":2013,"date_issued":"2013","date_published":"2013","updated_at":"2026-07-24T02:07:52Z","subjects":[],"languages":["eng"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["oai:discovery.dundee.ac.uk:studenttheses/39cd7ecc-d09b-4295-933e-725538437046"],"render_values":[{"text":"oai:discovery.dundee.ac.uk:studenttheses/39cd7ecc-d09b-4295-933e-725538437046","href":null,"code":true}]}]},"links":{"outbound_url":"https://discovery.dundee.ac.uk/en/studentTheses/39cd7ecc-d09b-4295-933e-725538437046","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Keyse, Stephen","Kohn, Maja","Krijgsveld , Jeroen","Lemke, Edward"]},{"key":"dc:creator","label":"Author","values":["Pavic, Karolina"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2013"]},{"key":"dc:date.issued","label":"Date","values":["2013"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Dundee","European Molecular Biology Laboratory"]},{"key":"dc:relation.isreferencedby","label":"Dc Relation Isreferencedby","values":["https://discovery.dundee.ac.uk/en/studentTheses/39cd7ecc-d09b-4295-933e-725538437046"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral Thesis"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["Doctor of Philosophy"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["oai:discovery.dundee.ac.uk:studenttheses/39cd7ecc-d09b-4295-933e-725538437046","https://discovery.dundee.ac.uk/en/studentTheses/39cd7ecc-d09b-4295-933e-725538437046"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://discovery.dundee.ac.uk/files/4439298/Pavic_phd_2013.pdf"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Abnormalities in the coordinated activities of protein phosphatases (PPs) and
protein kinases (PKs) contribute to the development of many diseases.
Phosphatase of regenerating liver (PRL)-3 and Vaccinia H1-Related (VHR) are
two members of the protein tyrosine phosphatase (PTP) family shown to be
involved in cancer. PRL-3 is a member of the PRL phosphatases containing a
unique post-translationally modifiable prenylation CAAX motif at the carboxy
(C)- terminal end. There is an immense body of evidence to support a role for
PRL-3 in the development of various types of cancer and in progression to
metastasic disease. However, many questions are still pending, especially with
respect to the identity of physiological substrates, and interacting partners in
general, of PRL-3. VHR is a model for a group of atypical dual specificity
protein phosphatases (DUSPs) with a role in cell cycle progression. Only a few
of VHR’s physiological substrates have been reported to date and there are
very few studies addressing its regulation and physiological role(s).
Generally, in order to isolate and identify transient phosphatase-substrate
interactions, substrate-trapping mutants of PTPs are employed. Mutants which
can function as substrate traps have the ability to recognise and bind
substrates, yet they lack functionality of the key catalytic residues and cannot
efficiently process the hydrolysis of the substrate. However, it is acknowledged
that the efficiency of such standard substrate-trapping mutants of PTPs is low.
In this work, the expanded genetic code approach was applied to develop more
efficient substrate trapping variants of the PTPs by incorporating the photocross-linkable amino acid para-benzoylphenylalanine (pBPA). The concept was optimised for PRL-3 and VHR, and for both proteins, pBPA-containing variantswere expressed at excellent yields and were highly purified.
By utilizing the photo-cross-linkable F68pBPA variant of VHR, dimerisation of
VHR was detected in an in vitro ultraviolet (UV) exposure-mediated crosslinking
assay. VHR dimerisation was further demonstrated to be a potential
novel regulatory mechanism for VHR, having a negative effect on the catalytic
activity of the protein. A specific region in VHR known as the variable insert
segment was pinpointed as a region in the protein, which is either at the dimer
interface or heavily contributing to dimeric association. Furthermore, the
intrinsic ability of VHR to self-associate was also demonstrated by
complementary methods.
For PRL-3 it was demonstrated that its D72pBPA variant could recognise and
bind to lipids, with a stronger signal detected in the UV-exposed sample, and
without altering the lipid binding profile with respect to the native protein. Lastly, the potential of exploiting photo-cross-linkable variants of the PTPs was also demonstrated by incubating PRL-3 variants, with or without selectively
introduced pBPA, with mammalian cell lysates, followed by UV exposure.
Western blot analysis detected new bands corresponding to covalently crosslinked PRL-3-protein complexes. Future work in our laboratory will follow up on these newly identified interactions."]},{"key":"dc:title","label":"Title","values":["The Development of Photo-crosslinkable Trapping Mutants as Tools to Investigate the Interactions of Protein Tyrosine Phosphatases"]}]}],"canonical_facts":{"dc:contributor.advisor":["Keyse, Stephen","Kohn, Maja","Krijgsveld , Jeroen","Lemke, Edward"],"dc:creator":["Pavic, Karolina"],"dc:date":["2013"],"dc:date.issued":["2013"],"dc:description.abstract":["Abnormalities in the coordinated activities of protein phosphatases (PPs) and
protein kinases (PKs) contribute to the development of many diseases.
Phosphatase of regenerating liver (PRL)-3 and Vaccinia H1-Related (VHR) are
two members of the protein tyrosine phosphatase (PTP) family shown to be
involved in cancer. PRL-3 is a member of the PRL phosphatases containing a
unique post-translationally modifiable prenylation CAAX motif at the carboxy
(C)- terminal end. There is an immense body of evidence to support a role for
PRL-3 in the development of various types of cancer and in progression to
metastasic disease. However, many questions are still pending, especially with
respect to the identity of physiological substrates, and interacting partners in
general, of PRL-3. VHR is a model for a group of atypical dual specificity
protein phosphatases (DUSPs) with a role in cell cycle progression. Only a few
of VHR’s physiological substrates have been reported to date and there are
very few studies addressing its regulation and physiological role(s).
Generally, in order to isolate and identify transient phosphatase-substrate
interactions, substrate-trapping mutants of PTPs are employed. Mutants which
can function as substrate traps have the ability to recognise and bind
substrates, yet they lack functionality of the key catalytic residues and cannot
efficiently process the hydrolysis of the substrate. However, it is acknowledged
that the efficiency of such standard substrate-trapping mutants of PTPs is low.
In this work, the expanded genetic code approach was applied to develop more
efficient substrate trapping variants of the PTPs by incorporating the photocross-linkable amino acid para-benzoylphenylalanine (pBPA). The concept was optimised for PRL-3 and VHR, and for both proteins, pBPA-containing variantswere expressed at excellent yields and were highly purified.
By utilizing the photo-cross-linkable F68pBPA variant of VHR, dimerisation of
VHR was detected in an in vitro ultraviolet (UV) exposure-mediated crosslinking
assay. VHR dimerisation was further demonstrated to be a potential
novel regulatory mechanism for VHR, having a negative effect on the catalytic
activity of the protein. A specific region in VHR known as the variable insert
segment was pinpointed as a region in the protein, which is either at the dimer
interface or heavily contributing to dimeric association. Furthermore, the
intrinsic ability of VHR to self-associate was also demonstrated by
complementary methods.
For PRL-3 it was demonstrated that its D72pBPA variant could recognise and
bind to lipids, with a stronger signal detected in the UV-exposed sample, and
without altering the lipid binding profile with respect to the native protein. Lastly, the potential of exploiting photo-cross-linkable variants of the PTPs was also demonstrated by incubating PRL-3 variants, with or without selectively
introduced pBPA, with mammalian cell lysates, followed by UV exposure.
Western blot analysis detected new bands corresponding to covalently crosslinked PRL-3-protein complexes. Future work in our laboratory will follow up on these newly identified interactions."],"dc:identifier":["oai:discovery.dundee.ac.uk:studenttheses/39cd7ecc-d09b-4295-933e-725538437046","https://discovery.dundee.ac.uk/en/studentTheses/39cd7ecc-d09b-4295-933e-725538437046"],"dc:identifier.uri":["https://discovery.dundee.ac.uk/files/4439298/Pavic_phd_2013.pdf"],"dc:language":["eng"],"dc:publisher.institution":["University of Dundee","European Molecular Biology Laboratory"],"dc:relation.isreferencedby":["https://discovery.dundee.ac.uk/en/studentTheses/39cd7ecc-d09b-4295-933e-725538437046"],"dc:title":["The Development of Photo-crosslinkable Trapping Mutants as Tools to Investigate the Interactions of Protein Tyrosine Phosphatases"],"dc:type":["Thesis"],"dc:type.qualificationlevel":["Doctoral Thesis"],"dc:type.qualificationname":["Doctor of Philosophy"]},"updated_at":"2026-07-24T02:07:52Z"}