title: Protein Dynamics and its Correlation to Protein Activity and Stability

authors: Clement, David

subjects: Incoherent neutron scattering

abstract: The aim of this thesis is to investigate the role of fast protein dynamics (picosecond
timescale) in enzyme activity and stability, and specifically to test the
hypothesis that enzyme activity and stability are inversely related by their internal
dynamics.
Activity   Dynamics (flexibility)   1/Stability
In order to test this hypothesis, the well known anti-cancer drug: methotrexate
was used as an informative ligand in the network established between these
properties. A multidisciplinary approach combining neutron scattering, circular
dichroism, UV absorption, isothermal titration calorimetry and X-ray crystallography
was undertaken to examine the current paradigm using the enzyme: dihydrofolate
reductase as a model.
As inferred by neutron spectroscopy, the binding of MTX influences the
dynamical behavior of DHFR. Macromolecular dynamics such as the resilience: lt;kgt;
(i.e. structural rigidity) was found to be increased and, inversely, the flexibility
decreased upon MTX binding. In addition, as revealed by circular dichroism, this
dynamical dependency upon MTX binding was correlated with an enhanced thermal
stability. Compared to the free enzyme, the melting temperature was found to be
increased by 13.8  C in the presence of MTX. The inhibitory power of MTX was also
examined by steady state kinetics and isothermal titration calorimetry. The Ki for
MTX was found to be in the nanomolar range Ki= 10.9 nM. Using isothermal
titration calorimetry, the binding thermodynamic signature between MTX and DHFR
was characterized. The binding event was found to be largely favourable (DGb=-12.1
Kcal mol-1), enthalpy driven (DHb= -16.8 Kcal mol-1) with an unfavourable entropy
DSb=-15.6 cal K-1mol-1.
In conclusion, the modulation of the macromolecular dynamics may reflect
how specific conformations are favoured for subsequent protein function in response
of the binding of specific ligand and how conformational substates approach to
protein function. In this context the unprecedented power of transition state analogs
such as MTX on protein function might therefore be dependent on fast protein
dynamics.

text: Protein Dynamics and its Correlation to Protein Activity and Stability The aim of this thesis is to investigate the role of fast protein dynamics (picosecond
timescale) in enzyme activity and stability, and specifically to test the
hypothesis that enzyme activity and stability are inversely related by their internal
dynamics.
Activity   Dynamics (flexibility)   1/Stability
In order to test this hypothesis, the well known anti-cancer drug: methotrexate
was used as an informative ligand in the network established between these
properties. A multidisciplinary approach combining neutron scattering, circular
dichroism, UV absorption, isothermal titration calorimetry and X-ray crystallography
was undertaken to examine the current paradigm using the enzyme: dihydrofolate
reductase as a model.
As inferred by neutron spectroscopy, the binding of MTX influences the
dynamical behavior of DHFR. Macromolecular dynamics such as the resilience: lt;kgt;
(i.e. structural rigidity) was found to be increased and, inversely, the flexibility
decreased upon MTX binding. In addition, as revealed by circular dichroism, this
dynamical dependency upon MTX binding was correlated with an enhanced thermal
stability. Compared to the free enzyme, the melting temperature was found to be
increased by 13.8  C in the presence of MTX. The inhibitory power of MTX was also
examined by steady state kinetics and isothermal titration calorimetry. The Ki for
MTX was found to be in the nanomolar range Ki= 10.9 nM. Using isothermal
titration calorimetry, the binding thermodynamic signature between MTX and DHFR
was characterized. The binding event was found to be largely favourable (DGb=-12.1
Kcal mol-1), enthalpy driven (DHb= -16.8 Kcal mol-1) with an unfavourable entropy
DSb=-15.6 cal K-1mol-1.
In conclusion, the modulation of the macromolecular dynamics may reflect
how specific conformations are favoured for subsequent protein function in response
of the binding of specific ligand and how conformational substates approach to
protein function. In this context the unprecedented power of transition state analogs
such as MTX on protein function might therefore be dependent on fast protein
dynamics.

year: 2009

title: Handmade pixels: Exposing the animation process

authors: Perrott, Lisa

abstract: Handmade Pixels seeks to expose those aspects of the animation process that are often relegated to ‘behind the scenes’ archives, ‘making of’ videos, or even discarded as rubbish. It aims to celebrate the distinctive approach of artists who experiment with diverse methods and techniques.
Many of the items selected here are quite different from the works typically exhibited in art galleries. Process materials such as working sketches and storyboards are rarely displayed as works of art in their own right. They are often archived or disposed of once the final film has been completed. These materials should be exhibited – not least because they communicate the creative genius and idiosyncratic craftwork of an animator.

text: Handmade pixels: Exposing the animation process Handmade Pixels seeks to expose those aspects of the animation process that are often relegated to ‘behind the scenes’ archives, ‘making of’ videos, or even discarded as rubbish. It aims to celebrate the distinctive approach of artists who experiment with diverse methods and techniques.
Many of the items selected here are quite different from the works typically exhibited in art galleries. Process materials such as working sketches and storyboards are rarely displayed as works of art in their own right. They are often archived or disposed of once the final film has been completed. These materials should be exhibited – not least because they communicate the creative genius and idiosyncratic craftwork of an animator.

year: 2011

title: Kia whakatōmuri te haere whakamua – A Māori framework for coastal climate change adaptation

authors: Bailey-Winiata, Akuhata

subjects: Climate Change Adaptation

abstract: Current climate change adaptation frameworks do not sufficiently represent or acknowledge the intricacies and complex nature of climate adaptation for all communities. This thesis contributes a Māori (Indigenous peoples of Aotearoa New Zealand (A-NZ)) climate adaptation framework that is informed by Te Ao Māori world views, mātauranga Māori (Māori knowledge), Te Tiriti o Waitangi (Treaty of Waitangi) and research at the interface of Western knowledge and mātauranga Māori. This is needed to promote a more equitable and culturally sensitive approach to the current climate change adaptation process for hapū (sub-tribes) and iwi (tribes). To achieve this, this thesis is rooted in the whakataukī (proverb) “Kia whakatōmuri te haere whakamua – I walk backwards into the future with my eyes fixed on my past”, which exemplifies the power of acknowledging Māori history and intergenerational knowledge, while moving forward to a prosperous future. This thesis had four key aims. First, I looked to the past to understand ways Māori ancestors adapted and relocated in response to natural hazards to inform a future climate adaptation or relocation process. Second, I took stock of the contemporary risk to coastal marae (Māori meeting grounds) from sea level rise. Third, I looked internationally at other Indigenous communities' adaptation challenges and how they have overcome them as a mutual learning opportunity. And finally, I developed a conceptual Māori climate adaptation framework based on existing models and informed by a wānanga (workshop) with over 100 Māori participants. This two-part framework emphasises the importance of fostering Te Tiriti-centric relationships and partnerships that are essential for climate adaptation with hapū and iwi. In addition, it serves as a guide to support adaptation decision-making for hapū and iwi Māori. This thesis took a multidisciplinary approach to achieve these aims, incorporating historical and archival analyses, semi-structured interviews, a systematic review, coastal flooding and exposure analyses using spatial information, and wānanga. The findings highlighted that relocation due to natural hazards is not uncommon for Māori, as this thesis identified 51 examples of where relocation was completed or discussed in response to natural hazards. Furthermore, in a case study with Tūhourangi and Ngāti Rangitihi, this thesis identified vital aspects that enabled their relocation following the 1886 Tarawera eruption, the most influential being tuku whenua – the gifting of land to relocate to. This thesis also identified that by 2150, under shared socio-economic pathway (SSP) 5-8.5, 27% and 28% of coastal marae (total of 186 nationally) are exposed to a 100–year and 1000–year annual recurrence interval (ARI) extreme sea level events, respectively. Overall, this thesis contributes to our understanding of the requirements to support hapū and iwi Māori in climate adaptation, with parallels to other Indigenous communities. Requirements include resourcing, partnerships, autonomy, intergenerational planning, recognition, respect and redress. In Chapter 8 – the discussion of this thesis, we focus on four overall contributions this thesis has made, which are: 1) Hapū and iwi Māori are at risk of climate change, 2) We’ve done it before we can do it again, 3) Adaptation approach cannot be one-size-fits-all, and 4) Adaptation in Aotearoa needs a Te Tiriti-centric approach. Ultimately, this thesis underscores the urgent need for inclusive climate adaptation strategies that honour Indigenous knowledge systems, ensuring that hapū and iwi Māori are not only heard but are actively supported in navigating the impacts of climate change.

text: Kia whakatōmuri te haere whakamua – A Māori framework for coastal climate change adaptation Current climate change adaptation frameworks do not sufficiently represent or acknowledge the intricacies and complex nature of climate adaptation for all communities. This thesis contributes a Māori (Indigenous peoples of Aotearoa New Zealand (A-NZ)) climate adaptation framework that is informed by Te Ao Māori world views, mātauranga Māori (Māori knowledge), Te Tiriti o Waitangi (Treaty of Waitangi) and research at the interface of Western knowledge and mātauranga Māori. This is needed to promote a more equitable and culturally sensitive approach to the current climate change adaptation process for hapū (sub-tribes) and iwi (tribes). To achieve this, this thesis is rooted in the whakataukī (proverb) “Kia whakatōmuri te haere whakamua – I walk backwards into the future with my eyes fixed on my past”, which exemplifies the power of acknowledging Māori history and intergenerational knowledge, while moving forward to a prosperous future. This thesis had four key aims. First, I looked to the past to understand ways Māori ancestors adapted and relocated in response to natural hazards to inform a future climate adaptation or relocation process. Second, I took stock of the contemporary risk to coastal marae (Māori meeting grounds) from sea level rise. Third, I looked internationally at other Indigenous communities' adaptation challenges and how they have overcome them as a mutual learning opportunity. And finally, I developed a conceptual Māori climate adaptation framework based on existing models and informed by a wānanga (workshop) with over 100 Māori participants. This two-part framework emphasises the importance of fostering Te Tiriti-centric relationships and partnerships that are essential for climate adaptation with hapū and iwi. In addition, it serves as a guide to support adaptation decision-making for hapū and iwi Māori. This thesis took a multidisciplinary approach to achieve these aims, incorporating historical and archival analyses, semi-structured interviews, a systematic review, coastal flooding and exposure analyses using spatial information, and wānanga. The findings highlighted that relocation due to natural hazards is not uncommon for Māori, as this thesis identified 51 examples of where relocation was completed or discussed in response to natural hazards. Furthermore, in a case study with Tūhourangi and Ngāti Rangitihi, this thesis identified vital aspects that enabled their relocation following the 1886 Tarawera eruption, the most influential being tuku whenua – the gifting of land to relocate to. This thesis also identified that by 2150, under shared socio-economic pathway (SSP) 5-8.5, 27% and 28% of coastal marae (total of 186 nationally) are exposed to a 100–year and 1000–year annual recurrence interval (ARI) extreme sea level events, respectively. Overall, this thesis contributes to our understanding of the requirements to support hapū and iwi Māori in climate adaptation, with parallels to other Indigenous communities. Requirements include resourcing, partnerships, autonomy, intergenerational planning, recognition, respect and redress. In Chapter 8 – the discussion of this thesis, we focus on four overall contributions this thesis has made, which are: 1) Hapū and iwi Māori are at risk of climate change, 2) We’ve done it before we can do it again, 3) Adaptation approach cannot be one-size-fits-all, and 4) Adaptation in Aotearoa needs a Te Tiriti-centric approach. Ultimately, this thesis underscores the urgent need for inclusive climate adaptation strategies that honour Indigenous knowledge systems, ensuring that hapū and iwi Māori are not only heard but are actively supported in navigating the impacts of climate change.

year: 2024-05-28