Quantitative approaches to defining normal and aberrant protein homeostasis
Lead Research Organisation:
University of Cambridge
Department Name: Chemistry
Abstract
The ability of all living systems to function requires a high level of regulation of the behaviour of proteins, which are the molecules that are involved in essentially all the biochemical reactions taking place within them. Proteins usually carry out their functions by adopting specific conformations, known as native states, which are encoded in their amino acid sequences. Much research in molecular biology has therefore been focused on the properties of native states of proteins. It is increasingly evident, however, that non-native states of proteins also play a fundamental role in determining the normal development of cellular activities. A variety of diseases, which include systemic conditions such as type II diabetes and dialysis-related amyloidosis, and neurodegenerative conditions such as Alzheimer's, Parkinson's and the various prion diseases, have been identified that are associated with the incorrect folding of proteins and their subsequent aggregation. Very considerable efforts, including much work by our own research groups, have been devoted in the last several years to addressing these problems by enhancing our ability of understanding the behaviour of proteins, including folding, misfolding and assembly. The approach that we propose in this application is based on two realisations. The first is that the investigation of protein homeostasis provides a general framework to formulate a comprehensive description of the behaviour of proteins in the cell. The second is that major advances can now be made by exploiting the opportunities offered by technical and conceptual developments that have taken place in disciplines such nanoscience, chemistry and neurobiology. We have thus brought together researchers from these disciplines that have already an established track record of successful collaborations to put forward an ambitious programme or research with the goal of increasing the level at which we can understand rationally and quantitatively the outcome of cellular processes. More specifically, we propose to carry out research at the Department of Chemistry (Prof Dobson and Dr Vendruscolo) to achieve a detailed determination, by a combination of experiment and theory, of the multiple possible states of proteins, including partially folded conformations, misfolding intermediates, amyloid fibrils, as well as of the pathways of their interconversion. The activity at the Nanoscience Centre (Prof Welland) will be devoted to the use of nanoscience techniques to establish quantitative relationships between different aspects of protein behaviour, including their aggregation rates and the mechanical properties of amyloid structures. Finally, at the Departments of Genetics (Dr. Crowther) and of Medicine (Prof Lomas) we will use in vivo Drosophila models in conjunction with theoretical predictions to enhance our understanding of the physico-chemical origin of misfolding diseases and to explore the development of rational strategies for their treatment.
Technical Summary
Cellular homeostasis depends on the presence of sophisticated quality control mechanisms that regulate the behaviour of proteins in their native and non-native states. A variety of diseases, which include systemic disorders such as type II diabetes and dialysis-related amyloidosis, and neurodegenerative conditions such as Alzheimer's and Parkinson's diseases, have been identified as being associated with incorrect processing of proteins in the cell. In this application we formulate a strategy for describing and potentially altering the behaviour of protein molecules in the cell, including their folding, misfolding and aggregation, based on a quantitative understanding of protein homeostasis. Our approach is based on the exploitation of the opportunities offered by technical developments in disciplines such as physics, nanoscience, chemistry and neurobiology. We have thus brought together researchers from such disciplines that have already an established track record of successful collaborations to put forward an ambitious programme to increase the level at which we can understand quantitatively cellular processes. The research at the Department of Chemistry will aim at the determination by a combination of experiment (Prof Dobson) and theory (Dr Vendruscolo) of multiple states of proteins, including partially folded conformations, misfolding intermediates, amyloid fibrils, and of the pathways of their interconversion. The activity at the Nanoscience Centre (Prof Welland) will involve the use of nanoscience techniques to establish quantitative relationships among different properties of proteins, including their aggregation rates and the mechanical properties of amyloids. At the Deparments of Genetics (Dr.Crowther) and of Medicine (Prof Lomas) we will use Drosophila models in conjunction with theoretical predictions to enhance our understanding of the origins of misfolding diseases and to explore the development of rational strategies for their treatment.
Publications
Abeln S
(2014)
A simple lattice model that captures protein folding, aggregation and amyloid formation.
in PloS one
Arosio P
(2014)
Chemical kinetics for drug discovery to combat protein aggregation diseases.
in Trends in pharmacological sciences
Baldwin AJ
(2011)
Metastability of native proteins and the phenomenon of amyloid formation.
in Journal of the American Chemical Society
Brorsson AC
(2010)
Intrinsic determinants of neurotoxic aggregate formation by the amyloid beta peptide.
in Biophysical journal
Buell AK
(2011)
Population of nonnative states of lysozyme variants drives amyloid fibril formation.
in Journal of the American Chemical Society
Buell AK
(2014)
Solution conditions determine the relative importance of nucleation and growth processes in a-synuclein aggregation.
in Proceedings of the National Academy of Sciences of the United States of America
Butler DC
(2014)
Differential nuclear localization of complexes may underlie in vivo intrabody efficacy in Huntington's disease.
in Protein engineering, design & selection : PEDS
Caporini MA
(2010)
Accurate determination of interstrand distances and alignment in amyloid fibrils by magic angle spinning NMR.
in The journal of physical chemistry. B
Chen SW
(2015)
Structural characterization of toxic oligomers that are kinetically trapped during a-synuclein fibril formation.
in Proceedings of the National Academy of Sciences of the United States of America
Ciryam P
(2013)
Widespread aggregation and neurodegenerative diseases are associated with supersaturated proteins.
in Cell reports
Ciryam P
(2013)
In vivo translation rates can substantially delay the cotranslational folding of the Escherichia coli cytosolic proteome.
in Proceedings of the National Academy of Sciences of the United States of America
Cohen S
(2011)
Nucleated Polymerisation in the Presence of Pre-Formed Seed Filaments
in International Journal of Molecular Sciences
Cohen SI
(2011)
Nucleated polymerization with secondary pathways. III. Equilibrium behavior and oligomer populations.
in The Journal of chemical physics
Cohen SI
(2014)
Spatial propagation of protein polymerization.
in Physical review letters
Cohen SI
(2012)
From macroscopic measurements to microscopic mechanisms of protein aggregation.
in Journal of molecular biology
Cohen SI
(2013)
Proliferation of amyloid-ß42 aggregates occurs through a secondary nucleation mechanism.
in Proceedings of the National Academy of Sciences of the United States of America
Cohen SI
(2011)
Nucleated polymerization with secondary pathways. II. Determination of self-consistent solutions to growth processes described by non-linear master equations.
in The Journal of chemical physics
Cohen SI
(2011)
Nucleated polymerization with secondary pathways. I. Time evolution of the principal moments.
in The Journal of chemical physics
De Genst E
(2012)
Nanobodies as structural probes of protein misfolding and fibril formation.
in Methods in molecular biology (Clifton, N.J.)
De Genst E
(2014)
Antibodies and protein misfolding: From structural research tools to therapeutic strategies.
in Biochimica et biophysica acta
De Simone A
(2011)
Experimental free energy surfaces reveal the mechanisms of maintenance of protein solubility.
in Proceedings of the National Academy of Sciences of the United States of America
Debelouchina GT
(2013)
Higher order amyloid fibril structure by MAS NMR and DNP spectroscopy.
in Journal of the American Chemical Society
Delivopoulos E
(2015)
Serum protein layers on parylene-C and silicon oxide: effect on cell adhesion.
in Colloids and surfaces. B, Biointerfaces
Dhulesia A
(2010)
Local cooperativity in an amyloidogenic state of human lysozyme observed at atomic resolution.
in Journal of the American Chemical Society
Fitzpatrick AW
(2011)
Inversion of the balance between hydrophobic and hydrogen bonding interactions in protein folding and aggregation.
in PLoS computational biology
Flagmeier P
(2016)
Mutations associated with familial Parkinson's disease alter the initiation and amplification steps of a-synuclein aggregation.
in Proceedings of the National Academy of Sciences of the United States of America
Francois-Moutal L
(2016)
Two-Step Membrane Binding of NDPK-B Induces Membrane Fluidity Decrease and Changes in Lipid Lateral Organization and Protein Cluster Formation.
in Langmuir : the ACS journal of surfaces and colloids
Fusco G
(2014)
Direct observation of the three regions in a-synuclein that determine its membrane-bound behaviour.
in Nature communications
Fusco G
(2012)
¹H, ¹³C and ¹5N resonance assignments of human muscle acylphosphatase.
in Biomolecular NMR assignments
Galvagnion C
(2016)
Chemical properties of lipids strongly affect the kinetics of the membrane-induced aggregation of a-synuclein.
in Proceedings of the National Academy of Sciences of the United States of America
Galvagnion C
(2015)
Lipid vesicles trigger a-synuclein aggregation by stimulating primary nucleation.
in Nature chemical biology
Guilliams T
(2013)
Nanobodies raised against monomeric a-synuclein distinguish between fibrils at different maturation stages.
in Journal of molecular biology
Hagan CL
(2010)
A non-natural variant of human lysozyme (I59T) mimics the in vitro behaviour of the I56T variant that is responsible for a form of familial amyloidosis.
in Protein engineering, design & selection : PEDS
Jahn TR
(2011)
Detection of early locomotor abnormalities in a Drosophila model of Alzheimer's disease.
in Journal of neuroscience methods
Knowles T
(2014)
The amyloid state and its association with protein misfolding diseases
in Nature Reviews Molecular Cell Biology
Knowles TP
(2012)
Twisting transition between crystalline and fibrillar phases of aggregated peptides.
in Physical review letters
Knowles TP
(2011)
Observation of spatial propagation of amyloid assembly from single nuclei.
in Proceedings of the National Academy of Sciences of the United States of America
Kohlhoff KJ
(2011)
The iFly tracking system for an automated locomotor and behavioural analysis of Drosophila melanogaster.
in Integrative biology : quantitative biosciences from nano to macro
Kumita JR
(2012)
Disease-related amyloidogenic variants of human lysozyme trigger the unfolded protein response and disturb eye development in Drosophila melanogaster.
in FASEB journal : official publication of the Federation of American Societies for Experimental Biology
Labrador-Garrido A
(2014)
Chaperoned amyloid proteins for immune manipulation: a-Synuclein/Hsp70 shifts immunity toward a modulatory phenotype.
in Immunity, inflammation and disease
Lee JE
(2018)
Mapping Surface Hydrophobicity of a-Synuclein Oligomers at the Nanoscale.
in Nano letters
Mossuto MF
(2011)
Disulfide bonds reduce the toxicity of the amyloid fibrils formed by an extracellular protein.
in Angewandte Chemie (International ed. in English)
Mossuto MF
(2010)
The non-core regions of human lysozyme amyloid fibrils influence cytotoxicity.
in Journal of molecular biology
O'Brien E
(2012)
Prediction of variable translation rate effects on cotranslational protein folding
in Nature Communications
O'Brien EP
(2011)
New scenarios of protein folding can occur on the ribosome.
in Journal of the American Chemical Society
O'Brien EP
(2014)
Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates.
in Nature communications
O'Brien EP
(2014)
Understanding the influence of codon translation rates on cotranslational protein folding.
in Accounts of chemical research
O'Brien EP
(2010)
Transient tertiary structure formation within the ribosome exit port.
in Journal of the American Chemical Society
O'Brien EP
(2012)
Trigger factor slows co-translational folding through kinetic trapping while sterically protecting the nascent chain from aberrant cytosolic interactions.
in Journal of the American Chemical Society
| Description | We have investigated the fundamental biophysical principles of protein homeostasis. Most notably, we have developed a chemical kinetics theory of protein aggregation and demonstrated that it can be used to develop innovative drug discovery strategies. |
| Exploitation Route | The drug discovery programme that we established following our discoveries are starting provide the first compounds with therapeutic activity against Alzheimer's and Parkinson's diseases. |
| Sectors | Chemicals,Pharmaceuticals and Medical Biotechnology |
| Description | Our research into the biophysical principles of protein homeostasis have opened the way to the development of a range of new methods for the characterisation of protein aggregation. In particular, the theory of chemical kinetics of protein aggregation is transforming the way in which this phenomenon can be studied and controlled in a quantitative manner by using small molecules, antibodies and molecular chaperones. |
| First Year Of Impact | 2012 |
| Sector | Chemicals,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Cultural,Societal,Economic |
| Description | Elan Pharmaceuticals |
| Amount | £20,000,000 (GBP) |
| Organisation | Perrigo |
| Department | Elan Pharmaceuticals |
| Sector | Private |
| Country | Ireland |
| Start | 01/2012 |
| End | 09/2021 |
| Title | Small molecules against aggregation |
| Description | We have developed a series of small molecules against protein aggregation. In particular, we have discovered a compound, called '228', which inhibits the toxicity of alpha-synuclein aggregates in an animal model of Parkinson's disease |
| Type Of Material | Model of mechanisms or symptoms - in vitro |
| Provided To Others? | No |
| Impact | The '228' compound is the first in our pipeline of drug discovery for neurodegeneration. |
| Description | Elan Pharmaceuticals |
| Organisation | Perrigo |
| Department | Elan Pharmaceuticals |
| Country | Ireland |
| Sector | Private |
| PI Contribution | We have collaborated on a drug discovery project for Alzheimer's and Parkinson's diseases with Elan, contributing our biophysical methods for the characterisation of the aggregation process of protein and peptides. |
| Collaborator Contribution | Elan Pharmaceuticals has been at the forefront of research in drug discovery for neurodegenerative diseases in the past 20 years. They have contributed to our programme with their expertise in drug development. |
| Impact | We have developed a compound, called '228', which has shown to be effective in reducing the toxicity of alpha-synuclein aggregates in animal models. |