Protein Homeostasis Diseases: Mechanisms and Novel Therapies

Chapter 1 - Protein folding: how, why, and beyond
	Outline
	Introduction
		Protein conformational landscapes
		Mutational perturbations to probe folding mechanisms and function
		Disordered proteins-regions and unfolded states
		Folding, stability, and binding in vivo
		“Real proteins” and beyond
	Acknowledgments
	References
Chapter 2 - Protein homeostasis and disease
	Outline
	Abbreviations
	Protein folding in vitro and in vivo
		Effects of intracellular milieu composition on protein folding, misfolding, and stability in vivo
		The first steps of in vivo folding and misfolding in the ribosomes: cotranslational versus posttranslational processes
		Protein homeostasis networks
			Molecular chaperones
			Protein degradation: proteasome versus autophagy
	Human misfolding diseases
		Loss-of-function diseases
		Gain-of-toxic function diseases
	Acknowledgments
	Conflict of interest
	Funding
	References
Chapter 3 - Caenorhabditis elegans as a model organism for protein homeostasis diseases
	Outline
	Abbreviations
	Caenorhabditis elegans as a model organism
		The proteostasis network is conserved in Caenorhabditis elegans
			The heat shock response
			The unfolded protein response of the endoplasmic reticulum and the mitochondria
			The insulin-like signaling pathway
			Caenorhabditis elegans as a model for protein misfolding diseases
		Alzheimer’s disease
			Disease mechanism
			Caenorhabditis elegans Amyloid-β models
			Utility of Caenorhabditis elegans Alzheimer’s disease models for drug discovery and identification of genetic modifiers
		Tauopathies
			Disease mechanism
			Caenorhabditis elegans models of tauopathy
			Utility of Caenorhabditis elegans tauopathy models for drug discovery and identification of genetic modifiers
		Parkinson’s disease
			Disease mechanism
			Caenorhabditis elegans Parkinson’s disease models
			Utility of Caenorhabditis elegans Parkinson’s disease models for drug discovery and identification of genetic modifiers
		Polyglutamine diseases
			Disease mechanism
			Caenorhabditis elegans models of Huntington’s disease
				Utility of Caenorhabditis elegans HD models for drug discovery and identification of genetic modifiers
			Caenorhabditis elegans models of spinocerebellar ataxia
				Utility of Caenorhabditis elegans spinocerebellar ataxia models for drug discovery and identification of genetic modifiers
		Amyotrophic lateral sclerosis
			Disease mechanism
			Caenorhabditis elegans models of amyotrophic lateral sclerosis
		Transthyretin amyloidosis
			Disease mechanism
			Caenorhabditis elegans disease models of transthyretin amyloidosis
		Type II diabetes mellitus
			Disease mechanism
			Caenorhabditis elegans model of diabetes mellitus
		Dialysis-related amyloidosis
			Disease mechanism
		Immunoglobulin light chain amyloidosis
			Disease mechanism
			Caenorhabditis elegans models of immunoglobulin light chain amyloidosis
		Prion diseases
	Conclusion
	References
Chapter 4 - Proteome-scale studies of protein stability
	Outline
	Abbreviations
	Introduction
	Protein stability and unfolding
	Biophysical methods to measure protein stability in vitro
	Protein stability in vivo
	Biological readouts to measure protein stability
		Proteome-scale analysis based on aggregation in vivo
		Proteome-scale analysis based on degradation in vivo
	Structural analyses of proteins and proteomes
		Cross-linking-based mass spectrometry
		Hydroxyl radical footprinting (HRF)
		Limited proteolysis-based mass spectrometry
	Proteome-scale methods involving experimental denaturation of proteins
		Denaturation probed by proteolysis sensitivity
		Thermal denaturation probed by aggregation
		Denaturation probed by methionine oxidation
	Contributions to basic and applied biomedical research
	Conclusions
	Acknowledgments
	References
Chapter 5 - Classifying disease-associated variants using measures of protein activity and stability
	Outline
	Abbreviations
	Introduction
	Selection of PTEN variants
	Comparing multiplexed assays and computational predictions to assess variant effects
	Loss of stability is a major source for loss of PTEN function
	Conclusions
	Methods
		Rosetta ∆∆G calculations
		Evolutionary sequence energies (Ẽ)
		Phosphatase-MAVE and VAMP-seq data
		Determining thresholds from receiver operating characteristic curves
		Analysis scripts
	Acknowledgments
	References
Chapter 6 - Protein destabilization and degradation as a mechanism for hereditary disease
	Outline
	Abbreviations
	Introduction to protein quality control
	Protein quality control in hereditary diseases
	Protein folding and refolding
	Protein quality control–mediated degradation via the ubiquitin-proteasome system
	Protein quality control degrons
	Local versus global unfolding
	Potential therapeutic approaches to protein quality control–linked hereditary diseases
	Acknowledgments
	Conflict of interest
	Funding
	References
Chapter 7 - Detection of amyloid aggregation in living systems
	Outline
	Abbreviations
	Introduction
	Techniques for detection of amyloid aggregation in vivo
		Förster resonance energy transfer detection and fluorescence lifetime imaging
		Bioluminescence imaging
		Optical fiber bundles and fluorescence imaging
		Cranial window or thinned-skull imaging using multiphoton microscopy
		In vivo microdialysis
		Positron emission tomography imaging
	Animal models to test in vivo amyloid formation
		Caenorhabditis elegans
		Zebrafish
		Mouse models
		Note on using animal models for in vivo protein aggregation studies
	In vivo complexity and how do in vivo detection assays provide insight into peripheral aspects contributing to neurodegener...
		Replicating the multicellular complexity of the brain
		Interaction of the brain with the periphery system
	Future outlook
	Acknowledgments
	References
Chapter 8 - Molecular mechanisms of amyloid aggregation in human proteinopathies
	Outline
	Introduction
	Protein aggregates: from dynamic oligomers to amyloid fibrils
		Amyloid fibrils
		Oligomers
		Protofibrils
	Mechanisms of amyloid aggregation
		Nucleation-Polymerization
		Nucleated conformational conversion
		More general mechanisms
	Application to different disease-related proteins
		Amyloid β peptides
		α-Synuclein
		hIAPP/amylin
	Concluding remarks
	Acknowledgments
	References
Chapter 9 - Metals and amyloid gain-of-toxic mechanisms in neurodegenerative diseases
	Outline
	Abbreviations
	Metal ions and amyloid formation in neurodegeneration
		Protein misfolding and metal ions in neurodegeneration
		Trace metal import and homeostasis in the brain
	Zinc and toxic protein aggregates in Alzheimer’s disease
		Zinc dyshomeostasis in Alzheimer’s disease
		Zinc binding and aggregation of Aβ
			Zinc binding to Aβ
			Influence of zinc on Aβ aggregation
		Zinc binding and tau aggregation
			Zinc binding to tau
			Influence of zinc on tau aggregation
	Metal chelation therapies
	Acknowledgments
	References
Chapter 10 - Vitamin B6-dependent enzymes and disease
	Abbreviations
	Clinical and genetic bases of misfolding diseases and natural ligand therapies
	Vitamin B6 enzymes and disease
	Primary hyperoxaluria type 1 due to deficiency of AGT
		Clinical and genetic features
		Molecular mechanisms leading to the AGT deficit in primary hyperoxaluria type 1
		The role of natural and unnatural ligands as chaperones for AGT
		Steps forward to new therapeutic approaches for primary hyperoxaluria type 1
	Conclusions
	Acknowledgments
	References
Chapter 11 - Galactosemia: opportunities for novel therapies
	Outline
	Abbreviations
	Introduction: four types of galactosemia
	Causes of pathology and current treatment
	Potential novel therapies
	Pharmacological chaperones for GALT deficiency
	Pharmacological chaperones for other types of galactosemia
	Conclusions
	Acknowledgments
	References
Chapter 12 - Protein homeostasis and regulation of intracellular trafficking of G protein-coupled receptors
	Outline
	Introduction
	Proteostasis and quality control systems
		Proteostasis
		Quality control systems
	Regulation of anterograde G protein-coupled receptor traffic from the endoplasmic reticulum to the cell surface plasma membrane
		Sequence motifs that promote/prevent upward trafficking of G protein-coupled receptors
		Posttranslational modifications in G protein-coupled receptors and intracellular trafficking
		Association of G protein-coupled receptors and intracellular trafficking
	Intracellular G protein-coupled receptor trafficking from the cell surface plasma membrane and beyond
		G protein-coupled receptor internalization via clathrin-coated pits and a central role of arrestins
		Divergent sorting of internalized G protein-coupled receptors and impact on receptor activity
		Sorting of G protein-coupled receptors to the regulated recycling pathway via multiple endosome types
		Sorting of G protein-coupled receptors to the lysosome
		Multilocation signaling of G protein-coupled receptors within the endocytic network
	Targeting misfolded G protein-coupled receptors with pharmacological chaperones
	Conclusions
	Acknowledgments
	References
Chapter 13 - Structure-guided discovery of pharmacological chaperones targeting protein conformational and misfolding diseases
	Outline
	Abbreviations
	Introduction
		The premise and promise of pharmacological chaperone therapy
		Advances in protein structural biology
	Structure-guided understanding of disease-causing variants
		Variants leading to decreased flexibility
		Variants leading to increased flexibility
		Variants that alter cofactor or substrate binding
		Variants that alter binding interface
	Structural basis of pharmacological chaperoning
		Active-site inhibitory pharmacological chaperones for lysosomal storage disorders
		Starting points for allosteric pharmacological chaperones
		Pharmacological chaperones for defects in channels, transporters, and receptors
		Pharmacological chaperones for structural proteins
	Structural methods used in primary compound screening
		Fragment-based approach
		Crystallography-based screening
	Concluding remarks
	Statements
	Acknowledgments
	References
Chapter 14 - Virtual screening in drug discovery: a precious tool for a still-demanding challenge
	Outline
	Abbreviations
	Introduction: the drug discovery process
	Accurate determination of binding affinity in a receptor–ligand complex
	Speeding up the search process through approximate scoring functions
	From binding properties to the identification of molecular descriptors
	Organizing distinct simulation techniques into a screening protocol
	References
Chapter 15 - Differential scanning fluorimetry in the screening and validation of pharmacological chaperones for soluble and membrane pr...
	Outline
	Abbreviations
	Background
	Initial high-throughput screening by differential scanning fluorimetry
		Differential scanning fluorimetry–monitored screening for soluble proteins
			Experimental setup
			Data analysis
			Filtering of hits
			Validation of primary hits by concentration-dependent differential scanning fluorimetry
		Differential scanning fluorimetry–monitored screening for membrane proteins
			Experimental setup
	Conclusion
	Acknowledgments
	References
Chapter 16 - Cellular high-throughput screening
	Outline
	Abbreviations:
	Introduction
	Cellular high-throughput screening
		Assay types
			Primary screen
			Negative screen
			Counter screen
			Positive control compound
		Pharmacoperone types
		Compound toxicity
	Genetic diseases potentially amenable to treatment with chemical or pharmacological chaperones: G protein-coupled receptors...
		G protein-coupled receptors
		Enzyme diseases
		Ion channel diseases
		Lysosomal storage disorders
	Challenges of high-throughput screening “hits”
	Conclusion
	Acknowledgments
	References
Chapter 17 - High-throughput screening for intrinsically disordered proteins by using biophysical methods
	Outline
	Abbreviations
	Introduction
		Drug discovery and biophysics
		Biophysical techniques and high-throughput screening
		Intrinsically disordered proteins
	Fluorescence
		Introduction to fluorescence
		Fluorescence intensity
		Fluorescence polarization or anisotropy
		Fluorescence resonance energy transfer
		Fluorescence temperature-related intensity change
		Fluorescence-based high-throughput screening: thermal shift assay
	Nuclear magnetic resonance
		Introduction to nuclear magnetic resonance
		Ligand-based nuclear magnetic resonance screening methods
			Relaxation-based methods
			Nuclear Overhauser effect-based methods
				Saturation transfer difference (STD) between protein and ligand via nuclear Overhauser effects
				Transfer of 1H-polarization from water to the ligand
		Target-based nuclear magnetic resonance screening methods
	Surface plasmon resonance
	Applications of biophysical techniques to hit identification and validation for intrinsically disordered proteins
	Funding
	References
Chapter 18 - Natural and pharmacological chaperones against accelerated protein degradation: uroporphyrinogen III synthase and congenita...
	Outline
	Abbreviations
	Introduction
		Heme group biosynthesis
		Uroporphyrinogen III synthase
		Congenital erythropoietic porphyria
	The UROIIIS “stability defect” analyzed in vitro
		UROIIIS is a kinetically stable protein
		Congenital erythropoietic porphyria–causing mutations accelerate protein degradation in vitro
		The irreversible unfolding of UROIIIS and the structure of the aggregates
	UROIIIS intracellular homeostasis and congenital erythropoietic porphyria
		UROIIIS intracellular concentration is altered in C73R-UROIIIS
		Quantitative roadmap of the pathogenic mutations that are affected by impaired homeostasis
		In vitro kinetic stability measures correlate with UROIIIS intracellular steady-state concentration for the congenital eryt...
		UROIIIS homeostasis and proteasomal degradation
		UROIIIS proteostasis restoration by proteasomal inhibition in animal models
	Ciclopirox as a pharmacological chaperone for congenital erythropoietic porphyria
		Pharmacological chaperones
		Ciclopirox and congenital erythropoietic porphyria
		Toward a modulation of the heme biosynthetic pathway
	Acknowledgments
	References