1. Structural Disorder and Its Connection with Misfolding Diseases; Veronika Csizmok and Peter Tompa. 1.1 The Concept of Protein Disorder. 1.2 Biophysical and Bioinformatics Characterization of Disorder. 1.2.1 Biophysical Techniques 1.2.2 Bioinformatics Techniques. 1.3 Disorder in Vivo, the Effect of Crowding? 1.4 Disorder and Aggregation. 1.5 Disorder in Neurodegenerative Diseases. 1.6 Physiological Prions. 1.7 Structural Transition to Amyloid: Partially Folded Intermediates. 1.8 The Structure of Amyloid: Cross-Beta Models and Flexibility. 1.9 Conclusions. References. 2 Intrinsic Disorder in Proteins Associated with Neurodegenerative Diseases Vladimir N. Uversky. 2.1 Neurodegenerative Diseases as Proteinopathies. 2.2 Introducing Intrinsically Disordered Proteins. 2.2.1 Concept. 2.2.2 Experimental Techniques for IDP Detection. 2.2.3 Sequence Peculiarities of IDPs and Predictors of Intrinsic Disorder. 2.2.4 Abundance of IDPs and their Functions. 2.3Abundance of IDPs in Neurodegenerative Diseases. Evidence from the Bioinformatics Analyses. 2.4 Intrinsic Disorder in Proteins Associated with -Protein and Alzheimer's Disease. 2.4.2 Neurodegenerative Diseases. 2.4.1 Amyloid Tau Protein in Alzheimer's Disease and Other Tauopathies. 2.4.3 Prion Protein and Prion Diseases. 2.4.4 Synucleins - and Synuclein and Synucleinopathies. 2.4.5 Parkinson's Disease and Dementia with Lewy Bodies. 2.4.6 Polyglutamine Repeat Diseases and Huntingtin, Ataxin-1, Ataxin-3, androgen Receptor and Atrophin-1. 2.4.7 Abri Peptide and Familial British Dementia. 2.4.8 Adan in Familial Danish Dementia. 2.4.9 Glial Fibrillary Acidic Protein and Alexander and Alpers Disease. 2.4.11DNA Disease. 2.4.10 Mitochondrial DNA Polymerase Excision Repair Protein ERCC-6 and Cockayne Syndrome. 2.4.12 Survival of Motor Neurons Protein and Spinal Muscular Atrophy. 2.5 Concluding Remarks: Another Illustration of the D2 Concept. References. 3 Dynamic Role of Ubiquitination in the Management of Misfolded Proteins Associated with Neurodegenerative Diseases. Esther S.P. Wong, Jeanne M.M. Tan and Kah-Leong Lim. 3.1 Protein Misfolding and the Ubiquitin-Proteasome System. 3.2 Protein Misfolding, UPS Disruption and Neurodegeneration. 3.3 Diversity of Ubiquitin Modifications. 3.4 Non-Proteolytic Ubiquitination and Protein Inclusions Biogenesis. 3.5 Aggresomes Formation and Clearance. 3.6 K63-Linked Polyubiquitination - A Novel Cargo Recognition Signal For Autophagic Degradation. 3.7 A Model of Inclusion Biogenesis and Clearance. 3.8 E2/E3 Pairs - Triage officers?. 3.9 Conclusions. References. 4. Protein Misfolding and Axonal Protection in Neurodegenerative Diseases. Haruhisa Inoue, Takayuki Kondo and Ryosuke Takahashi. 4.1 Neuronal Dysfunction in Neurodegeneration Are Reversible Process. 4.2 Neuronal Dysfunction Is Not Treatable by Anti-Cell Death Therapy. 4.3 Morphological Aspects of Neuronal Dysfunction Caused by Protein Aggregation/Misfolding in Human Neurodegenerative Disorder. 4.4 Protein Misfolding and Axonal Degeneration in Experimental Animal Models. 4.5 Therapeutic approaches to treat neuronal dysfunction by axonal protection. 4.5.1 Axonal regeneration. 4.5.2 Anti-Wallerian Degeneration. 4.5.3 Autophagy Enhancement. 4.5.4 Stabilization of Microtubules. 4.6 Concluding remarks. References. 5. Endoplasmic Reticulum Stress in Neurodegeneration Jeroen J.M. Hoozemans and Wiep Scheper. 5.1Introduction. 5.2 Protein Quality Control in the Endoplasmic Reticulum. 5.2.2 Triage: ERAD. 5.2.3 Degradation: Ubiquitin Proteasome System and Autophagy. 5.2.4 Stress Response: The Unfolded Protein Response. 5.2.5 ER-Stress-Induced Cell Death. 5.3. ER Stress in Neurodegenerative Disorders. 5.3.1 Alzheimer's Disease. 5.3.2 Parkinson's Disease 5.3.3 Prion Disease. 5.3.4 Tauopathies. 5.3.5 Polyglutamine Diseases. 5.3.6 Amyotrophic Lateral Sclerosis. 5.3.7 White Matter Disorders. 5.4 Conclusions .References. 6. Involvement of Alpha-2 Domain in Prion Protein Conformationally-Induced Diseases Luisa