ISSN 0026-8933, Molecular Biology, 2012, Vol. 46, No. 3, pp. 362–374. © Pleiades Publishing, Inc., 2012. Original Russian Text © T.A. Shelkovnikova, A.A. Kulikova, Ph.O. Tsvetkov, O. Peters, S.O. Bachurin, V.L. Buchman, N.N. Ninkina, 2012, published in Molekulyarnaya Biologiya, 2012, Vol. 46, No. 3, pp. 402–415. 362 INTRODUCTION New cell technologies, bioinformatic approaches, and methods of targeted manipulations with animal genomes led to a substantial progress in biomedicine in the past two decades; in particular, basic processes underlying a number of common neurodegenerative disorders (NDDs) were identified. As a result, several concepts were revisited and changes made to the NDD nomenclature in regard to new data on the molecular mechanisms of NDDs. A large number of clinically different NDDs proved to have a similar pathogenetic molecular mechanism, including patho- logical aggregation of proteins, the formation of insol- uble fibrillar structures, and their deposition in the form of histopathological inclusions in the nervous system [1]. The majority of histopathological deposits formed by aggregation-prone proteins displays properties of amyloid (senile plaques, Lewy bodies, etc.). However, relatively recent studies revealed the proteins that pro- duce non-amyloid inclusions, and the common term “amyloidosis of the nervous system” failed to include all of the disorders characterized by metabolic alter- ations, aggregation, and deposition of proteins in tis- sues of the nervous system. A more general term came to be needed for this group of disorders. Historically, pathological protein inclusions were first identified in Parkinson’s disease (PD, α-synuclein deposition in the form of Lewy bodies) and various dementias (tau protein depositions). The disorders were consequently termed synucleinopathies and tauopathies, respec- tively (protein pathology of synuclein or tau protein). More recently, several types of pathological inclusions formed by different proteins proved to occur simulta- neously in the nervous system of some patients. The term “proteinopathy” (or proteopathy) consequently came to be broadly used to designate the group of dis- orders characterized by protein pathology. Thus, the NDD forms whose pathogenesis is based on the struc- tural changes and/or metabolic alterations of certain proteins that result in their aggregation or lead to aggregation of pathogenic peptides with the subse- quent formation of characteristic histopatological protein or peptide deposits are now classified as pro- teinopathies [2]. Proteinopathies include Alzheimer’s disease (AD), which is characterized by extracellular amyloid plaques and intracellular neurofibrillary tangles; PD, which is characterized by Lewy bodies; prion diseases; trinucleotide repeat disorders, such as Huntington’s disease; motor neuron disease, including amyotrophic lateral sclerosis; and several rare NDDs. Amyloid- pathological inclusions in tissues of various parts of the nervous system were described in classical works on Proteinopathies, Neurodegenerative Disorders with Protein Aggregation-Based Pathology T. A. Shelkovnikova a, c , A. A. Kulikova c , Ph. O. Tsvetkov c , O. Peters b , S. O. Bachurin a , V. L. Buchman b , and N. N. Ninkina a, b a Institute of Physiologically Active Compounds, Russian Academy of Sciences, Chernogolovka, Moscow oblast, 142432 Russia; e-mail: sta.ipac@gmail.com b Cardiff University, Cardiff, CF10 3 US United Kingdom c Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia Received August 21, 2011; in final form, October 14, 2011 Abstract—A number of neurodegenerative disorders were recently coalesced into a group of proteinopathies based on the similarity of molecular mechanisms underlying their pathogenesis. A key step in the develop- ment of proteinopathies is a structural change that triggers aggregation of the proteins that are intrinsically prone to form aggregates owing to their physical and chemical properties. The review considers the recent progress in the field of proteinopathies with a special focus on the properties of aggregation-prone proteins, the main stages of the development of molecular pathology, and the role of cell clearance systems in the pro- gression of neurodegeneration. Recent modifications made to the nomenclature of neurodegenerative dis- eases on the basis of the molecular mechanism of neurodegeneration are also addressed. DOI: 10.1134/S0026893312020161 Keywords: neurodegenerative disorders, proteinopathies, amyloid, synuclein, prions UDC 575.2:577.29:616.8 Abbreviations: NDD, neurodegenerative disorder; AD, Alzhe- imer’s disease; PD, Parkinson’s disease; UPS, ubiquitin–pro- teasomal system; APP, β-amyloid precursor protein.