Differential mitochondrial protein expression profiling in neurodegenerative diseases

Alterations in mitochondrial structure or function have been described in a variety of human diseases for nearly half a century. The complete sequence of the human mitochondrial genome has been published in 1981. The mitochondrial proteome database however, is still incomplete. Here I give a short review on recent advances to determine the complete set of mitochondrial proteins. The main emphasis is put on gel-based proteomic approaches to identify differentially expressed mitochondrial proteins in neurodegenerative diseases.     

Neuronal autophagy and neurodegenerative diseases

Autophagy is a dynamic cellular pathway involved in the turnover of proteins, protein complexes, and organelles through lysosomal degradation. The integrity of postmitotic neurons is heavily dependent on high basal autophagy compared to non-neuronal cells as misfolded proteins and damaged organelles cannot be diluted through cell division. Moreover, neurons contain the specialized structures for intercellular communication, such as axons, dendrites and synapses, which require the reciprocal transport of proteins, organelles and autophagosomes over significant distances from the soma. Defects in autophagy affect the intercellular communication and subsequently, contributing to neurodegeneration. The presence of abnormal autophagic activity is frequently observed in selective neuronal populations afflicted in common neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Huntington's disease and amyotrophic lateral sclerosis. These observations have provoked controversy regarding whether the increase in autophagosomes observed in the degenerating neurons play a protective role or instead contribute to pathogenic neuronal cell death. It is still unknown what factors may determine whether active autophagy is beneficial or pathogenic during neurodegeneration. In this review, we consider both the normal and pathophysiological roles of neuronal autophagy and its potential therapeutic implications for common neurodegenerative diseases.     

Alpha-synuclein misfolding and neurodegenerative diseases

Alpha-synuclein is an abundant presynaptic brain protein, misfolding, aggregation and fibrillation of which are implicated as critical factors in several neurodegenerative diseases. The list of the well-known synucleinopathies includes such devastating disorders as Parkinson's disease, Lewy body variant of Alzheimer's disease, diffuse Lewy body disease, dementia with Lewy bodies, multiple system atrophy, and neurodegeneration with brain iron accumulation type I. The precise functions of alpha-synuclein remain elusive, but there are evidence indicating its involvement in regulation vesicular release and/or turnover and synaptic function in the central nervous system. It might play a role in neuronal plasticity responses, bind fatty acids, regulate certain enzymes, transporters, and neurotransmitter vesicles, be involved in neuronal survival and even can act as a molecular chaperone. Structurally, alpha-synuclein is an illustrative member of the rapidly growing family of natively unfolded (or intrinsically disordered) proteins and considerable knowledge has been accumulated about its structural properties and conformational behavior. The molecular mechanisms underlying misfolding, aggregation and fibrillation of alpha-synuclein and the role of various environmental and genetic factors in stimulation and inhibition of these processes are relatively well understood. Here, the main structural features of alpha-synuclein, its functions, and involvement in various human diseases are summarized providing a foundation for better understanding of the biochemistry, biophysics and neuropathology of alpha-synuclein aggregation.     

Degradation of misfolded proteins in neurodegenerative diseases: therapeutic targets and strategies

Mammalian cells remove misfolded proteins using various proteolytic systems, including the ubiquitin (Ub)-proteasome system (UPS), chaperone mediated autophagy (CMA) and macroautophagy. The majority of misfolded proteins are degraded by the UPS, in which Ub-conjugated substrates are deubiquitinated, unfolded and cleaved into small peptides when passing through the narrow chamber of the proteasome. The substrates that expose a specific degradation signal, the KFERQ sequence motif, can be delivered to and degraded in lysosomes via the CMA. Aggregation-prone substrates resistant to both the UPS and the CMA can be degraded by macroautophagy, in which cargoes are segregated into autophagosomes before degradation by lysosomal hydrolases. Although most misfolded and aggregated proteins in the human proteome can be degraded by cellular protein quality control, some native and mutant proteins prone to aggregation into β-sheet-enriched oligomers are resistant to all known proteolytic pathways and can thus grow into inclusion bodies or extracellular plaques. The accumulation of protease-resistant misfolded and aggregated proteins is a common mechanism underlying protein misfolding disorders, including neurodegenerative diseases such as Huntington''s disease (HD), Alzheimer''s disease (AD), Parkinson''s disease (PD), prion diseases and Amyotrophic Lateral Sclerosis (ALS). In this review, we provide an overview of the proteolytic pathways in neurons, with an emphasis on the UPS, CMA and macroautophagy, and discuss the role of protein quality control in the degradation of pathogenic proteins in neurodegenerative diseases. Additionally, we examine existing putative therapeutic strategies to efficiently remove cytotoxic proteins from degenerating neurons.     

The role of mitochondrial DNA mutation on neurodegenerative diseases

Many researchers have reported that oxidative damage to mitochondrial DNA (mtDNA) is increased in several age-related disorders. Damage to mitochondrial constituents and mtDNA can generate additional mitochondrial dysfunction that may result in greater reactive oxygen species production, triggering a circular chain of events. However, the mechanisms underlying this vicious cycle have yet to be fully investigated. In this review, we summarize the relationship of oxidative stress-induced mitochondrial dysfunction with mtDNA mutation in neurodegenerative disorders.     

蛋氨酸亚砜还原酶的结构特征及与神经退行性疾病的关系

蛋氨酸易被氧化为蛋氨酸亚砜,使生物体中氧化还原平衡失调,诱发各种疾病.蛋氨酸亚砜还原酶(Msrs)能将蛋氨酸亚砜还原成蛋氨酸,恢复蛋白的结构与功能,对调控多种氧化应激相关疾病具有重要作用.本文结合本课题组的研究结果,介绍了Msrs的分类进化、结构特征、催化机理和基因工程表达;综述了Msrs与衰老、帕金森病和阿尔茨海默病的关系,以探讨有关Msrs研究的发展方向和应用前景.     

基于质谱的蛋白质组学技术在神经退行性疾病生物标志物研究中的应用

蛋白质组学是在整体水平上研究细胞、组织或生物体蛋白质组成及变化规律的科学.与传统的生物学研究相比,蛋白质组学具有快速、灵敏、高通量的优点.神经退行性疾病是一类由神经系统内特定神经细胞的进程性病变或丢失而导致神经功能障碍的疾病,严重危害人类健康.近年来,基于质谱的蛋白质组学技术在神经退行性疾病的研究中得到了广泛应用.本文简要介绍了蛋白质组学在样品分离、多肽定量、质谱检测及生物标志物临床验证等方面的技术发展,并结合实例综述了基于质谱的蛋白质组学在神经退行性疾病生物标志物发现与验证中的研究进展.     

1,2,4-Thiadiazoles as promising multifunctional agents for treatment of neurodegenerative diseases

Detailed studies of properties of new 3-substituted 5-anilino-1,2,4-thiadiazoles containing different substituents at position 3 of the thiadiazole ring were carried out, in particular, their esterase profile and antioxidant properties. It was found that the presence in the molecule of 2-aminopropyl fragment determines an efficient and selective inhibition of butyrylcholinesterase as compared to acetylcholinesterase and carboxylesterase, with radical-scavenging activity being weak. The compounds containing a 2-aminopropenyl fragment possess a high radicalscavenging activity, weakly inhibit cholinesterases, and exhibit anticarboxylesterase activity. A wide spectrum of activity of 3-substituted 5-anilino-1,2,4-thiadiazoles as inhibitors of cholinesterases and highly efficient scavengers of free radicals gives a basis for the optimization of structure and development in this series of original agents for therapy of neurodegenerative diseases.     

茜素红与蛋白质分子Langmuir吸附聚集反应研究

在pH4.3的B-R缓冲体系中,用微相吸附-光谱修正技术[1]研究了茜素红(ARS)与牛血清白蛋白(BSA)、人血清白蛋白(HSA)的结合反应。其吸附结合常数分别为:KBSA-ARS=3.950×104,KHSA-ARS=4.377×104。染料与蛋白的最大结合数分别为NARS∶NBSA=9∶1,NARS∶NHSA=7∶1。经光谱修正技术计算结合产物的实际摩尔吸光系数分别为εBSA-ARS(537nm)=2.517×104L.mol-1.cm-1,εHSA-ARS(519nm)=2.051×104L.mol-1.cm-1,检出限BSA为19mg/L,HSA为23mg/L。经探讨该结合反应机理符合Langmuir吸附聚集反应方程。     

The implication of topology for protein structure and aggregation

For proteins, it is discussed which intrinsic dynamical modes can be present when all static forces are screened. Excitations involving a wringing of the polypeptide chain around its path exists. It is suggested that the existence of such wringons is the underlying cause for the uniqueness of protein folding, and that they may be determinant for aggregation.     

Advances in electrochemical detection for probing protein aggregation

Electrochemistry provides an array of methods to investigate protein aggregation and determine biomarkers of neurodenenerative diseases. Biosensors detecting monomeric or oligomeric biomarkers of Alzheimer's disease and Parkinson's disease evolved toward femtomolar, multiplexed detection in blood and biological fluids for less invasive diagnosis. The biosensors also serve as complementary tools in studies investigating putative biomarkers for the assessment of patient's cognitive decline. The study of protein aggregation via the direct electrochemical oxidation focused recently on enhanced sensitivity and on establishing correlations between protein structure and aggregation propensity. Departing from classic approaches, nanopore resistive pulse sensing and single-particle collision electrochemistry enable studying aggregates in solution. Growing applications converge toward accurate evaluation of aggregate populations and method adoption beyond proof of principle.     

Influence of backbone conformation on protein aggregation

Effect(s) of organic solvents on an all beta-sheet protein are investigated to understand the influence of backbone conformation on protein aggregation. Results obtained in the present study reveal that protein aggregation is accompanied by the formation of non-native beta-sheet conformation. In contrast, induction of non-native helical segments in the protein is found to inhibit aggregation. The differential effects of the secondary structures on protein aggregation are proposed to stem from the disparity in the nature of the hydrogen bonds and packing of the side chains of hydrophobic residues in the beta-sheet and alpha-helix conformation. In our opinion, the results of the present study provide useful hints to develop methods to alleviate the problems of both in vitro and in vivo protein aggregation.     

General aspects of protein adsorption

The study of protein adsorption on a mechanistic and quantitative basis is still a relatively young science and a general theory encompassing all aspects cannot be given. Till now the possibility of synthesizing surfaces in a controlled way, to elucidate the mechanism of protein adsorption - a possibility existing since the advent of affinity chromatography nearly two decades ago - has only been utilized to a small extent. Since this technique, however, has allowed the derivation of some general principles of protein adsorption and protein adsorption kinetics, which would otherwise not have been amenable for study, these results will be mainly referred to here.     

Colloid-chemical aspects of protein crystallization

Problems and prospects of the crystallization of water-soluble and membrane proteins are discussed. The main focus is on colloid-chemical aspects of crystallization processes and the use of surfactants and various structured dispersions (surfactant-based gels and lyotropic phases). Advantages of the protein crystallization on solid supports of different nature, including biopolymer supports, are considered. Apparently, we are witnesses to the rise of a new field, nanocrystallography, dealing with the determination of protein structures from the investigation of nanocrystals.     

Colloidal aspects of protein digestion

The increase in food related health issues has sparked an interest in research on the digestion processes of the gastrointestinal tract. Because of the difficulty and expense of undertaking human trials or even animal experiments, much of the current research uses in vitro models that simulate various aspects of digestion. The results of this research indicate that the rate and extent of protein digestion is governed by accessibility of the cleavage sites to enzymes and local flexibility of the substrate molecule. However, results have also shown that digestion of an allergenic protein to small fragments does not necessarily mean that it will no longer be immunologically active. Other factors are also important. For example, adsorption to an interface increased rates of digestion as did the presence of bile acids. In fact, interaction with a range of physiological surfactants has been shown to be extremely important in protein digestion. When protein is adsorbed to an emulsified food it can be displaced by the surfactants in either the stomach or the small intestine. Lipid interaction with the protein in solution has been demonstrated to be important in effecting rates of proteolysis and phospholipids in particular have provided a protective effect for some milk proteins. Conversely the presence of specific proteins has been shown to affect rates of lipid digestion. The number of such colloidal interactions that we now know may play a role in protein digestion highlights the importance of this area to understanding how we can produce food that optimises nutrition for the consumer.     

In silico strategies for the selection of chelating compounds with potential application in metal-promoted neurodegenerative diseases

The development of new strategies to find commercial molecules with promising biochemical features is a main target in the field of biomedicine chemistry. In this work we present an in silico-based protocol that allows identifying commercial compounds with suitable metal coordinating and pharmacokinetic properties to act as metal-ion chelators in metal-promoted neurodegenerative diseases (MpND). Selection of the chelating ligands is done by combining quantum chemical calculations with the search of commercial compounds on different databases via virtual screening. Starting from different designed molecular frameworks, which mainly constitute the binding site, the virtual screening on databases facilitates the identification of different commercial molecules that enclose such scaffolds and, by imposing a set of chemical and pharmacokinetic filters, obey some drug-like requirements mandatory to deal with MpND. The quantum mechanical calculations are useful to gauge the chelating properties of the selected candidate molecules by determining the structure of metal complexes and evaluating their stability constants. With the proposed strategy, commercial compounds containing N and S donor atoms in the binding sites and capable to cross the BBB have been identified and their chelating properties analyzed.