Analyses of protein sequences using inter-residue average distance statistics to study folding processes and the significance of their partial sequences

One of the goals of molecular bioinformatics is decoding amino acid sequences to extract information on the principles of protein folding. However, this is difficult to perform with standard bioinformatics techniques such as multiple sequence alignment and so on. Thus, we propose a technique based on inter-residue average distance statistics to make predictions regarding the protein folding mechanisms of amino acid sequences. Our method involves constructing a kind of predicted contact map called an Average Distance Map (ADM) based on average distance statistics to pinpoint regions of possible folding nuclei for proteins. Only information on the amino acid sequence of a given protein is required for the present method. In this article, we summarize the results of studies using our method to analyze how specific protein sequences affect folding properties. In particular, we present studies on proteins in the phage lysozyme, such as the globin, fatty acid binding protein-like, and the cupredoxin-like fold families. In the present review, we characterize the 3D architectures of these proteins through the properties of the protein ADMs. Furthermore, we combine the information on the conserved residues within the regions predicted by the ADMs with our results obtained so far. Such information may help identify the folding characteristics of each protein. We discuss this possibility in the present review.     

RNA-interference in the regulation of axonal transport

Until now, in the world since literature, there has been no direct evidence indicating that RNA-interference controls local protein synthesis in the mammalian motor neuron axons. In the present review we have summarized the results on intraaxonal protein synthesis, its role in the axonal transport, and mechanisms regulating local protein synthesis in the axoplasm. The new mechanisms regulating axonal transport based on RNA-interference presented in the review let us discuss the questions about pathogenesis of the neurodegenerative diseases. The estimated role of the intraaxonal protein synthesis on axonal transport suggested applying short interfering RNA for degradation of the mutant gene RNA for blocking synthesis of the aberrant protein along the whole axon.     

In-vivo and in-vitro nutrient-gene interactions

Association studies of gene variants and response to dietary challenges represent one way of investigating gene-nutrient interactions. Several studies reported in the present review concentrate on evaluating variation at the apolipoprotein AI-CIII-AIV and apolipoprotein E gene loci, as well as the fatty acid binding protein gene. In addition, the effect of nutrients can be directly evaluated at the level of gene expression, and reports of in-vitro studies of control of fatty acid and triglycerides synthesis are discussed in the present review.     

Surfactant-free purification of membrane proteins with intact native membrane environment

In order to study the structure and function of a protein, it is generally required that the protein in question is purified away from all others. For soluble proteins, this process is greatly aided by the lack of any restriction on the free and independent diffusion of individual protein particles in three dimensions. This is not the case for membrane proteins, as the membrane itself forms a continuum that joins the proteins within the membrane with one another. It is therefore essential that the membrane is disrupted in order to allow separation and hence purification of membrane proteins. In the present review, we examine recent advances in the methods employed to separate membrane proteins before purification. These approaches move away from solubilization methods based on the use of small surfactants, which have been shown to suffer from significant practical problems. Instead, the present review focuses on methods that stem from the field of nanotechnology and use a range of reagents that fragment the membrane into nanometre-scale particles containing the protein complete with the local membrane environment. In particular, we examine a method employing the amphipathic polymer poly(styrene-co-maleic acid), which is able to reversibly encapsulate the membrane protein in a 10?nm disc-like structure ideally suited to purification and further biochemical study.     

植物蛋白磷酸酶及其在植物抗逆中的作用

随着多种蛋白磷酸酶在植物中的发现,可逆磷酸化作用在植物各种生理活动中的研究有许多重要的进展。本文概述了蛋白磷酸酶的类型与特点,并着重介绍近年来植物中多种磷酸酶的活性、基因、蛋白等各个水平上的鉴定工作。讨论了几类主要蛋白磷酸酶参与植物抵抗逆境胁迫的有关研究成果。     

植物蛋白磷酸酶及其在植物抗逆中的作用

随着多种蛋白磷酸酶在植物中的发现,可逆磷酸化作用在植物各种生理活动中的研究有许多重要的进展。本文概述了蛋白磷酸酶的类型与特点,并着重介绍近年来植物中多种磷酸酶的活性、基因、蛋白等各个水平上的鉴定工作。讨论了几类主要蛋白磷酸酶参与植物抵抗逆境胁迫的有关研究成果。     

Tau Protein Function in Axonal Formation

Tau protein is a predominantly neuronal microtubule-associated protein that is enriched in axons and is capable of promoting microtubule assembly and stabilization. In the present article we review some of the key experiments directed to obtain insights about tau protein function in developing neurons. Aspects related to whether or not tau has essential, unique, or complementary functions during axonal formation are discussed.     

Review: what can structural classifications reveal about protein evolution?

In this article we present a review of the methods used for comparing and classifying protein structures. We discuss the hierarchies and populations of fold groups and evolutionary families in some of the major classifications and we consider some of the problems confronting any general analyses of structural evolution in protein families. We also review some more recent analyses that have expanded these classifications by identifying sequence relatives in the genomes and thereby reveal interesting trends in fold usage and recurrence.     

Protein inference: a review

Assembling peptides identified from tandem mass spectra into a list of proteins, referred to as protein inference, is a critical step in proteomics research. Due to the existence of degenerate peptides and 'one-hit wonders', it is very difficult to determine which proteins are present in the sample. In this paper, we review existing protein inference methods and classify them according to the source of peptide identifications and the principle of algorithms. It is hoped that the readers will gain a good understanding of the current development in this field after reading this review and come up with new protein inference algorithms.     

FADD adaptor in cancer

FADD (Fas Associated protein with Death Domain) is a key adaptor molecule transmitting the death signal mediated by death receptors. In addition, this multiple functional protein is implicated in survival/proliferation and cell cycle progression. FADD functions are regulated via cellular sublocalization, protein phosphorylation, and inhibitory molecules. In the present review, we focus on the role of the FADD adaptor in cancer. Increasing evidence shows that defects in FADD protein expression are associated with tumor progression both in mice and humans. Better knowledge of the mechanisms leading to regulation of FADD functions will improve understanding of tumor growth and the immune escape mechanisms, and could open a new field for therapeutic interventions.     

Compressibility of protein transitions

We review the results of compressibility studies on proteins and low molecular weight compounds that model the hydration properties of these biopolymers. In particular, we present an analysis of compressibility changes accompanying conformational transitions of globular proteins. This analysis, in conjunction with experimental compressibility data on protein transitions, were used to define the changes in the hydration properties and intrinsic packing associated with native-to-molten globule, native-to-partially unfolded, and native-to-fully unfolded transitions of globular proteins. In addition, we discuss the molecular origins of predominantly positive changes in compressibility observed for pressure-induced denaturation transitions of globular proteins. Throughout this review, we emphasize the importance of compressibility data for characterizing protein transitions, while also describing how such data can be interpreted to gain insight into role that hydration and intrinsic packing play in modulating the stability of and recognition between proteins and other biologically important compounds.     

Engineering of non-conventional yeasts for efficient synthesis of macromolecules: the methylotrophic genera

Methylotrophic yeasts, named after their ability to grow on methanol as the sole carbon source, have raised large interest as recombinant protein factories. In this review, we explain the basic mechanisms underlying this interest and describe the minimal requirements to transform the two genera recognized as methylotrophic, Pichia and Candida, into a powerful protein production tool. We present a comparison between this group of yeasts and the conventional yeasts used as expression system in view of productivity, level of secretion and quality of post-translational modifications. Selected examples of recombinant protein produced by methylotrophic yeast are also included.     

Partial effects of estrogens and 19-nortestoron derivatives]

In the present review the extragenital effects of steroidal estrogens and 19-norandrogen derivatives on mammalian organs and tissues are described. In detail experimental and clinical findings concerning the influence of these compounds on carbohydrate-, lipid- and protein metabolism, on the cardio-vascular system, the blood coagulation, the bone-tissue, the connective-tissue, the central nervous system and the immune system are summarised. These effects are mainly discussed as possible side effects and also as base for new therapeutic concepts.     

Higher-order assemblies in innate immune and inflammatory signaling: A general principle in cell biology

Higher-order supramolecular complexes–dubbed signalosomes carry out key signaling and effector functions in innate immunity and inflammation. In this review, we present several recently discovered signalosomes that are formed either by stable protein–protein interactions or by dynamic liquid–liquid phase separation. Structural features of these signalosomes are highlighted to elucidate their functions and biological insights.     

Activity-based probes as a tool for functional proteomic analysis of proteases

Traditional proteomics methodology allows global analysis of protein abundance but does not provide information on the regulation of protein activity. Proteases, in particular, are known for their multilayered post-translational activity regulation that can lead to a significant difference between protease abundance levels and their enzyme activity. To address these issues, the field of activity-based proteomics has been established in order to characterize protein activity and monitor the functional regulation of enzymes in complex proteomes. In this review, we present structural features of activity-based probes for proteases and discuss their applications in proteomic profiling of various catalytic classes of proteases.     

Activity-based probes as a tool for functional proteomic analysis of proteases

Traditional proteomics methodology allows global analysis of protein abundance but does not provide information on the regulation of protein activity. Proteases, in particular, are known for their multilayered post-translational activity regulation that can lead to a significant difference between protease abundance levels and their enzyme activity. To address these issues, the field of activity-based proteomics has been established in order to characterize protein activity and monitor the functional regulation of enzymes in complex proteomes. In this review, we present structural features of activity-based probes for proteases and discuss their applications in proteomic profiling of various catalytic classes of proteases.     

Heterologous protein production in the yeast Kluyveromyces lactis

Kluyveromyces lactis is both scientifically and biotechnologically one of the most important non-Saccharomyces yeasts. Its biotechnological significance builds on its history of safe use in the food industry and its well-known ability to produce enzymes like lactase and bovine chymosin on an industrial scale. In this article, we review the various strains, genetic techniques and molecular tools currently available for the use of K. lactis as a host for protein expression. Additionally, we present data illustrating the recent use of proteomics studies to identify cellular bottlenecks that impede heterologous protein expression.     

Tau phosphorylation and aggregation in Alzheimer's disease pathology

In this article I shall review how tau phosphorylation and aggregation participates in Alzheimer's disease (AD) and other tauopathies. Tau, a microtubule associated protein, is the main component, in phosphorylated form, of the aberrant paired helical filaments found in AD. Tau is present in phosphorylated and aggregated form not only in AD, but in other pathologies (tauopathies). In this review, the phosphorylation of tau, its aggregation, and the possible relation between tau phosphorylation and aggregation is, briefly, described. Also, it is discussed the toxicity of modified tau. In addition, I propose a working model detailing the progression of tau pathologies.