Assisting functional assignment for hypothetical Heamophilus influenzae gene products through structural genomics

The three-dimensional structures of Haemophilus influenzae proteins whose biological functions are unknown are being determined as part of a structural genomics project to ask whether structural information can assist in assigning the functions of proteins. The structures of the hypothetical proteins are being used to guide further studies and narrow the field of such studies for ultimately determining protein function. An outline of the structural genomics methodological approach is provided along with summaries of a number of completed and in progress crystallographic and NMR structure determinations. With more than twenty-five structures determined at this point and with many more in various stages of completion, the results are encouraging in that some level of functional understanding can be deduced from experimentally solved structures. In addition to aiding in functional assignment, this effort is identifying a number of possible new targets for drug development.     

以整合素为作用靶点的精氨酸-甘氨酸-天冬氨酸模体毒素研究进展

整合素为一类αβ异源二聚体膜蛋白,调节细胞外基质与胞内细胞骨架间的相互作用。精氨酸-甘氨酸-天冬氨酸（RGD）序列为整合素的结合位点,存在于多种重要的细胞外基质蛋白中。整合素与RGD序列结合可调节多种细胞生理活动,RGD模体还存在于来自蛇毒和其他物种来源的多种毒素蛋白中,这些RGD模体毒素能够特异性抑制整合素与细胞外基质的结合,从而成为整合素的强效拮抗剂。本文对整合素的结构与功能、去整合素作为整合素拮抗剂的结构特征做一综述,并对整合素和以RGD为模体结构作为潜在药物靶点的应用加以讨论。     

Creating the next generation of protein therapeutics through rational drug design

Biopharmaceuticals, or protein drugs, have proven to be safe and effective therapies in many disease indications. However, the first generation of biopharmaceuticals has largely been limited to replicating the functions of native human proteins, or inhibiting these functions through the use of monoclonal antibodies. Recent advances in the design of biopharmaceuticals include computational approaches to manipulate protein structure, improved screening processes to synthesize and assay libraries of novel proteins, and new methods to modify proteins post-translationally and during production. Protein drug structure and function can now be optimized in the same way that small molecules are optimized via medicinal chemistry. This review addresses recent developments in the field of protein 'medicinal biology', and provides examples of how these tools are being applied to create the next generation of biopharmaceuticals possessing optimized drug properties and novel functions.     

Insights into immunophilin structure and function

The immunophilins are proteins which are capable of influencing the immune response in combination with an immunosuppressive drug. Their natural function, however, is mainly the cis/trans isomerization of peptidyl-prolyl bonds in other proteins. This review lists all immunophilin structure coordinates currently available in the RCSB protein data bank and highlights the key active-site factors that define their catalytic and immunological action. In addition, an overview of biologically-relevant functions is provided for various immunophilin members.     

细菌脂蛋白生物合成调控研究进展

细菌脂蛋白是一组具有多种功能的膜蛋白。由于其广泛的功能，这些蛋白质对细菌的正常生长、分化和发育是必须的。脂蛋白的经典生物合成路径需要细胞质膜的3种酶：前脂蛋白二酰甘油基转移酶(Lgt)，脂蛋白信号肽酶Ⅱ(LspA)和脂蛋白N-酰基转移酶(Lnt)相继发挥催化作用，产生成熟的三酰化脂蛋白。这3种酶的缺失会导致革兰阴性菌的死亡及革兰阳性菌活力和致病能力的下降，并且这3种酶是原核生物所特有的，在人体中无同源类似物。因此这些酶是下一代广谱抗生素研发的潜在靶标。近几年来，这些酶的晶体结构已被相继解析出来，从而可以开展基于结构的药物设计。本文主要综述细菌脂蛋白生物合成路径以所涉及到的3种酶的晶体结构和生物学功能。     

The structure and function of histone deacetylases: the target for anti-cancer therapy

Histone deacetylases (HDACs) and Histone acetyltransferases (HATs) are two kinds of enzymes, which can, by reversible deacetylation and acetylation, modify the structure and function of chromatin histones that are involved in the regulation of gene expression, as well as many non-histone proteins that regulate cell function in eukaryotes. Compared with HATs, HDACs have attracted more and more attentions for two main reasons over the past few years. First, the relationship of HDACs and cancer, as well as several other diseases has been confirmed. Second, many HDAC inhibitors (HDACi) have entered pre-clinical or clinical research as anti-cancer agents and shown satisfying effects. HDACs, including 18 members at least, are subdivided into 4 classes that generally have high structure similarity and related substrate specificity within classes, but have divergent sequence and different functions even between within classes. This review will introduce the relationship between HDACs and cancer along with the enzymes' structure and main function.     

RNA as a small-molecule drug target: doubling the value of genomics

Recent advances in the determination of RNA structure and function have led to new opportunities that will have a significant impact on the pharmaceutical industry. RNA, which, among other functions, serves as a messenger between DNA and proteins, was thought to be an entirely flexible molecule without significant structural complexity. However, recent studies have revealed a surprising intricacy in RNA structure. This observation unlocks opportunities for the pharmaceutical industry to target RNA with small molecules. Because both proteins and their specific mRNAs are potential drug-binding sites, the number of targets revealed from genome sequencing efforts is effectively doubled. Perhaps more importantly, drugs that bind to RNA might produce effects that cannot be achieved by drugs that bind to proteins.     

Antibacterial and antiviral effects of milk proteins and derivatives thereof

Milk forms a rich source of biologically interesting components. In particular, its protein fraction is known to encompass many kinds of biological functions. In this review we focus on antibacterial and antiviral properties of milk proteins and milk protein derivatives. The latter include chemically modified proteins and enzymatically induced peptides. If such peptides are released by enzymes present within the digestive tract (e.g. trypsin or pepsin), it is likely that they play a role in the health defense system. This is especially the case when the active fragments can survive the intestinal conditions long enough to arrive at the right place to exert their beneficial function. In the first part of this paper attention is paid to the antibacterial proteins lactoferrin, lactoperoxidase, and lysozyme. Furthermore, antibacterial peptides originating from caseins and whey proteins are described. The second part reports on studies of antiviral effects of milk proteins and derivatives thereof. Special focus is directed to the antiviral action towards the human immunodeficiency virus (HIV) and the human cytomegalovirus (HCMV). Unmodified milk proteins are generally not active against these viruses. An exception is lactoferrin, which shows significant antiviral activity against both HIV and HCMV. Several other milk proteins tested showed strong antiviral effects only after chemical modification, i.e. by making them polyanionic (for anti-HIV activity) or polycationic (for anti-HCMV activity). In a number of cases, conclusions are drawn concerning possible relationships between antibacterial/antiviral activity and molecular structure of the components described.     

细菌ClpP蛋白酶功能及其抗菌药物靶点的研究进展

摘要：ClpP(Casein lytic proteinase P)是一种广泛存在于真核细胞和原核生物中的丝氨酸蛋白酶，可与多种类型AAA+ (ATPase associated with various cellular activity)超家族ATP酶组成多种ClpP蛋白酶复合物，其主要功能是清除或降解细菌胞内合成不当、受损伤、变性聚集或无用的蛋白，并维持正常代谢和压力刺激下胞内蛋白质的动态平衡。近年研究表明，细菌ClpP可协助病原菌在宿主体内生存、繁殖和播散，ClpP在细菌致病过程中发挥重要作用，其相关致病机制也受到广泛关注。近年，细菌对抗生素耐药性不断增强，已严重威胁人类健康，ClpP蛋白酶因其独特的蛋白水解作用而成为抗菌药物研究的新靶点。本文综述了ClpP在不同病原体中的结构、分子功能和不同作用以及相应药物开发方面的研究进展。     

Using property based sequence motifs and 3D modeling to determine structure and functional regions of proteins

Homology modeling has become an essential tool for studying proteins that are targets for medical drug design. This paper describes the approach we developed that combines sequence decomposition techniques with distance geometry algorithms for homology modeling to determine functionally important regions of proteins. We show here the application of these techniques to targets of medical interest chosen from those included in the CASP5 (Critical Assessment of Techniques for Protein Structure Prediction) competition, including the dihydroneopterin aldolase from Mycobacterium tuberculosis, RNase III of Thermobacteria maritima, and the NO-transporter nitrophorin from saliva of the bedbug Cimex lectularius. Physical chemical property (PCP) motifs, identified in aligned sequences with our MASIA program, can be used to select among different alignments returned by fold recognition servers. They can also be used to suggest functions for hypothetical proteins, as we illustrate for target T188. Once a suitable alignment has been made with the template, our modeling suite MPACK generates a series of possible models. The models can then be selected according to their match in areas known to be conserved in protein families. Alignments based on motifs can improve the structural matching of residues in the active site. The quality of the local structure of our 3D models near active sites or epitopes makes them useful aids for drug and vaccine design. Further, the PCP motif approach, when combined with a structural filter, can be a potent way to detect areas involved in activity and to suggest function for novel genome sequences.     

Trial to predict interactions between proteins and biomolecules based on their three-dimensional structures

A vast amount of DNA sequence data, protein three-dimensional (3D) structure data, and RNA expression data have been produced by the efforts of genome sequencing, structural genomics, and omics projects, and we are at the stage where comprehensive views of cell activity and molecular mechanisms of life can be deduced. But in reality, we are inundated with massive amounts of data and are still in the process of finding ways to fully utilize the data. In this report, I would like to present our observations on the growth of protein 3D structure data and our effort to deduce the functions from the 3D structures. We found that the 3D structure of quite a high proportion of proteins derived from genome sequences can be now predicted and methods to predict the functions from 3D structures are in high demand. The methods we have developed can be used to predict some functions, namely RNA and ligand interfaces, based on those 3D structures and DNA sequences with relatively high accuracy. The methods enable predictions that are accurate enough to help with deducing the atomic structures of the complexes.     

The role of neuropeptides in sleep modulation

Several neuropeptides affect the sleep-wake cycle, for example, vasoactive intestinal polypeptide, cholecystokinin octapeptide, orexin, somatostatin, insulin, leptin, ghrelin, neuropeptide Y and cortistatin, which regulate food ingestion. There are also proteins from the immunological system: tumor necrosis factor-alpha, interleukin (IL)-1beta IL-4, IL-10, IL-13, as well as trophic molecules, such as growth hormone-releasing hormone, growth hormone, prolactin, brain-derived neurotrophic factor and nerve growth factor, neurotrophin-3 and neurotrophin-4. Based on this information, we believe that some functions of sleep can be suggested. One of these functions could be the regulation of energy, since many, if not all, of the neuropeptides that regulate feeding affect the level of alertness. Likewise, the immunological system and the trophic molecules establish a dialog with the brain during sleep in order to reestablish neuronal structure. These proteins are the expression of genes that accomplish the function of regulating our waking and our sleep, suggesting the important control the genome is exerting on this activity.     

Interactions of hepatotoxic agents with proteins and subcellular structures

Two proteins with high affinity for amatoxins have been characterized in calf thymus nucleic, the RNA-polymerase II (or B) and a 100 K protein of unknown function. Most of the toxic effects of amatoxins are based on the inhibited synthesis of mRNA. The 100 K protein may be involved in functions of cytokinesis as suggested by experiments with PtK1 cells and a fluorescent labelled amatoxin. The molecular toxicity of phallotoxins can be understood in terms of their affinity for actin. By interaction with rabbit muscle actin the concentration of action monomers is decreased. In hepatocytes, the phallotoxins change the structure of the microfilamentous web.     

Role of Ena/VASP proteins in homeostasis and disease

The actin cytoskeleton is required for many important processes during embryonic development. In later stages of life, important homeostatic processes depend on the actin cytoskeleton, such as immune response, haemostasis and blood vessel preservation. Therefore, the function of the actin cytoskeleton must be tightly regulated, and aberrant regulation may cause disease. A growing number of proteins have been described to bind and regulate the actin cytoskeleton. Amongst them, Ena/VASP proteins function as anti-capping proteins, thereby directly modulating the actin ultrastructure. Ena/VASP function is regulated by their recruitment into protein complexes downstream of plasma membrane receptors and by phosphorylation. As regulators of the actin ultrastructure, Ena/VASP proteins are involved in crucial cellular functions, such as shape change, adhesion, migration and cell-cell interaction and hence are important targets for therapeutic intervention. In this chapter, we will first describe the structure, function and regulation of Ena/VASP proteins. Then, we will review the involvement of Ena/VASP proteins in the development of human diseases. Growing evidence links Ena/VASP proteins to important human diseases, such as thrombosis, cancer, arteriosclerosis, cardiomyopathy and nephritis. Finally, present and future perspectives for the development of therapeutic molecules interfering with Ena/VASP-mediated protein-protein interactions are presented.     

Peptide and peptoid foldamers in medicinal chemistry

Introduction: Proteins and other biologics comprise emerging therapeutic class with efficacies against targets for which development of small-molecule antagonists has been unsuccessful. The biological function of a protein is intimately tied to its sequence-dependent folding. A variety of unnatural oligomer backbones show folding behavior analogous to proteins. Often termed 'foldamers,' these compounds have the potential to provide the benefits of existing protein therapeutics while overcoming some drawbacks, such as protease susceptibility. Areas covered: This review surveys work toward the development of foldamer therapeutics based on β-peptides, α-peptoids, β-peptoids and heterogeneous backbones composed of mixtures of these monomers with natural α-residues. Bioactivities targeted by foldamers are diverse but can be broadly divided into two categories: i) functions that require the simple separation of charged and hydrophobic functional groups and ii) functions that require a precise and complex three-dimensional display of side chains in the folded state. Expert opinion: A long-term goal in research on foldamers is to recreate the entire range of structure and function manifested by natural proteins on unnatural backbones. Successes in the development of bioactive foldamers not only show their promise, but also highlight the challenges associated with the invention of general and reliable design strategies. While there is still a long way to go to a clinically used foldamer drug, significant advances in recent years demonstrate the potential of such scaffolds for use in the discovery of new therapeutics.     

Prediction of protein function in the absence of significant sequence similarity

Tremendous progress in DNA sequencing has yielded the genomes of a host of important organisms. The utilisation of these resources requires understanding of the function of each gene. Standard methods of functional assignment involve sequence alignment to a gene of known function; however such methods often fail to find any significant matches. Here we discuss a number of recent alternative methods that may be of use when sequence alignment fails. Function can be defined in a number of ways including E.C. number and MIPS and KEGG functional classes. Phylogenetic profiles show the pattern of presence or absence of a protein between genomes. Protein-protein interactions can be identified by searching for interacting pairs of proteins that are fused to a single protein chain in another organism. The gene neighbour method uses the observation that if the genes that encode two proteins are close on a chromosome, the proteins tend to be functionally related. More general methods use sequence properties such as amino acid composition, mean hydrophobicity, predicted secondary structure and post-translational modification sites. Data mining methods devise rules in the form of IF...THEN statements that make predictions of function using sequence based attributes, predicted secondary structure and sequence similarity. Finally, structural features can be used, after modelling the structure of a protein from its sequence or solving its structure. Protein fold class can be strongly indicative of function, while other structural features, such as secondary structure content, cleft size and 3D structural motifs are also useful.     

Alcohol induced conformational transitions of proteins and polypeptides

Integral enthalpies of solution of diglycine in tert.-butyl alcohol + water and of diglycine and β-alanine in ethanol + water mixtures were measured at 298.15 K as a function of alcohol concentration. Enthalpies of transfer of the solutes from water to aqueous alcohol mixtures were evaluated from these data. Entropies of transfer of a peptide backbone unit (CH₂CONH) and peptide group (CONH) from water to aqueous ethanol solutions were derived from the enthalpy of transfer data and the free energies of transfer of glycine, α-alanine, β-alanine and diglycine. The thermodynamic transfer functions are discussed in terms of “water structure” mediated solute-solute interactions. The observed trends in the thermodynamic transfer functions have also been utilized to rationalize the effect of alcohols on the conformational stability of proteins and polypeptides in aqueous solutions