染色质重塑复合物

人基因组伸展开来长约 1 .8米 ,而人细胞核的直径不到 6微米 ,ＤＮＡ在细胞核中以核小体的形式被高度压缩。这种结构在保证遗传物质稳定性的同时也阻碍了其它生物大分子接近ＤＮＡ双螺旋。许多重要生命过程的发生又都依赖功能大分子与ＤＮＡ的相互作用。机体内必然存在使核小体稳定性发生变化的调节机制以适应不同情况的需要。通常把染色质和单个核小体内发生的任何可检测到的变化称为染色质重塑。对核心组蛋白尾部的修饰 ,尤其是乙酰化修饰 ,与染色质结构变化密切相关。另有一类复合物也可以改变核小体稳定性 ,它们都含有一个ＤＮＡ依赖的…     

Protein Complexes in Bacteria

Large-scale analyses of protein complexes have recently become available for Escherichia coli and Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometry-characterized protein complexes with the 285 “gold standard” protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: well-conserved complexes, complexes with a conserved core, and complexes with partial conservation but no conserved core. Expanding the comparison to 894 distinct bacterial genomes illustrates fractional conservation and the limits of co-conservation among components of protein complexes: just 14 out of 285 model protein complexes are perfectly conserved across 95% of the genomes used, yet we predict more than 180 may be partially conserved across at least half of the genomes. No clear relationship between gene essentiality and protein complex conservation is observed, as even poorly conserved complexes contain a significant number of essential proteins. Finally, we identify 183 complexes containing well-conserved components and uncharacterized proteins which will be interesting targets for future experimental studies.     

Benchmarking Human Protein Complexes to Investigate Drug-Related Systems and Evaluate Predicted Protein Complexes

Protein complexes are key entities to perform cellular functions. Human diseases are also revealed to associate with some specific human protein complexes. In fact, human protein complexes are widely used for protein function annotation, inference of human protein interactome, disease gene prediction, and so on. Therefore, it is highly desired to build an up-to-date catalogue of human complexes to support the research in these applications. Protein complexes from different databases are as expected to be highly redundant. In this paper, we designed a set of concise operations to compile these redundant human complexes and built a comprehensive catalogue called CHPC2012 (Catalogue of Human Protein Complexes). CHPC2012 achieves a higher coverage for proteins and protein complexes than those individual databases. It is also verified to be a set of complexes with high quality as its co-complex protein associations have a high overlap with protein-protein interactions (PPI) in various existing PPI databases. We demonstrated two distinct applications of CHPC2012, that is, investigating the relationship between protein complexes and drug-related systems and evaluating the quality of predicted protein complexes. In particular, CHPC2012 provides more insights into drug development. For instance, proteins involved in multiple complexes (the overlapping proteins) are potential drug targets; the drug-complex network is utilized to investigate multi-target drugs and drug-drug interactions; and the disease-specific complex-drug networks will provide new clues for drug repositioning. With this up-to-date reference set of human protein complexes, we believe that the CHPC2012 catalogue is able to enhance the studies for protein interactions, protein functions, human diseases, drugs, and related fields of research. CHPC2012 complexes can be downloaded from http://www1.i2r.a-star.edu.sg/xlli/CHPC2012/CHPC2012.htm.     

Nucleoprotein Complexes Containing Replicating Simian Virus 40 DNA: Comparison with Polyoma Nucleoprotein Complexes

Procedures for isolating nucleoprotein complexes containing replicating polyoma DNA from infected mouse cells were used to prepare short-lived nucleoprotein complexes (r-SV40 complexes) containing replicating simian virus 40 (SV40) DNA from infected monkey cells. Like the polyoma complexes, r-SV40 complexes were only partially released from nuclei by cell lysis but could be extracted from nuclei by prolonged treatment with solutions containing Triton X-100. r-SV40 complexes sedimented faster than complexes containing SV40 supercoiled DNA (SV40 complex) in sucrose gradients, and both types of SV40 nucleoprotein complexes sedimented ahead of polyoma complexes containing supercoiled polyoma DNA (py complex). The sedimentation rates of py complex and SV40 complex were 56 and 61S, respectively, based on the sedimentation rate of the mouse large ribosomal subunit as a marker. r-SV40 complexes sedimented as multiple peaks between 56 and 75S. Sedimentation and buoyant density measurements indicated that protein is bound to all forms of SV40 DNA at about the same ratio of protein to DNA (1-2/1) as was reported for polyoma nucleoproteins.     

Immune Complexes in Cystic Fibrosis

Circulating immune complexes were detected in serum and sputum of patients with cystic fibrosis (C.F.). There were extensive deposits of immunoglobulins and complement immune complexes in several of the C.F. organs, especially the respiratory and gastrointestinal tracts, but not in the kidneys. Significant concentrations of IgG and of complement complexes could be eluted from the lungs of the C.F. patients but not from those of controls. Studies involving immunoabsorption, autoradiography, and molecular sieving through Sephadex G-200 columns identified both bovine serum albumin and staphylococcal α-haemolysin as two of the antigens present in the immune complexes. The sedimentation constant of the immune complexes was about 8S to 11S. The clinical significance of these immune complexes and the wide variety of antibodies detected in C.F. patients are discussed.     

Electrostatic Interactions in Aminoglycoside-RNA Complexes

Electrostatic interactions often play key roles in the recognition of small molecules by nucleic acids. An example is aminoglycoside antibiotics, which by binding to ribosomal RNA (rRNA) affect bacterial protein synthesis. These antibiotics remain one of the few valid treatments against hospital-acquired infections by Gram-negative bacteria. It is necessary to understand the amplitude of electrostatic interactions between aminoglycosides and their rRNA targets to introduce aminoglycoside modifications that would enhance their binding or to design new scaffolds. Here, we calculated the electrostatic energy of interactions and its per-ring contributions between aminoglycosides and their primary rRNA binding site. We applied either the methodology based on the exact potential multipole moment (EPMM) or classical molecular mechanics force field single-point partial charges with Coulomb formula. For EPMM, we first reconstructed the aspherical electron density of 12 aminoglycoside-RNA complexes from the atomic parameters deposited in the University at Buffalo Databank. The University at Buffalo Databank concept assumes transferability of electron density between atoms in chemically equivalent vicinities and allows reconstruction of the electron densities from experimental structural data. From the electron density, we then calculated the electrostatic energy of interaction using EPMM. Finally, we compared the two approaches. The calculated electrostatic interaction energies between various aminoglycosides and their binding sites correlate with experimentally obtained binding free energies. Based on the calculated energetic contributions of water molecules mediating the interactions between the antibiotic and rRNA, we suggest possible modifications that could enhance aminoglycoside binding affinity.     

Complexes in ternary cholesterol-phospholipid mixtures

Recent work by Veatch and Keller has described micron-scale liquid-liquid immiscibility in giant unilamellar vesicles composed of ternary mixtures of cholesterol, dipalmitoylphosphatidylcholine (DPPC), and dioleoylphosphatidylcholine (DOPC). Significantly, they do not observe micron-scale immiscibility in any of the three corresponding binary mixtures under the same conditions. It is shown here that this unexpected result can be accounted for by the formation of a complex between cholesterol and DPPC. The complex is miscible with DPPC and cholesterol, and immiscible with DOPC. A simple, idealized thermodynamic treatment of this model leads to theoretical ternary phase diagrams that are similar to the experimental diagram reported by Veatch and Keller. The model also accounts for significant qualitative features of the deuterium NMR spectra of these mixtures in bilayers.     

Functional Characterization of Septin Complexes

Septins belong to a family of conserved GTP-binding proteins found in majority of eukaryotic species except for higher plants. Septins form nonpolar complexes that further polymerize into filaments and associate with cell membranes, thus comprising newly acknowledged cytoskeletal system. Septins participate in a variety of cell processes and contribute to various pathophysiological states, including tumorigenesis and neurodegeneration. Here, we review the structural and functional properties of septins and the regulation of their dynamics with special emphasis on the role of septin filaments as a cytoskeletal system and its interaction with actin and microtubule cytoskeletons. We also discuss how septins compartmentalize the cell by forming local protein-anchoring scaffolds and by providing barriers for the lateral diffusion of the membrane proteins.     

Getting a Grip on Complexes

We are witnessing tremendous advances in our understanding of the organization of life. Complete genomes are being deciphered with ever increasing speed and accuracy, thereby setting the stage for addressing the entire gene product repertoire of cells, towards understanding whole biological systems. Advances in bioinformatics and mass spectrometric techniques have revealed the multitude of interactions present in the proteome. Multiprotein complexes are emerging as a paramount cornerstone of biological activity, as many proteins appear to participate, stably or transiently, in large multisubunit assemblies. Analysis of the architecture of these assemblies and their manifold interactions is imperative for understanding their function at the molecular level. Structural genomics efforts have fostered the development of many technologies towards achieving the throughput required for studying system-wide single proteins and small interaction motifs at high resolution. The present shift in focus towards large multiprotein complexes, in particular in eukaryotes, now calls for a likewise concerted effort to develop and provide new technologies that are urgently required to produce in quality and quantity the plethora of multiprotein assemblies that form the complexome, and to routinely study their structure and function at the molecular level. Current efforts towards this objective are summarized and reviewed in this contribution.Key Words: Proteome, interactome, multiprotein assemblies, structural genomics, robotics, multigene expression, multiBac, BEVS, ACEMBL, complexomics.     

BK通道功能性复合体的研究进展

离子通道可以与其他蛋白质耦合形成稳定的大分子复合物,以确保信号转导的效率和准确性。大电导、钙离子激活的钾离子通道（BK通道）的核心是由形成孔区的d亚基组成的四聚体,它具有BK通道的基本生理功能。在不同的组织内,BKα可以与不同的辅助性亚基结合,使通道功能变得复杂多样。BK通道可以将细胞兴奋性与细胞内的钙离子信号联接在一起,在血流、泌尿、免疫、神经递质释放等许多生命过程中发挥着重要的调节作用。近年来,大量的研究工作表明。BK通道可以与钙离子通道、细胞骨架蛋白、蛋白激酶等生物大分子形成功能性复合物,这对通道功能调控和信号转导等生命活动具有重要的生理意义。本文综述了这些BK通道功能复合体的主要分类、功能特性以及生理学意义,并对其未来的研究前景进行展望。     

BK通道功能性复合体的研究进展

离子通道可以与其他蛋白质耦合形成稳定的大分子复合物,以确保信号转导的效率和准确性。大电导、钙离子激活的钾离子通道(BK通道)的核心是由形成孔区的α亚基组成的四聚体,它具有BK通道的基本生理功能。在不同的组织内,BKα可以与不同的辅助性亚基结合,使通道功能变得复杂多样。BK通道可以将细胞兴奋性与细胞内的钙离子信号联接在一起,在血流、泌尿、免疫、神经递质释放等许多生命过程中发挥着重要的调节作用。近年来,大量的研究工作表明,BK通道可以与钙离子通道、细胞骨架蛋白、蛋白激酶等生物大分子形成功能性复合物,这对通道功能调控和信号转导等生命活动具有重要的生理意义。本文综述了这些BK通道功能复合体的主要分类、功能特性以及生理学意义,并对其未来的研究前景进行展望。     

Complexes of bilirubin with proteins

Complexes of bilirubin with chymotrypsin, lysozyme and apomyoglobin in neutral aqueous solution are characterized by circular dichroism spectra in the visible region. These are analogous to previously investigated bilirubin-serum albumin complexes. Ferriprotoporphyrin IX displaces bilirubin from its apomyoglobin complex.     

Structure of Pna-Nucleic Acid Complexes

Abstract

The solution structure of the PNA-DNA hybrid H-GCTATGTC-NH₂d(GACATAGC), determined by NMR methods, shows a new conformation which has elements of both A- and B-form DNA. Comparison with other PNA-nucleic acid complexes points to common structural features, but also demonstrates the ability of PNA to conform to nucleic acid partners of different conformations.