治疗性克隆研究的进展，机遇和挑战

治疗性克隆为很多疾病的治疗提供了新的策略 . 以韩国科学家最近在这一领域的突破性进展为基点,回顾近年来这一领域的主要进展,着重对“核移植重编程”以及“人胚胎干细胞的建系,扩增和分化”这两个治疗性克隆策略中的关键问题进行评述,并对治疗性克隆的发展前景和目前所遇到的挑战进行了展望 .     

Transcription factors do it together: the hows and whys of studying protein-protein interactions

Protein–protein interactions are intrinsic to virtually every cellular process. Recent breakthroughs in techniques to study protein-interaction and the availability of fully sequenced plant genomes have attracted many plant scientists to undertake the first steps in the field of protein interactions. High-throughput screening systems allow the discovery of protein functions. Even without performing laborious functional assays, in planta functional homologues and redundant proteins can be accurately predicted based on protein-interaction maps. Therefore, protein–protein-interaction screenings are an essential supplement to the current functional-genomics toolbox.     

Expanded bed adsorption of protein with DEAE Spherodex M

In this article, the bed expansion behavior and the hydrodynamic and protein adsorption properties of the DEAE Spherodex M in expanded bed with mobile phases of different viscosities have been studied. The axial liquid-phase dispersion coefficient is found to be on the order of 10(-6) m(2)/s, falling into the common range from 1.0 x 10(-6) to 1.0 x 10(-5) m(2)/s observed previously in expanded bed operation. Because of the small size of the adsorbent, the high pore diffusivity of protein and the favorable column efficiency (low dispersion coefficient), the dynamic binding capacity (DBC) of bovine serum albumin (BSA) at 5% breakthrough in the expanded bed reaches over 80% that of the equilibrium adsorption density (EAD). Moreover, a theoretical model with unadjustable model parameters is used for the prediction of the breakthrough curves. Computer simulations show that the model agrees well with the experimental results at breakthrough less than about 50%. It indicates that the model is promising in the prediction of protein breakthrough behavior because breakthrough profiles at 5-50% breakthrough points are more important in practical applications.     

Biopharmaceutical liquid formulation: a review of the science of protein stability and solubility in aqueous environments

Formulation scientists employed in the biopharmaceutical industry face the challenge of creating liquid aqueous formulations for proteins that never had evolutionary pressure to be exceptionally stable or soluble. Yet commercial products usually need a shelf life of 2 years to be economically viable. The research done in this field is dominated by physical chemists who have developed theories like preferential interaction, preferential hydration and excluded volume to explain the mechanisms for the interaction between salt, small organic molecules and proteins. This review aims to translate the research findings on protein stability and solubility produced by the physical chemists and make it accessible to formulation scientists working within the biopharmaceutical industry.     

大规模蛋白质相互作用组实验技术及其应用

大规模蛋白质相互作用研究的主要实验技术包括酵母双杂交技术、串联亲和纯化技术和蛋白质芯片技术,随着这些技术的不断发展和完善,科学家们在模式生物、哺乳动物、病原微生物中展开了大规模的蛋白质相互作用组研究,并进行了药物研发方面的研究,绘制了多种生物的蛋白质相互作用连锁图,揭示了多种蛋白质的新功能,为全面研究蛋白质（群）的分子作用机制、药物研发和疾病的临床预防与治疗等提供了崭新的线索。     

Automated technologies and novel techniques to accelerate protein crystallography for structural genomics

The sequence infrastructure that has arisen through large-scale genomic projects dedicated to protein analysis, has provided a wealth of information and brought together scientists and institutions from all over the world. As a consequence, the development of novel technologies and methodologies in proteomics research is helping to unravel the biochemical and physiological mechanisms of complex multivariate diseases at both a functional and molecular level. In the late sixties, when X-ray crystallography had just been established, the idea of determining protein structure on an almost universal basis was akin to an impossible dream or a miracle. Yet only forty years after, automated protein structure determination platforms have been established. The widespread use of robotics in protein crystallography has had a huge impact at every stage of the pipeline from protein cloning, over-expression, purification, crystallization, data collection, structure solution, refinement, validation and data management- all of which have become more or less automated with minimal human intervention necessary. Here, recent advances in protein crystal structure analysis in the context of structural genomics will be discussed. In addition, this review aims to give an overview of recent developments in high throughput instrumentation, and technologies and strategies to accelerate protein structure/function analysis.     

The 2002 Olympic Games of protein structure prediction

The summer of every even year is considered by the protein structure prediction community as the Olympic Games season, because in addition to a number of continuous benchmarking experiments such as LiveBench, much effort is invested in the blind prediction experiments CASP and CAFASP. Here we report the major advances registered in the field since the last Games of 2000, as measured by the recently completed LiveBench-4 experiment. These results provide a timely measure of the capabilities of current methods and of their expected performance in the upcoming CASP-5 and CAFASP-3 experiments. We also describe the initiation of the two new, community-wide experiments, PDB-CAFASP and MR-CAFASP. These new experiments extend the scope of previous efforts and may have important implications for structural genomics.     

转基因禽蛋——新一代基因工程生物反应器

利用转基因禽蛋作为生物反应器生产重组蛋白可能是未来基因工程最佳的表达系统之一,具有重要的经济价值,已引起越来越多的公司和研究人员的重视。由于禽类转基因的困难,尽管多年来人们在这个领域作过不懈的努力,但至今在其商业化进程方面仍未见有重要的突破。对该领域的研究进展和动向作出简要的评述。     

中国科学家在解析独脚金内酯调控水稻株型的分子机制研究中取得突破性进展

阐明植物激素作用的分子机理一直是植物学研究的前沿和热点。如何调控作物的株型等重要农艺性状是绿色革命的核心内容。最近, 中国科学家在解析新型植物激素独脚金内酯的信号途径和阐明独脚金内酯调控水稻(Oryza sativa)株型的分子机制等方面所取得的重大原创成果入选“2014年度中国科学十大进展”。     

Filamentous fungi as cell factories for heterologous protein production

Filamentous fungi have been used as sources of metabolites and enzymes for centuries. For about two decades, molecular genetic tools have enabled us to use these organisms to express extra copies of both endogenous and exogenous genes. This review of current practice reveals that molecular tools have enabled several new developments. But it has been process development that has driven the final breakthrough to achieving commercially relevant quantities of protein. Recent research into gene expression in filamentous fungi has explored their wealth of genetic diversity with a view to exploiting them as expression hosts and as a source of new genes. Inevitably, the progress in the 'genomics' technology will further develop high-throughput technologies for these organisms.     

Modern analytical ultracentrifugation in protein science: a tutorial review

Analytical ultracentrifugation (AU) is reemerging as a versatile tool for the study of proteins. Monitoring the sedimentation of macromolecules in the centrifugal field allows their hydrodynamic and thermodynamic characterization in solution, without interaction with any matrix or surface. The combination of new instrumentation and powerful computational software for data analysis has led to major advances in the characterization of proteins and protein complexes. The pace of new advancements makes it difficult for protein scientists to gain sufficient expertise to apply modern AU to their research problems. To address this problem, this review builds from the basic concepts to advanced approaches for the characterization of protein systems, and key computational and internet resources are provided. We will first explore the characterization of proteins by sedimentation velocity (SV). Determination of sedimentation coefficients allows for the modeling of the hydrodynamic shape of proteins and protein complexes. The computational treatment of SV data to resolve sedimenting components has been achieved. Hence, SV can be very useful in the identification of the oligomeric state and the stoichiometry of heterogeneous interactions. The second major part of the review covers sedimentation equilibrium (SE) of proteins, including membrane proteins and glycoproteins. This is the method of choice for molar mass determinations and the study of self-association and heterogeneous interactions, such as protein-protein, protein-nucleic acid, and protein-small molecule binding.     

The SecY complex: conducting the orchestra of protein translocation

Like the conductor of an orchestra, the Sec protein translocation channel is the platform needed to bring together the many different players required for the constitutive and obligatory process of protein transport. This conserved membrane channel, termed SecY in bacteria and Sec61 in eukaryotes, creates a ubiquitous protein-conducting pathway by which thousands of newly synthesized polypeptides make their way through the lipid bilayer. The channel is not a simple passive pore, however; it displays remarkable complexity by interacting with numerous soluble partners, including SecA, Syd, FtsY and the ribosome in bacteria. For several decades, scientists have been fascinated by the sophistication and versatility of this transport channel. In this review, we cover the current state of the field including some of the newest and most exciting findings on channel structure and mechanism of action.     

Prediction of protein secondary structure with a reliability score estimated by local sequence clustering

Most algorithms for protein secondary structure prediction are based on machine learning techniques, e.g. neural networks. Good architectures and learning methods have improved the performance continuously. The introduction of profile methods, e.g. PSI-BLAST, has been a major breakthrough in increasing the prediction accuracy to close to 80%. In this paper, a brute-force algorithm is proposed and the reliability of each prediction is estimated by a z-score based on local sequence clustering. This algorithm is intended to perform well for those secondary structures in a protein whose formation is mainly dominated by the neighboring sequences and short-range interactions. A reliability z-score has been defined to estimate the goodness of a putative cluster found for a query sequence in a database. The database for prediction was constructed by experimentally determined, non-redundant protein structures with <25% sequence homology, a list maintained by PDBSELECT. Our test results have shown that this new algorithm, belonging to what is known as nearest neighbor methods, performed very well within the expectation of previous methods and that the reliability z-score as defined was correlated with the reliability of prediction. This led to the possibility of making very accurate predictions for a few selected residues in a protein with an accuracy measure of Q3 > 80%. The further development of this algorithm, and a nucleation mechanism for protein folding are suggested.     

Investigations on protein adsorption to agarose-dextran composite media

A new stationary phase for protein purification was investigated with regard to its performance during capture of selected model proteins. The commercially available matrix consists of a porous agarose backbone, to which dextran is covalently attached. The dextran carries ion-exchange ligands, thus providing a binding space of high ligand density. Breakthrough of various proteins during frontal application to packed beds was measured and the experiments were analyzed in terms of equilibrium and breakthrough capacity. A significant increase of static capacity, as compared with conventional porous matrices, was found. Good dynamic properties allowed utilization of a high percentage of the equilibrium capacity at 10% breakthrough. For all proteins, a decreasing ratio of breakthrough to equilibrium capacity was detected with increasing feed concentration. This observation suggested a significant contribution of solid diffusion to the transport of proteins into the adsorbent particles. The specific architecture of the stationary phase, where the agarose base structure is derivatized with ion-exchange ligand-bearing dextran, may lead to this behavior.     

Lipid metabolism modulation by the P2X7 receptor in the immune system and during the course of infection: new insights into the old view

For decades, scientists have described numerous protein pathways and functions. Much of a protein’s function depends on its interactions with different partners, and those partners can change depending on the cell type or system. The P2X7 receptor (P2X7R) is one such multifunctional protein that is related to multiple partners and signaling pathways. The relationship between P2X7R and different enzymes involved in lipid metabolism represents a relatively new field in P2X7R research. This field of research began in epithelial cells and currently includes immune and nervous cells. The P2X7R-lipid metabolism pathway is related to many biological functions of P2X7R, such as cell death and pathogen clearance, and this signaling pathway may be involved in many functions that are dependent on bioactive lipids. In the present review, we will attempt to summarize data related to the P2X7R-lipid metabolism pathway, focusing on signaling pathways and their biological relevance to the immune system and infection.     

Recent advances in N- and C-terminus cysteine protein bioconjugation

Advances in the site-specific chemical modification of proteins, also referred to as protein bioconjugation, have proved instrumental in revolutionary approaches to designing new protein-based therapeutics. Of the sites available for protein modification, cysteine residues or the termini of proteins have proved especially popular owing to their favorable properties for site-specific modification. Strategies that, therefore, specifically target cysteine at the termini offer a combination of these favorable properties of cysteine and termini bioconjugation. In this review, we discuss these strategies with a particular focus on those reported recently and provide our opinion on the future direction of the field.     

Application of magnetic agarose support in liquid magnetically stabilized fluidized bed for protein adsorption

A novel magnetic agarose support (MAS) was fabricated for application in a liquid magnetically stabilized fluidized bed (MSFB). It was produced by water-in-oil emulsification method using a mixture of agarose solution and nanometer-sized superparamagnetic Fe(3)O(4) particles as the aqueous phase. The MAS showed good superparamagnetic responsiveness in a magnetic field. A reactive triazine dye, Cibacron blue 3GA (CB), was coupled to the gel to prepare a CB-modified magnetic agarose support (CB-MAS) for protein adsorption. Lysozyme was used as a model protein to test the adsorption equilibrium and kinetic behavior of the CB-MAS. The dependence of bed expansion in the MSFB with a transverse magnetic field on liquid velocity and magnetic field intensity was investigated. Liquid-phase dispersion behavior in the MSFB was examined by measurements of residence time distributions and compared with that obtained in packed and expanded beds. Dynamic lysozyme adsorption in the MSFB was also compared with those in packed and expanded beds. The dynamic binding capacity at 10% breakthrough was estimated at 55.8 mg/mL in the MSFB, higher than that in the expanded bed (31.1 mg/mL) at a liquid velocity of 45 cm/h. The results indicate that the CB-MAS is promising for use in liquid MSFB for protein adsorption.     

50 Years of poly(ADP-ribosyl)ation

The seminal paper published in 1963 by Chambon, Weil and Mandel reporting a new NAD-dependent protein modification now known as poly(ADP-ribosyl)ation (PARylation) marked the launch of a new era in both protein research and cell biology. In the coming decades, the identity, biochemical characteristics and regulation of enzymes responsible for the synthesis and degradation of protein-bound poly(ADP-ribose) have been discovered and the surprisingly multifarious biological roles of PARylation have not ceased to amaze cell and molecular biologists ever since. The review series on PARylation following this preface is comprised of ten papers written by great experts of the field and aims to provide practicing physicians and basic scientists with the state-of-the-art on the “writers, readers and erasers” of poly(ADP-ribose), some recent paradigm shifts of the field and its translational potential.     

Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model

A new, efficient method for the assembly of protein tertiary structure from known, loosely encoded secondary structure restraints and sparse information about exact side chain contacts is proposed and evaluated. The method is based on a new, very simple method for the reduced modeling of protein structure and dynamics, where the protein is described as a lattice chain connecting side chain centers of mass rather than Cαs. The model has implicit built-in multibody correlations that simulate short- and long-range packing preferences, hydrogen bonding cooperativity and a mean force potential describing hydrophobic interactions. Due to the simplicity of the protein representation and definition of the model force field, the Monte Carlo algorithm is at least an order of magnitude faster than previously published Monte Carlo algorithms for structure assembly. In contrast to existing algorithms, the new method requires a smaller number of tertiary restraints for successful fold assembly; on average, one for every seven residues as compared to one for every four residues. For example, for smaller proteins such as the B domain of protein G, the resulting structures have a coordinate root mean square deviation (cRMSD), which is about 3 Å from the experimental structure; for myoglobin, structures whose backbone cRMSD is 4.3 Å are produced, and for a 247-residue TIM barrel, the cRMSD of the resulting folds is about 6 Å. As would be expected, increasing the number of tertiary restraints improves the accuracy of the assembled structures. The reliability and robustness of the new method should enable its routine application in model building protocols based on various (very sparse) experimentally derived structural restraints. Proteins 32:475–494, 1998. © 1998 Wiley-Liss, Inc.     

Tuning microbial hosts for membrane protein production

The last four years have brought exciting progress in membrane protein research. Finally those many efforts that have been put into expression of eukaryotic membrane proteins are coming to fruition and enable to solve an ever-growing number of high resolution structures. In the past, many skilful optimization steps were required to achieve sufficient expression of functional membrane proteins. Optimization was performed individually for every membrane protein, but provided insight about commonly encountered bottlenecks and, more importantly, general guidelines how to alleviate cellular limitations during microbial membrane protein expression. Lately, system-wide analyses are emerging as powerful means to decipher cellular bottlenecks during heterologous protein production and their use in microbial membrane protein expression has grown in popularity during the past months.