Cluster Formation of Anchored Proteins Induced by Membrane-Mediated Interaction

Computer simulations were used to study the cluster formation of anchored proteins in a membrane. The rate and extent of clustering was found to be dependent upon the hydrophobic length of the anchored proteins embedded in the membrane. The cluster formation mechanism of anchored proteins in our work was ascribed to the different local perturbations on the upper and lower monolayers of the membrane and the intermonolayer coupling. Simulation results demonstrated that only when the penetration depth of anchored proteins was larger than half the membrane thickness, could the structure of the lower monolayer be significantly deformed. Additionally, studies on the local structures of membranes indicated weak perturbation of bilayer thickness for a shallowly inserted protein, while there was significant perturbation for a more deeply inserted protein. The origin of membrane-mediated protein-protein interaction is therefore due to the local perturbation of the membrane thickness, and the entropy loss—both of which are caused by the conformation restriction on the lipid chains and the enhanced intermonolayer coupling for a deeply inserted protein. Finally, in this study we addressed the difference of cluster formation mechanisms between anchored proteins and transmembrane proteins.     

蛋白冠与纳米粒子的相互作用

近年来,尽管纳米粒子在生物医学领域的研究中取得了巨大的进展,但很少能进入临床试验阶段,其中,很大程度取决于人们缺乏对纳米粒子与生理环境之间相互作用的认知,对纳米粒子进入体内后的生物学特性了解有限。在生理环境下,蛋白质会吸附于纳米粒子表面,从而形成蛋白冠,这种纳米粒子-蛋白冠复合物的形成严重影响纳米粒子的生物学特性,限制了纳米粒子的临床应用,因此,蛋白质与纳米粒子之间的相互作用应该被深入研究。目前,对纳米粒子-蛋白冠复合物的研究属于一个相对较新的研究领域。概括了蛋白冠的研究现状,对蛋白冠与纳米粒子相互作用所产生的影响进行了重点阐述,也介绍了预防和减少蛋白冠形成的方法,为纳米粒子的进一步研发提供了思路。     

Interaction between Plate Make and Protein in Protein Crystallisation Screening

Background

Protein crystallisation screening involves the parallel testing of large numbers of candidate conditions with the aim of identifying conditions suitable as a starting point for the production of diffraction quality crystals. Generally, condition screening is performed in 96-well plates. While previous studies have examined the effects of protein construct, protein purity, or crystallisation condition ingredients on protein crystallisation, few have examined the effect of the crystallisation plate.

Methodology/Principal Findings

We performed a statistically rigorous examination of protein crystallisation, and evaluated interactions between crystallisation success and plate row/column, different plates of same make, different plate makes and different proteins. From our analysis of protein crystallisation, we found a significant interaction between plate make and the specific protein being crystallised.

Conclusions/Significance

Protein crystal structure determination is the principal method for determining protein structure but is limited by the need to produce crystals of the protein under study. Many important proteins are difficult to crystallise, so that identification of factors that assist crystallisation could open up the structure determination of these more challenging targets. Our findings suggest that protein crystallisation success may be improved by matching a protein with its optimal plate make.     

Interaction between Protein Subunits from Model Studies

A molecular model of hemoglobin was constructed which made it possible to visualize the relation between various amino acid residues in the molecule. The model indicates that electrostatic forces might play a significant role in holding the subunits of hemoglobin together. This would explain why myoglobin does not form a tetramer while four β-chains, which are structurally similar to myoglobin, do assemble into a hemoglobin H molecule. Also, as far as the primary structures of hemoglobin chains of various species are known, the proposed ionic links between subunits are consistent with the fact that mammalian hemoglobins form stable tetramers while the peptide chains of lamprey hemoglobin are only weakly associated. The different behavior of hemoglobin H and of normal hemoglobin upon oxygen uptake is briefly discussed in terms of allosteric effects.     

SND1蛋白与HuR蛋白的相互结合作用

人源SND1（staphylococcal nuclease domain containing 1）蛋白由N端的SN（staphylococcal nucleases）结构域和C端的TSN (Tudor SN5) 结构域组成,其中SN结构域又包含SN1～SN4四个重复的功能片段. 本课题组前期研究结果表明,SND1蛋白可以通过SN结构域与G3BP（Ras GAP SH3 domain binding protein）蛋白相互结合,共同参与细胞应激颗粒（stress granules,SGs）的形成. SGs是真核细胞在受到氧化应激、病毒感染等外界刺激时在胞浆内形成的与RNA代谢相关的颗粒状结构. 对于SGs的成分鉴定及相互作用的分析一直是学者们研究的热点. 本研究中,免疫共沉淀实验结果表明,以抗SND1抗体可以共沉淀出HeLa细胞内另一个重要的应激相关人类抗原R（human antigen R,HuR）蛋白. 另外,利用脂质体转染法将pcDNA3 FLAG HuR重组质粒瞬时转染入HeLa细胞,成功过表达外源性的FLAG HuR融合蛋白,再以抗FLAG标签抗体又可以反向共沉淀出内源性SND1蛋白,证明SND1与HuR之间存在蛋白质间的相互结合作用. 细胞免疫荧光实验结果表明,当给予HeLa细胞05 mmol/L亚砷酸钠氧化应激时,SND1与HuR蛋白共同定位于胞浆中的SGs结构中. GST pulldown实验结果进一步表明截短的SN结构域可以结合HuR蛋白,其中以SN1功能片段的结合能力最强,表明SND1蛋白是通过SN结构域与HuR蛋白形成应激复合物,参与SGs的胞浆组装.并不定位于SGs的TSN结构域亦可结合HuR蛋白,提示SND1 HuR的蛋白相互作用可能并不局限于SGs,具有其它方面的功能意义.     

Thermodynamic Framework of the Interaction between Protein and Solvent Drives Protein Folding

Abstract

We use internal coordinate molecular mechanics calculations to study the impact of abasic sites on the conformation and the mechanics of the DNA double helix. Abasic sites, which are common mutagenic lesions, are shown to locally modify both the groove geometry and the curvature of DNA in a sequence dependent manner. By controlled twisting and bending, it is also shown that these lesions modify the deformability of the duplex, generally increasing its flexibility, but again to an extent which depends on the nature of the abasic site and on the surrounding base sequence. Both the conformational and mechanical influence of this type of DNA damage may be significant for recognition and repair mechanisms.     

酪氨酸激酶Jak3与核小体组装蛋白Nap1的相互作用

在白细胞介素－２（ｉｎｔｅｒｌｅｕｋｉｎ－２,ＩＬ－２）的信号转导过程中,酪氨酸激酶Ｊａｋ３起着至关重要的作用。它不但参与Ｊａｋ－Ｓｔａｔ通路的传递,而且通过与一些未知的信号分子相互作用调节一些原癌基因的表达,如ｃ－ｆｏｓ,ｃ－ｍｙｃ等。由于目前越来越多的证据表明在信号转导过程中两个蛋白质之间的相互作用需要磷酸酪氨酸的存在,为此构建了酪氨酸磷酸化相关原酵母双杂交系统,以进一步阐释Ｊａｋ３在ＩＬ－２     

A Pareto-Optimal Refinement Method for Protein Design Scaffolds

Computational design of protein function involves a search for amino acids with the lowest energy subject to a set of constraints specifying function. In many cases a set of natural protein backbone structures, or “scaffolds”, are searched to find regions where functional sites (an enzyme active site, ligand binding pocket, protein – protein interaction region, etc.) can be placed, and the identities of the surrounding amino acids are optimized to satisfy functional constraints. Input native protein structures almost invariably have regions that score very poorly with the design force field, and any design based on these unmodified structures may result in mutations away from the native sequence solely as a result of the energetic strain. Because the input structure is already a stable protein, it is desirable to keep the total number of mutations to a minimum and to avoid mutations resulting from poorly-scoring input structures. Here we describe a protocol using cycles of minimization with combined backbone/sidechain restraints that is Pareto-optimal with respect to RMSD to the native structure and energetic strain reduction. The protocol should be broadly useful in the preparation of scaffold libraries for functional site design.     

Critical Interaction Domains between Bloom Syndrome Protein and RAD51

The American Cancer Society’s 2009 statistics estimate that 1 out of every 4 deaths is cancer related. Genomic instability is a common feature of cancerous states, and an increase in genomic instability is the diagnostic feature of Bloom Syndrome. Bloom Syndrome, a rare disorder characterized by a predisposition to cancer, is caused by mutations of the BLM gene. This study focuses on the partnerships of BLM protein to RAD51, a Homologous Recombination repair protein essential for survival. A systematic set of BLM deletion fragments were generated to refine the protein binding domains of BLM to RAD51 and determine interacting regions of BLM and ssDNA. Results show that RAD51 and ssDNA interact in overlapping regions; BLM_100–214 and BLM_1317–1367. The overlapping nature of these regions suggests a preferential binding for one partner that could function to regulate homologous recombination and therefore helps to clarify the role of BLM in maintaining genomic stability.     

Protein Interaction Networks

The study of protein interactions is playing an ever increasing role in our attempts to understand cells and diseases on a system-wide level. This article reviews several experimental approaches that are currently being used to measure protein–protein, protein–DNA and gene–gene interactions. These techniques have now been scaled up to produce extensive genome-wide data sets that are providing us with a first glimpse of global interaction networks. Complementing these experimental approaches, several computational methodologies to predict protein interactions are also reviewed. Existing databases that serve as repositories for protein interaction information and how such databases are used to analyze high-throughput data from a pathway perspective is also addressed. Finally, current efforts to combine multiple data types to obtain more accurate and comprehensive models of protein interactions are discussed. It is clear that the evolution of these experimental and computational approaches is rapidly changing our view of biology, and promises to provide us with an unprecedented ability to model cells and organisms at a system-wide level.     

A Model for Shaping Membrane Sheets by Protein Scaffolds

Membranes of peripheral endoplasmic reticulum form intricate morphologies consisting of tubules and sheets as basic elements. The physical mechanism of endoplasmic-reticulum shaping has been suggested to originate from the elastic behavior of the sheet edges formed by linear arrays of oligomeric protein scaffolds. The heart of this mechanism, lying in the relationships between the structure of the protein scaffolds and the effective intrinsic shapes and elastic properties of the sheets’ edges, has remained hypothetical. Here we provide a detailed computational analysis of these issues. By minimizing the elastic energy of membrane bending, we determine the effects of a rowlike array of semicircular arclike membrane scaffolds on generation of a membrane fold, which shapes the entire membrane surface into a flat double-membrane sheet. We show, quantitatively, that the sheet’s edge line tends to adopt a positive or negative curvature depending on the scaffold’s geometrical parameters. We compute the effective elastic properties of the sheet edge and analyze the dependence of the equilibrium distance between the scaffolds along the edge line on the scaffold geometry.     

Using Protein Dimers to Maximize the Protein Hybridization Efficiency with Multisite DNA Origami Scaffolds

DNA origami provides a versatile platform for conducting ‘architecture-function’ analysis to determine how the nanoscale organization of multiple copies of a protein component within a multi-protein machine affects its overall function. Such analysis requires that the copy number of protein molecules bound to the origami scaffold exactly matches the desired number, and that it is uniform over an entire scaffold population. This requirement is challenging to satisfy for origami scaffolds with many protein hybridization sites, because it requires the successful completion of multiple, independent hybridization reactions. Here, we show that a cleavable dimerization domain on the hybridizing protein can be used to multiplex hybridization reactions on an origami scaffold. This strategy yields nearly 100% hybridization efficiency on a 6-site scaffold even when using low protein concentration and short incubation time. It can also be developed further to enable reliable patterning of a large number of molecules on DNA origami for architecture-function analysis.     

疏水作用和蛋白质

疏水作用及疏水和亲水的平衡在蛋白质结构与功能的方方面面都起着重要的作用。本文将以此为主题,就４０年来,疏水作用对蛋白质影响的研究作一概要的回顾。１．“疏水作用”这一概念的提出１９５９年,Ｋａｕｚｍａｎｎ在《蛋白质化学进展》上发表了一篇题为“影响蛋白质...     

Studies of the Interaction between Rad52 Protein and the Yeast Single-Stranded DNA Binding Protein RPA

The RFA1 gene encodes the large subunit of the yeast trimeric single-stranded DNA binding protein replication protein A (RPA), which is known to play a critical role in DNA replication. A Saccharomyces cerevisiae strain carrying the rfa1-44 allele displays a number of impaired recombination and repair phenotypes, all of which are suppressible by overexpression of RAD52. We demonstrate that a rad52 mutation is epistatic to the rfa1-44 mutation, placing RFA1 and RAD52 in the same genetic pathway. Furthermore, two-hybrid analysis indicates the existence of interactions between Rad52 and all three subunits of RPA. The nature of this Rad52-RPA interaction was further explored by using two different mutant alleles of rad52. Both mutations lie in the amino terminus of Rad52, a region previously defined as being responsible for its DNA binding ability (U. H. Mortenson, C. Beudixen, I. Sunjeuaric, and R. Rothstein, Proc. Natl. Acad. Sci. USA 93:10729–10734, 1996). The yeast two-hybrid system was used to monitor the protein-protein interactions of the mutant Rad52 proteins. Both of the mutant proteins are capable of self-interaction but are unable to interact with Rad51. The mutant proteins also lack the ability to interact with the large subunit of RPA, Rfa1. Interestingly, they retain their ability to interact with the medium-sized subunit, Rfa2. Given the location of the mutations in the DNA binding domain of Rad52, a model incorporating the role of DNA in the protein-protein interactions involved in the repair of DNA double-strand breaks is presented.     

Interaction between Connexin50 and Mitogen-activated Protein Kinase Signaling in Lens Homeostasis

Both connexins and signal transduction pathways have been independently shown to play critical roles in lens homeostasis, but little is known about potential cooperation between these two intercellular communication systems. To investigate whether growth factor signaling and gap junctional communication interact during the development of lens homeostasis, we examined the effect of mitogen-activated protein kinase (MAPK) signaling on coupling mediated by specific lens connexins by using a combination of in vitro and in vivo assays. Activation of MAPK signaling pathways significantly increased coupling provided by Cx50, but not Cx46, in paired Xenopus laevis oocytes in vitro, as well as between freshly isolated lens cells in vivo. Constitutively active MAPK signaling caused macrophthalmia, cataract, glucose accumulation, vacuole formation in differentiating fibers, and lens rupture in vivo. The specific removal or replacement of Cx50, but not Cx46, ameliorated all five pathological conditions in transgenic mice. These results indicate that MAPK signaling specifically modulates coupling mediated by Cx50 and that gap junctional communication and signal transduction pathways may interact in osmotic regulation during postnatal fiber development.     

SARS-CoV N蛋白与病毒mRNA相互作用的初步研究

SARS冠状病毒(SARS-CoV)是一种新型的冠状病毒,其基因组大小约为30,000 nt,为单股正链RNA.病毒基因中的1-72个核甘酸为前导序列.核衣壳(Nucleocapsid,N)蛋白是冠状病毒的主要结构蛋白,它在病毒基因转录,翻译以及病毒颗粒包装中起重要作用.在本研究中,我们通过PCR的方法从SARS-CoV cDNA中克隆N基因,将基因克隆到大肠杆菌表达载体中,经表达纯化获得大量重组蛋白,通过亲和层析和凝胶过滤层析获得高纯度的N蛋白.同时构建前导RNA的转录模板,经体外转录得到地高辛标记的RNA.使用Northwestern分析技术,我们证实纯化的N蛋白在体外可以与RNA发生特异性的结合.N蛋白与病毒RNA的结合特性及其在病毒生活周期中的所起作用的初步研究,为下一步设计出有效的阻断病毒周期从而达到抗病毒目的的药物或疫苗奠定了基础.     

Functional Interaction between Ribosomal Protein L6 and RbgA during Ribosome Assembly

RbgA is an essential GTPase that participates in the assembly of the large ribosomal subunit in Bacillus subtilis and its homologs are implicated in mitochondrial and eukaryotic large subunit assembly. How RbgA functions in this process is still poorly understood. To gain insight into the function of RbgA we isolated suppressor mutations that partially restored the growth of an RbgA mutation (RbgA-F6A) that caused a severe growth defect. Analysis of these suppressors identified mutations in rplF, encoding ribosomal protein L6. The suppressor strains all accumulated a novel ribosome intermediate that migrates at 44S in sucrose gradients. All of the mutations cluster in a region of L6 that is in close contact with helix 97 of the 23S rRNA. In vitro maturation assays indicate that the L6 substitutions allow the defective RbgA-F6A protein to function more effectively in ribosome maturation. Our results suggest that RbgA functions to properly position L6 on the ribosome, prior to the incorporation of L16 and other late assembly proteins.     

血清蛋白与4,5-二溴荧光素相互作用及其分析应用的研究

在 0 .10mol/mL的醋酸溶液中 ,4,5 二溴荧光素能与血清蛋白形成稳定的复合物 ,最大吸收波长 482nm ,与试剂比较 ,红移了 12nm。据此建立了测定血清蛋白的方法 ,用于BSA和HSA的测定 ,分别在 2～ 14mg·L-1有线性关系 ,表观摩尔吸光系数分别为 3.12× 10 5L·mol-1·cm-1和 3.2 7× 10 5L·mol-1·cm-1。应用该法测定了人血清样品总蛋白含量 ,结果令人满意。