The molten globule protein conformation probed by disulphide bonds

The molten globule is a compact protein conformation that has a secondary structure content like that of the native protein, but poorly defined tertiary structure. It is a stable state for a few proteins under particular conditions and could be a ubiquitous kinetic intermediate in protein folding. The extent to which native interactions, above the level of the secondary structure, are preserved in this conformation is not so far known. Here we report that alpha-lactalbumin can adopt a molten globule conformation when one of its four disulphide bonds is reduced. In this state, the three other disulphide bonds rearrange spontaneously, at the same rate as when the protein is fully unfolded, to a number of different disulphide bond isomers that tend to maintain the molten globule conformation. That the molten globule state is compatible with a variety of disulphide bond pairings suggests that it is unlikely to be stabilized by many specific tertiary interactions.     

Atom-by-atom analysis of global downhill protein folding

Protein folding is an inherently complex process involving coordination of the intricate networks of weak interactions that stabilize native three-dimensional structures. In the conventional paradigm, simple protein structures are assumed to fold in an all-or-none process that is inaccessible to experiment. Existing experimental methods therefore probe folding mechanisms indirectly. A widely used approach interprets changes in protein stability and/or folding kinetics, induced by engineered mutations, in terms of the structure of the native protein. In addition to limitations in connecting energetics with structure, mutational methods have significant experimental uncertainties and are unable to map complex networks of interactions. In contrast, analytical theory predicts small barriers to folding and the possibility of downhill folding. These theoretical predictions have been confirmed experimentally in recent years, including the observation of global downhill folding. However, a key remaining question is whether downhill folding can indeed lead to the high-resolution analysis of protein folding processes. Here we show, with the use of nuclear magnetic resonance (NMR), that the downhill protein BBL from Escherichia coli unfolds atom by atom starting from a defined three-dimensional structure. Thermal unfolding data on 158 backbone and side-chain protons out of a total of 204 provide a detailed view of the structural events during folding. This view confirms the statistical nature of folding, and exposes the interplay between hydrogen bonding, hydrophobic forces, backbone conformation and side-chain entropy. From the data we also obtain a map of the interaction network in this protein, which reveals the source of folding cooperativity. Our approach can be extended to other proteins with marginal barriers (less than 3RT), providing a new tool for the study of protein folding.     

Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy

Protein folding is inherently a heterogeneous process because of the very large number of microscopic pathways that connect the myriad unfolded conformations to the unique conformation of the native structure. In a first step towards the long-range goal of describing the distribution of pathways experimentally, F?rster resonance energy transfer (FRET) has been measured on single, freely diffusing molecules. Here we use this method to determine properties of the free-energy surface for folding that have not been obtained from ensemble experiments. We show that single-molecule FRET measurements of a small cold-shock protein expose equilibrium collapse of the unfolded polypeptide and allow us to calculate limits on the polypeptide reconfiguration time. From these results, limits on the height of the free-energy barrier to folding are obtained that are consistent with a simple statistical mechanical model, but not with the barriers derived from simulations using molecular dynamics. Unlike the activation energy, the free-energy barrier includes the activation entropy and thus has been elusive to experimental determination for any kinetic process in solution.     

Role of a subdomain in the folding of bovine pancreatic trypsin inhibitor.

The disulphide-bonded intermediates that accumulate in the oxidative folding of bovine pancreatic trypsin inhibitor (BPTI) were characterized some time ago. Structural characterization of these intermediates would provide an explanation of the kinetically preferred pathways of folding for BPTI. When folding occurs under strongly oxidizing conditions, more than half the molecules become trapped in an intermediate, designated N*, which is similar to the native protein but lacks the 30-51 disulphide bond. We have tested the hypothesis that the precursor to N* is the one-disulphide intermediate [5-55], which contains the most stable disulphide in BPTI, and present evidence here that this is the case. A peptide model of [5-55], corresponding to a subdomain of BPTI, seems to fold into a native-like conformation, explaining why [5-55] does not lead to native protein and why it folds rapidly to N*. A native-like subdomain structure in a peptide model of [30-51], the other crucial one-disulphide intermediate, may explain the route by which [30-51] folds to native protein. Thus, much of the folding pathway of BPTI can be explained by the formation of a native-like subdomain in these two early intermediates. This suggests that a large part of the protein folding problem can be reduced to identifying and understanding subdomains of native proteins.     

HMM in predicting protein secondary structure

We introduced a new method—duration Hidden Markov Model (dHMM) to predicate the secondary structure of Protein. In our study, we divide the basic second structure of protein into three parts: H (α-Helix), E (β-sheet) and O (others, include coil and turn). HMM is a kind of probabilistic model which more thinking of the interaction between adjacent amino acids (these interaction were represented by transmit probability), and we use genetic algorithm to determine the model parameters. After improving on the model and fixed on the parameters of the model, we write a program HMMPS. Our example shows that HMM is a nice method for protein secondary structure prediction. Foundation item: Supported by the National Natural Science Foundation of China (30170214) Biography: Huang Jing (1977-), female, Master candidate, research direction: bioinformatics.     

Dependence of mutual information of big protein sequence

The mutual information function is used to describe the auto-correlation of amino acids in protein. We find two interesting phenomenon: (1) for any given big protein, the mutual information function l(k) is almost a const, where k is the length of gap. (2) for any two sequence similar proteins, the mutual information are nearly the same. As a consequent, we may use mutual information of protein as a character for sequences comparison. Foundation item: Supported by the National Natural Science Foundation of China (30170214) Biography: Shi Feng ( 1966-), male, Ph. D, Associate professor, research direction: bioinformatics.     

Purification and Characterization of an Antibacterial Protein from the Cultured Mycelia of Cordyceps sinensis

0 IntroductionAlnattie mdicfrroobmiala p wriodteei nvsar iheatdy boefe linv ifnogun odr gaanndis ismos--Bacteria[1], fungi[2 ,3], plants[4]and ani mals[5].Those proteins displayed a wide spectrumof anti mi-crobial activity against different species of viruses ,bacteria andfungi .Over the past few years ,several anti microbialpeptides and proteins were foundinfungus ,such asAFP fromAspergillus giganteus[6], Anafp fromAspergillus niger[7], Zygocin fromthe yeastZy-gosaccharomyces bailii[8],an…     

Computer simulation of protein folding.

A new and very simple representation of protein conformations has been used together with energy minimisation and thermalisation to simulate protein folding. Under certain conditions, the method succeeds in "renaturing" bovine pancreatic trypsin inhibitor from an open-chain conformation into a folded conformation close to that of the native molecule.     

小蛋白天然结构与折叠速度关系的分子动力学模拟研究

用分子动力学模拟方法研究了小蛋白天然结构集合与其折叠速度的关系．根据蛋白质内存在接触的不同定义方式．利用分子动力学模拟方法得到了10个小蛋白的一系列构象集合,分析了其拓扑参数与折叠速度的关系,并与PDB单构象的情况进行了比较．用含主链重原子的方式定义接触,所计算的结果较好,天然结构集合所计算的拓扑参数与蛋白质折叠速度的关系可以更真实地反映实际情况．     

Solving integer programming by evolutionary soft agent

Many practical problems in commerce and industry involve finding the best way to allocate scarce resources a-mong competing activities. This paper focuses on the problem of integer programming, and describes an evolutionary soft a-gent model to solve it. In proposed model, agent is composed of three components: goal, environment and behavior. Experimental shows the model has the characters of parallel computing and goal driving. Foundation item: Supported by the National Natural Science Foundation of China( 60205007) , Natural Science Foundation of Guangdong Province(001264), Research Foundation of Software Technology Key Laboratory in Guangdong Province and Research Foundation of State Key Laboratory for Novel Software Technology at Nanjing University Biography: Yin Jian ( 1968-), male, Associate professor, research direction: artificial intelligence, data mining.     

The Effect of cdk-5 Overexpression and Overactivation on Tau Hyperphosphorylation in Cultured N2a Cells

Neurofibrillary tangles (NFTs) are one of the neuropathological hallmarks of Alzheimer‘s disease (AD) and abnormally hyperphosphorylated tau is the major protein of NFTs. It was reported that cyclin-dependent kinase5 (Cdk-5) could phosphorylate tau at most AD-related epitopes in vivo. In this study, we investigated the effect of cdk-5 overexpression on tau hyperphosphorylation in neuroblastoma N2a cells. We demonstrated that overexpression of cdk-5 whieh rcsul-ted in a 3.5-fold Cdk-5 activation in the transfected cells induced a dramatic increase in phosphorylation of tau at several phosphorylation sites. Overexpression of cdk-5 led to a reduced staining with antibody Tau-1 and an enhanced staining with antibody PHF-1, suggesting hyperphosphorylation of tau at Ser199/202 and Ser396/404 sites. It implies that in vitro overexpression of cdk-5 leads to Cdk-5 overactivation and tau hyperphosphorylation may be the underline mechanism.     

The evolutionary computation techniques for protein structure prediction: A survey

In this paper, the applications of evolutionary al gorithm in prediction of protein secondary structure and tertiary structures are introduced, and recent studies on solving protein structure prediction problems using evolutionary algorithms are reviewed, and the challenges and prospects of EAs applied to protein structure modeling are analyzed and discussed. Foundation item: Supported by the National Natural Science Foundation of China( 60133010,70071042,60073043) Biography: Zou Xiu-fen ( 1966-), female, Associate professor, research direction:evolutionary computing, parallel computing, bioinformatics.     

Sensitive Determination of DNA by RLS Enhancement of Metal Ions

0　IntroductionThequantitativeanalysisofnucleicacids,especiallythemi cro determinationofnucleicacids,isbecomingmoreandmoreimportantinmanybiologicalstudies.Recently ,apromisingspectraltechnique ,whichwasbasedonthemeasurementofen hancedresonancelightscattering (RLS) [1 ,2 ] ,hasgivenrisetostronginterestbyanalystsandbiochemistsfornucleicacidsandproteinassay[3 9] .Uptonow ,manykindscompoundshavebeenfoundRLSenhancementwhilebindingtoDNA ,andallthesecompoundsarecharacterizedofpositivechargewhicha…     

A New ID-Based Proxy Multi-Signature Scheme from Bilinear Pairings

ID-based public key cryptosystem can be a good alternative for certifieate-based public key setting. This paper provides an efficient ID-based proxy multi signature scheme from pairings. In the random oracle model, we prove that our new scheme is secure against existential delegation forgery with the assumption that Hess＇s scheme-1 is existential unforgeable, and that our new scheme is secure against existential proxy multi-signature forgery under the hardness assumption of the computational Diffie-Hellman problem.     

Cloning,expression of<Emphasis Type="Italic">Crocus sativus</Emphasis> phytoene desaturase gene and preparation of antiserum against it

A 2 149 bp full length phytoene desaturase (PDS) cDNA was first cloned from saffron (Crocus sativus L.) stigma using RT-PCR technique and a rapid amplification of cDNA end (RACE) strategy. The cDNA has an open reading frame of 1 697 bp, which encodes a polypeptide of 565 amino acids. The coding region of the cDNA was inserted into a prokaryotic expression vector pET-21a(+) and over-expressed inE. coli BL21 (DE3). The fusion proteins were found largely in an insoluble inclusion bodies. The purified fusion protein was used to immunize rabbits to obtain polyclonal antiserum with titer of 1×10⁵. Western blot analysis by using this particular antiserum showed that the higher expression level of PDS in mature stigma than in leaves and stamen, and the higher expression level of PDS in mature stigma than in young stigma. Foundation item: Supported by the Doctoral Foundation of the Ministry of Education, P. R. China and the Young Science Foundation of Sichuan University (Grant 0020405505012) Biography: Bai Jie (1968-), female, Ph. D candidate, research direction: plant developmental biology and reproductive engineering.     

The synthesis of a fluorescent chemosensor containing two thiourea groups and its recognition behavior for dicarboxylate anions

A novel anion receptor 2 bearing anthracene flurophore and thiourea was synthesized and identified by ^1H NMR,MS,IR and elemental analysis. The interaction between receptor 2 and various α,ω-dicarboxylate anions was studied by fluorescence spectrum. The obtained fluorescence data indicate that 1：1 stoichiometry complex is formed between receptor 2 with diferent dicarboxylate anions through a hydrogen-bonging interaction. The selectivity of 2 for recognition of different dicarboxylates deponds on chain length of the anionic species.     

Effects of interactions among surfactants,water and oil on equilibrium configuration of surfactant-water-oil systems

The distribution and configuration of surfactants at interface in surfactant-water-oil systems have been investigated using discontinuous molecular dynamic simulations. There exists a certain equilibrium concentration of surfactants at interface for the systems with certain interactions among surfactant, water and oil. The interface length and equilibrium morphology of the systems are dependent on the equilibrium concentration of surfactants at interface and the total amount of surfactants. The interaction strengths among surfactant, water and oil determine the equilibrium concentration of surfactants at interface. Three typical configurations of surfactants at interface have been observed: ① surfactant molecules are perpendicular to the interface and arranged closely; ② perpendicular to the interface and arranged at interval of two particles; ③ lie down in the interface partly.     

Trust Based Pervasive Computing

Pervasive computing environment is a distributed and mobile space. Trust relationship must be established and ensured between devices and the systems in the pervasive computing environment. The trusted computing （TC） technology introduced by trusted computing group is a distributed-system-wide approach to the provisions of integrity protection of resources. The TC＇s notion of trust and security can be described as conformed system behaviors of a platform environment such that the conformation can be attested to a remote challenger. In this paper the trust requirements in a pervasive/ubiquitous environment are analyzed. Then security schemes for the pervasive computing are proposed using primitives offered by TC technology.     

Binding of Euplotes octocarinatus centrin with target peptide melittin

Interactions between model target peptide melittin (ME) and Euplotes octocarinatus centrin (EoCen) were investigated by fluorescence spectra, circular dichroism (CD) spectra and native polyacrylamide gel electrophoresis (PAGE). In 0.1 mol/L N-2-hydroxyethylpiperazine-N-2-ethanesulfonic acid (Hepes) and 150 mmol/L NaCl at pH 7.4, EoCen and isolated short C-terminal domain of EoCen (SC-EoCen) form 1:1 peptide:protein complexes. However, no detectable signal changes can be observed while isolated N-terminal domain of EoCen (N-EoCen) or isolated long C-terminal domain of EoCen (LC-EoCen) was added into solution of ME. The interaction between EoCen and ME is specified exclusively for the short C-terminal domain of EoCen. On the basis of fluorescence titration curves, the conditional binding constants of ME with EoCen and SC-EoCen were calculated to be logKME-EoCen = 6.81±0.33 and log- KME-SC-EoCen = 6.51±0.45, respectively.     

Effect of thrombin on the apoptosis of hippocampal neurons in vitro

Hippocampal neurons were treated by thrombin and thrombin receptor activating peptides (TRAP). Cell survival rate was decreased in a dose-dependent manner by MTT assay. The numbers of apoptotic cell and apoptotic rate of hippocampal neurons treated by different concentrations of thrombin were increased in a dose-dependent manner by terminal deoxynucleotidyl transferase (TdT) mediated dUTP-biotin nick end-labeling (TUNEL) method and Flow Cytometry. When the concentration of thrombin is 40 U/mL, TUNEL positive cells and apoptotic rate of hippocampal neurons reached peak value, were 27.3±4.0 and (29.333±4.633)%, respectively. Immunocytochemistry assay show that Bcl-2 protein expression was down-regulated and Bax protein expression was up-regulated with the concentration of thrombin increased. TRAP can mimic the effect of thrombin to induce apoptosis on hippocampal neurons. These data demonstrated that thrombin induced hippocampal neuron apoptosis in a dose-dependent manner through activating protease-activated protein-1 (PAR-1). The change in expression of Bcl-2 and Bax was related with the effect of high concentration thrombin induced apoptosis on hippocampal neurons. Foundation item: Supported by the Natural Science Foundation of Hainan Province (N30215) Biography: YANG Wen-qiong (1968-), female, Ph.D. candidate, research direction: cerebrovascular disease.