The natively helical chain segment 169-188 of Escherichia coli adenylate kinase is formed in the latest phase of the refolding transition

The refolding transition of Escherichia coli adenylate kinase (AK) was investigated by monitoring the refolding kinetics of a selected 20 residue helical segment in the CORE domain of the protein. Residues 169 and 188 were labeled by 1-acetamido-methyl-pyrene, and by bimane, respectively. The experiment combines double-jump stopped-flow fast mixing initiation of refolding and time-resolved F?rster energy transfer spectroscopy for monitoring the conformational transitions (double-kinetics experiment). Two kinetic phases were found in the denaturant-induced unfolding of AK. In the first phase, the fluorescence quantum yields of both probes decreased. The distribution of the distances between them transformed from the native state's narrow distribution with the mean distance corresponding to the distance in the crystal structure, to a distribution compatible with an unordered structure. In the second, slow step of denaturation, neither the fluorescence parameters of the probes nor the distance distribution between them changed. This step appeared to be a transformation of the fast-folding species formed in the first phase, to the slow-folding species. Refolding of the fast-folding species of the denatured state of AK was also a two-phase process. During the first fast phase, within less than 5ms, the fluorescence emission of both probes increased, but the distance distribution between the labeled sites was unchanged. Only during the second slow refolding step did the intramolecular distance distribution change from the characteristic of the denatured state to the narrow distribution of the native state. This experiment shows that for the case of the CORE domain of AK, the large helical segment of residues 169-188 was not formed in the first compaction step of refolding. The helical conformation of this segment is established only in the second, much slower, refolding phase, simultaneously with the completion of the native structure.     

Block of Voltage-dependent Calcium Channel by the Green Mamba Toxin Calcicludine

A number of peptide toxins derived from marine snails and various spiders have been shown to potently inhibit voltage-dependent calcium channels. Here, we describe the effect of calcicludine, a 60 amino-acid peptide isolated from the venom of the green mamba (Dendroaspis angusticeps), on transiently expressed high voltage-activated calcium channels. Upon application of calcicludine, L-type (α_{1 C} ) calcium channels underwent a rapid, irreversible decrease in peak current amplitude with no change in current kinetics, or any apparent voltage-dependence. However, even at saturating toxin concentrations, block was always incomplete with a maximum inhibition of 58%, indicating either partial pore block, or an effect on channel gating. Block nonetheless was of high affinity with an IC₅₀ value of 88 nm. Three other types of high voltage activated channels tested (α_{1 A} , α_{1 B} , and α_{1 E} ) exhibited a diametrically different response to calcicludine. First, the maximal inhibition observed was around 10%, furthermore, the voltage-dependence of channel activation was shifted slightly towards more negative potentials. Thus, at relatively hyperpolarized test potentials, calcicludine actually upregulated current activity of (N-type) α_{1 B} channels by as much as 50%. Finally, the use of several chimeric channels combining the major transmembrane domains of α_{1 C} and α_{1 E} revealed that calcicludine block of L-type calcium channels involves interactions with multiple structural domains. Overall, calcicludine is a potent and selective inhibitor of neuronal L-type channels with a unique mode of action. Received: 22 September 1999/Revised: 1 December 1999     

Differential response of DPI-modified cardiac Na+ channels to antiarrhythmic drugs: No flicker blockade by lidocaine

Summary Elementary Na⁺ currents were recorded in cell attached patches from short-time cultured neonatal cardiocytes in order to test the hypothesis whether the open state of DPI-modified, noninactivating cardiac Na⁺ channels is basically sensitive to blocking drug molecules such as antiarrhythmics.Lidocaine (300 mol/liter) effectively reduced the open probability of cardiac Na⁺ channels and, at a stimulation rate of 1 Hz, depressed the reconstructed macroscopic peak I _Na to 40+ 3.5% of the predrug value. The same drug concentration failed to influence DPI-modified Na⁺ channels. Their open state proved almost insensitive to lidocaine. _open decreased only slightly to 85 ±2%. Still more importantly, the number of transitions between the conducting and a nonconducting configuration did not increase. At –40 mV, lidocaine may interfere with the open state with an association rate constant of 1.3×10⁵ mol^–1sec^–1 which is about two orders of magnitude smaller than the rate constant obtained with propafenone or prajmalium. Moreover, propafenone (10–20 mol/liter) or prajmalium (30 mol/liter) led to a tremendous increase in the number of transitions between the open and a nonconducting configuration. Lidocaine also failed to evoke a fast flicker blockade with reaction kinetics in the microsecond range.It is concluded that DPI-modified cardiac Na⁺ channels discriminate between lidocaine and other antiarrhythmic drugs. As a tentative explanation, this might be indicative for multiple binding sites for those drugs in cardiac Na⁺ channels.This work was supported by a grant from the Deutsche Forschungs-gemeinschagt (Ko 778/2–3), Bonn.     

In silico protein design by combinatorial assembly of protein building blocks

Utilizing concepts of protein building blocks, we propose a de novo computational algorithm that is similar to combinatorial shuffling experiments. Our goal is to engineer new naturally occurring folds with low homology to existing proteins. A selected protein is first partitioned into its building blocks based on their compactness, degree of isolation from the rest of the structure, and hydrophobicity. Next, the protein building blocks are substituted by fragments taken from other proteins with overall low sequence identity, but with a similar hydrophobic/hydrophilic pattern and a high structural similarity. These criteria ensure that the designed protein has a similar fold, low sequence identity, and a good hydrophobic core compared with its native counterpart. Here, we have selected two proteins for engineering, protein G B1 domain and ubiquitin. The two engineered proteins share approximately 20% and approximately 25% amino acid sequence identities with their native counterparts, respectively. The stabilities of the engineered proteins are tested by explicit water molecular dynamics simulations. The algorithm implements a strategy of designing a protein using relatively stable fragments, with a high population time. Here, we have selected the fragments by searching for local minima along the polypeptide chain using the protein building block model. Such an approach provides a new method for engineering new proteins with similar folds and low homology.     

基于直线电机连续-步进运动的快速光声显微成像系统

报道了一种利用直线电机连续-步进的扫描方式进行光声显微成像的系统,该系统在运动时走弓字型路线,其中直线电机在X轴方向上连续运动,在Y轴方向上以步进的方式运动,采集卡只在X轴电机运动的过程中连续采集。该成像系统较之前振镜扫描的方式扫描的范围更大,可达到厘米尺度范围内的生物组织光声成像;较之前的步进电机逐点扫描的方式扫描速度明显提高。同时本文采用电机带动光和超声换能器一同扫描的方式,较光和超声换能器不动电机带动样品扫描的方式更灵活。另外利用包埋碳丝的模拟样品和在体小鼠耳朵血管来验证系统的成像能力。实验结果表明,这种快速光声显微成像方法及其系统可以实现在体组织的高分辨率成像,有望成为一种无创、实时的光声显微镜应用于生物医学当中。     

人类基因组单核苷酸多态性和单体型的分析及应用

单核苷酸多态性是人类基因组中最丰富的遗传变异。单体型是指位于一条染色体上或某一区域的一组相关联的SNP等位位点,单体型已经成为近年来人类遗传研究的组成部分。人类基因组单体型图（HapMap）计划的目标就是构建人类DNA序列中多态位点的常见模式,找出代表整个人类基因图谱之中的SNP集合的标签SNP。在复杂性疾病研究中,由多个变异位点组合构成的单体型分析优于单个SNP的分析。文章论述了SNPs、基因型、表现型的定义与HapMap计划的一些情况,综述了单体型的3种推断算法和单体域的不同定义与构建方法,同时介绍了标签SNP的选择及单体型与复杂疾病关联分析的方法,可利用公共SNP数据库的情况以及SNPs与单体型在复杂疾病与药物反应方面的应用。     

The economics of producing sustainable aviation fuel: a regional case study in Queensland,Australia

The airline industry has a strong interest in developing sustainable aviation fuels, in order to reduce their exposure to increasing oil prices and cost liability for greenhouse gas emissions. The feasibility and cost of producing sustainable biomass‐based jet fuels at a sufficient scale to materially address these issues is an enormous challenge. This paper builds directly on the biophysical study by H.T. Murphy, D.A. O'Connell, R.J. Raison, A.C. Warden, T.H. Booth, A. Herr, A.L. Braid, D.F. Crawford, J.A. Hayward, T. Javonovic, J.G. McIvor, M.H. O'Connor, M.L. Poole, D. Prestwidge, N. Raisbeck‐Brown & L. Rye, In review, which examined a 25 year scale‐up strategy to produce 5% of projected jet fuel demand in Australia in 2020 (470 mL) in the Fitzroy region of Queensland, Australia. The strategy was based on the use of a mixed ligno‐cellulosic biomass feedstock and assumed, for the sake of exploring and quantifying the scenario, a simplified two‐step conversion process – conversion of biomass to crude bio‐oil within the region, and upgrade to jet fuel at a central Brisbane facility. This paper provides details on the costs of production in this scenario, focusing on two different strategies for biomass utilization, and two types of novel small–medium scale conversion technologies. The cost analyses have taken into account technology learning curves, different economies of scale and key cost sensitivities. The cost of biomass‐based jet fuels is estimated to be between 0.70 and 1.90 The airline industry has a strong interest in developing sustainable aviation fuels, in order to reduce their exposure to increasing oil prices and cost liability for greenhouse gas emissions. The feasibility and cost of producing sustainable biomass‐based jet fuels at a sufficient scale to materially address these issues is an enormous challenge. This paper builds directly on the biophysical study by H.T. Murphy, D.A. O'Connell, R.J. Raison, A.C. Warden, T.H. Booth, A. Herr, A.L. Braid, D.F. Crawford, J.A. Hayward, T. Javonovic, J.G. McIvor, M.H. O'Connor, M.L. Poole, D. Prestwidge, N. Raisbeck‐Brown & L. Rye, In review, which examined a 25 year scale‐up strategy to produce 5% of projected jet fuel demand in Australia in 2020 (470 mL) in the Fitzroy region of Queensland, Australia. The strategy was based on the use of a mixed ligno‐cellulosic biomass feedstock and assumed, for the sake of exploring and quantifying the scenario, a simplified two‐step conversion process – conversion of biomass to crude bio‐oil within the region, and upgrade to jet fuel at a central Brisbane facility. This paper provides details on the costs of production in this scenario, focusing on two different strategies for biomass utilization, and two types of novel small–medium scale conversion technologies. The cost analyses have taken into account technology learning curves, different economies of scale and key cost sensitivities. The cost of biomass‐based jet fuels is estimated to be between 0.70 and 1.90 $ L^?1 when the efficiency of conversion of biomass to biocrude and subsequently to aviation fuel is varied by ±10% of published values, with an average value of 1.10 $ L^?1. This is within the range of the projected 2035 conventional jet fuel price of 1.50 $ L^?1. Therefore, biomass‐based jet fuel has the potential to contribute to supply of Australia's jet fuel needs in the future.