光合作用系统II外周蛋白——P23k去折叠的热力学和动力学

利用荧光光谱学等方法结合高压力技术研究了光合作用系统II中的一个外周蛋白——— 2 3kD(以P2 3k表示 )蛋白的去折叠。热力学研究表明 ,在 2 0℃、180MPa(1MPa =10 .0大气压 )可使该蛋白质完全去折叠 ,而在3℃ ,16 0MPa即可使该蛋白质完全去折叠 ,这是迄今为止有关研究中最易被高压力去折叠的一个蛋白质。在2 0℃ ,该蛋白质在常压下去折叠反应的标准自由能与标准体积变化分别为 2 3.4 5kJ mol和 - 15 0 .3ml mol;动力学研究揭示该蛋白质的折叠反应的活化体积ΔV f 为正值 (84 .1ml mol) ,而去折叠反应的活化体积ΔV u 为负值(- 6 6 .2ml mol)。在常压下 ,折叠和去折叠反应的速度常数 (K0f,K0u)分别为 1.87s- 1 和 1.3× 10 - 4s- 1 ,这些结果为解释该蛋白质易被压力去折叠提供了线索     

工业微生物常用计量单位符号简介

为执行国务院发布的《关于在我国统一实行法定计量单位的命令》的规定,根据中华人民共和国国家标准(GB3100~3102-93)《量和单位》一书所述内容,现将本刊常用的计量单位符号介绍如下,请广大作者参照执行。日(天)—d;时—h;分—min;秒—s;吨—t;公斤(千克)—kg;克—g;毫克—mg;微克—μg;纳克—ng;升—L;毫升—mL;微升—μL;克分子浓度(M):废用,改为摩尔每升mol/L;当量浓度(N):废用,换算成相应的mol/L;旋转速度—r/min;蒸汽压力、压强:帕(斯卡)—Pa(许用);kg/cm2(废用);磅(废用);0.55kg/cm2(8磅)≈0.55×105Pa,1.05kg/cm2(15磅)≈1×105P…     

温度和食物浓度对三品系萼花臂尾轮虫实验种群动态的影响

应用个体培养方法,研究了温度(20、25和30℃)和藻类食物浓度(1．5×10^6、3．0×10^6、6．0×10^6和9．0×10^6cells·ml^-1)对青岛、芜湖、广州三品系萼花臂尾轮虫种群动态的影响．结果表明,温度仅对轮虫的世代时间和种群内禀增长率有显著影响,而品系对所有生命表参数均无显著影响．轮虫种群的内禀增长率随培养温度的升高而增大,世代时间则随培养温度的升高而缩短．食物浓度仅对轮虫的生命期望值和平均寿命有显著影响,品系对轮虫的净生殖率、世代时间、生命期望值和平均寿命也有显著影响．三品系间,以广州品系轮虫的净生殖率、世代时间、生命期望值和平均寿命最大,芜湖品系最短．当食物浓度为3．0×10^6cells·ml^-1时,轮虫的生命期望值和平均寿命最长,9．0×10^6cells·ml^-1时最短．各品系轮虫的净生殖率、世代时间、总生殖率、生命期望值和平均寿命均随培养温度的升高而减小,广州品系的净生殖率除外．轮虫种群的内禀增长率和广州品系轮虫的总生殖率则随培养温度的升高而增大．青岛和广州品系轮虫的各生命表参数,均与食物浓度呈曲线相关,但芜湖品系仅世代时间、平均寿命和生命期望值随食物浓度的增大而缩短．     

北方粳稻光合速率、气孔导度对光强和CO2浓度的响应

 以东北地区主栽的粳稻（Oryza sativa var. japonica）品种为对象,用美国LI-cor公司生产的Li 6400光合作用测定仪控制光强、CO2浓度和温度等环境条件,阐述了光合作用和气孔导度对光和CO2浓度的响应特征及其耦合关系。结果表明,光合速率随光强或CO2浓度的提高而增大,均遵循米氏响应;在不同CO2浓度下,表观量子效率随CO2浓度的提高而增大,但CO2浓度达到800 μmol•mol－1以上时,表观量子效率有所减小;在不同光强下,表观羧化效率也随光的增强而增大,但光强达到1 600 μmol•m-2•s-1以上时,表观羧化效率也有所减小;在光强和CO2浓度协同作用下,光合速率的响应遵循双底物的米氏方程,在光强和CO2浓度均趋于饱和时,北方粳稻（品种：辽粳294）剑叶的潜在最大光合速率为71.737 8 μmol•m-2•s-1,表观量子效率为0.056 0 μmolCO2•μmol-1 photons,表观羧化效率为0.103 1 μmol•m-2•s-1/μmol•mol－1。气孔导度也随光的增强而增大,对光强的响应规律也可以用Michaelis-Menten曲线模拟,而叶面CO2浓度的提高会使气孔导度减小,气孔导度（Gs）对叶面CO2浓度（Cs）的响应可以用Gs=Gmax,c/(1+Cs/Cs0)的双曲线方程模拟。在光强(PFD)和CO2浓度协同作用下,气孔导度可以用式Gs=Gmax(PFD/PFDc)/［(1+PFD/PFDc)(1+Cs/Cs0)］+Gct估算,当CO2浓度趋于0而光强趋于饱和时,北方粳稻的潜在最大气孔导度（Gmax）为0.670 9 mol•m-2•s-1。在光强和CO2浓度协同作用下,Ball-Berry模型及其修正形式依然能很好地表达气孔导度-光合速率的耦合关系,并且用叶面饱和水汽压差（Ds）修正耦合关系中的相对湿度可以提高模拟精度。     

一种新型蚯蚓纤溶酶的部分性质研究

为获得一种高效的溶栓药物。从赤子爱胜蚓(Eiseniafoelida)中分离纯化得到了一种纤溶酶组分。用Lowry法测定蛋白质浓度,SDSPAGE鉴定纯度为98%,表观相对分子质量(Mr)为14850,纤维蛋白平板法测定其总纤溶活性为65.51×103mm2/mg,直接纤溶活性为15.61×103mm2/mg,间接纤溶活性为26.34×103mm2/mg。水解BAEE的米氏常数(Km)为1.82×105mol/L。水解ChromozymPL的米氏常数(Km)3.98×105mol/L,水解ChromozymtPA的米氏常数(Km)5.55×105mol/L活性,N端氨基酸序列测定的结果为VIGGTNAIPGEFPYQ。结果表明该纤溶酶分子量较小,间接活性较高,适宜作为一种新型的溶栓药物。     

双歧杆菌双元蛋白酸奶中特定菌含量及酸度的检测

目的 :检测双歧杆菌双元蛋白酸奶中发酵前后以及在贮藏期间的双歧杆菌和乳酸菌活菌数及酸度的变化。方法 :应用改良MRS琼脂平板法检测含菌量 ,应用吉尔涅尔度表示酸度 (°T)。结果 :双歧杆菌双元蛋白酸奶中双歧杆菌含量为 3 1× 10 7CFU/ml,乳酸菌含量为 4 1× 10 8CFU/ml;°T为 6 5± 5。随着贮藏进程的延长 ,特定菌的含量随贮藏期进程而下降 ,第 4～ 5天下降明显 ;°T随贮藏期延长而逐渐上升 ,保质期内°T为 75～ 110之间。结论 :双歧双元蛋白酸奶符合酸奶国家GB2 74 6～ 1999标准。     

防治西花蓟马的病原真菌-白僵菌微菌核的液体培养

微菌核是许多植物病原真菌产生的越冬结构,目前还没有关于白僵菌微菌核的报道。用含不同氮源的介质培养出了2株白僵菌菌株,RSB和SZ21的微菌核。在液体培养条件下,2株菌株不仅能产生典型的芽孢和菌丝,还能产生微菌核。在以玉米粉(RSB和SZ21菌株分别为6.5×102和6.3×102mL-1)为氮源的介质中产生的微菌核浓度高于以大豆粉(RSB和SZ21菌株分别为2.5×102和2.2×102mL-1)为氮源的介质。菌株SZ21产生的芽孢浓度(在以大豆粉和玉米粉为氮源的介质中,分别为17.9×105和7.4×105L-1)高于RSB菌株的芽孢浓度(在以大豆粉和玉米粉为氮源的介质中,分别为14.8×105和6.2×105L-1)。含有硅藻土的微菌核制剂能在真空干燥(<5%湿度)后存活下来,并且对于活力没有显著影响。干燥后的微菌核颗粒在水洋菜培养基上复水和培养后,能够萌发菌丝和产生高浓度的分生孢子。将微菌核颗粒预混到土壤中能引起西花蓟马Frankliniella occidentalis(Pergande)土栖阶段的高死亡率。这是首次报道白僵菌的微菌核的培养,并为用虫生真菌防治土栖昆虫提供了一个新的方法。     

蛋白质折叠速度与其拓扑结构关系的研究

以6种不同的方式来定义蛋白质内存在的接触,进而运用分子动力学模拟等不同方法,对10个小蛋白进行分析,研究了不同的接触定义及不同的拓扑参数计算方法下,蛋白质的折叠速度与其拓扑参数的关系.结果表明,用含主链重原子的方式定义接触,所计算的拓扑参数与蛋白质折叠速度的相关性较好;用含侧链原子的方式定义接触,得到的拓扑参数与β型蛋白质的折叠速度的相关性较好.对不同的蛋白质,其拓扑结构与相应折叠速度间的相关程度不同。     

不同EGF和胰岛素水平对体外培养的大熊猫皮肤成纤维细胞的影响

用DME∶Ham sF12(1∶1)培养液,添加3个水平的EGF和2个水平的胰岛素,组合成6种培养体系(CS)分别培养大熊猫皮肤成纤维细胞。通过对细胞生长速度和染色体数目变异率进行测定,测得在添加10μg/ml的胰岛素和40 ng/ml的表皮生长因子的培养体系中,以1.673±0.185×105/ml密度接种细胞,经3.5天,密度达到6.890×105/ml,其生长速度最快;染色体数目为二倍体的百分率为75.77%。综合衡量,CS-5在本研究中更适合大熊猫皮肤成纤维细胞的培养。     

从量子跃迁观点对蛋白质折叠速率的统计分析

理解蛋白质折叠速率是探明蛋白质结构和折叠机制物理基础的关键.蛋白质折叠速率的温度依赖关系是当前一个未解决的难题.假定蛋白质折叠是一个分子构象间的量子跃迁,导出了一个蛋白质折叠速率的解析公式.由此公式出发,计算了资料库中二态蛋白质的折叠速率和研究了它们的温度依赖性.从第一性原理出发,对实验给出的16个二态蛋白质折叠速率的非阿列尼乌斯(non-Arrhenius)温度关系给予成功解释,进而预测了这些蛋白质解折叠速率的温度依赖关系.依据量子折叠理论,给出了一个预测二态蛋白质折叠速率的统计公式,用于65个蛋白的资料库,理论和实验比较的相关系数为0.73.此外,理论还给出了与实验结果一致的最大和最小折叠速率估计.     

Effects of Hyperbaric Pressure on a Deep-Sea Archaebacterium in Stainless Steel and Glass-Lined Vessels

The effects of hyperbaric helium pressures on the growth and metabolism of the deep-sea isolate ES4 were investigated. In a stainless steel reactor, cell growth was completely inhibited but metabolic gas production was observed. From 85 to 100°C, CO₂ production proceeded two to three times faster at 500 atm (1 atm = 101.29 kPa) than at 8 atm. At 105°C, no CO₂ was produced until the pressure was increased to 500 atm. Hydrogen and H₂S were also produced biotically but were not quantifiable at pressures above 8 atm because of the high concentration of helium. In a glass-lined vessel, growth occurred but the growth rate was not accelerated by pressure. In most cases at temperatures below 100°C, the growth rate was lower at elevated pressures; at 100°C, the growth rates at 8, 250, and 500 atm were nearly identical. Unlike in the stainless steel vessel, CO₂ production was exponential during growth and continued for only a short time after growth. In addition, relatively little H₂ was produced in the glass-lined vessel, and there was no growth or gas production at 105°C at any pressure. The behavior of ES4 as a function of temperature and pressure was thus very sensitive to the experimental conditions.     

Microsecond simulations of the folding/unfolding thermodynamics of the Trp‐cage miniprotein

We study the unbiased folding/unfolding thermodynamics of the Trp‐cage miniprotein using detailed molecular dynamics simulations of an all‐atom model of the protein in explicit solvent using the Amberff99SB force field. Replica‐exchange molecular dynamics simulations are used to sample the protein ensembles over a broad range of temperatures covering the folded and unfolded states at two densities. The obtained ensembles are shown to reach equilibrium in the 1 μs/replica timescale. The total simulation time used in the calculations exceeds 100 μs. Ensemble averages of the fraction folded, pressure, and energy differences between the folded and unfolded states as a function of temperature are used to model the free energy of the folding transition, ΔG(P, T), over the whole region of temperatures and pressures sampled in the simulations. The ΔG(P, T) diagram describes an ellipse over the range of temperatures and pressures sampled, predicting that the system can undergo pressure‐induced unfolding and cold denaturation at low temperatures and high pressures, and unfolding at low pressures and high temperatures. The calculated free energy function exhibits remarkably good agreement with the experimental folding transition temperature (T_f = 321 K), free energy, and specific heat changes. However, changes in enthalpy and entropy are significantly different than the experimental values. We speculate that these differences may be due to the simplicity of the semiempirical force field used in the simulations and that more elaborate force fields may be required to describe appropriately the thermodynamics of proteins. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Studying pressure denaturation of a protein by molecular dynamics simulations

Many globular proteins unfold when subjected to several kilobars of hydrostatic pressure. This “unfolding‐up‐on‐squeezing” is counter‐intuitive in that one expects mechanical compression of proteins with increasing pressure. Molecular simulations have the potential to provide fundamental understanding of pressure effects on proteins. However, the slow kinetics of unfolding, especially at high pressures, eliminates the possibility of its direct observation by molecular dynamics (MD) simulations. Motivated by experimental results—that pressure denatured states are water‐swollen, and theoretical results—that water transfer into hydrophobic contacts becomes favorable with increasing pressure, we employ a water insertion method to generate unfolded states of the protein Staphylococcal Nuclease (Snase). Structural characteristics of these unfolded states—their water‐swollen nature, retention of secondary structure, and overall compactness—mimic those observed in experiments. Using conformations of folded and unfolded states, we calculate their partial molar volumes in MD simulations and estimate the pressure‐dependent free energy of unfolding. The volume of unfolding of Snase is negative (approximately ?60 mL/mol at 1 bar) and is relatively insensitive to pressure, leading to its unfolding in the pressure range of 1500–2000 bars. Interestingly, once the protein is sufficiently water swollen, the partial molar volume of the protein appears to be insensitive to further conformational expansion or unfolding. Specifically, water‐swollen structures with relatively low radii of gyration have partial molar volume that are similar to that of significantly more unfolded states. We find that the compressibility change on unfolding is negligible, consistent with experiments. We also analyze hydration shell fluctuations to comment on the hydration contributions to protein compressibility. Our study demonstrates the utility of molecular simulations in estimating volumetric properties and pressure stability of proteins, and can be potentially extended for applications to protein complexes and assemblies. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Heat and cold denaturation of yeast frataxin: The effect of pressure

Yfh1 is a yeast protein with the peculiar characteristic to undergo, in the absence of salt, cold denaturation at temperatures above the water freezing point. This feature makes the protein particularly interesting for studies aiming at understanding the rules that determine protein fold stability. Here, we present the phase diagram of Yfh1 unfolding as a function of pressure (0.1–500 MPa) and temperature 278–313 K (5–40°C) both in the absence and in the presence of stabilizers using Trp fluorescence as a monitor. The protein showed a remarkable sensitivity to pressure: at 293 K, pressures around 10 MPa are sufficient to cause 50% of unfolding. Higher pressures were required for the unfolding of the protein in the presence of stabilizers. The phase diagram on the pressure-temperature plane together with a critical comparison between our results and those found in the literature allowed us to draw conclusions on the mechanism of the unfolding process under different environmental conditions.     

Folding thermodynamics of β‐hairpins studied by replica‐exchange molecular dynamics simulations

We study the differences in folding stability of β‐hairpin peptides, including GB1 hairpin and a point mutant GB1 K10G, as well as tryptophan zippers (TrpZips): TrpZip1, TrpZip2, TrpZip3‐1, and TrpZip4. By performing replica‐exchange molecular dynamics simulations with Amber03* force field (a modified version of Amber ff03) in explicit solvent, we observe ab initio folding of all the peptides except TrpZip3‐1, which is experimentally known to be the least stable among the peptides studied here. By calculating the free energies of unfolding of the peptides at room temperature and folding midpoint temperatures for thermal unfolding of peptides, we find that TrpZip4 and GB1 K10G peptides are the most stable β‐hairpins followed by TrpZip1, GB1, and TrpZip2 in the given order. Hence, the proposed K10G mutation of GB1 peptide results in enhanced stability compared to wild‐type GB1. An important goal of our study is to test whether simulations with Amber 03* model can reproduce experimentally predicted folding stability differences between these peptides. While the stabilities of GB1 and TrpZip1 yield close agreement with experiment, TrpZip2 is found to be less stable than predicted by experiment. However, as heterogenous folding of TrpZip2 may yield divergent thermodynamic parameters by different spectroscopic methods, mismatching of results with previous experimental values are not conclusive of model shortcomings. For most of the cases, molecular simulations with Amber03* can successfully reproduce experimentally known differences between the mutated peptides, further highlighting the predictive capabilities of current state‐of‐the‐art all‐atom protein force fields. Proteins 2015; 83:1307–1315. © 2015 Wiley Periodicals, Inc.     

How do chemical denaturants affect the mechanical folding and unfolding of proteins?

We present the first single-molecule atomic force microscopy study on the effect of chemical denaturants on the mechanical folding/unfolding kinetics of a small protein GB1 (the B1 immunoglobulin-binding domain of protein G from Streptococcus). Upon increasing the concentration of the chemical denaturant guanidinium chloride (GdmCl), we observed a systematic decrease in the mechanical stability of GB1, indicating the softening effect of the chemical denaturant on the mechanical stability of proteins. This mechanical softening effect originates from the reduced free-energy barrier between the folded state and the unfolding transition state, which decreases linearly as a function of the denaturant concentration. Chemical denaturants, however, do not alter the mechanical unfolding pathway or shift the position of the transition state for mechanical unfolding. We also found that the folding rate constant of GB1 is slowed down by GdmCl in mechanical folding experiments. By combining the mechanical folding/unfolding kinetics of GB1 in GdmCl solution, we developed the “mechanical chevron plot” as a general tool to understand how chemical denaturants influence the mechanical folding/unfolding kinetics and free-energy diagram in a quantitative fashion. This study demonstrates great potential in combining chemical denaturation with single-molecule atomic force microscopy techniques to reveal invaluable information on the energy landscape underlying protein folding/unfolding reactions.     

The exclusion of glycine betaine from anionic biopolymer surface: why glycine betaine is an effective osmoprotectant but also a compatible solute

Paradoxically, glycine betaine (N,N,N-trimethyl glycine; GB) in vivo is both an effective osmoprotectant (efficient at increasing cytoplasmic osmolality and growth rate) and a compatible solute (without deleterious effects on biopolymer function, including stability and activity). For GB to be an effective osmoprotectant but not greatly affect biopolymer stability, we predict that it must interact very differently with folded protein surface than with that exposed in unfolding. To test this hypothesis, we quantify the preferential interaction of GB with the relatively uncharged surface exposed in unfolding the marginally stable lacI helix-turn-helix (HTH) DNA binding domain using circular dichroism and with the more highly charged surfaces of folded hen egg white lysozyme (HEWL) and bovine serum albumin (BSA) using all-gravimetric vapor pressure osmometry (VPO) and compare these results with results of VPO studies (Hong et al. (2004), Biochemistry, 43, 14744-14758) of the interaction of GB with polyanionic duplex DNA. For these four biopolymer surfaces, we observe that the extent of exclusion of GB per unit of biopolymer surface area increases strongly with increasing fraction of anionic oxygen (protein carboxylate or DNA phosphate) surface. In addition, GB is somewhat more excluded from the surface exposed in unfolding the lacI HTH and from the folded surface of HEWL than expected from their small fraction of anionic surface, consistent with moderate exclusion of GB from polar amide surface, as predicted by the osmophobic model of protein stability (Bolen and Baskakov (2001) J. Mol. Biol. 310, 955-963). Strong exclusion of GB from anionic surface explains how it can be both an effective osmoprotectant and a compatible solute; analysis of this exclusion yields a lower bound on the hydration of anionic protein carboxylate surface of two layers of water (>or=0.22 H(2)O A(-)(2)).     

Amino acids conserved at the C-terminal half of the ribonuclease T2 family contribute to protein stability of the enzymes

The ribonuclease MC1 (RNase MC1) from the seeds of the bitter gourd belongs to the RNase T2 family. We evaluated the contribution of 11 amino acids conserved in the RNase T2 family to protein folding of RNase MC1. Thermal unfolding experiments showed that substitution of Tyr(101), Phe(102), Ala(105), and Phe(190) resulted in a significant decrease in themostability; the T(m) values were 47-58 degrees C compared to that for the wild type (64 degrees C). Mutations of Pro(125), Gly(127), Gly(144), and Val(165) caused a moderate decrease in thermostability (T(m): 60-62 degrees C). In contrast, mutations of Asp(107) and Gly(173) did little effect on thermostability. The contribution of Tyr(101), Phe(102), Pro(125), and Gly(127) to protein stability was further corroborated by means of Gdn-HCl unfolding and protease digestions. Taken together, it appeared that Tyr(101), Phe(102), Ala(105), Pro(125), Gly(127), Gly(144), Leu(162), Val(165), and Phe(190) conserved in the RNase T2 family play an important role in the stability of the proteins.     

Pressure denaturation of staphylococcal nuclease studied by neutron small-angle scattering and molecular simulation

We studied the pressure-induced folding/unfolding transition of staphylococcal nuclease (SN) over a pressure range of approximately 1-3 kilobars at 25 degrees C by small-angle neutron scattering and molecular dynamics simulations. We find that applying pressure leads to a twofold increase in the radius of gyration derived from the small-angle neutron scattering spectra, and P(r), the pair distance distribution function, broadens and shows a transition from a unimodal to a bimodal distribution as the protein unfolds. The results indicate that the globular structure of SN is retained across the folding/unfolding transition although this structure is less compact and elongated relative to the native structure. Pressure-induced unfolding is initiated in the molecular dynamics simulations by inserting water molecules into the protein interior and applying pressure. The P(r) calculated from these simulations likewise broadens and shows a similar unimodal-to-bimodal transition with increasing pressure. The simulations also reveal that the bimodal P(r) for the pressure-unfolded state arises as the protein expands and forms two subdomains that effectively diffuse apart during initial stages of unfolding. Hydrophobic contact maps derived from the simulations show that water insertions into the protein interior and the application of pressure together destabilize hydrophobic contacts between these two subdomains. The findings support a mechanism for the pressure-induced unfolding of SN in which water penetration into the hydrophobic core plays a central role.     

Abstracts: Albany 2007, The 15th Conversation

Abstract

Forty nine molecular dynamics simulations of unfolding trajectories of the segment B1 of streptococcal protein G (GB1) provide a direct demonstration of the diversity of unfolding pathway and give a statistically utmost unfolding pathway under the physical property space. Twelve physical properties of the protein were chosen to construct a 12-dimensional property space. Then the 12-dimentional property space was reduced to a 3-dimentional principle component property space. Under the property space, the multiple unfolding trajectories look like “trees”, which have some common characters. The “root of the tree” corresponds to the native state, the “bole” homologizes the partially unfolded conformations, and the “crown” is in correspondence to the unfolded state. These unfolding trajectories can be divided into three types. The first one has the characters of straight “bole” and “crown” corresponding to a fast two-state unfolding pathway of GB1. The second one has the character of “the standstill in the middle tree bole”, which may correspond to a three-state unfolding pathway. The third one has the character of “the circuitous bole” corresponding to a slow two-state unfolding pathway. The fast two-state unfolding pathway is a statistically utmost unfolding pathway or preferred pathway of GB1, which occupies 53% of 49 unfolding trajectories. In the property space all the unfolding trajectories construct a thermal unfolding pathway ensemble of GB1. The unfolding pathway ensemble resembles a funnel that is gradually emanative from the native state ensemble to the unfolded state ensemble. In the property space, the thermal unfolded state distribution looks like electronic cloud in quantum mechanics. The unfolded states of the independent unfolding simulation trajectories have substantial overlaps, indicating that the thermal unfolded states are confined by the physical property values, and the number of protein unfolded state are much less than that was believed before.