白细胞介素－2中某些残基替换对活性的影响

用基因定点突变法研究了白细胞介素－２（ＩＬ－２）中某些氨基酸对生物活性的影响。将ＩＬ－２中３９Ｍｅｔ和４３Ｌｙｓ分别改为Ｐｒｏ,企图破坏此处α螺旋,突变体的ＣＤ图谱和生物活性均,不变,说明此处可能原来就不存在α螺旋．而将５２Ｇｌｕ．５３Ｌｅｕ,５４Ｌｙｓ分别改为Ｐｒｏ后,ＣＤ谱发生了变化,生物活性也显著下降。表明这些氨基酸处在α螺旋中,将它们改为Ｐｒｏ后,影响了ＩＬ－２的结构,并导致活性下降     

Predicting the Functional Effect of Amino Acid Substitutions and Indels

As next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of sequence variations and narrow down the search of casual variants for disease phenotypes. Different classes of sequence variations at the nucleotide level are involved in human diseases, including substitutions, insertions, deletions, frameshifts, and non-sense mutations. Frameshifts and non-sense mutations are likely to cause a negative effect on protein function. Existing prediction tools primarily focus on studying the deleterious effects of single amino acid substitutions through examining amino acid conservation at the position of interest among related sequences, an approach that is not directly applicable to insertions or deletions. Here, we introduce a versatile alignment-based score as a new metric to predict the damaging effects of variations not limited to single amino acid substitutions but also in-frame insertions, deletions, and multiple amino acid substitutions. This alignment-based score measures the change in sequence similarity of a query sequence to a protein sequence homolog before and after the introduction of an amino acid variation to the query sequence. Our results showed that the scoring scheme performs well in separating disease-associated variants (n = 21,662) from common polymorphisms (n = 37,022) for UniProt human protein variations, and also in separating deleterious variants (n = 15,179) from neutral variants (n = 17,891) for UniProt non-human protein variations. In our approach, the area under the receiver operating characteristic curve (AUC) for the human and non-human protein variation datasets is ∼0.85. We also observed that the alignment-based score correlates with the deleteriousness of a sequence variation. In summary, we have developed a new algorithm, PROVEAN (Protein Variation Effect Analyzer), which provides a generalized approach to predict the functional effects of protein sequence variations including single or multiple amino acid substitutions, and in-frame insertions and deletions. The PROVEAN tool is available online at http://provean.jcvi.org.     

氨基酸序列突变对TFPI生物半衰期和生物活性的影响

通过对个别氨基酸突变的研究,获得了保持良好生物活性的长半衰期组织因子途径抑制因子(tissue factor pathwayinhibitor,TFPI)重组蛋白的有效途径.采用定点诱变和基因重组技术,首先在TFPI cDNA特定位点形成一个位点的沉默突变,以提高TFPI在毕赤酵母细胞内的表达量,此cDNA称为mTFPI.在此基础上,通过系列位点突变,形成3个羧基端突变体:m0TFPI、m1TFPI和m2TFPI.将上述4种TFPI cDNA与表达质粒pPic9连接,转染大肠杆菌,通过PCR和DNA测序确认重组质粒,转染酵母细胞GS115,甲醇诱导表达重组蛋白.采用层析方法纯化TFPI重组蛋白,用125I标记重组蛋白,静脉注射给药,比较四者在SD大鼠体内血浆代谢清除速度.用底物显色法测定重组蛋白抑制凝血因子Xa(Fxa)的活性,比较各株TFPI重组蛋白突变体在体内、体外对FXa的抑制作用及肝素对各株TFPI重组蛋白功能的影响.结果显示,相比野生型TFPI重组蛋(mTFPI)而言,3株羧基端突变体m0TFPI、m1TFPI、m2TFPI在SD大鼠体内血浆代谢清除时间均有不同程度延长,其生物代谢半衰期分别是mTFPI的1.5倍、1.9倍和大于2倍,与m-TFPI相比,3个rTFPI突变体在体内、体外抑制FXa的作用无明显减弱,与肝素的结合能力及协同能力也无明显减弱.结果表明,m0TFPI、m1TFPI和m2TFPI在生物半衰期得到明显延长的同时,仍保持良好的抑制Fxa的生物活性.     

Molecular Dynamics Study of the Structure,Flexibility and Dynamics of Thermostable L1 Lipase at High Temperatures

Molecular Dynamics (MD) simulations have been used to understand how protein structure, dynamics, and flexibility are affected by adaptation to high temperature for several years. We report here the results of the high temperature MD simulations of Bacillus stearothermophilus L1 (L1 lipase). We found that the N-terminal moiety of the enzyme showed a high flexibility and dynamics during high temperature simulations which preceded and followed by clear structural changes in two specific regions; the small domain and the main catalytic domain or core domain of the enzyme. These two domains interact with each other through a Zn²⁺-binding coordination with Asp-61 and Asp-238 from the core domain and His-81 and His-87 from the small domain. Interestingly, the His-81 and His-87 were among the highly fluctuated and mobile residues at high temperatures. The results appear to suggest that tight interactions of Zn²⁺-binding coordination with specified residues became weak at high temperature which suggests the contribution of this region to the thermostability of the enzyme. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

衰老对大鼠脑区氨基酸水平的影响

本文测定了正常青龄组（３月龄）和老龄组（２０月龄）大鼠不同脑区（皮层、小脑海马、纹状体和下丘脑）谷氨酸、天门冬氨酸、甘氨酸、ｒ－氨基丁酸和牛磺酸的含量。结果表明：在衰老过程中大鼠某些脑区谷氨酸、天门冬氨酸、甘氨酸和牛磺酸水平显著降低;而纹状体γ－氨基丁酸含量则显著升高。     

The Complete Amino Acid Substitutions at Position 131 That Are Positively Involved in Cold Adaptation of Subtilisin BPN′

To ascertain whether position 131 of a mesophilic protease, subtilisin BPN′, is a potential critical site for cold adaptation as screened by evolutionary engineering (S. Taguchi, A. Ozaki, and H. Momose, Appl. Environ. Microbiol. 64:492–495, 1998), a full set of subtilisin BPN′ mutants with mutations at position 131 was constructed by site-saturation mutagenesis. All mutated enzymes were measured for specific activity at 10°C by the quantitative titer microplate assay system using polyclonal antibody against subtilisin BPN′ and a synthetic chromogenic substrate. All the mutants exhibited proteolytic activities almost the same as or higher than that of the wild-type enzyme, suggesting that position 131 may be important for cold adaptation. In comparison with the wild type, purified mutants G131F, G131R, G131M, and G131W were found to acquire proteolytic activities (k_cat/K_m) at 10°C that were 150, 94, 84, and 50% higher, respectively. In particular, for the G131F mutant, temperature dependency in enzyme activity was shown by an increase in k_cat and a decrease in K_m. All of these amino acid substitution mutants, G131F, G131R, G131M, and G131W, acquired increased proteolytic activities at 10°C for three different synthetic peptide substrates but no increase in caseinolytic activity. Furthermore, they all conferred thermolability on the enzyme to differing extents in terms of the half-life of enzyme inactivation at 60°C. No significant correlation was found between the amino acids preferred for cold adaptation surveyed here and those present at position 131 of subtilisin of psychrophilic cells naturally occurring in cold environments. Based on these findings, position 131 is a contributor in artificial evolution for acquiring a cold-active character and may not be related to physiological requirements for subtilisin-producing cells living in cold environments. Therefore, saturation mutagenesis would be effective in achieving rapid improvement in protein properties via evolutionary engineering.     

陆地棉脂肪酶基因克隆及氨基酸序列分析

根据陆地棉(Gossypium hirsutum L.)EST序列设计一对引物,采用RT-PCR方法从萌发的棉籽中获得了脂肪酶(triacylglycerol acylhydrolases,EC 3.1.1.3)基因,该基因编码483个氨基酸;比对结果显示,棉籽脂肪酶与拟南芥、水稻、蓖麻等脂肪酶相似性较低,具有由Ser-Asp-His组成的三联体催化活性中心,在亲核Ser残基周围有GXSXG保守序列.软件预测显示该脂肪酶为可溶性蛋白,分子量约为55.4 kD,等电点为9.07,不含N端信号肽,亚细胞定位可能是过氧化物酶体或胞质溶胶.     

Changes in Targeting Efficiencies of Proteins to Plant Microbodies Caused by Amino Acid Substitutions in the Carboxy-terminal Tripeptide

It has been demonstrated that the carboxyl terminus of microbodyenzymes functions as a targeting signal to microbodies in higherplants. We have examined an ability of 24 carboxy-terminal aminoacid sequences to facilitate the transport of a cytosolic passengerprotein, ß-glucuroni-dase, into microbodies in greencotyledonary cells of trans-genic Arabidopsis. Immunoelectronmicroscopic analysis revealed that carboxy-terminal tripeptidesequences of the form [C/A/S/P]-[K/R]-[I/L/M] function as amicrobody-targeting signal, although tripeptides with prolineat the first amino acid position and isoleucine at the carboxylterminus show weak targeting efficiencies. All known micro-bodyenzymes that are synthesized in a form similar in size to themature molecule, except catalase, contain one of these tripeptidesequences at their carboxyl terminus. (Received April 14, 1997; Accepted April 8, 1997)     

Single Amino Acid Substitutions in the Chemotactic Sequence of Urokinase Receptor Modulate Cell Migration and Invasion

The receptor for urokinase-type plasminogen activator (uPAR) plays an important role in controlling cell migration. uPAR binds urokinase and vitronectin extracellular ligands, and signals in complex with transmembrane receptors such as Formyl-peptide Receptors (FPR)s and integrins. Previous work from this laboratory has shown that synthetic peptides, corresponding to the uPAR_88–92 chemotactic sequence, when carrying the S90P or S90E substitutions, up- or down-regulate cell migration, respectively. To gain mechanistic insights into these opposite cell responses, the functional consequences of S90P and S90E mutations in full-length uPAR were evaluated. First, (HEK)-293 embryonic kidney cells expressing uPAR^S90P exhibit enhanced FPR activation, increased random and directional cell migration, long-lasting Akt phosphorylation, and increased adhesion to vitronectin, as well as uPAR/vitronectin receptor association. In contrast, the S90E substitution prevents agonist-triggered FPR activation and internalization, decreases binding and adhesion to vitronectin, and inhibits uPAR/vitronectin receptor association. Also, 293/uPAR^S90P cells appear quite elongated and their cytoskeleton well organized, whereas 293/uPAR^S90E cells assume a large flattened morphology, with random orientation of actin filaments. Interestingly, when HT1080 cells co-express wild type uPAR with uPAR S90E, the latter behaves as a dominant-negative, impairing uPAR-mediated signaling and reducing cell wound repair as well as lung metastasis in nude mice. In contrast, signaling, wound repair and in vivo lung metastasis of HT1080 cells bearing wild type uPAR are enhanced when they co-express uPAR^S90P. In conclusion, our findings indicate that Ser⁹⁰ is a critical residue for uPAR signaling and that the S90P and S90E exert opposite effects on uPAR activities. These findings may be accommodated in a molecular model, in which uPAR^S90E and uPAR^S90P are forced into inactive and active forms, respectively, suggesting important implications for the development of novel drugs targeting uPAR function.     

Myasthenia Gravis: Effect on Antibody Binding of Conservative Substitutions of Amino Acid Residues Forming the Main Immunogenic Region of the Nicotinic Acetylcholine Receptor

Abstract

In Myasthenia Gravis most anti-acetylcholine receptor (AChR) antibodies are against a highly conserved area of the AChR α-subunit called the Main Immunogenic Region (MIR). Amino acid residues critical for MIR formation have been located within the sequence α67–76. In the present study, binding of anti-AChR monoclonal antibodies (mAbs) to synthetic peptide analogues of the sequence α67–76 of human and Torpedo AChRs containing conservative single-residue substitutions identified the amino acid residues most important to the antigenicity of the MIR sequence, and offered clues to its tridimensional structure.

Conservative substitutions of residues Asn₆₈ and Asp₇₁ greatly diminished mAb binding, identifying them as critical contact residues for anti-MIR mAbs. Substitutions at Asp₇₀ and Tyr₇₂ moderately affected binding. Cross-reactive mAbs originally raised against Electrophorus AChR bound single residue-substituted synthetic peptides in a manner consistent with the possibility that Electrophorus AChR may have a glutamic acid residue at position α70 or α71. Substitutions at residues Asp/Ala₇₀ and Val/Ile₇₀ between human and Torpedo α-subunits may be size-compensating, suggesting these amino acids in the native AChR may be in closer proximity than proposed in previous models of the MIR.     

Positively Charged Amino Acid Substitutions in the E2 Envelope Glycoprotein Are Associated with the Emergence of Venezuelan Equine Encephalitis Virus

Epidemic-epizootic Venezuelan equine encephalitis (VEE) viruses (VEEV) have emerged repeatedly via convergent evolution from enzootic predecessors. However, previous sequence analyses have failed to identify common sets of nucleotide or amino acid substitutions associated with all emergence events. During 1993 and 1996, VEEV subtype IE epizootics occurred on the Pacific Coast of the states of Chiapas and Oaxaca in southern Mexico. Like other epizootic VEEV strains, when inoculated into guinea pigs and mice, the Mexican isolates were no more virulent than closely related enzootic strains, complicating genetic studies of VEE emergence. Complete genomic sequences of 4 of the Mexican strains were determined and compared to those of closely related enzootic subtype IE isolates from Guatemala. The epizootic viruses were less than 2% different at the nucleotide sequence level, and phylogenetic relationships confirmed that the equine-virulent Mexican strains probably evolved from enzootic progenitors on the Pacific Coast of Mexico or Guatemala. Of 35 amino acids that varied among the Guatemalan and Mexican isolates, only 8 were predicted phylogenetically to have accompanied the phenotypic change. One mutation at position 117 of the E2 envelope glycoprotein, involving replacement of Glu by Lys, resulted in a small-plaque phenotype characteristic of epizootic VEEV strains. Analysis of additional E2 sequences from representative enzootic and epizootic VEEV isolates implicated similar surface charge changes in the emergence of previous South American epizootic phenotypes, indicating that E2 mutations are probably important determinants of the equine-virulent phenotype and of VEE emergence. Maximum-likelihood analysis indicated that one change at E2 position 213 has been influenced by positive selection and convergent evolution of the epizootic phenotype.     

Viability of Chlamydomonas Mutants with Amino Acid Substitutions in the Precursor D1 Protein at the Carboxyl-Terminal Processing Site: an Analysis by Mixed-Culture Growth Experiments

Department of Biology, Faculty of Science, Okayama University,3-1-1, Tsushima-naka, Okayama, 700-8530 Japan In order to analyzethe influence of amino acid substitutions at the carboxyl-terminalprocessing site of the D1 precursor protein, mixed-culture growthexperiments were conducted for psbA directed mutants of Chlamydomonasreinhardtii. Wild type and D1 mutants were mixed in the sameculture and their viability was compared. Replacement of Ser-345by Gly or Val at the cleavage site markedly affected the relativegrowth rate of the mutant in the high intensity light, but notin a dim light or the darkness. This was consistent with theprevious result obtained by in vitro analysis using substitutedcarboxyl-terminal oligopeptides as substrates [Taguchi et al.(1995) J Biol. Chem. 270: 10711], This is a clear indicationthat the rate of carboxyl-terminal processing of the D1 precursorin the photosystem II reaction center is a rate-limiting stepfor growth under some environmental stress conditions. (Received June 9, 1998; Accepted September 25, 1998)     

Identification and Structural Analysis of Amino Acid Substitutions that Increase the Stability and Activity of Aspergillus niger Glucose Oxidase

Glucose oxidase is one of the most conspicuous commercial enzymes due to its many different applications in diverse industries such as food, chemical, energy and textile. Among these applications, the most remarkable is the manufacture of glucose biosensors and in particular sensor strips used to measure glucose levels in serum. The generation of ameliorated versions of glucose oxidase is therefore a significant biotechnological objective. We have used a strategy that combined random and rational approaches to isolate uncharacterized mutations of Aspergillus niger glucose oxidase with improved properties. As a result, we have identified two changes that increase significantly the enzyme''s thermal stability. One (T554M) generates a sulfur-pi interaction and the other (Q90R/Y509E) introduces a new salt bridge near the interphase of the dimeric protein structure. An additional double substitution (Q124R/L569E) has no significant effect on stability but causes a twofold increase of the enzyme''s specific activity. Our results disclose structural motifs of the protein which are critical for its stability. The combination of mutations in the Q90R/Y509E/T554M triple mutant yielded a version of A. niger glucose oxidase with higher stability than those previously described.     

Preferential Accumulation by Mesophyll Cells at Low and by Veins at High Exogenous Amino Acid and Sugar Concentrations in Commelina benghalensis L. Leaves

The contribution to solute uptake by mesophyll cells and veinsin leaf discs, was assessed through a study of uptake in relationto concentration for ¹⁴C-labelled substrates (sucrose, glucose,arginine, proline, valine and -aminoisobutyric acid) using isolatedmesophyll cells and stripped leaf discs of Commelina benghalensisL. Uptake per unit fresh weight was higher in mesophyll cellsthan in discs at low substrate concentrations (lower than about0·5 mol m^–3). At higher concentrations, uptakeby discs exceeded that by mesophyll cells except for glucoseuptake which was higher in mesophyll cells over the whole concentrationrange. The profiles of uptake versus concentration displayedbiphasic kinetics in mesophyll cells and discs. Comparison ofthe uptake characteristics obtained by iterative fitting confirmedthat the high-affinity systems of uptake prevail in the mesophyllcells, whereas the low-affinity systems are dominant in theveins. The results provide good evidence that, supplementaryto direct vein loading, a pathway via the mesophyll contributesstrongly to the photosynthate loading by veins in stripped discs. Key words: Commelina benghalensis L., amino acid uptake, mesophyll, minor veins, phloem loading, sugar uptake     

Three Amino Acid Substitutions in the L Protein of the Human Parainfluenza Virus Type 3 cp45 Live Attenuated Vaccine Candidate Contribute to Its Temperature-Sensitive and Attenuation Phenotypes

Studies were initiated to define the genetic basis of the temperature-sensitive (ts), cold adaptation (ca), and attenuation (att) phenotypes of the human parainfluenza virus type 3 (PIV3) cp45 live attenuated vaccine candidate. Genetic data had previously suggested that the L polymerase protein of cp45, which contains three amino acid substitutions at positions 942, 992, and 1558, contributed to its temperature sensitivity (R. Ray, M. S. Galinski, B. R. Heminway, K. Meyer, F. K. Newman, and R. B. Belshe, J. Virol. 70:580–584, 1996; A. Stokes, E. L. Tierney, C. M. Sarris, B. R. Murphy, and S. L. Hall, Virus Res. 30:43–52, 1993). To study the individual and aggregate contributions that these amino acid substitutions make to the ts, att, and ca phenotypes of cp45, seven PIV3 recombinant viruses (three single, three double, and one triple mutant) representing all possible combinations of the three amino acid substitutions were recovered from full-length antigenomic cDNA and analyzed for their ts, att, and ca phenotypes. None of the seven mutant recombinant PIVs was cold adapted. The substitutions at L protein amino acid positions 992 and 1558 each specified a 10⁵-fold reduction in plaque formation in cell culture at 40°C, whereas the substitution at position 942 specified a 300-fold reduction. Thus, each of the three mutations contributes individually to the ts phenotype. The triple recombinant which possesses an L protein with all three mutations was almost as temperature sensitive as cp45, indicating that these mutations are the major contributors to the ts phenotype of cp45. The three individual mutations in the L protein each contributed to restricted replication in the upper or lower respiratory tract of hamsters, and this likely contributes to the observed stability of the ts and att phenotypes of cp45 during replication in vivo. Importantly, the recombinant virus possessing L protein with all three mutations was as restricted in replication as was the cp45 mutant in both the upper and lower respiratory tracts of hamsters, indicating that the L gene of the cp45 virus is a major attenuating component of this candidate vaccine.Human parainfluenza virus type 3 (PIV3), a member of the genus Paramyxovirus of the family Paramyxoviridae, has a single-stranded, negative-sense RNA genome that is 15,462 nucleotides (nt) in length. PIV3 is a major cause of serious lower respiratory illness requiring hospitalization of infants and young children (4). A vaccine is needed to prevent the severe disease caused by this virus, and two live attenuated candidate PIV3 vaccines are currently being evaluated in humans (21, 22). One of these is a bovine strain of PIV3 that is discussed elsewhere (21). The other was produced by passaging the human PIV3 wild type (wt), JS strain, at low temperature for 45 passages to yield the PIV3 cold-passaged 45 (cp45) candidate vaccine virus (1). The cp45 vaccine virus possesses temperature-sensitive (ts), cold adaptation (ca), and attenuation (att) phenotypes (1, 6). The att phenotype is manifested by attenuation of replication in the upper and lower respiratory tracts of rodents and nonhuman primates (6, 15, 16). In addition, the virus appears to be satisfactorily attenuated, phenotypically stable, and immunogenic in seronegative infants and children (22) and therefore is a promising vaccine candidate. Comparison of the complete nucleotide sequences of the cp45 and wt (JS strain) viruses indicated that cp45 possesses multiple point mutations in coding and noncoding regions of the genome, including three point mutations in the L polymerase gene that each encode an amino acid substitution (34).Previously, we recovered recombinant PIV3 from a full-length antigenomic cDNA clone of wt PIV3 (JS strain), the parent of cp45, and demonstrated that the recovered virus was not temperature sensitive and replicated to a level in the respiratory tract of rodents comparable to that of the biologically derived wt (JS strain) virus (9). This meant that it was now possible to systematically examine the genetic basis of the att phenotype of PIV3 candidate vaccines such as cp45. Since the polymerase genes are the sites of many att and ts mutations for influenza virus and respiratory syncytial virus (RSV) (8, 11, 20, 24, 32) and since preliminary data suggested that the L gene of cp45 possesses a ts mutation (30), we initiated our studies to examine the genetic basis of attenuation of cp45 by introducing the mutations yielding the seven possible combinations of the three amino acid substitutions present in the L gene of cp45 into the cDNA clone of its wt (JS strain) parent. Seven recombinant viruses (three single, three double, and one triple mutant) were isolated and analyzed for their ts and att phenotypes. Analysis of these mutants indicated that each of the three mutations in the L protein is a major separate contributor to the ts and att phenotypes of this promising vaccine candidate. Furthermore, this study illustrates the usefulness of the newly developed reverse-genetics systems for characterizing and manipulating a nonsegmented negative-strand virus.     

The Effect of Sucrose Supply on the Energization of Amino Acid Uptake by Cotyledons of Euphorbia lathyris L

The cotyledons of Euphorbia lathyris L. take up sucrose andamino acids from the endosperm. The interaction between theuptake of sucrose and that of amino acids by cotyledons of intactseedlings was investigated. Sucrose (100 mol m^–3) reducedvaline uptake to 75% of the control rate; the active uptakecomponent of valine uptake was reduced from 45 to 25 % of thetotal uptake rate. In a reverse experiment, 100 mol m^–3valine inhibited sucrose uptake by 25%. At 500 mol m^–3sucrose, valine uptake was completely restored to the controlrate, whereas high valine concentrations failed to restore sucroseuptake. The stimulation of valine uptake by sucrose is linkedto the role of sucrose as a primary respiratory substrate. Whenthe cotyledons were bathed in sucrose concentrations rangingfrom 0 to 100 mol m^–3 (these concentrations are non-saturatingwith respect to sucrose uptake), a constant 1.8% of the sucrosetaken up was respired. The K_m of the concentration-dependentsucrose oxidation (44±6 mol m^–3) agreed reasonablywell with that for sucrose uptake (29±6 mol m^–3).When the external sucrose concentration was increased from 100to 600 mol m^–3, the sucrose uptake increased by 30% again,while sucrose oxidation was increased by 300%. This increasewas not due to an increased engagement of the alternative (cyanide-resistant)pathway for respiration. Alternative pathway, Euphorbia lathyris L., fermentation, seedling, sucrose uptake, valine uptake