Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing

The controversy surrounding the idea that neutral mutations dominate protein evolution is attributable in part to the inadequacy of the tools available to evolutionary investigators. With a few exceptions, most investigations into the force driving protein evolution have relied on indirect criteria for distinguishing neutral and non-neutral variants. To investigate a particular pathway of molecular evolution, we have reconstructed by site-directed mutagenesis likely ancestral variants of the lysozymes of modern game birds (order Galliformes), tested their activity and thermostability and determined their three-dimensional structure. We focused on amino acids at three positions that are occupied in all known game birds either by the triplet Thr 40, Ile 55, Ser 91, or by the triplet Ser 40, Val 55, Thr 91. We have synthesized proteins representing intermediates along the possible three-step evolutionary pathways between these triplets. Although all of these are active and stable, none of these intermediates is found in known lysozymes. A comparison of the structures and thermostabilities of the variants reveals a linear correlation between the side-chain volume of the triplet and the thermostability of the protein. Each pathway connecting the two extant triplet sequences includes a variant with a thermostability outside the range of the extant proteins. This observation is consistent with a non-neutral evolutionary pathway. The existence of variants that are more stable than the extant proteins suggests that selection for maximum thermostability may not have been an important factor in the evolution of this enzyme.     

Detection of single base substitutions in total genomic DNA

Certain single base substitutions causing genetic diseases or resulting in polymorphisms linked to mutant alleles, alter a restriction enzyme cleavage site and can therefore be detected in total genomic DNA using DNA blots. Many base substitutions do not lead to an altered restriction site, but these can be detected using synthetic oligonucleotides as hybridization probes if the DNA sequence surrounding the base substitution is known. In the case of beta-thalassaemia, where 22 different single base mutations have been identified, a large number of probes would be required for diagnosis. An approach which was used to detect mutations in viral DNA involves the S1 nuclease treatment of heteroduplexes formed between wild-type and mutant DNA. Although certain single base mismatches are cleaved by S1 nuclease (ref. 11 and T. Shenk, personal communication), many other mismatches examined by this procedure are not cleaved (B. Seed, personal communication; R.M.M., unpublished data). Heteroduplexes between mutant and wild-type subgenomic fragments of double-stranded reovirus RNA migrate slower than the corresponding homoduplexes in polyacrylamide gels containing 7 M urea, but it is not known whether this method is applicable to DNA heteroduplexes containing single base mismatches. Here we describe a procedure that involves the electrophoretic separation of DNA heteroduplexes in a well-characterized gel system. We show that four different human beta-thalassaemia alleles with known single base mutations can be detected with as little as 5 micrograms of total genomic DNA. The method should be useful in the localization and diagnosis of mutations associated with genetic diseases.     

Protein dispensability and rate of evolution.

If protein evolution is due in large part to slightly deleterious amino acid substitutions, then the rate of evolution should be greater in proteins that contribute less to individual fitness. The rationale for this prediction is that relatively dispensable proteins should be subject to weaker purifying selection, and should therefore accumulate mildly deleterious substitutions more rapidly. Although this argument was presented over twenty years ago, and is fundamental to many applications of evolutionary theory, the prediction has proved difficult to confirm. In fact, a recent study showed that essential mouse genes do not evolve more slowly than non-essential ones. Thus, although a variety of factors influencing the rate of protein evolution have been supported by extensive sequence analysis, the relationship between protein dispensability and evolutionary rate has remained unconfirmed. Here we use the results from a highly parallel growth assay of single gene deletions in yeast to assess protein dispensability, which we relate to evolutionary rate estimates that are based on comparisons of sequences drawn from twenty-one fully annotated genomes. Our analysis reveals a highly significant relationship between protein dispensability and evolutionary rate, and explains why this relationship is not detectable by categorical comparison of essential versus non-essential proteins. The relationship is highly conserved, so that protein dispensability in yeast is also predictive of evolutionary rate in a nematode worm.     

Counting integral numbers of amino acid residues per polypeptide chain

Proteins have integral numbers of each of the 20 amino acids. However, all the currently accepted methods of determining this number measure the ratio of moles of amino acid residue per mole of protein. This value is rarely close to an integer, due to experimental errors in determination of the molar amounts of both amino acid residues and polypeptide chain. A simple method which gives integral values of amino acid residues per polypeptide chain, independent of any other properties of the protein, would be useful in characterising proteins. We describe here one method; it is illustrated for the case of Cys residues, although the approach should be useful for many of the other 19 usual amino acids.     

Calculation of electrostatic potentials in an enzyme active site

To be able to calculate the contributions of individual amino acids to the electrostatic field of a protein would be of considerable value in designing proteins of enhanced or altered function and stability. Recent studies on the serine protease subtilisin provide direct measurements of the electrostatic potential in the active site of the enzyme produced by two charged amino acids. We have used these results to test a recently developed method for the calculation of electrostatic interactions between two specific sites on a protein. The extent of agreement between the theoretical and experimental results suggests that the continuum solvent model used in the calculations reproduces the essential features of the interaction.     

Three-dimensional structure of an antigenic mutant of the influenza virus haemagglutinin

Antigenic variation in the haemagglutinin (HA) glycoprotein of influenza virus is associated with recurrent epidemics of respiratory disease in man (for review see ref. 1). We have examined the size of structural changes necessary to alter the antigenicity of HA by determining the three-dimensional structure of the HA from an antigenic mutant containing a single amino acid substitution which was selected by growth of virus in the presence of monoclonal antibodies. Here we present evidence that the simple addition of an amino acid side chain which results in only minor local distortions of the structure of the HA is sufficient structural alteration for a virus to escape neutralization by a monoclonal antibody. Our results also demonstrate that single amino acid substitutions can cause only local changes in the HA structure, verifying the assumption made in several studies to locate antigenic sites on the HA and other molecules, and indicate that proposals of large conformational changes to account for variations in HA antigenicity are unnecessary in this case. The structure of the variant antigen has independently been successfully predicted (M. Karplus, personal communication).     

The yeast ubiquitin gene: head-to-tail repeats encoding a polyubiquitin precursor protein

Ubiquitin, a 76-residue protein, occurs in cells either free or covalently joined to a variety of protein species, from chromosomal histones to cytoplasmic proteins. Conjugation of ubiquitin to proteolytic substrates is essential for the selective degradation of intracellular proteins in higher eukaryotes. We show here that a protein homologous to human ubiquitin exists in the yeast Saccharomyces cerevisiae, and that yeast extracts conjugate human ubiquitin to a variety of endogenous proteins in an ATP-dependent reaction. We have isolated the S. cerevisiae ubiquitin gene and found it to contain six consecutive ubiquitin-coding repeats in a found it to contain six consecutive ubiquitin-coding repeats in a head-to-tail arrangement. This apparently unique gene organization suggests that yeast ubiquitin is generated by processing of a precursor protein in which several exact repeats of the ubiquitin amino acid sequence are joined directly via Gly-Met peptide bonds between the last and first residues of mature ubiquitin, respectively. Ubiquitin-coding yeast DNA repeats are restricted to a single genomic locus; although the sequenced repeats differ in up to 27 of 228 bases per repeat, they encode identical amino acid sequences. As this predicted amino acid sequence differs in only 3 of 76 residues from that of ubiquitin in higher eukaryotes, ubiquitin is apparently the most conserved of known proteins.     

二硫键影响GH11木聚糖酶稳定性研究进展

低聚木糖具有改善肠道微生态的益生作用,在降血糖、降血压、防止便秘等方面表现出良好的保健效果。近年来,利用生物酶技术制备功能性低聚木糖的相关研究受到广泛关注。糖苷水解酶(glycoside hydrolase, GH)11家族木聚糖酶具有底物特异性强和催化效率高的特点,在低聚木糖生产应用中表现出显著优势；然而,大多数天然GH11木聚糖酶存在稳定性较差的问题,无法满足工业生产中高温、酸、碱等极端条件的要求。利用酶工程技术对天然木聚糖酶进行分子改造,以适应高温、酸、碱等生产条件,使底物特异性强、催化效率高的酶相对稳定地发挥作用,对于制备功能性低聚木糖的工业生产具有重要的实际意义。根据GH11木聚糖酶的分子结构及其特点,通过比较其分子内相互作用力对酶热稳定性的影响,发现二硫键在改善酶的稳定性方面具有十分显著的优势。基于对GH11木聚糖酶结构的分析,总结了引入二硫键的常规策略,比较了酶在不同区域引入不同数量二硫键对GH11木聚糖酶稳定性的改善效果,对引入二硫键后酶稳定性显著变化的几个区域进行定位,并指出多个二硫键对改善酶稳定性的作用方式,希望为提高酶稳定性的酶分子改造研究提供基础数据,为拓宽GH11木聚糖酶工业应用范围提供科学参考。     

人类乙型肝炎样病毒核心蛋白中第7位疏水性氨基酸重复肚段区域的突变可以抑制病毒核衣壳的组装

人类乙型肝炎病毒的核衣壳由核心蛋白的二聚体所组成．但是,核心蛋白亚单位与亚单位之间相互作用的机制至今尚不清楚．研究发现,在人类乙型肝炎样病毒──土拨鼠肝炎病毒（WHV）核心蛋白的氨基端,存在着4个保守的疏水氨基酸残基（氨基酸位置101～102）．它们分别是亮氨酸101,亮氨酸108,缬氨酸115和苯丙氨酸122．这4个疏水氨基酸残基以每隔6个氨基酸残基而重复出现1次．它们被称为“第7位疏水性氨基酸重复肽段（hhr）”．由于蛋白质中的疏水键往往在蛋白质的相互作用中起重要作用,因此就在培养细胞系统中研究WHV核心蛋白的hhr区域在…     

A universal trend of amino acid gain and loss in protein evolution

Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G + C)-rich (or (A + T)-rich) genomes contain more (or fewer) amino acids encoded by (G + C)-rich codons. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day.     

Mimicking the alloantigenicity of proteins with chemically synthesized peptides differing in single amino acids

Recent studies have shown that short chemically synthesized peptides very often induce antibodies which react with the cognate sequence in the intact folded protein. Since such antibodies react with known regions of proteins, they are of predetermined specificity and offer a precision not previously possible with immunological probes. A basic concept emerging from the use of such antibodies in viral systems is that the differential immunogenicity of closely related proteins can be mimicked by short peptides which span the regions of sequence variation. To generalize this concept, we have studied the two Thy-1 proteins which vary by only a single amino acid. Chemically synthesized peptides differing in only one out of 19 amino acids were able to induce allospecific antisera. Thus, single amino acid changes have similar effects on the immunogenicity of proteins and small peptides, even though the latter are free from constraints provided by neighbouring structures in the tertiary configuration of the intact folded proteins.     

A novel thermophilic endoglucanase from a mesophilic fungus Fusarium oxysporum

Cellulose is an abundant and renewable energy re- source on earth. Microorganisms produce multiple en- zymes to degrade cellulose, known as cellulase sys- tem[1]. Components of cellulase system were first clas- sified based on their modes of catalytic act…     

鱼露外加酶工艺的探讨

通过对鱼露外加酸发酵及自然发酵过程中氨基态氮、挥发性盐基氨的分析，可比较出鱼露在外加酶发酵及自然发酵过程中的成分变化．以市售优质天然鱼露作对照，检测外加酶鱼露产品的氨基酸及多肽的组成，得出了外加酶发酵的意义．     

5个产地羊角药材中氨基酸比较研究

本文采用高效液相柱前衍生异硫氰酸苯酯法(PITC-HPLC)检测了5个产地羊角药材的氨基酸种类及含量,为完善羊角药材质量标准提供依据。结果表明,5个产地羊角药材氨基酸HPLC与氨基酸标准品溶液的出峰顺序一致,出峰时间接近,PITC-HPLC可用于氨基酸的检测。四川山羊角药材样品中氨基酸总量为94.3%,且多种氨基酸含量较高,远超过其他4个产地样品氨基酸总量。山东菏泽产药材的氨基酸总量也较高,为68.10%,山东平邑、山东莱芜、河北衡水产羊角药材氨基酸含量相近。氨基酸含量应作为羊角药材质量的内在控制指标。     

大肠杆菌L—谷氨酸脱羧酶酶促特性的研究

本文主要研究大肠杆菌505L-谷氨酸脱羧酶脱羧作用的最适浓度、pH、温度、耐热性、底物浓度以及它对天冬氨酸等十二种氨基酸是否具有脱羧性能,从而发现目前L-谷氨酸发酵生产中测定存在的问题。     

蚯蚓纤溶酶的分离及其生物学特性

经过分离纯化，从人工养殖的赤子爱胜蚓中提取出两种既有纤维蛋白溶酶原激活因子活性又能直接溶解纤维蛋白的组分。ＰＡＧＥ检测各为一条区带，证明已达电泳纯。对这两组分的生物学性质进行了研究，包括分子量、酶活力，Ｎ－末端氨基酸残基，氨基酸组成，温度的稳定性及对苯甲酸精氨酸乙酯（ＢＡＥＥ）的酶促反应动力学特性。还分析了其中一个组分（ＢⅡ）从Ｎ末端开始的 ２５个氨基酸残基序列。     

The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine

Pyrrolysine, the twenty-second amino acid found to be encoded in the natural genetic code, is necessary for all of the known pathways by which methane is formed from methylamines. Pyrrolysine comprises a methylated pyrroline carboxylate in amide linkage to the ε-amino group of L-lysine. In certain Archaea, three methyltransferases initiate methanogenesis from the various methylamines, and these enzymes are encoded by genes with an in-frame amber codon that is translated as pyrrolysine. Escherichia coli that has been transformed with the pylTSBCD genes from methanogenic Archaea can incorporate endogenously biosynthesized pyrrolysine into proteins. The decoding of UAG as pyrrolysine requires pylT, which produces tRNA(Pyl) (also called tRNA(CUA)), and pylS, which encodes a pyrrolysyl-tRNA synthetase. The pylB, pylC and pylD genes are each required for tRNA-independent pyrrolysine synthesis. Pyrrolysine is the last remaining genetically encoded amino acid with an unknown biosynthetic pathway. Here we provide genetic and mass spectrometric evidence for a pylBCD-dependent pathway in which pyrrolysine arises from two lysines. We show that a newly uncovered UAG-encoded amino acid, desmethylpyrrolysine, is made from lysine and exogenous D-ornithine in a pylC-dependent process followed by a pylD-dependent process, but it is not further converted to pyrrolysine. These results indicate that the radical S-adenosyl-L-methionine (SAM) protein PylB mediates a lysine mutase reaction that produces 3-methylornithine, which is then ligated to a second molecule of lysine by PylC before oxidation by PylD results in pyrrolysine. The discovery of lysine as the sole precursor to pyrrolysine will further inform discussions of the evolution of the genetic code and amino acid biosynthetic pathways. Furthermore, intermediates of the pathway may provide new avenues by which the pyl system can be exploited to produce recombinant proteins with useful modified residues.     

四螺旋桨家族蛋白质序列——结构关系研究

蛋白质的三级结构唯一地由其氨基酸序列决定,这是广为人所接受的。然而,很多具有规则三级结构的蛋白质其氨基酸序列接近随机,这使得人们感到很困惑。本文将以四螺旋桨家族蛋白质为例,通过简化氨基酸残基,根据相似性方法把序列中的隐含对称性显示出来。结果表明氨基酸序列中的隐含对称性与三级结构的四重准对称性一致。     

中性植酸酶结构与功能关系研究进展

中性植酸酶是一种新型、绿色环保的饲料用酶。从中性植酸酶的微生物来源、酶学性质、序列结构特点及分子改造研究等方面进行综述,以期为改善中性植酸酶的热稳定性及催化活性提供参考。