Engineering enzyme specificity by "substrate-assisted catalysis"

A novel approach to engineering enzyme specificity is presented in which a catalytic group from an enzyme is first removed by site-directed mutagenesis causing inactivation. Activity is then partially restored by substrates containing the missing catalytic functional group. Replacement of the catalytic His with Ala in the Bacillus amyloliquefaciens subtilisin gene (the mutant is designated His64Ala) by site-directed mutagenesis reduces the catalytic efficiency (kcat/Km) by a factor of a million when assayed with N-succinyl-L-Phe-L-Ala-L-Ala-L-Phe-p-nitroanilide (sFAAF-pNA). Model building studies showed that a His side chain at the P2 position of a substrate bound at the active site of subtilisin could be virtually superimposed on the catalytic His side chain of this serine protease. Accordingly, the His64Ala mutant hydrolyzes a His P2 substrate (sFAHF-pNA) up to 400 times faster than a homologous Ala P2 or Gln P2 substrate (sFAAF-pNA or sFAQF-pNA) at pH 8.0. In contrast, the wild-type enzyme hydrolyzes these three substrates with similar catalytic efficiencies. Additional data from substrate-dependent pH profiles and hydrolysis of large polypeptides indicate that the His64Ala mutant enzyme can recover partially the function of the lost catalytic histidine from a His P2 side chain on the substrate. Such "substrate-assisted catalysis" provides a new basis for engineering enzymes with very narrow and potentially useful substrate specificities. These studies also suggest a possible functional intermediate in the evolution of the catalytic triad of serine proteases.     

Redesigning trypsin: alteration of substrate specificity

A general method for modifying eukaryotic genes by site-specific mutagenesis and subsequent expression in mammalian cells was developed to study the relation between structure and function of the proteolytic enzyme trypsin. Glycine residues at positions 216 and 226 in the binding cavity of trypsin were replaced by alanine residues, resulting in three trypsin mutants. Computer graphic analysis suggested that these substitutions would differentially affect arginine and lysine substrate binding of the enzyme. Although the mutant enzymes were reduced in catalytic rate, they showed enhanced substrate specificity relative to the native enzyme. This increased specificity was achieved by the unexpected differential effects on the catalytic activity toward arginine and lysine substrates. Mutants containing alanine at position 226 exhibited an altered conformation that may be converted to a trypsin-like structure upon binding of a substrate analog.     

A specific amino acid binding site composed of RNA

A specific, reversible binding site for a free amino acid is detectable on the intron of the Tetrahymena self-splicing ribosomal precursor RNA. The site selects arginine among the natural amino acids, and prefers the L- to the D-amino acid. The dissociation constant is in the millimolar range, and amino acid binding is at or in the catalytic rG splicing substrate site. Occupation of the G site by L-arginine therefore inhibits splicing by inhibiting the binding of rG, without inhibition of later reactions in the splicing reaction sequence. Arginine binding specificity seems to be directed at the side chain and the guanidino radical, and the alpha-amino and carboxyl groups are dispensable for binding. The arginine site can be placed within the G site by structural homology, with consequent implications for RNA-amino acid interaction, for the origin of the genetic code, for control of RNA activities, and for further catalytic capabilities for RNA.     

5'-腺苷磷酰硫酸激酶及其R68K突变体对5'-腺苷一磷酸3'羟基的磷酸化

硫作为生命活动的必需元素,主要以-2价和+6价发挥生物学功能。硫的同化代谢包括胞内活化、转移以及还原等反应。其活化是同化代谢的关键反应,包括ATP硫酸化酶(ATP sulfurylase,ATPS)催化硫酸盐与ATP反应生成腺苷-5'-磷酰硫酸(adenosine 5'-phosphosulfate,APS)和焦磷酸(pyrophosphate,PPi)以及腺苷-5'-磷酰硫酸激酶(adenosine 5'-phosphosulfate kinase,APSK)催化APS 3'羟基磷酸化生成3'-磷酸腺苷-5'-磷酰硫酸(3'-phosphoadenosine 5'-phosphosulfate,PAPS),APSK催化APS磷酸机理已经较为清楚。利用APSK对AMP的磷酸化进行了初步分析,发现AMP可作为APSK的底物,反应生成3,5'二磷酸腺苷(3'-phosphoadenosine 5'-phosphate,PAP);对APSK的三维结构进行分析发现,R68同时和APS的磷酸根和硫酸根形成氢键,稳定APS的结合,而K侧链基团比R短2.4魡,R68K突变将导致K不能和距离较远的硫酸根离子相互作用,从而减弱APS的亲和力,而增加与磷酸根离子的相互作用,可能提高AMP的亲和力。研究结果表明,R68K突变体的最适底物变为AMP,KmAMP是对照的0.2倍,而催化效率是对照的5倍。以R68K为偶联酶成功测定了具有较低KmPAP的酵母3,5二磷酸核苷酸酶(3',5'-bisphosphate nucleotidase,YND)动力学常数,为分析测定AMP底物的酶活提供了工具。     

Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase

The structure of a 20-amino acid peptide inhibitor bound to the catalytic subunit of cyclic AMP-dependent protein kinase, and its interactions with the enzyme, are described. The x-ray crystal structure of the complex is the basis of the analysis. The peptide inhibitor, derived from a naturally occurring heat-stable protein kinase inhibitor, contains an amphipathic helix that is followed by a turn and an extended conformation. The extended region occupies the cleft between the two lobes of the enzyme and contains a five-residue consensus recognition sequence common to all substrates and peptide inhibitors of the catalytic subunit. The helical portion of the peptide binds to a hydrophobic groove and conveys high affinity binding. Loops from both domains converge at the active site and contribute to a network of conserved residues at the sites of magnesium adenosine triphosphate binding and catalysis. Amino acids associated with peptide recognition, nonconserved, extend over a large surface area.     

Design and synthesis of a peptide having chymotrypsin-like esterase activity

A peptide having enzyme-like catalytic activity has been designed and synthesized. Computer modeling was used to design a bundle of four short parallel amphipathic helical peptides bearing the serine protease catalytic site residues serine, histidine, and aspartic acid at the amino end of the bundle in the same spatial arrangement as in chymotrypsin (ChTr). The necessary "oxyanion hole" and substrate binding pocket for acetyltyrosine ethyl ester, a classical ChTr substrate, were included in the design. The four chains were linked covalently at their carboxyl ends. The peptide has affinity for ChTr ester substrates similar to that of ChTr and hydrolyzes them at rates approximately 0.01 that of ChTr; total turnovers greater than 100 have been observed. The peptide is inhibited by ChTr specific inhibitors and is inactive toward benzoyl arginine ethyl ester, a trypsin substrate. The peptide is inactivated by heating above 60 degrees C, but recovers full catalytic activity upon cooling and lyophilization from acetic acid.     

Structural basis for substrate delivery by acyl carrier protein in the yeast fatty acid synthase

In the multifunctional fungal fatty acid synthase (FAS), the acyl carrier protein (ACP) domain shuttles reaction intermediates covalently attached to its prosthetic phosphopantetheine group between the different enzymatic centers of the reaction cycle. Here, we report the structure of the Saccharomyces cerevisiae FAS determined at 3.1 angstrom resolution with its ACP stalled at the active site of ketoacyl synthase. The ACP contacts the base of the reaction chamber through conserved, charge-complementary surfaces, which optimally position the ACP toward the catalytic cleft of ketoacyl synthase. The conformation of the prosthetic group suggests a switchblade mechanism for acyl chain delivery to the active site of the enzyme.     

Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase

The crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase complexed with a 20-amino acid substrate analog inhibitor has been solved and partially refined at 2.7 A resolution to an R factor of 0.212. The magnesium adenosine triphosphate (MgATP) binding site was located by difference Fourier synthesis. The enzyme structure is bilobal with a deep cleft between the lobes. The cleft is filled by MgATP and a portion of the inhibitor peptide. The smaller lobe, consisting mostly of amino-terminal sequence, is associated with nucleotide binding, and its largely antiparallel beta sheet architecture constitutes an unusual nucleotide binding motif. The larger lobe is dominated by helical structure with a single beta sheet at the domain interface. This lobe is primarily involved in peptide binding and catalysis. Residues 40 through 280 constitute a conserved catalytic core that is shared by more than 100 protein kinases. Most of the invariant amino acids in this conserved catalytic core are clustered at the sites of nucleotide binding and catalysis.     

Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions

The crystal structure of a complex containing the DNA-binding domain of lambda repressor and a lambda operator site was determined at 2.5 A resolution and refined to a crystallographic R factor of 24.2 percent. The complex is stabilized by an extensive network of hydrogen bonds between the protein and the sugar-phosphate backbone. Several side chains form hydrogen bonds with sites in the major groove, and hydrophobic contacts also contribute to the specificity of binding. The overall arrangement of the complex is quite similar to that predicted from earlier modeling studies, which fit the protein dimer against linear B-form DNA. However, the cocrystal structure reveals important side chain-side chain interactions that were not predicted from the modeling or from previous genetic and biochemical studies.     

Antarctic stratospheric chemistry of chlorine nitrate, hydrogen chloride, and ice: release of active chlorine

The reaction rate between atmospheric hydrogen chloride (HCl) and chlorine nitrate (ClONO(2)) is greatly enhanced in the presence of ice particles; HCl dissolves readily into ice, and the collisional reaction probability for ClONO(2) on the surface of ice with HCl in the mole fraction range from approximately 0.003 to 0.010 is in the range from approximately 0.05 to 0.1 for temperatures near 200 K. Chlorine (Cl(2)) is released into the gas phase on a time scale of at most a few milliseconds, whereas nitric acid (HNO(3)), the other product, remains in the condensed phase. This reaction could play an important role in explaining the observed depletion of ozone over Antarctica; it releases photolytically active chlorine from its most abundant reservoir species, and it promotes the formation of HNO(3) and thus removes nitrogen dioxide (NO(2)) from the gas phase. Hence it establishes the necessary conditions for the efficient catalytic destruction of ozone by halogenated free radicals. In the absence of HCl, ClONO(2) also reacts irreversibly with ice with a collision efficiency of approximately 0.02 at 200 K; the product hypochlorous acid (HOCI) is released to the gas phase on a time scale of minutes.     

The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling

The mammalian target of rapamycin (mTOR) protein kinase is a master growth promoter that nucleates two complexes, mTORC1 and mTORC2. Despite the diverse processes controlled by mTOR, few substrates are known. We defined the mTOR-regulated phosphoproteome by quantitative mass spectrometry and characterized the primary sequence motif specificity of mTOR using positional scanning peptide libraries. We found that the phosphorylation response to insulin is largely mTOR dependent and that mTOR exhibits a unique preference for proline, hydrophobic, and aromatic residues at the +1 position. The adaptor protein Grb10 was identified as an mTORC1 substrate that mediates the inhibition of phosphoinositide 3-kinase typical of cells lacking tuberous sclerosis complex 2 (TSC2), a tumor suppressor and negative regulator of mTORC1. Our work clarifies how mTORC1 inhibits growth factor signaling and opens new areas of investigation in mTOR biology.     

Network context and selection in the evolution to enzyme specificity

Enzymes are thought to have evolved highly specific catalytic activities from promiscuous ancestral proteins. By analyzing a genome-scale model of Escherichia coli metabolism, we found that 37% of its enzymes act on a variety of substrates and catalyze 65% of the known metabolic reactions. However, it is not apparent why these generalist enzymes remain. Here, we show that there are marked differences between generalist enzymes and specialist enzymes, known to catalyze a single chemical reaction on one particular substrate in vivo. Specialist enzymes (i) are frequently essential, (ii) maintain higher metabolic flux, and (iii) require more regulation of enzyme activity to control metabolic flux in dynamic environments than do generalist enzymes. Furthermore, these properties are conserved in Archaea and Eukarya. Thus, the metabolic network context and environmental conditions influence enzyme evolution toward high specificity.     

SDS水相胶束体系中酶促反应的热动力学研究

在298.15K十二烷基硫酸钠(SDS)的水相胶束体系中,利用微量热方法研究了辣根过氧化物酶(HRP)催化H2O2氧化邻苯二胺(OPD)的反应.SDS作为一种蛋白质变性剂,不仅能够使HRP变性失去部分活性,而且还能使HRP对底物OPD的米氏常数Km(OPD)和最大反应速率都比其在缓冲体系中小;而在SDS溶胶中,OPD相对过量时,HRP对底物H2O2不符合米氏机理.     

Acid catalysis in basic solution: a supramolecular host promotes orthoformate hydrolysis

Although many enzymes can promote chemical reactions by tuning substrate properties purely through the electrostatic environment of a docking cavity, this strategy has proven challenging to mimic in synthetic host-guest systems. Here, we report a highly charged, water-soluble, metal-ligand assembly with a hydrophobic interior cavity that thermodynamically stabilizes protonated substrates and consequently catalyzes the normally acidic hydrolysis of orthoformates in basic solution, with rate accelerations of up to 890-fold. The catalysis reaction obeys Michaelis-Menten kinetics and exhibits competitive inhibition, and the substrate scope displays size selectivity, consistent with the constrained binding environment of the molecular host.     

Structural basis of energy transduction in the transport cycle of MsbA

We used site-directed spin-labeling and electron paramagnetic resonance spectroscopy to characterize the conformational motion that couples energy expenditure to substrate translocation in the multidrug transporter MsbA. In liposomes, ligand-free MsbA samples conformations that depart from the crystal structures, including looser packing and water penetration along the periplasmic side. Adenosine triphosphate (ATP) binding closes the substrate chamber to the cytoplasm while increasing hydration at the periplasmic side, consistent with an alternating access model. Accentuated by ATP hydrolysis, the changes in the chamber dielectric environment and its geometry provide the likely driving force for flipping amphipathic substrates and a potential exit pathway. These results establish the structural dynamic basis of the power stroke in multidrug-resistant ATP-binding cassette (MDR ABC) transporters.     

树脂负载Fe(Ⅲ)/Cu(Ⅱ)非均相光Fenton体系降解罗丹明B模拟废水研究

采用浸渍法制备负载有Fe(Ⅲ)/Cu(Ⅱ)、Fe(Ⅲ)和Cu(Ⅱ)的阳离子交换树脂(R)催化剂,在H_2O_2和节能灯照射条件下降解罗丹明B(Rh B)模拟印染废水。在H_2O_2浓度为20 mmol/L、曝气、30℃和光照条件下,0.05 g/L Fe(Ⅲ)/Cu(Ⅱ)/R催化剂在29 h内将20 mg/L的Rh B溶液降解完全,30 h后COD去除率为73.7%,且Fe(Ⅲ)/Cu(Ⅱ)/R催化剂具有最大的反应速率。Fe(Ⅲ)/Cu(Ⅱ)/R催化剂的稳定试验和重复试验表明,该催化剂在78 h光催化反应后,溶液中含有的Fe(Ⅲ)和Cu(Ⅱ)浓度分别为0.5和0.2 mg/L,且在连续使用6次后仍具有较高的催化效率。Fe(Ⅲ)/Cu(Ⅱ)/R催化剂对Rh B的较高催化性能主要归因于铁、铜离子间的协同作用及光照的共同作用。     

296位氨基酸位阻效应影响黄花蒿没药醇合酶环化反应的起始

【目的】探究黄花蒿没药醇合酶第296位氨基酸突变抑制环化反应的机制。【方法】利用Quik Change?Multi Site-Directed Mutagenesis的方法将黄花蒿没药醇合酶的296位氨基酸残基由苏氨酸突变成异亮氨酸。原核表达,蛋白纯化后测定其催化特异性。【结果】黄花蒿没药醇合酶T296I体外催化(2E,6E)-法尼基焦磷酸主产物为非环化的法尼烯;但是将T296I蛋白与中间体(3R,6E)-橙花叔醇焦磷酸一起孵育时可生成环化的主产物α-bisabolol,野生型酶的天然产物。【结论】黄花蒿没药醇合酶T296I点突变进一步证明氨基酸残基的空间体积和立体化学是自然环化反应起始的控制关键,其位阻效应能够抑制法尼基焦磷酸向橙花叔醇焦磷酸转化。     

Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A

The three-dimensional structures of an antibody to a peptide and its complex with the peptide antigen have been determined at 2.8 A resolution. The antigen is a synthetic 19-amino acid peptide homolog of the C helix of myohemerythrin (Mhr). The unliganded Fab' crystals are orthorhombic with two molecules per asymmetric unit, whereas the complex crystals are hexagonal with one molecule per asymmetric unit. The Fab' and the Fab'-peptide complex structures have been solved independently by molecular replacement methods and have crystallographic R factors of 0.197 and 0.215, respectively, with no water molecules included. The amino-terminal portion of the peptide sequence (NH2-Glu-Val-Val-Pro-His-Lys-Lys) is clearly interpretable in the electron density map of the Fab'-peptide complex and adopts a well-defined type II beta-turn in the concave antigen binding pocket. This same peptide amino acid sequence in native Mhr is alpha-helical. The peptide conformation when bound to the Fab' is inconsistent with binding of the Fab' to native Mhr, and suggests that binding of the Fab' to conformationally altered forms of the native Mhr or to apo-Mhr. Immunological mapping previously identified this sequence as the peptide epitope, and its fine specificity correlates well with the structural analysis. The binding pocket includes a large percentage of hydrophobic residues. The buried surfaces of the peptide and the antibody are complementary in shape and cover 460 A2 and 540 A2, respectively. These two structures now enable a comparison of a specific monoclonal Fab' both in its free and antigen complexed state. While no major changes in the antibody were observed when peptide was bound, there were some small but significant side chain and main chain rearrangements.     

查尔酮合酶蛋白表达技术、结构、活性和进化

查尔酮合酶(CHS)是类黄酮途径的首步关键酶,参与合成所有类黄酮和异黄酮物质,参与决定多种植物重要性状。NCBI已有2917条CHS序列登录和释放。单个物种基因组中的CHS普遍由基因家族编码,通过基因加倍而产生。CHS蛋白的表达技术目前均是基于大肠杆菌的原核表达,多采用Novagen公司的pET载体系统,最通行参数为37℃条件下1 mmol/L IPTG诱导3h,表达蛋白普遍采用His-Tag进行亲和纯化,采用质谱或免疫分析技术进行身份检测,通过对生化反应底物和产物的HPLC检测可以精确分析酶活。苜蓿等植物的CHS蛋白已完成X射线晶体衍射研究,获得了三维结构和活性位点构象的初步解析,并与植物Ⅲ型PKS超家族中的其它酶类进行了比较。CHS蛋白的催化活性中心含有一个Cys-His-Asn三联体,另外CoA结合通道和内部的起始/延伸/环化腔关系到CHS蛋白的底物特异性及聚酮化合物链延伸的长度。植物Ⅲ型PKS超家族中,其它酶的结构骨架和催化方式与CHS相似,但活性位点残基的变化可能会造成活性中心结构的改变,进而产生底物特异性、催化能力和产物种类的显著变化,是蛋白水平进化的根本动力。