Cys146-Cys146分子间二硫键在人瘦素二聚化过程中起主导作用

在前期研究中,已发现人瘦素（leptin）在体外再折叠过程中会形成稳定的二聚体,但其二聚化机制尚不清楚. 本研究旨在分析瘦素二聚体的结构特性,并重点研究体外再折叠过程中瘦素二聚化的机制. 相较与瘦素单体,瘦素二聚体保留了约75％免疫活性及15％受体结合活性,同时显示出明显慢的天然电泳迁移率. 圆二色性分析显示,二聚体基本保留了单体α螺旋索结构特征. 还原性及非还原性凝胶电泳分析和自由巯基测定结果表明,瘦素二聚体是由一对分子间二硫键连接2个单体而成的.为了确定瘦素二聚化过程中起主导作用的分子间二硫键,利用PCR定点突变技术构建了C96S和C146S两个突变体瘦素. 通过分析C96S及C146S突变体瘦素的体外再折叠特性及过程,并与野生型瘦素相比较,揭示C96S瘦素的二聚体显示出与野生型瘦素二聚体相似的特性,而C146S瘦素不能形成结构稳定的二聚体. 以上研究结果表明,Cys146-Cys146分子间二硫键在人瘦素二聚化过程中起主导作用.     

BLUF蛋白TePixD Y8F突变体的结构

目的 TePixD（Tll0078）是一种来自细长嗜热聚球藻（Thermosynechococcus elongatus BP-1）的blue light-using flavin（BLUF）感光蛋白。TePixD蛋白在FAD口袋周围有一个保守的Tyr8-Gln50-Met93三联体,以介导质子偶联电子转移（proton-coupled electron transfer,PCET）过程。但具体的光响应机制有待进一步研究。本文的目的是解析TePixD在光响应关键位点突变体的结构以及生化性质,以此分析TePixD的光响应过程。方法 利用X射线衍射法解析TePixD Y8F突变体的晶体结构,Tyr8侧链在PCET过程中有重要作用,而突变体Phe8的侧链失去了羟基从而使分子无法介导PCET。本文比较了TePixD野生型和Y8F突变体之间的结构,并比较了同蛋白家族的SyPixD Y8F与TePixD Y8F的结构。此外,使用多角度光散射法分析几种TePixD在光响应关键位点突变体（Y8F、Q50L、W91F、Y8F/W91F和Q50L/W91F）在溶液中的生化特性。结果 本文以2.54 ?分辨率解析了TePixD Y8F突变体的晶体结构,发现其与TePixD野生型的整体结构相似,而与SyPixD Y8F存在显著差异。生化分析表明,对比黑暗和光照条件时,TePixD突变体与野生型的分子质量变化以及洗脱峰表现出差异,表明突变体对光诱导蛋白质构象变化产生干扰。结论 本文的结构测定和生化分析为揭示BLUF蛋白的光响应机制提供了新信息。     

A7—B7二硫键缺失对胰岛素原重折叠及结构的影响

为研究A7 B7二硫键在胰岛素原结构和折叠中的作用 ,构建了A7 B7二硫键缺失的胰岛素原突变体 ,研究了其与野生型胰岛素原在体外重折叠产率、自由巯基氧化速度、CD谱、受体及抗体结合活性 ,以及对胰蛋白酶酶切敏感性的差别。结果表明 ,A7 B7二硫键缺失可导致胰岛素原α 螺旋明显减少以及对胰蛋白酶的酶切敏感性显著增加 ,其对胰岛素原结构的影响主要导致了受体结合活性的大幅度降低。突变体在体外重折叠 1h后巯基氧化速率较野生型明显减慢 ,但其最终折叠产率与野生型相当。由此提出一个胰岛素原折叠的可能途径 ,即A链链内二硫键最先形成 ,然后是两对链间二硫键。且A2 0 B19二硫键比A7 B7二硫键很可能先形成 ,在折叠中更重要。     

白色念珠菌CYP51蛋白功能性氨基酸残基定点突变、蛋白表达及活性测定

实验设计了白色念珠菌CYP51蛋白功能性氨基酸残基突变体Y118A、Y118F、Y118T、S378A、S378T、H310A、H310R, 并转入基因工程菌D12667中表达。用Western及紫外分光光度法定性、定量检测蛋白, 用GC-MS法测定蛋白代谢活性。结果表明, 成功表达目标蛋白, 蛋白诱导表达量接近微粒体蛋白总量的25%。活性测定表明, 表达的野生型蛋白保持其对天然底物的代谢能力; 相较于野生型蛋白, 突变体蛋白代谢活性不同程度改变, 最多可下降1/2左右。因此, 本研究中成功表达了野生型和     

抗赤霉病小麦地方品种黄方柱和海盐种EMS突变体的变异分析

突变体对增加小麦资源的遗传多样性,克隆和解析重要农艺、产量和抗性相关基因具有重要的意义。本研究以高抗赤霉病小麦品种黄方柱(HFZ)及其11个甲磺酸乙酯(EMS)诱导的纯合突变体(F2~F12,Mu4),以及海盐种(HYZ)及其12个EMS纯合突变体(Y2~Y13,Mu4)为材料,在扬花期利用单花滴注鉴定赤霉病扩展抗性,灌浆期测定了分蘖数、株高、旗叶长、旗叶宽、叶绿素含量,收获后测定千粒重、粒长、粒宽、每穗小穗数和每穗粒数共计11个性状。每一个突变体至少在一个性状上与野生型存在显著差异。黄方柱突变系F6、F9和F12以及海盐种突变系Y6、Y7和Y9病小穗率均显著高于相应野生型,达中感或高感水平,因此,这6个突变体是研究赤霉病扩展抗性的理想材料。此外,海盐种突变体株高、千粒重、每穗粒数和粒宽均低于或显著低于野生型。对野生型和突变体采用了基于最小组内平方和距离的动态聚类分析方法,综合评价了野生型与突变体以及突变体相互之间的相似情况。株高等农艺性状显著优于野生型但赤霉病抗性与野生型类似的突变体(如F2、F7、Y2、Y3、Y4、Y8、Y10和Y12)可为农艺性状的遗传研究和抗赤育种亲本选配提供重要的资源。     

Ⅱ型抗癌晶体蛋白抗肝癌作用的关键芳香族氨基酸

为探讨Ⅱ型抗癌晶体蛋白(Parasporin-2)上与抗肝癌作用相关的关键氨基酸,利用5-BU对Parasporin-2活性区编码DNA(P2Y)进行PCR诱变,之后在大肠杆菌中表达,产物纯化后经MTT法检测其对肝癌细胞系和正常肝细胞系的作用。获得的9个突变体其抗肝癌活性差异极大,其中P2M1和P2M8对两种肝癌细胞系SMMC7721和Bel7402均有较强的细胞毒杀作用而不影响正常肝细胞系Chang-liver。比较了P2M1、P2M8和P2Y的二级结构与三级结构,发现二级结构上的变化如β折叠变长或α螺旋增加影响着Ⅱ型抗癌晶体蛋白的抗肝癌活性。基于突变体间氨基酸序列比对、突变体与受体间分子对接以及模拟突变等研究的结果表明,位点52、56、58和208上的氨基酸残基特别是芳香族氨基酸在Parasporin-2与受体间的互作中可能起着重要作用。     

通过N端引入芳香族氨基酸提高木聚糖酶的热稳定性

耐热的木聚糖酶具有用于造纸、麻类脱胶和饲料生产等工业领域的巨大潜力,为了提高11家族碱性木聚糖酶Xyn11A-LC的热稳定性,通过理性设计在N-末端引入了芳香族氨基酸(T9Y和D14F)。测定野生型和突变体的性质表明,突变体的最适反应温度和热稳定性均获得了提高。突变体的最适反应温度比野生型提高了5℃。野生型在65℃的Tris/HCl缓冲液(pH 8.0)中的半衰期为22 min,而突变体在此条件下的半衰期为106 min。圆二色光谱测定结果显示野生型和突变体的Tm分别为55.3℃和67.9℃。因此,通过在N-末端引入芳香族氨基酸可以提高11家族木聚糖酶的热稳定性和在高温下的活性。     

丙型肝炎病毒F蛋白缺失对病毒复制及感染性的影响

探索了F蛋白缺失及核心蛋白(Core)二级结构改变对丙型肝炎病毒(HCV)复制和感染性的影响．利用定点突变方法,将J6JFH1的核心基因引进5个终止密码子以中断F蛋白的表达,从而获得F蛋白缺失的病毒复制子J6JFH1/ΔF．体外制备RNA转录体,并电穿孔转染Huh7.5.1细胞,采用免疫荧光、实时荧光定量PCR方法以及病毒感染等方法,观察F蛋白缺失对病毒复制、蛋白质表达及转染细胞上清感染性病毒颗粒产生的影响．在此基础上,构建5个单一突变病毒体,对HCV核心蛋白进行二级结构分析,观察核心蛋白二级结构对HCV复制和翻译的影响．结果显示,转染48 h后,J6JFH1/ΔF与野生型J6JFH1相比,J6JFH1/ΔF转染阳性细胞数明显降低,细胞内HCV RNA 水平降低约95%,J6JFH1/ΔF转染后不同时间点细胞上清中HCV RNA拷贝数和病毒颗粒也明显降低．5个单一突变体不影响核心基因二级结构,病毒在细胞内复制和感染性与野生型水平一致．J6JFH1/ΔF所产生的改变可能是由于5处突变导致核心基因二级结构改变而造成的．结果说明,HCV F蛋白缺失不影响病毒的复制翻译及病毒颗粒的包装释放,核心蛋白二级结构的改变对病毒复制和翻译则产生较大影响．     

P450cam突变体蛋白表达、纯化与结晶的改进及其四突变体（F87L/Y96F/L244A/V247A）晶体结构

在P450cam突变体蛋白纯化过程中使用280 nm/392 nm双波长比值检测蛋白质纯度, 采用β-巯基乙醇对蛋白质进行还原性保护,有效地缩短了纯化进程,纯化效率相应提高.以PEG 8000为沉淀剂经悬滴汽相扩散法筛选得到适合衍射的P450cam四突变体（F87L/Y96F/L244A/V247A）晶体,在Mar-Research面探测器系统上收集了0.22 nm分辨率的X射线衍射数据.采用同晶差值傅立叶法解析结构,最后的晶体学R因子和R_free分别为0.197和0.247,键长偏差为0.001 77 nm,键角偏差为1.96°.结构测定显示P450cam四突变体（F87L/Y96F/L244A/V247A）和P450cam野生型的整体构象无重大变化,突变后活性口袋变大而疏水性增加,这与突变设计预期目标一致.     

人白细胞介素-2结构与镇痛功能关系的研究

免疫调节因子白细胞介素-2(IL-2)具有中枢镇痛功能。实验采用基因定位突变技术,获得系列IL-2突变体,并测定其免疫学活性和镇痛能力,发现无免疫学活性的IL-2突变体20Leu-IL-2仍具有中枢镇痛能力,而44Leu-IL-2,45 Val-IL-2虽保留了免疫学活性,但其镇痛能力显著性下降或消失,阿片受体拮抗剂纳洛酮能够阻断IL-2的中枢镇痛作用,而不能影响IL-2对CTLL-2细胞的增殖作用。抗内源性阿片肽血清与IL-2能发生明显的交叉反应。实验结果提示,IL-2分子是通过由第45位Tyr残基及空间上相近的Phe残基等组成的镇痛功能位点与阿片受体相结合而发挥镇痛效应。     

Structure and calcium-binding studies of a recoverin mutant (E85Q) in an allosteric intermediate state

Recoverin, a member of the EF-hand superfamily, serves as a calcium sensor in retinal rod cells. A myristoyl or related fatty acyl group covalently attached to the N-terminus of recoverin facilitates the binding of recoverin to retinal disk membranes by a mechanism known as the Ca2+-myristoyl switch. Previous structural studies revealed that the myristoyl group of recoverin is sequestered inside the protein core in the absence of calcium. The cooperative binding of two calcium ions to the second and third EF-hands (EF-2 and EF-3) of recoverin leads to the extrusion of the fatty acid. Here we present nuclear magnetic resonance (NMR), fluorescence, and calcium-binding studies of a myristoylated recoverin mutant (myr-E85Q) designed to abolish high-affinity calcium binding to EF-2 and thereby trap the myristoylated protein with calcium bound solely to EF-3. Equilibrium calcium-binding studies confirm that only one Ca2+ binds to myr-E85Q under the conditions of this study with a dissociation constant of 100 microM. Fluorescence and NMR spectra of the Ca2+-free myr-E85Q are identical to those of Ca2+-free wild type, indicating that the E85Q mutation does not alter the stability and structure of the Ca2+-free protein. In contrast, the fluorescence and NMR spectra of half-saturated myr-E85Q (one bound Ca2+) look different from those of Ca2+-saturated wild type (two bound Ca2+), suggesting that half-saturated myr-E85Q may represent a structural intermediate. We report here the three-dimensional structure of Ca2+-bound myr-E85Q as determined by NMR spectroscopy. The N-terminal myristoyl group of Ca2+-bound myr-E85Q is sequestered within a hydrophobic cavity lined by many aromatic residues (F23, W31, Y53, F56, F83, and Y86) resembling that of Ca2+-free recoverin. The structure of Ca2+-bound myr-E85Q in the N-terminal region (residues 2-90) is similar to that of Ca2+-free recoverin, whereas the C-terminal region (residues 100-202) is more similar to that of Ca2+-bound wild type. Hence, the structure of Ca2+-bound myr-E85Q represents a hybrid between the structures of recoverin with zero and two Ca2+ bound. The binding of Ca2+ to EF-3 leads to local structural changes within the EF-hand that alter the domain interface and cause a 45 degrees swiveling of the N- and C-terminal domains, resulting in a partial unclamping of the myristoyl group. We propose that Ca2+-bound myr-E85Q may represent a stable intermediate state in the kinetic mechanism of the calcium-myristoyl switch.     

Site-directed mutagenesis of glutathione S-transferase YaYa. Important roles of tyrosine 9 and aspartic acid 101 in catalysis.

The roles of tyrosine 9 and aspartic acid 101 in the catalytic mechanism of rat glutathione S-transferase YaYa were studied by site-directed mutagenesis. Replacement of tyrosine 9 with phenylalanine (Y9F), threonine (Y9T), histidine (Y9H), or valine (Y9V) resulted in mutant enzymes with less than 5% catalytic activity of the wild type enzymes. Kinetic studies with purified Y9F and Y9T mutants demonstrated poor catalytic efficiencies which were largely due to a drastic decrease in kcat. The estimated pK alpha values of the sulfhydryl group of glutathione bound to Y9F and Y9T mutant enzymes were 8.5 to 8.7, similar to the chemical reaction, in contrast to the estimated pK alpha value of 6.7 to 6.8 for the glutathione enzyme complex of wild type glutathione S-transferase. These results indicate that tyrosine 9 is directly responsible for the lowering of the pKa of the sulfhydryl group of glutathione, presumably due to the stabilization of the thiolate anion through hydrogen bonding with the hydroxyl group of tyrosine. To examine the role of aspartic acid in the binding of glutathione to YaYa, 4 conserved aspartic acid residues at positions 61, 93, 101, and 157 were changed to glutamic acid and asparagine. All mutant enzymes retained either full or partial activity except D157N, which was virtually inactive. Kinetic studies with four mutant enzymes (D93E, D93N, D101E, and D101N) indicate that only D101N exhibited a 5-fold increase in Km toward glutathione. Also, the binding of this mutant to the affinity column was greatly reduced. These results demonstrate that aspartic acid 101 plays an important role in glutathione interaction to YaYa. The role of aspartic acid 157 in catalysis remains to be determined.     

Mutation of tyrosine 332 to phenylalanine converts dopa decarboxylase into a decarboxylation-dependent oxidative deaminase

A flexible loop (residues 328-339), presumably covering the active site upon substrate binding, has been revealed in 3,4-dihydroxyphenylalanine decarboxylase by means of kinetic and structural studies. The function of tyrosine 332 has been investigated by substituting it with phenylalanine. Y332F displays coenzyme content and spectroscopic features identical to those of the wild type. Unlike wild type, during reactions with l-aromatic amino acids under both aerobic and anaerobic conditions, Y332F does not catalyze the formation of aromatic amines. However, analysis of the products shows that in aerobiosis, l-aromatic amino acids are converted into the corresponding aromatic aldehydes, ammonia, and CO(2) with concomitant O(2) consumption. Therefore, substitution of Tyr-332 with phenylalanine results in the suppression of the original activity and in the generation of a decarboxylation-dependent oxidative deaminase activity. In anaerobiosis, Y332F catalyzes exclusively a decarboxylation-dependent transamination of l-aromatic amino acids. A role of Tyr-332 in the Calpha protonation step that catalyzes the formation of physiological products has been proposed. Furthermore, Y332F catalyzes oxidative deamination of aromatic amines and half-transamination of d-aromatic amino acids with k(cat) values comparable with those of the wild type. However, for all the mutant-catalyzed reactions, an increase in K(m) values is observed, suggesting that Y --> F replacement also affects substrate binding.     

Structure-function analysis of the human sialyltransferase ST3Gal I: role of n-glycosylation and a novel conserved sialylmotif

All eukaryotic sialyltransferases have in common the presence in their catalytic domain of several conserved peptide regions (sialylmotifs L, S, and VS). Functional analysis of sialylmotifs L and S previously demonstrated their involvement in the binding of donor and acceptor substrates. The region comprised between the sialylmotifs S and VS contains a stretch of four highly conserved residues, with the following consensus sequence (H/y)Y(Y/F/W/h)(E/D/q/g). (Capital letters and lowercase letters indicate a strong or low occurrence of the amino acid, respectively.) The functional importance of these residues and of the conserved residues of motif VS (HX(4)E) was assessed using as a template the human ST3Gal I. Mutational analysis showed that residues His(299) and Tyr(300) of the new motif, and His(316) of the VS motif, are essential for activity since their substitution by alanine yielded inactive enzymes. Our results suggest that the invariant Tyr residue (Tyr(300)) plays an important conformational role mainly attributable to the aromatic ring. In contrast, the mutants W301F, E302Q, and E321Q retained significant enzyme activity (25-80% of the wild type). Kinetic analyses and CDP binding assays showed that none of the mutants tested had any significant effect in nucleotide donor binding. Instead the mutant proteins were affected in their binding to the acceptor and/or demonstrated lower catalytic efficiency. Although the human ST3Gal I has four N-glycan attachment sites in its catalytic domain that are potentially glycosylated, none of them was shown to be necessary for enzyme activity. However, N-glycosylation appears to contribute to the proper folding and trafficking of the enzyme.     

Conserved tyrosine-369 in the active site of Escherichia coli copper amine oxidase is not essential.

Copper amine oxidases are homodimeric enzymes that catalyze two reactions: first, a self-processing reaction to generate the 2,4,5-trihydroxyphenylalanine (TPQ) cofactor from an active site tyrosine by a single turnover mechanism; second, the oxidative deamination of primary amine substrates with the production of aldehyde, hydrogen peroxide, and ammonia catalyzed by the mature enzyme. The importance of active site residues in both of these processes has been investigated by structural studies and site-directed mutagenesis in enzymes from various organisms. One conserved residue is a tyrosine, Tyr369 in the Escherichia coli enzyme, whose hydroxyl is hydrogen bonded to the O4 of TPQ. To explore the importance of this site, we have studied a mutant enzyme in which Tyr369 has been mutated to a phenylalanine. We have determined the X-ray crystal structure of this variant enzyme to 2.1 A resolution, which reveals that TPQ adopts a predominant nonproductive conformation in the resting enzyme. Reaction of the enzyme with the irreversible inhibitor 2-hydrazinopyridine (2-HP) reveals differences in the reactivity of Y369F compared with wild type with more efficient formation of an adduct (lambda(max) = 525 nm) perhaps reflecting increased mobility of the TPQ adduct within the active site of Y369F. Titration with 2-HP also reveals that both wild type and Y369F contain one TPQ per monomer, indicating that Tyr369 is not essential for TPQ formation, although we have not measured the rate of TPQ biogenesis. The UV-vis spectrum of the Y369F protein shows a broader peak and red-shifted lambda(max) at 496 nm compared with wild type (480 nm), consistent with an altered electronic structure of TPQ. Steady-state kinetic measurements reveal that Y369F has decreased catalytic activity particularly below pH 6.5 while the K(M) for substrate beta-phenethylamine increases significantly, apparently due to an elevated pK(a) (5.75-6.5) for the catalytic base, Asp383, that should be deprotonated for efficient binding of protonated substrate. At pH 7.0, the K(M) for wild type and Y369F are similar at 1.2 and 1.5 microM, respectively, while k(cat) is decreased from 15 s(-1) in wild type to 0.38 s(-1), resulting in a 50-fold decrease in k(cat)/K(M) for Y369F. Transient kinetics experiments indicate that while the initial stages of enzyme reduction are slower in the variant, these do not represent the rate-limiting step. Previous structural and solution studies have implicated Tyr369 as a component of a proton shuttle from TPQ to dioxygen. The moderate changes in kinetic parameters observed for the Y369F variant indicate that if this is the case, then the absence of the Tyr369 hydroxyl can be compensated for efficiently within the active site.     

Role of Phe283 in enzymatic reaction of cyclodextrin glycosyltransferase from alkalophilic Bacillus sp.1011: Substrate binding and arrangement of the catalytic site

Cyclodextrin glycosyltransferase (CGTase) belonging to the alpha-amylase family mainly catalyzes transglycosylation and produces cyclodextrins from starch and related alpha-1,4-glucans. The catalytic site of CGTase specifically conserves four aromatic residues, Phe183, Tyr195, Phe259, and Phe283, which are not found in alpha-amylase. To elucidate the structural role of Phe283, we determined the crystal structures of native and acarbose-complexed mutant CGTases in which Phe283 was replaced with leucine (F283L) or tyrosine (F283Y). The temperature factors of the region 259-269 in native F283L increased >10 A(2) compared with the wild type. The complex formation with acarbose not only increased the temperature factors (>10 A(2)) but also changed the structure of the region 257-267. This region is stabilized by interactions of Phe283 with Phe259 and Leu260 and plays an important role in the cyclodextrin binding. The conformation of the side-chains of Glu257, Phe259, His327, and Asp328 in the catalytic site was altered by the mutation of Phe283 with leucine, and this indicates that Phe283 partly arranges the structure of the catalytic site through contacts with Glu257 and Phe259. The replacement of Phe283 with tyrosine decreased the enzymatic activity in the basic pH range. The hydroxyl group of Tyr283 forms hydrogen bonds with the carboxyl group of Glu257, and the pK(a) of Glu257 in F283Y may be lower than that in the wild type.     

A distal tyrosine residue is required for ligand discrimination in DevS from Mycobacterium tuberculosis

DevS is a heme-based sensor kinase required for sensing environmental conditions leading to nonreplicating persistence in Mycobacterium tuberculosis. Kinase activity is observed when the heme is a ferrous five-coordinate high-spin or six-coordinate low-spin CO or NO complex but is strongly inhibited in the oxy complex. Discrimination between these exogenous ligands has been proposed to depend on a specific hydrogen bond network with bound oxygen. Here we report resonance Raman data and autophosphorylation assays of wild-type and Y171F DevS in various heme complexes. The Y171F mutation eliminates ligand discrimination for CO, NO, and O2, resulting in equally inactive complexes. In contrast, the ferrous-deoxy Y171F variant exhibits autokinase activity equivalent to that of the wild type. Raman spectra of the oxy complex of Y171F indicate that the environment of the oxy group is significantly altered from that in the wild type. They also suggest that a solvent molecule in the distal pocket substitutes for the Tyr hydroxyl group to act as a poorer hydrogen bond donor to the oxy group. The wild-type CO and NO complexes exist as a major population in which the CO or NO groups are free of hydrogen bonds, while the Y171F mutation results in a mild increase in the distal pocket polarity. The Y171F mutation has no impact on the proximal environment of the heme, and the activity observed with the five-coordinate ferrous-deoxy wild type is conserved in the Y171F variant. Thus, while the absence of an exogenous ligand in the ferrous-deoxy proteins leads to a moderate kinase activity, interactions between Tyr171 and distal diatomic ligands turn the kinase activity on and off. The Y171F mutation disrupts the on-off switch and renders all states with a distal ligand inactive. This mechanistic model is consistent with Tyr171 being required for distal ligand discrimination, but nonessential for autophosphorylation activity.     

Cytochrome b5 reductase: role of the si-face residues, proline 92 and tyrosine 93, in structure and catalysis

The conserved sequence motif "RxY(T)(S)xx(S)(N)" coordinates flavin binding in NADH:cytochrome b(5) reductase (cb(5)r) and other members of the flavin transhydrogenase superfamily of oxidoreductases. To investigate the roles of Y93, the third and only aromatic residue of the "RxY(T)(S)xx(S)(N)" motif, that stacks against the si-face of the flavin isoalloxazine ring, and P92, the second residue in the motif that is also in close proximity to the FAD moiety, a series of rat cb(5)r variants were produced with substitutions at either P92 or Y93, respectively. The proline mutants P92A, G, and S together with the tyrosine mutants Y93A, D, F, H, S, and W were recombinantly expressed in E. coli and purified to homogeneity. Each mutant protein was found to bind FAD in a 1:1 cofactor:protein stoichiometry while UV CD spectra suggested similar secondary structure organization among all nine variants. The tyrosine variants Y93A, D, F, H, and S exhibited varying degrees of blue-shift in the flavin visible absorption maxima while visible CD spectra of the Y93A, D, H, S, and W mutants exhibited similar blue-shifted maxima together with changes in absorption intensity. Intrinsic flavin fluorescence was quenched in the wild type, P92S and A, and Y93H and W mutants while Y93A, D, F, and S mutants exhibited increased fluorescence when compared to free FAD. The tyrosine variants Y93A, D, F, and S also exhibited greater thermolability of FAD binding. The specificity constant (k(cat)/K(m)(NADH)) for NADH:FR activity decreased in the order wild type > P92S > P92A > P92G > Y93F > Y93S > Y93A > Y93D > Y93H > Y93W with the Y93W variant retaining only 0.5% of wild-type efficiency. Both K(s)(H4NAD) and K(s)(NAD+) values suggested that Y93A, F, and W mutants had compromised NADH and NAD(+) binding. Thermodynamic measurements of the midpoint potential (E degrees ', n = 2) of the FAD/FADH(2) redox couple revealed that the potentials of the Y93A and S variants were approximately 30 mV more positive than that of wild-type cb(5)r (E degrees ' = -268 mV) while that of Y93H was approximately 30 mV more negative. These results indicate that neither P92 nor Y93 are critical for flavin incorporation in cb(5)r and that an aromatic side chain is not essential at position 93, but they demonstrate that Y93 forms contacts with the FAD that effectively modulate the spectroscopic, catalytic, and thermodynamic properties of the bound cofactor.     

Spectroscopy and a high-resolution crystal structure of Tyr263 mutants of cyanobacterial phytochrome Cph1

Phytochromes are biliprotein photoreceptors that can be photoswitched between red-light-absorbing state (Pr) and far-red-light-absorbing state (Pfr). Although three-dimensional structures of both states have been reported, the photoconversion and intramolecular signaling mechanisms are still unclear. Here, we report UV-Vis absorbance, fluorescence and CD spectroscopy along with various photochemical parameters of the wild type and Y263F, Y263H and Y263S mutants of the Cph1 photosensory module, as well as a 2.0-Å-resolution crystal structure of the Y263F mutant in its Pr ground state. Although Y263 is conserved, we show that the aromatic character but not the hydroxyl group of Y263 is important for Pfr formation. The crystal structure of the Y263F mutant (Protein Data Bank ID: 3ZQ5) reaffirms the ZZZssa chromophore configuration and provides a detailed picture of its binding pocket, particularly conformational heterogeneity around the chromophore. Comparison with other phytochrome structures reveals differences in the relative position of the PHY (phytochrome specific) domain and the interaction of the tongue with the extreme N-terminus. Our data support the notion that native phytochromes in their Pr state are structurally heterogeneous.