Allostery and Conformational Dynamics in cAMP-binding Acyltransferases

Mycobacteria harbor unique proteins that regulate protein lysine acylation in a cAMP-regulated manner. These lysine acyltransferases from Mycobacterium smegmatis (KATms) and Mycobacterium tuberculosis (KATmt) show distinctive biochemical properties in terms of cAMP binding affinity to the N-terminal cyclic nucleotide binding domain and allosteric activation of the C-terminal acyltransferase domain. Here we provide evidence for structural features in KATms that account for high affinity cAMP binding and elevated acyltransferase activity in the absence of cAMP. Structure-guided mutational analysis converted KATms from a cAMP-regulated to a cAMP-dependent acyltransferase and identified a unique asparagine residue in the acyltransferase domain of KATms that assists in the enzymatic reaction in the absence of a highly conserved glutamate residue seen in Gcn5-related N-acetyltransferase-like acyltransferases. Thus, we have identified mechanisms by which properties of similar proteins have diverged in two species of mycobacteria by modifications in amino acid sequence, which can dramatically alter the abundance of conformational states adopted by a protein.

Structural requirements for catalysis: studies on RTEM-1 β-lactamase

β-lactamases are a group of enzymes that confer resistance to penam and cephem antibiotics by hydrolysis of the β-lactam ring, thereby inactivating the antibiotic. Crystallographic and computer modeling studies of RTEM-1 β-lactamase have indicated that Asp 132, a strictly conserved residue among the class A β-lactamases, appears to be involved in substrate binding, catalysis, or both. To study the contribution of residue 132 to β-lactamase function, site saturation mutagenesis was used to generate mutants coding for all 20 amino acids at position 132. Phenotypic screening of all mutants indicated that position 132 is very sensitive to amino acid changes, with only N132C, N132D, N132E, and N132Q showing any appreciable activity. Kinetic analysis of three of these mutants showed increases in K_M, along with substantial decreases in k_(cat). Efforts to trap a stable acyl-enzyme intermediate were unsuccessfuL These results indicate that residue 132 is involved in substrate binding, as well as catalysis, and supports the involvement of this residue in acylation as suggested by Strynadka et al.

Crystallographic and computer modeling studies of RTEM-1 β-lactamase have indicated that Lys 73 and Glu 166, two strictly conserved residues among the class A β-lactamases, appear to be involved in substrate binding, catalysis, or both. To study the contribution of these residues to β-lactamase function, site saturation mutagenesis was used to generate mutants coding for all 20 amino acids at positions 73 and 166. Then all 400 possible combinations of mutants were created by combinatorial mutagenesis. The colonies harboring the mutants were screened for growth in the presence of ampicillin. The competent colonys' DNA were sequenced, and kinetic parameters investigated. It was found that lysine is essential at position 73, and that position 166 only tolerated fairly conservative changes (Aspartic acid, Histidine, and Tyrosine). These functional mutants exhibited decreased kcat's, but K_M was close to wild-type levels. The results of the combinatorial mutagenesis experiments indicate that Lysis absolutely required for activity at position 73; no mutation at residue 166 can compensate for loss of the long side chain amine. The active mutants found--K73K/E166D, K73KIE166H, and K73KIE166Y were studied by kinetic analysis. These results reaffirmed the function of residue 166 as important in catalysis, specifically deacylation.

The identity of the residue responsible for enhancing the active site serine (Ser 70) in RTEM-1 β-lactamase has been disputed for some time. Recently, analysis of a crystal structure of RTEM-1 β-lactamase with covalently bound intermediate was published, and it was suggested that Lys 73, a strictly conserved residue among the class A β-lactamases, was acting as a general base, activating Ser 70. For this to be possible, the pK_a of Lys 73 would have to be depressed significantly. In an attempt to assay the pK_a of Lys 73, the mutation K73C was made. This mutant protein can be reacted with 2-bromoethylamine, and activity is restored to near wild type levels. ^(15)N-2-bromoethylamine hydrobromide and ^(13)C-2-bromoethylamine hydrobromide were synthesized. Reacting these compounds with the K73C mutant gives stable isotopic enrichment at residue 73 in the form of aminoethylcysteine, a lysine homologue. The pK_a of an amine can be determined by NMR titration, following the change in chemical shift of either the ^(15)N-amine nuclei or adjacent Be nuclei as pH is changed. Unfortunately, low protein solubility, along with probable label scrambling in the Be experiment, did not permit direct observation of either the ^(15)N or ^(13)C signals. Indirect detection experiments were used to observe the protons bonded directly to the ^(13)C atoms. Two NMR signals were seen, and their chemical shift change with pH variation was noted. The peak which was determined to correspond to the aminoethylcysteine residue shifted from 3.2 ppm down to 2.8 ppm over a pH range of 6.6 to 12.5. The pK_a of the amine at position 73 was determined to be ~10. This indicates that residue 73 does not function as a general base in the acylation step of the reaction. However the experimental measurement takes place in the absence of substrate. Since the enzyme undergoes conformational changes upon substrate binding, the measured pK_a of the free enzyme may not correspond to the pK_a of the enzyme substrate complex.

Studies of the serotonin type 3A receptor and the chemical preparation of tRNA

This thesis describes studies surrounding a ligand-gated ion channel (LGIC): the serotonin type 3A receptor (5-HT₃AR). Structure-function experiments using unnatural amino acid mutagenesis are described, as well as experiments on the methodology of unnatural amino acid mutagenesis. Chapter 1 introduces LGICs, experimental methods, and an overview of the unnatural amino acid mutagenesis.

In Chapter 2, the binding orientation of the clinically available drugs ondansetron and granisetron within 5-HT₃A is determined through a combination of unnatural amino acid mutagenesis and an inhibition based assay. A cation-π interaction is found for both ondansetron and granisetron with a specific tryptophan residue (Trp183, TrpB) of the mouse 5-HT₃AR, which establishes a binding orientation for these drugs.

In Chapter 3, further studies were performed with ondansetron and granisetron with 5-HT₃A. The primary determinant of binding for these drugs was determined to not include interactions with a specific tyrosine residue (Tyr234, TyrC2). In completing these studies, evidence supporting a cation-π interaction of a synthetic agonist, meta-chlorophenylbiguanide, was found with TyrC2.

In Chapter 4, a direct chemical acylation strategy was implemented to prepare full-length suppressor tRNA mediated by lanthanum(III) and amino acid phosphate esters. The derived aminoacyl-tRNA is shown to be translationally competent in Xenopus oocytes.

Appendix A.1 gives details of a pharmacological method for determining the equilibrium dissociation constant, K_B, of a competitive antagonist with a receptor, known as Schild analysis. Appendix A.2 describes an examination of the inhibitory activity of new chemical analogs of the 5-HT₃A antagonist ondansetron. Appendix A.3 reports an organic synthesis of an intermediate for a new unnatural amino acid. Appendix A.4 covers an additional methodological examination for the preparation of amino-acyl tRNA.

Friedel-crafts反应合成芳香环状齐聚物与开环聚合

芳香环状低聚物的合成是二十世纪八十年代末发展起来的研究领域，其特有的环状结构和可进行可控的开环聚合决定了芳香环状低聚物具有广阔的应用前景。本文从研究单体结构与成环反应的关系出发，开拓了一种合成芳香环状聚醚酮的新方法—改进的Friedel-Crafte反应法，采用该方法成功地合成了一系列新型结构的大环化合物，并首次利用流变仪对开环聚合过程中的流变行为进行了较为系统的观测。根据acoson-Stockmayer环化理论，应用基质辅助激光解吸离子化飞行时间质谱（MAIDL-TOF MS），对一系列芳香环状低聚物组分分布进行分析，研究了芳香环状低聚物的产率、组分分布与单体结构的关系。结果表明：芳香聚醋、聚麟酸醋及芳香聚醚环状低聚物系列中，InCn与1nn呈良好的线性关系，符合J-S理论分布。环状齐聚物的产率与组分分布受单体的中心键角影响，单体的中心键角在100°～120°范围内，其中心键角愈小，γ值愈大。γ值愈大，反应产物中小环化合物的含量越高，而小环化合物的含量的增加是高产率地合成环状齐聚物的前提之一。在此理论的指导下，通过对单体结构的模拟，高选择性地合成了一种新型结构的芳香环状聚硫醋二聚体，对其结构进行了精确的表征，在不同溶剂中得到了该环状二聚体的单晶，单晶X闪ray衍射表明该二聚体为环张力极小的大环化合物。基于上述理论，以有利于成环的邻苯二酞氯为酞基化试剂，对Friedel-Crafts酞基化反应在合成芳香环状齐聚物中的应用进行了系统研究，开拓了一种合成芳香环状预聚体的新方法—改进的Friedel-Crafts酞基化反应法。发现反应体系中Lewis碱的存在有利于选择性地形成环状产物。并进一步确定反应最佳条件为： Lewis碱和催化剂Alcl3与富电单体的摩尔比分别为1.2和3.4; 1,2-二氯乙烷为本反应的最佳溶剂；等当量的反应单体要求缓慢滴加到形成“假高稀”的溶剂体系中；Lewis碱NMP，DMF等都适用于本反应体系。在此优化条件下，以邻苯二酞氯和间苯二酞氯为酞基化试剂，室温下，合成了一系列芳香环状聚醚酮酮、聚醚酮、聚醚矾酮等新型结构的环状齐聚物，利用MALDI-TOF-MS，NMR，GPC，FTIR，DSC，元素分析等手段对环状结构进行了精确的表征；DSC分析表明含邻苯二拨基结构的环状齐聚物为无定型材料；部分产物的产率高达90％。在阴离子引发剂联苯双酚钾存在下，制备的环状齐聚物成功进行了熔融开环聚合，得到了相应结构的高分子量的线性开环聚合产物。其中，含邻苯二拨基结构的环状聚醚酮酮、环状聚醚酮矾的开环聚合产物的比浓粘度分别达到0.42dL／g，0.36 dL／g（0.5％的DMF溶液，25士0.1℃）；四种含间苯二锁基结构的环状齐聚物的开环聚合产物的Tg与常规亲电沉淀反应合成的线性高聚物的Tg相同。含侧甲基的开环聚合产物的Tg比对应的开环聚合的产物的Tg高约5℃。研究结果表明用亲电缩聚方法制备芳香环状聚醚酮与亲核缩聚法相比较，具有成本低廉、反应条件温和丫产率高、易于大规模制备等优势，开拓了一种制备环状化合物的方法。自从美国G.E.公司利用环状聚碳酸酷的开环聚合制备线性聚碳酸醋以来，对芳香环状低聚物的开环聚合过程的研究仅局限在由GPC监测反应某一时刻的产物的分子量，而缺乏对与应用更为接近的开环聚合中的粘度的变化的研究。本文以界面缩聚反应高产率地合成芳香环状双酚A聚酷二聚体为对象，研究了流变仪在开环聚合中的应用。利用流变仪对环状二聚体开环聚合过程进行了较为系统的观测，研究了不同条件下的开环聚合中的流变行为，结果表明，开环聚合存在引发期，而且在引发期，熔融体的粘度低于10Pa·S，超过引发期，粘度呈指数级增长。引发期的长短可以通过引发剂的种类、浓度、开环聚合的温度等条件进行有效地控制。芳香环状聚酷二聚体与环状聚碳酸醋的开环共聚合的流变行为的研究结果表明：开环共聚合可以降低开环聚合的温度，调整引发期，是提高聚合产物的分子量的有效途径。用流变仪对以改进的Friedel-Crafts反应合成的芳香环酮齐聚物的开环聚合中的流变行为进行了监控。在330℃，剪切速率为0.05S-l下，熔融的环状齐聚物的粘度为2.0Pa·S。通过对开环聚合的反应条件的控制，同样实现了开环聚合的可控，通过改变其开环聚合的引发期的长短及粘度的变化规律，可、适应不。条一定为加工设计与成型加工提供理论指导和模型设计，必将进一步推进开环聚合工 艺向应用方向的发展。

天然产物Standishinal 的首次全合成研究

具有1，1，4α-三甲基氢化芴骨架结构的天然三环二萜化合物自然界中不常见。在该类化合物中，Standishinal 具有良好的芳香化酶抑制活性和细胞毒活性。迄今未发现有Standishinal 的全合成报道，因此，我们对Standishinal 的全合成进行了探索，在该过程中得到以下实验结果： 1. 发现MSA/P2O5、MSA 在无溶剂条件下，25 °C 时烷氧基苯即可实现向苯酚的转化，但在CH3NO2 中，温度升高至80 °C 并未发生反应。 2. 烷氧基苯或对溴苯酚与α-环香叶酸在不同温度下以MSA/P2O5、MSA、PPA为催化剂以CH3NO2 为溶剂或以BF3·Et2O为催化剂时均不发生Friedel-Crafts酰化反应。 3. 对溴苯酚与香叶酸在p-TsOH 催化作用下发生了香叶酸向α-环香叶酸环化、α-环香叶酸环与对溴苯酚的酯化，得到了唯一产物α-环香叶酸对溴苯酯，产率68%。 Standishinal is one of tricyclic-diterpenes possessing the uncommon 1, 1,4a-trimethylhydrofluorene skeleton. Standishinal possesses cytotoxic and aromataseinhibitory activities. Till now, no synthesis of standishinal has been reported. Inattempt to synthesize standishinal, the following phenomenon were observed: 1. Alkyloxybenzenes could be transformed into corresponding phenol at 25 °C inthe presence of MSA/P2O5 or MSA under solvent free condition. ButAlkyloxybenzenes are stable in presence of MSA/P2O5 or MSA in CH3NO2 even at 80 °C. 2. Friedel-Crafts acylation of alkyloxybenzenes and p-bromophenol withα-cyclogeranic acid could not be realized under catalysis of MSA/P2O5, MSA or PPAin CH3NO2, or under catalysis of BF3·Et2O without CH3NO2. 3. The reaction of 4-bromaophenol and geranic acid in the presecnce of p-TsOHafforded 4-bromophenol α-cyclogeranoate in which cyclization of geranic acid toα-cyclogeranic acid was followed by esterification of α-cyclogeranic acid with p-bromophenol.

环糊精衍生物的设计、合成及其对环辛烯光异构化研究

环糊精(Cyclodextrins, CDs)经化学修饰后可以得到各种类型的衍生物，不仅可以扩展其原有的键合能力，而且还可以改变其选择性，是当代超分子化学的一个研究热点。环糊精第二面的仲羟基比第一面的伯羟基有着更好的催化性能，第二面的选择性修饰将产生更多有价值的衍生物，可用于催化、酶模拟、手性识别等方面。 取代苯甲酰基修饰环糊精对顺式环辛烯(cis-cyclooctene)光异构化反应有非常重要的影响作用，苯环上取代基的性质和取代位置与产物的%ee值和对映体构型之间存在某种内在联系。有目的地选择适宜取代基，设计、合成新型环糊精光增感剂, 有可能按预定目的得到更高%ee值的反式环辛烯；同时，取代苯甲酰基修饰环糊精对cis-cyclooctene光异构化的增感机理有待于进一步阐明。 本论文工作对环糊精的化学修饰以及超分子体系对cis-cyclooctene不对称光异构化反应方面的进展进行了调研。合成了一系列单-6-位取代苯甲酰基修饰环糊精，用于cis-cyclooctene光异构化增感反应，并用圆二色光谱滴定法研究这些环糊精衍生物与cis-cyclooctene的相互作用，以探索光增感反应机理。在此基础上，探讨了环糊精第二面的选择性修饰方法。内容主要包括： 1. 简要介绍了超分子化学的概况，并对环糊精的选择性修饰方法和超分子体系对cis-cyclooctene不对称光异构化反应的主要成果和最新进展进行了评述。 2. 合成了12种单-6-O-(取代苯甲酰基)-β-环糊精，其中10种为新化合物。采用紫外光谱、红外光谱、核磁共振波谱以及质谱等手段对化合物的结构进行了表征。 3. 探索了直接选择性修饰环糊精第二面的便捷新方法。用取代苯甲酰咪唑酯为酰化试剂，0.2M碳酸盐缓冲溶液(pH=9.9)作催化剂，能够有效地活化2-位仲羟基，对环糊精第二面进行选择性修饰，此方法既简便又经济；同时，发现取代苯甲酰基能够在β-CD第二面的2-位、3-位羟基间相互迁移。 4. 用单-6-O-(取代苯甲酰基)-β-环糊精作光增感剂，对cis-cyclooctene光异构化反应进行研究。实验结果证明：取代苯甲酰基上的取代基性质、位置、长度对反应的对映选择性有很大影响；此外，反应体系溶剂极性对产物的%ee值和对映体构型也有重大影响。用单-6-O-(3-甲氧苯甲酰基)-β-CD作增感剂，cis-cyclooctene光异构化反应产物(R)-trans-cyclooctene的对映选择性为45.8%ee，是到目前为止取得的最好对映选择性。 5. 采用圆二色光谱滴定法研究环糊精衍生物与cis-cyclooctene的相互作用，计算包结物的平衡常数，研究包结物的相对稳定性，为探索光增感反应机理提供基础。我们猜测：电子效应对cis-cyclooctene光异构化反应的影响，可能比取代基位置对反应的影响更大，借助电子效应有希望获得更高的%ee值。 Cyclodextrins can be subjected to diverse modifications to give a wide variety of cyclodextrin derivatives, which could not only extend their original molecular binding ability, but also alter their molecular selectivity. Therefore, cyclodextrin chemistry is currently a significant topic in supramolecular chemistry. The more open secondary hydroxyl side of CDs is stated to be catalytically very important, modifications of this face are believed to produce valuable derivatives for catalysis, enzyme mimic, chiral discrimination, etc. Mono-6-O-(substituted benzoyl)-β-CDs as novel supramolecular photosensitizing hosts have recently excited considerable attention in photochirogenesis. The supramolecular photosenstization of cis-cyclooctene mediated by them gave chiral trans-cyclooctene, enantiomeric excess of which was critically affected by the substituent introduced to the sensitizer moiety. In order to enhance the photoenantiodifferentiating ability, and elucidate the origin mechanisms of substituent-dependent enantioselectivity, in this work a series of mono-6-O-(substituted benzoyl)-β-CDs have been synthesized, and applied for enantiodifferentiating photoisomerization of cis-cyclooctene. The major contents are as follows: 1. The general aspects of supramolecular chemistry were descibed briefly. The new progress and important achievements on methods of selective modification of cyclodextrin and supramolecular enantiodifferentiating photoisomerization of cis-cyclooctene were reviewed. 2. Twelve mono-6-O-(substituted benzoyl)-β-CDs including ten novel compounds have been synthesized. Their structures have been characterized by using UV-vis, IR, NMR and MS methods. 3. A new convenient strategy for direct acylation of β-cyclodextrin on the secondary hydroxyl face was achieved by using the combination of N-benzoylimidazole and carbonate buffer in DMF, and the acyl migration between the C-2 and C-3 hydroxyl groups of β-cyclodextrin was found. 4. Experiments using mono-6-O-(substituted benzoyl)-β-CDs as chiral sensitizing hosts for mediating the enantiodifferentiating photoisomerization of cis-cyclooctene, were carried out. The results indicate that enantiomeric excess was critically affected, or even switched in sign, by the substituent introduced to the sensitizer moiety, and polarity of solvent. Using mono-6-O-(3-methoxybenzoyl)-β-CD as chiral sensitizing host, (R)-trans-cyclooctene was obtained in up to 45.8% enantiomeric excess, which is the highest value ever reported for supramolecular photochirogenesis with analogous hosts. 5. The conformational variation of these modified CDs and their complexation behaviors with cis-cyclooctene were examined by circular dichroism spectroscopy in water-methanol mixed solvents, which reveal that the orientation of chromophore was highly sensitive to the type, position and length of the introduced substituents. In the end, the complex stability constants(Ks) were calculated, and the mechanisms of reaction were discussed. Maybe, electronic effects are more important than positions of substituents for mediating the enantiodifferentiating photoisomerization of cis-cyclooctene.

N-arylamides from selenium-catalyzed reactions of nitroaromatics and amides in the presence of carbon monoxide and mixed organic bases

N-Arylamides were exclusively obtained in moderate to good yields from selenium-catalyzed reactions of nitroaromatics with amides in the presence of CO and mixed organic bases Et3N and DBU.

The synthesis and properties of meso-tetra(4-alkylamidophenyl)porphyrin liquid crystals and their Zn complexes

A series of novel, long-chain-substituted, porphyrin derivatives, meso-tetra (4-alkylamidophenyl) porphyrin ligands and their Zn complexes (alkyl = 8,10,12,14,16,18) were prepared by acylation of the amino groups of 5,10,15,20-tetra(4-aminophenyl)porphyrin by alkyl chloride. Mesomorphism was investigated by DSC, polarized optical microscopy (POM) and X-ray diffraction (XRD). Only ligands containing chains > 12 carbon atoms displayed liquid crystalline behaviour, which exhibited a high phase transition temperature and a broad mesophase temperature span, Zn complexes showed no liquid crystalline behaviour. Cyclic voltammetry, luminescence spectra and surface photovoltage spectroscopy revealed that covalent linking of an alkylamido group to the tetraphenylporphyrin molecule influences, significantly, the properties of the porphyrin macrocycle.

Synthesis and characterization of hyperbranched aromatic poly(ether imide)s

The four AB(2) monomers, N-[3- or 4-bis(4-hydroxyphenyl)toluoyl]-4-chlorophthalimide and N-{3- or 4-[1,1-bis(4-hydroxyphenyl)]ethylphenyl}-4-chlorophthalimides, were prepared and used for synthesis of hyperbranched poly(ether imide)s bearing hydroxyl end groups. These hyperbranched poly(ether imide)s had moderate molecular weights with broad distributions and showed glass-transition temperatures (Tgs) between 177 and 230 degreesC. The thermogravimetric analytic measurement revealed the decomposition temperature at 5% weight-loss temperatures (T-d(5%)) ranging from 240 to 281 degreesC. Analysis using H-1 NMR spectroscopy revealed the four types of hyperbranched poly(ether imide)s to have similar degrees of branching (ca. 60%). These polymers were modified by acylation or nucleophilic substitution reaction at the hydroxyl end groups. The conversion effectiveness depended on the type of modification reaction, modifier, and reaction conditions. The thermal stability and solubility of hyperbranched poly(ether imide)s were improved by the modification of the end groups.

Synthesis and crystallization of a novel poly(ether ketone ether ketone ketone) containing meta-phenylene linkage: PEKEKK(T/I)

Poly(ether ketone ether ketone ketone) containing meta-phenylene linkage (PEKEKK(T/I)) was synthesized by electrophilic Friedel-Crafts acylation condensation of 1, 4-diphenoxybenzophenone with terephthaloyl chloride (T) and isophthaloyl chloride (I) with a T/I ratio of 1 and characterized by LR,DSC,TGA and WAXD. PEKEKK(T/I) has two different crystal structures: a conventional Farm I structure, the same as that observed in PEEK and PEK, wich is usually developed from melt crystallization, and a new Form II structure which can be developed from cold crystallization or solvent induced crystallization (by exposing the glassy sample to methylene chloride).

Electrospray ionization multiple-stage tandem mass spectrometric analysis of diglycosyldiacylglycerol glycolipids from the bacteria Bacillus pumilus

Electrospray ionization (ESI) combined with multiple-stage tandem mass spectrometry (MSn) was used to directly analyze the glycolipid mixture from bacteria Bacillus pumilus without preliminary separation. Full scan ESI-MS revealed the composition of picomole quantities of glycerolglycolipid species containing C-14-C-19 fatty acids, some of which were monounsaturated, Two main components were identified from their molecular masses and fragmentation pathways. The fragmentation pathway of the known compound compared with the investigated compound verified the proposed structure as 1(3)-acyl-2-pentadecanoyl-3(1)-O-[beta-D-glucopyranosyl-(1-->6)-O-beta-D-glucopyranosyl]-sn-glycerols. A comparison of the multiple tandem mass spectra of the different alkali-metal cation adducts indicates that the intensity of fragments and the dissociation pathways are dependent on the alkali-metal type, The basic structures of glycerolglycolipids were reflected clearly from the fragmentation patterns of the sodium cations, The intense fragments of the sugar residue from the precursor ions were obtained from the lithiated adduct ions. ESI-MSn spectra of [M + K](+) ions did not provide as much fragmentation as [M + Na](+) and [M + Li](+) adducts, but their spectra allow the position of glycerol acylation to be determined. On the basis of MS2 spectra of[M + K](+) ions, it was established that all components have a C-15:0 fatty acid at the sn-2 position of the glycerol backbone and C-14-C-19 acids at the sn-1 position of the glycerol backbone. Copyright (C) 1999 John Wiley & Sons, Ltd.