Dissertations / Theses on the topic 'Side-chain effect'

Thesis (Ph.D.)--University of Cincinnati, 2009.
Advisors: H. Brian Halsall PhD (Committee Chair), William Heineman PhD (Committee Co-Chair), Patrick Limbach PhD (Committee Member), Pearl Tsang PhD (Committee Member). Title from electronic thesis title page (viewed July 25, 2009). Keywords: Chlorine; hypochlorous acid; immunoassay; tryptophan; indole acetic acid; paramagnetic microbead. Includes abstract. Includes bibliographical references.

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations.

By flavin's unique structure, nature predestined riboflavin and its derivatives to the participation in redox processes within the bodies of all the living organisms. These biomolecules draw attention with intriguing optical properties and photosensitising abilities. Nature-inspired flavin derivatives share these qualities, and there is also a possibility of fine-tuning for the particular application from the chemical point of view. The thesis deals with two main aims. The first aim handles the synthesis of the trimer heteroaromatic precursor and 1,2-diketone. These key intermediates are essential for the future synthesis of the central aromatic core of the novel NH-free non-fused flavin derivative. The thesis introduces and verifies three approaches, including oxidation of diarylalkynes, nucleophilic addition of a corresponding organolithium compound to a Weinreb amide and benzoin condensation. The second aim covers the properties customization of NH-free fused systems by implementation of linear and bulky alkyl side-chains on the nitrogen atoms N1 and N3 of the alloxazine dilactam. N,N-alkylation introduced an increase in solubility in common organic solvents dichloromethane and chloroform. For the derivatives with 2-(adamantan-1-yl)ethyl substituents, high thermal stability was observed via TGA.

Anthocyanins are plant pigments offering a range of colours to fruits and flowers. Many properties of anthocyanins are influenced by the degree and type of side chain modifications. Though much is known about the biosynthesis of anthocyanins and the enzymes involved in side-chain decoration, there is limited understanding of the structural features of anthocyanin acyltransferases that determine their substrate preference. Anthocyanin acyltransferases belong to the BAHD family of enzymes and are involved in acylation. Through mutagenesis I showed that an arginine positioned close to motif-1 in aliphatic anthocyanin acyltransferase determines the enzyme’s specificity for malonyl transfer. Modification of arginine to phenylalanine in Ch3MAT, led to gain of acetylation property. This study thus suggests that CoA interacting residues are conserved in aliphatic acyltansferases. A phenylalanine in a similar position, close to motif 1 in aromatic anthocyanin acyltransferases is crucial for the specificity for aromatic-CoA of aromatic acyltransferases. To understand the influence of different side-chain modifications on the formation of anthocyanic vacuolar inclusions (AVIs), I showed that coumaroylation of anthocyanins leads to AVI formation when high levels of anthocyanins are accumulating. Malonylation does not lead to the formation of AVIs, suggesting that the ability of aromatic moieties to form intra-molecular stacks can cause formation of AVIs. Neither the presence of flavonols nor light or high amounts of anthocyanins can lead to the formation of AVIs. Therefore, the type of decoration mainly aromatic acylation of anthocyanins is responsible for AVI formation. From understanding the molecular mechanisms of acyltransferases for side chain decoration to their activity, anthocyanins can be engineered by anthocyanin acyltransferases in plants for novel functionalities. I showed that coumaroylation of anthocyanins promotes copigmentation more effectively than 5-glucosylation. 5- glucosylation, together with coumaroylation, offered stability to anthocyanins, both invitro and in-vivo. I also showed that flavonols copigment better than phenolics with anthocyanins, a property which could be useful for developing natural food colours. Thus, my study provided an in-depth investigation from molecular mechanisms to final applications of side chain decoration of anthocyanins.

The work presented in this thesis deals with the analysis of protein crystal structures with an emphasis on the stereochemical aspects of the folded conformation of proteins. The various analyses described have been performed on a data-set of 250 high resolution and non-homologous protein structures derived from the Protein Data Bank. The overall objective of the work has been to analyse conformational features of the non-secondary structural regions in proteins and identify structural motifs present therein. The results can be useful in the three-dimensional modelling of proteins, altering the stability of proteins, design of peptide mimics and in understanding the structural rules that guide protein folding. The contents of this thesis can be broadly classified into three parts, (a) Conformational preferences of amino acid residues to occur in the partially allowed regions of the Ramachandran map, (b) conformational features of structural motifs formed by side-chain/main-chain hydrogen bonds by polar residues and (c) analysis and characteristic features of isolated β-strands. Chapter 1 of the thesis gives an introduction, briefly discussing the conformation of polypeptide chains, structural features of globular proteins and applications of protein structural analysis etc. Chapter 2 describes the occurrence of left-handed α-helical conformation in protein structures. A data-set of 250 high resolution (< 2.0A) non-homologous protein crystal structures derived from the Protein Data Bank (PDB) has been analysed for occurrences of left-handed α-helical (αL) conformations. A total of 2,573 αL residues were identified from the data-set. About 59% of the observed examples of at conformations were found to be glycyl residues and about 41% non-glycyl. Continuous long stretches of αL residues are seldom found in protein structures. They are most commonly found as singlets represented by 78% of the observed αL examples. The doublets, triplets and quadruplets account for a very minor fraction of the observed examples. There is only a single example of a stretch of four contiguous αL residues, from the protein thermolysin, which forms a single turn of a left-handed α-helix. A majority of the αL residues are nevertheless part of well-defined substructures in proteins. They play singular roles as part of β-turns and helix termination sites in maintaining the characteristic main-chain hydrogen bonds needed for the stability of these structures. They are also found to be effective in the termination of β-strands. The stereo-chemistry and sequence environment around such structures are discussed. The analysis of the side-chain torsion angles of αL residues indicate that the g+ rotamer is highly unfavourable due to stereo-chemical violations posed by the atoms of the side-chain with those of the backbone. The αL residues are highly conserved by residue type as well as conformation among related proteins indicating their vital importance in protein structures Chapter 3 provides an explanation for the unusual preference of glycyl residues to occur in the bridge regions of the Ramachandran map. The Ramachandran steric map and energy diagrams for the glycyl residue are fully symmetric. Though a plot of the (Φ,Ψ) angles of glycyl residues derived from a data-set of 250 non-homologous and high-resolution protein structures is also largely symmetric, there is a clear aberration in the symmetry. While there is a cluster of points corresponding to the right-handed a-helical region, the "equivalent" cluster is shifted to centre around the (Φ,Ψ)values of (90°, 0°) instead of being centred at the left-handed a-helical region of (60°, 40°). An analysis of glycyl conformations in small peptide structures and in "coil" proteins, which are largely devoid of helical and sheet regions, shows that glycyl residues prefer to adopt conformations around (±90°, 0°) instead of right and left handed a-helical regions. Using theoretical calculations, such conformations are shown to have highest solvent accessibility in a system of two-linked peptide units with glycyl residue at the central Cα atom. This is found to be consistent with the observations from 250 non-homologous protein structures where glycyl residues with conformations close to (±90°, 0°) are seen to have high solvent accessibility. Analysis of a sub-set of non-homologous structures with very high resolution (1.5A or better) shows that water molecules are indeed present at distances suitable for hydrogen bond interaction with glycyl residues possessing conformations close to (±90°, 0°). It is concluded that water molecules play a key role in determining and stabilising these conformations of glycyl residues and explains the aberration in the symmetry of glycyl conformations in proteins. Chapter 4 discusses an analysis of backbone mimicry performed by polar side-chains in protein structures. Backbonemimicry bythe formation of closed loop C7, C10, C13 (mimics of γ-, β- and α-turns) conformations through side-chain main-chain hydrogen bonds by polar groups is found to be a frequent observation in protein structures. A data-set of 250 non-homologous and high-resolution protein structures was used to analyse these conformations for their characteristic features. Seven out of the nine polar residues (Ser, Thr, Asn, Asp, Gin, Glu and His) have hydrogen bonding groups in their side-chains which can participate in such mimicry and as many as 15% of all these polar residues engage in such conformations. The distributions of dihedral angles of these mimics indicate that only certain combinations of the involved dihedral angles aids the formation of these mimics. The observed examples have been categorised into various classes based on these combinations resulting in well-defined motifs. Asn and Asp residues show a very high capability to perform such backbone secondary structural mimicry. The most highly mimicked backbone structure is of the Cio conformation by the Asx residues. The mimics formed by His, Ser, Thr and Glx residues are also discussed. The role of such conformations in initiating the formation of regular secondary structures during the course of protein folding seems significant. Chapter 5 presents a description of deterministic features of side-chain main-chain hydrogen bonds as observed in protein structures. A total of 19,835 polar residues from the data set of 250 non-homologous and highly resolved protein crystal structures were used to identify side-chain main-chain (SC-MC) hydrogen bonds. The ratio of the total number of polar residues to the number of SC-MC hydrogen bonds is close to 2:1, indicating the ubiquitous nature of such hydrogen bonds. Close to 56% of the SC-MC hydrogen bonds are local involving side-chain acceptor/donor (‘i’) and a main-chain donor/acceptor within the window i-5 to i+5. These short-range hydrogen bonds form well defined conformational motifs characterised by specific combinations of backbone and side-chain torsion angles. Some of the salient features of such hydrogen bonds are as follows, (a) The Ser/Thr residues show the greatest preference in forming intra-helical hydrogen bonds between the atoms Oyi and Oi-4 Such hydrogen bonds form motifs of the form αRαRαRαR(g") and are most commonly observed at the middle of α-helices. (b) These residues also show great preference to form hydrogen bonds between OYi and Oi-3, which are closely related to the previous type and though intra-helical, these hydrogen bonds are more often found at the C-termini of helices than at the middle. The motif represented by αRαRαRaR(g+) is most preferred in these cases, (c) The Ser, Thr and Glu (between the side-chain and main-chain of the same residue), (d) The side-chain acceptor atoms of Asn/Asp and Ser/Thr residues show high preference to form hydrogen bonds with acceptors two residues ahead in the chain, which are characterised by the motifs β(tt’)αR and β(t)αR, respectively. These hydrogen bonded segments referred to as Asx turns, are known to provide stability to type I and type I’ β-turns. (e) Ser/Thr residues often form a combination of SC-MC hydrogen bonds, with the side-chain donor hydrogen bonded to the carbonyl oxygen of its own peptide backbone and the side-chain acceptor hydrogen bonded to an amide hydrogen three residues ahead in the sequence. Such motifs are quite often seen at the beginning of a-helices, which are characterised by the β (g+)αRαR motif. A remarkable majority of all these hydrogen bonds are buried from the protein surface, away from the surrounding solvent. This strongly indicates the possibility of side-chains playing the role of the backbone, in the protein interiors, to satisfy the potential hydrogen bonding sites and maintaining the network of hydrogen bonds which is crucial to the structure of the protein. Chapter 6 provides a detailed characterisation of isolated β-strands. Reason for the formation of β-strands in proteins is often associated with the formation of β -sheets. However β-strands, not part of β-sheets, commonly occur in proteins. This raises questions about the structural role and stability of such isolated β-strands. Using a data set consisting of 250 proteins, 518 isolated β-strands have been identified from 187 proteins. The two important features that distinguish isolated β-strands from p-strands occurring in β-sheets are (i) the high preponderance of prolyl residues to occur in isolated β-strands and (ii) their high solvent exposure. It is shown that the high propensity for proline residues to occur in isolated β-strands is not due to the occurrence of polyproline type segments in the data-set. The propensities of other amino acids to occur in isolated β-strands follows the same trend as those for β-sheet forming β-strands. Isolated β-strands are characterised often by their main-chain amide and carbonyl groups involved in hydrogen bonding with polar side-chains or water. They are often flanked by irregular loop structures indicating that they are part of long of loops. Analysis of the conservation of such strands among families of homologous protein structures indicates that a sizeable fraction of them are highly conserved. It is suggested that though the formation of isolated β-strands are driven by the intrinsic preferences of amino acid residues, they have many characteristics like loop segments but with repetitive (Φ,Ψ) values falling within the β-region of the Ramachandran map. In addition of the material described in the six chapters above, the thesis also contains the details of work carried out on an aspect slightly different from the main theme of the thesis. This pertains to the comparative analysis of the members of a family of cytokine receptors to derive information to model new members of the family. The three dimensional modelling of the leptin receptor has been used as a case study and the details are included as an appendix. Appendix describes the 3-dimensional model of the satiety factor receptor (the leptin receptor) modelled using principles of homology modelling. Recessive mutations in the mouse obese (ob) and diabetes (db) genes result in obesity and diabetes in a syndrome resembling human obesity. Data from parabiosis (cross circulation) experiments suggested that the ob gene coded, and was responsible for the generation of a circulating factor called leptin which regulated energy balance and the db gene encoded the receptor for this factor. While the structure of the leptin has been determined that of its cognate receptor is as yet unknown. The leptin receptor shows low but clear sequence similarity to the members of the interleukin type 6 family of receptors. The structures of the members of this family are characterised by two p-sandwich like domains connected by a short 4-residue helical linker. The 3-dimensional models for the N- and C-terminal domains of the leptin receptor was generated using the corresponding structures of the signal transducing component of gpl30, the erythropoetin receptor and the prolactin receptor. Further using the evidence that the leptin binds to its receptor with a stoichiometry of 1:1, the relative orientation of the two domains was modelled based on the structure of the human growth hormone receptor, which also binds its ligand with similar stoichiometry. The complex of leptin with its receptor was also modelled based on the structure of human growth hormone/receptor complex. The final energy minimised model of the complex elucidates the mode of interaction between the leptin and its receptor.

Les cristaux liquides discotiques ont 20 ans. La perspective d'applications exploitant le comportement photoconducteur et les caracteristiques optiques de composes de cette famille a fortement stimule leur developpement. Ces applications requierent en general une grande stabilite mecanique et thermique des proprietes anisotropes mises en jeu. Cette these decrit l'utilisation de la photopolymerisation in-situ de molecules discotiques fonctionnalisees par des groupements acrylate pour stabiliser l'ordre present dans leurs phases liquides cristallines. Cette technique de polymerisation, deja employee avec succes pour les cristaux liquides calamitiques, consiste a d'abord aligner uniformement les monomeres liquides cristallins dans la phase choisie et a ensuite amorcer la polymerisation par voie photochimique. Pour realiser cette etude, nous avons synthetise des derives de benzoates de triphenylene avec 1 a 6 groupements acrylate par molecule. La photopolymerisation de ces monomeres orientes dans la phase nematique discotique n#d conduit, selon qu'ils ont un ou plusieurs groupements acrylate, a des polymeres lineaires a chaines laterales ou a des reseaux polymerises fortement reticules. Ces derniers ont une birefringence negative stable depuis la temperature ambiante jusqu'a plus de 200c, et dont la valeur peut etre ajustee grace a la temperature de polymerisation. Ce manuscrit detaille la synthese, les proprietes liquides cristallines, et la cinetique de polymerisation des monomeres, ainsi que les caracteristiques optiques et structurales de certains des polymeres obtenus. Nous discutons l'influence de la nature chimique des differents monomeres synthetises sur les proprietes finales des materiaux apres polymerisation, et en particulier l'effet du nombre de groupements polymerisables par molecule et celui de la longueur des espaceurs. La photopolymerisation dans les phases cholesterique n#d#* et colonnaire d#h#d, ainsi que la synthese et l'etude de derives du benzene et du phenanthrene, sont egalement abordees.

碩士
國立中興大學
化學工程學系所
100
A hydroxyl group-containing [3-(4-(4-(3,3-dimethyl-2,4- dioxoazetidin-1-yl)benzyl)phenyl)-1,1-bis(2-hydroxyethyl)urea] with reactive azetidine-2,4-dione group was prepared and introduced into polyurethane backbone. The polyurethanes with reactive pendent azetidine-2,4-dione groups were further crosslinked by short-chain aliphatic diamine or modified by silane coupling agent (3-aminopropyltriethoxysilane; APS) following by a sol-gel reaction to bring about Si–O–Si crosslinked organic/inorganic hybrid polyurethanes with shape memory function. X-ray diffraction (WXRD) and differential scanning calorimeter (DSC) showed that the crystallinity of polyurethane decreased with the increase of crosslinking density. The glass transition temperatures (Tg), tensile strength and storage modulus increased with increasing crosslinking density and hard-segment rigidity. Dynamic mechanical analysis (DMA) and shape recovery tests revealed the close relationship between shape memory behaviors and polymeric structures. The high ratio of storage moduli below and above transition temperature accounted for excellent temporary shape fixing at low temperatures and faster shape recovery speed at high temperatures. In addition, phase separation was characterized by atomic force microscopy (AFM). By introducing the chemically crosslinked structures, the deformed samples completely recovered to their original shape in less than 6 second without any deficiency during shape recovery tests. Shape recovery went up to 99% during cyclic thermomechanical tensile tests, indicating that the polyurethanes with chemical crosslinking effects exhibited higher impact than did the linear and dendritic side-chain polyurethanes. Consequently, these novel crosslinked polyurethanes with excellent shape-memory effect have been successfully developed in this work.

碩士
國立臺灣大學
化學研究所
99
More than 30% of protein residues adopt an α-helical conformation. Intrahelical ion-pairing interactions can stabilize the helix conformation. To investigate how side chain length (of charged residues) and relative spacing (between charged residues) affect helicity, peptides AghAsp3, AghGlu3, AspAgp5, GluAgp5, AgbAsp4, and AgbGlu4 were synthesized. The helical content of the peptides were determined by circular dichorism spectroscopy (CD). The helical content of peptides at pH 7 follows the trend AghGlu3 > AghAsp3, GluAgp5 > AspAgp5, AgbGlu4 > AgbAsp4. This trend is consistent with the helix propensity trend Glu > Asp. Peptides with modified sequences of GCN4 basic region were synthesized to investigate the effects of Arg side chain charge on DNA recognition. Peptides WtArgGCN4ss as well as MinArg11Ass, and the mutants with individual Arg residues replaced with citrulline (Cit) at various positions were synthesized. The binding affinity and specificity of the GCN4-based peptides for cAMP response element (CRE) were determined by gel shift assays. The WtArgGCN4ss mutants showed higher affinity than the MinArg11Ass mutants. Further, WtCit18GCN4ss exhibited lower specificity and affinity than WtArgGCN4ss and other WtArgGCN4ss mutants. Min11ACit2ss showed highest affinity and specificity compared to MinArg11Ass and other MinArg11Ass mutants. The results were further corroborated by molecular mechanics calculations.

碩士
國立臺灣大學
化學研究所
101
β-Sheet is one of the secondary structures in proteins. A β-sheet consists of two or more β-strands linked and stabilized by hydrogen bonds between adjacent strands. Moreover, sheet propensity of amino acids may affect the β-sheet stability. Interestingly, the side chain length of natural charged amino acids are all different. To investigate how the side chain length affects stability, β-hairpin, the simplest antiparallel β-sheet, was used as a model system. Three negative charged side chains with different side chain length were investigated: Aad, Glu, and Asp. Water-soluble monomeric β-hairpin peptides with different aspartate analogs were synthesized by solid phase peptide synthesis using Fmoc-based chemistry: HPTZbbAla and HPTAlaZbb (Zbb = Asp, Glu, and Aad). The fully folded peptides and unfolded peptides were also synthesized as reference peptides. The structure and quantitation the population of β-hairpin were derived based on 2D-NMR spectroscopy. The percent folded for the Asp analog β-hairpin peptides followed the trends: HPTAspAla > HPTGluAla > HPTAadAla and HPTAlaAad > HPTAlaGlu > HPTAlaAsp. β-Hairpin peptides with Asp analogues showed length dependence with opposite trends depending on the guest position due to non- equivalence of the two guest positions. Unexpected long-range electrostatic attraction may decrease the stability with increasing side chain length. The HIV-1 Rev protein is an RNA binding protein that regulates viral gene expression. Rev binds to the RRE RNA located within the env gene of HIV. The structure of arginine-rich RNA binding domain of Rev is a short alpha-helix. Previous studies showed that arginine is important in RNA binding, but varying the side chain length of arginine may affect the helicity. The side chain-side chain cyclization method was used to maintain the helicity of short peptides before the effect of side chain length of arginine on binding affinity was studied. The constrained peptides were synthesized by solid phase peptide synthesis using Fmoc-based chemistry. All the six constrained peptides showed lower helicity than wild-type Rev. The gel shift assay also showed minimal binding to RRE. The constrained sequence might form another structure rather than alpha-helix. In summary, the side chain-side chain cyclization method via D-amino acid linker was not suitable in this case.

碩士
中興大學
化學工程學系所
95
Intelligent material is a new functional material which can sense external stimulus and respond to it, and self-diagnose. The most famous intelligent material is shape-memory material which can be divided into three types (1) metal alloy (2) ceramic material (3) polymer. Moreover, the polymeric material attracts most attention because of its low cost, ease of processing, and facile modification. Dendrimers are nanostructures with specific, precise and predictable physical properties (lower intrinsic viscosity and higher solubility). This makes them especially useful for various areas including drug delivery, self-assembly systems, electro-optical materials, catalysts, etc. Herein, we focus on a thermo-responsive side chain dendritic polyurethane system. The pursuit of developing nano-scaled polyurethanes with shape memory effect is approached in two aspects: (1) linear polyurethane: hard domain consists of methylene di-p-phenyl diisocynate (MDI) and diethylene glycol (DEG) and Tone polyol 0260 (Mn=3000) is used as soft domain. (2) side chain dendritic polyurethane : Employing a polyurea/malonamide dendrons as chain extender to modify traditional linear polyurethanes. By embedding different generations of dendrimers in polyurethanes, the physical properties will be enhanced because of the presence of interactions such as hydrogen bonding, dipole-dipole interactions and van Der Waals forces. To probe into the influences of different generation dendritic diols and hard segment/soft segment ratios, we utilized DSC and tensile measurement to examine thermal properties and mechanical properties, respectively. In addition, phase separation was characterized by AFM. In shape-memory test, the dendritic polyurethanes possessed great recovery ability because of the presence of embedded dendrimers. After incorporation of the dendritic structures, the recovery ratio could improve from 85% to 100%, and the primary shape was fully recovered within 3 second. It was found that somewhat phase-mixed morphology was present in the dendritic polyurethanes by the study of DSC and AFM. These phase-mixed materials would further improve recovery capacity under strong molecular interactions. It is important to note that the polyurethane consisting of generation one dendrimer possessed the better mechanical properties. The elongation at break was up to 700% and the tensile strength reached as high as 18.8Mpa. Hence, novel side chain dendritic polyurethanes with excellent shape-memory effect have been successfully developed in this work.

碩士
輔仁大學
化學學系
82
In spite of the ever increasing quantity of experimental data , the correlation between the motions of the main chain and the pendent mesogenic unit is not well understood. In most cases it is not possible to find a consistent and satisfactory agreement between different laboratories on the interpretation of results in the current literature. In the present paper,the structure and phase transitions of the two stilbene carboxylic ester based side chain liquid crystalline polysiloxane were studies by DSC, dielectric analyser and polarizing optical microscopy ( POM ) on the aligned and unaligned sample. In addition ,this study investigated different molecular structures of the mesogenic pendant group ,and analyse the effect of each part of the side chain on the dielectric relaxation behavior , in order to indentify the origin of the relaxation mechanism.

博士
國立臺灣大學
化學研究所
102
The guanidinium bearing side chain of arginine (Arg) is unique and critical for various bioactivities. However, the functional role of the three hydrophobic methylenes linking the hydrophilic guanidinium group to the backbone of Arg remains unclear. As such, the effect of arginine side chain length on RNA recognition and cellular uptake has been investigated. The 11-amino acid basic region of HIV Tat protein (human immunodeficiency virus transactivator of transcription protein, residues 47-57) binds to the transactivator response element (TAR) RNA, and is responsible for cell penetration. The six arginines in the Tat(47-57) peptide were all simultaneously replaced by arginine analogs (S)-2-amino-6-guanidinohexanoic acid (Agh, 4 methylenes) or (S)-2-amino- 4-guanidinobutyric acid (Agb, 2 methylenes). These Tat-derived peptides were synthesized by solid phase peptide synthesis (SPPS). The binding specificity was determined by electrophoretic mobility shift assays (EMSA). The cellular uptake into Jurkat cells were determined by flow cytometry. Lengthening the Arg side chain length by one methylene to give AghTat greatly diminished specific binding of TAR RNA, with slightly increased cellular uptake. Surprisingly, shortening the Arg side chain length to give AgbTat enhanced both TAR RNA binding specificity and cellular uptake. As such, AgbTat may be useful for developing drug delivery vehicles or anti-HIV therapeutics. The effect of side chain length at the different positions of Tat(47-57) for binding TAR RNA was explored. For position 57, Arg and Agb exhibited similar binding specificity. For position 56, the TAR RNA binding specificity followed the trend Agb > Agp > Arg > Agh (Agp, side chain two methylenes shorter than Arg). For position 55, Arg and Agp exhibited similar binding specificity. For 53 position, the TAR RNA binding specificity followed the trend Agp > Agb ~ Arg > Agh. For positions 52 and 49, the TAR RNA binding specificity followed the trend Agp > Arg > Agb > Agh. The potentially most optimal Tat-derived peptide for specific binding to TAR RNA with Arg analogs of mixed side chain lengths was designed by combining the Arg analogs with the highest binding affinity at each position. The Tat-CX peptides exhibited higher TAR RNA binding specificity and cellular uptake compared to ArgTat. Furthermore, a portion of the cellular uptake for the Tat CX peptides apparently occurred via non-endocytotic pathways. The non-natural amino acids containing Tat-CX peptides exhibited high resistance to trypsin proteolysis and intracellular degradation. Importantly, most Tat-CX peptides inhibited Tat-dependent luciferase gene expression more than native ArgTat. These results suggest that the non-natural Tat-derived peptides (Tat-CX) may be effective peptide transporters for drug delivery application and anti-HIV therapeutics. Preliminary temperature dependence studies on cellular uptake of Tat-derived peptides suggested non-endocytotic uptake. Accordingly, analogous Tat-derived peptides (XaaTatC) were conjugated onto MSNs with different sizes to affect the cellular uptake efficiency of the MSNs. The uptake into HeLa cells were investigated by flow cytometry and confocal microscopy. Results showed size dependence in cellular uptake efficiency and mechanism of the MSNs. Furthermore, endosome trapping of the 300 nm MSN was circumvented by improving the efficiency of endosomal escape and even enhancing non-endocytotic pathways. Importantly, introducing cell-penetrating peptides containing non-natural amino acids analogs with varying side chain lengths should be a useful strategy for the design of nanoparticle surface ligands for biomedical applications.

碩士
國立交通大學
應用化學系
83
The goal of this research is to study the effect of lateral fluoro-substituent on the mesomorphic properties of the prepared polymers. Two series of side-chain liquid crystalline polymethacrylates and polysiloxanes were prepared. The polymethacrylates containing one to tree oligooxethylene units spacers, a (2S)-2-chloro-4-methylvaleric acid chiral end group and a biphenyl 3-fluorobenzoate mesogen. All of the prepared polymethacrylates exhibits only an enantiotropic smectic A phase. The second series of polysiloxanes and copolysiloxanes containing three to eleven methylene unit spacers, a 4-(S)-2- methyl-1-butanol chiral end group and a phenyl benzoate or a phenyl 3-fluorobenzoate mesogen. Both polysiloxanes containing three methylene units in the spacer present no mesophase. Six polysiloxanes containing respectively four, five or six methylene units in the spacers exhibit only an enantiotropic smectic A phase, while both polysiloxanes containing eleven methylene units in the spacer reveal two enantiotropic smectic phases. All of the copolysiloxanes show very similar mesomorphic behavior as their corresponding polysiloxanes. The results demonstrate that incorporation of the lateral fluoro- substituent in the mesogenic side groups depresses the thermal stability of the mesophase formed. The copolymers show much lower thermal transition temperature than their corresponding homopolymers.

碩士
國立臺北科技大學
有機高分子研究所
105
In recent years, the tendency of organic conjugated polymers to be applied to optoelectronic devices has been greatly increased, because of the advantages of low cost, stretchable, flexibility and light-weight, over organic small-molecular counterparts. In the common conjugated polymer materials, it is found the side chain structure design, such as increase the alkyl chain length or modified low glass transition temperature chains, can effectively control the solubility of the polymer, molecular packing motifs, stretch ability and thin film morphology. The objective of this research is to develop the low glass transition temperature PBA chain PBA chain equip to the stiff conjugated backbone for improving the ductility of the polymeric active layer in organic electronics. The amount of bulky PBA side groups incorporated, importantly, was controlled systematically to investigate the structure-property relationships between chemical structure, molecular packing orientation, thin film stretch ability, and charge transport ability. The details of explorations are summarized as follows: 1. Synthesis and Characterization of Butyl Acrylate Side Chain Engineered Isoindigo -Based Polymeric Semiconductors (Chapter 2): a system of studied isoindigo-based conjugated copolymers, including PII2T, PII2T-PBA5, PII2T-PBA10 and PII2T-PBA20, they used donor moiety (2T) through Stille coupling polymerization and control butyl acrylate (PBA) side-chain contents design to synthesize. PII2T (-5.23 eV), PII2T-PBA5 (-5.20 eV) and PII2T-PBA10 (-5.27 eV) have similar HOMO level and deeper, due to their backbone molecular has more ordered packing than PII2T-PBA20. Moreover we observe PII2T-PBA20 showed a longer lamellar d-spacing (27.0 Å) than other studied polymers on X-ray diffraction (GIXD), which was mainly also due to the PBA moiety contents most. In the field-effect transistors (FETs), PII2T exhibit the highest hole mobility of 1.2 cm2V-1s-1, with an on/off current ratio around 106, and other polymers mobility of PII2T-PBA5, PII2T-PBA10 and PII2T-PBA20 is 0.4, 0.2 and 0.06 cm2V-1s-1, respectively, proving the studied polymers were suitable using for electronic device applications. 2. Butyl Acrylate Side Chain Engineered Isoindigo-Based Polymeric Semiconductors for Stretchable Transistor Applications (Chapter 3): The studied polymers firstly dissolved in processing solvent and then use spin-coating to form polymer thin film, moreover use the elastic poly(dimethylsiloxane) (PDMS) substrate to transfer polymer thin film and stretch. In mechanical properties of material, PII2T-PBA20 exhibits a tensile modulus of 0.12 GPa. In addition, in electrical performance, when subjected on tensile strain (up to 80%), PII2T-PBA10 still keep the mobility of 0.04 cm2V-1s-1, which hints our studied materials can effective for stretchable electronic applications.

碩士
國立臺北科技大學
有機高分子研究所
98
Single wall carbon nanotubes are used as active material in fabricating transparent conducting film, because they have excellent mechanical strength and conductivity. Moreover, we can easily incorporate the said material into flexible substrates which in turn are suitable for optoelectronic device applications. Due to Van der Waal’s interaction between individual carbon nanotubes, they are difficult to disperse in organic solvent. In this study, we used conducting polymer (poly(3-alkylthiophene) as surfactant in aiding the dispersion of the nanotubes. We used different side chain length and various molecular weight of poly(3-alkylthiophene). By doing so, we observed that the dispersion of carbon nanotubes and the transmittance and conductance of the fabricated films vary. To differentiate the dispersion property of the carbon nanotube-polymer solutions, the zetasizer was used to obtain difference in zeta-potential and carbon nanotube diameter. From the result, we have concluded that as the alkyl side chain of P3AT gets longer, the diameter of the carbon nanotube decreases and the zeta-potential value increases. This indicates that the dispersion of the solution gets better as longer alkyl side chain is used. Furthermore, dispersion enhancement can be done when the carbon nanotube-polymer solutions were subjected under ultrasonication process and removal of amorphous carbon by centrifugation. By doing this, less aggregation can be observed after film fabrication. To coat the solution onto the substrate, we use ultrasonic spray which gives a more uniform film.

碩士
國立中山大學
光電工程學系研究所
97
P3DDT (3-dodecylthiophene-2,5-diyl) and PCBM( [6,6]-phenyl C61-butyric acid methyl ester) were fabricated to the active layer of Bulk Heterojunction Organic Solar Cells .We obtained the device efficiency was 0.64 % by evaporating solvent at room temperature. We measured Thermal decomposition Temperature (Td) of P3DDT was 487℃. But operational temperature was over 90℃, it could affect the roughness of thin film and make efficiency to be 4×10-3(%). For results of experiments, we know that roughness changed by the crystallization of side chain and exciton dissociation modified by the morphology between P3DDT and PCBM. Thin film solar cell has a large effect on the formation of active layer, such as heat treatment, choices of solvents, composition ratio, and speed of spin coating. The efficiency of solar cell has been shown to be highly sensitive to the size, composition and crystallization of the formed domains. We studied two kinds of conjugated polythiophenes with the same main chain but different side chain. When the number of carbon atoms of alkyl side chains is more than 10, some orderly arrangements will occur for side chains between the layers. We tried to explain the crystallization caused by long alkyl side chains determined which intrinsic phenomena are the most evident for altering the PCE of solar cell. After recrystallization, the layered structures of P3DDT can be improved, but those orderly degrees of the arrangements with PCBM are further aggregated. The main point for low PEC and Jsc by heat treatment is the unfavorable and roughened morphology. Charge transfer only occurs at the boundary ,which is interfacial area between donor and acceptor materials, hence, the low Jsc could be caused by poor charge transfer between P3DDT and PCBM. The redistributed arrangement of P3DDT domains exclude PCBM from original space, and it makes PCBM to aggregate large particles, from nanophase to mesophase scales, which reduce mutual solubility to be the source of PCE and Jsc reduction.

碩士
國立臺北大學
國際企業研究所
102
The supply chain functions indeed have a great influence on the channel performance, especially the leanness of supply chain. We recommend that if the garment industry wants to raise their channel performance and sales performance. They should sincerely think about supply chain function as strategy to elevate the channel and sales performance. To be clearly, the implementation of leanness of supply chain would raise the level of supportive innovation. Through supportive innovation strengthens good channel performance and sales performance.

碩士
國立臺灣大學
化學研究所
105
Electrostatics is important for protein structure stability. Charged amino acids contribute to these electrostatic interactions. β-Sheet is one of the protein secondary structures and is involved in various protein mis-folding diseases. Different amino acids have different propensities for β-sheet formation. Therefore, it is important to study the propensity of charged amino acids for β-sheet formation. This research focuses on the propensity of arginine (Arg) and arginine analogs with longer and shorter side chains (Agh, Agb, and Agp), and the position dependence of the corresponding sheet propensity. β-Hairpins are the simplest β-sheet structure. Hairpin peptides with arginine and arginine analogs incorporated at different guest sites were synthesized by Fmoc-based solid phase peptide synthesis. Collagen triple helix consists of three polyproline II helices. In this project, different numbers of POG triplets were inserted in the middle of all three heterotrimeric collagen triple helix forming peptides. Thermal denaturation experiments were used to determine the melting temperatures of the collagen triple helices. Thermal equilibration was found to be extremely long at temperatures around the melting transition, and up to 2000 minutes were required for reversible denaturation and renaturation. The melting temperatures were derived by fitting with the thermal denaturation curve, assuming a two-state trimer to monomer equilibrium. The POG triplet was found to stabilize the polyproline II structure in a collagen triple helix. Specificity was gradually decreased with the addition of more POG triplets. This study provides insights into how to use POG triplets to tune the stability and specificity of a collagen triple helix.

碩士
崑山科技大學
材料工程研究所
100
In this work, we provided insights into effects of the side-chain structure of polyfluorenes; poly(9,9-dioctylfluorene) (PF8) and poly[9,9-di-(2-ethylhexyl)-fluorenyl-2,7-diyl] (PF2/6) on the morphology, microstroctore and photophysical properties of electrosppining nanofibers through the optical microscope (OM), polarized optical microscope (POM), scanning electron microscope (SEM), differential scanning calorimeter (DSC), Wide angle X-ray Diffraction (WAXD), UV-vis absorption (UV-vis) and photoluminescence (PL) spectra. In the second chapter, the effect of the prepare condition on the morphology, microstructure and photophysical properties of PF8 electrosppining nanofiber. The conclusion of the charpt as shown in below: In the concentration higher than 12.0wt%, PF8 cnjugated solution can format a uniform and homogenous electrospun fiber with diameter ca. 0.5 – 2.0 ?慆, which presente a clearly green-blue emission profile attributed to more ??-phase domains accompanied with high-extended PF8 polymer chains in the fiber axes. Compared with the drop-casted thin-film, the microstructure of PF8 electrospun fiber shows a red-shifted in the UV-vis, while that presents a blue-sifted in the PL spectra, attributing to the high-extended of PF8 chains in the fiber axes of PF8 electrospping fiber promote a higher energy in the absorption and emission behavior. However, compared with drop-casted thin film, the microstructure of PF8 electrospun fiber presentes the amorphous metastable structure; therefore, more complexly thermal properties of the PF8 electrospun fiber displaies in DSC. In heating trace the thermal behavior of PF8 electrospun fiber shows a stress-relief peak at ca. 57 oC and a cooling crystallization exothermic peak at ca. 80 oC, and then presents a crystallization transition peak at ca. 120 oC followed by a melting endothermic peak at ca. 145 oC. Moreover, these crystallization and crystal structure transition behaviors of PF8 electrospun fiber also provide by the heat-dependence wide angle X-ray diffraction (WAXD) technical. In the third chapter, we study the effects of the prepare condition on the morphology, microstructure and photophysical properties of PF2/6 electrospun fiber, the conclusion of the chapter as shown in below: Herein, PF2/6 conjugated polymer also could prepare a uniform and homogenous morphology with diameter ca. 1.0 – 2.0 ?慆 electrospun fiber. The PF2/6 electrospun fiber presentes a clearly deep-blue emission attributed to a more high-extended PF2/6 polymer chains and small content ??-?? stacking ??-phase domains in the PF2/6 fiber axes. Therefore, PF2/6 electrospun fiber shows a more blue-sifted in the UV-vis and PL spectra, respectively. Moreover, compared with the PF2/6 drop-casted thin film, the photophysical properties of PF2/6 electrospun nanofiber also presents a red-shifted in the UV-vis, while that shows a blue-sifted in the PL spectra, corresponding to the high-extended of PF2/6 chains in the fiber axes of PF2/6 electrospun fiber promote a higher energy in the absorption and emission behavior. On the other hand, the broadness of the UV-vis and PL spectra in PF2/6 electrospun fiber corresponds to the heterogeneous of the fiber dimension and nanoporous on the fiber surface. The XRD result displaies some ordered ??-form crystals in the PF2/6 thin-film, thus it showed a melting endothermic peak at ca. 158 oC. Whereas, the PF2/6 electrospun fiber displaies an amorphous structure; therefore, the thermal behavior of PF2/6 electrospun fiber shows a very small melting endothermic peak at 147.8 oC. These results indicates that PF2/6 polymer chains presente a high-extended PF2/6 polymer chains in the PF2/6 electrospun fiber axes by the drafting force of the electrospping technology.

碩士
國立臺灣大學
高分子科學與工程學研究所
102
We employed all-atom molecular dynamics (AAMD) simulation and the quantum mechanical (QM) methods to explore the correlation between the molecular conformation and the UV absorption behaviors of terthiophene-based conjugated polymers. The four model systems examined here are PBTTTV-v, PBTTTV-h, H-PBTTTV-v and H-PBTTTV-h. We focus on the effects of side-chain architecture on the two-dimensional extended conjugation properties of the UV absorption spectra of polythiophenes. First, we observe the molecular conformation displaying disordered state of polymer chains within dilute solution via AAMD. In the PBTTTV-v, PBTTTV-h, H-PBTTTV-v and H-PBTTTV-h molecules, due to a large steric hindrance from the linkage between main chain and side chain, they have broader torsional angle distribution of main chain (τMain chain_A) and side chain (τSide chain_B). Because of the free motion of single bonds, the single bond linkages between main chain and side chain don’t intend to preserve a coplanar conformation as the H-PBTTTV-v and H-PBTTTV-h molecules. In contrast, as for the PBTTTV-v and PBTTTV-h polymers with vinyl linkage tend to keep a coplanar conformation. Then, we explore the UV absorption spectra of PBTTTV-v and PBTTTV-h molecules via QM. We notice that PBTTTV-v and PBTTTV-h have the two-dimensional extended conjugation properties in the UV absorption spectra, which make the UV absorption spectra more complicated. On the other hand, we observe the molecular orbital and discover the electron cloud may scatter along the main chain to side chain. As a result, we constitute several segments from the molecular orbitals by adjusting each segment’s fraction. The resultant UV absorption spectra of PBTTTV-v and PBTTTV-h show good match to the experimental results. When the single bonds are substituted for the vinyl linkages, the UV absorption spectra of H-PBTTTV-v and H-PBTTTV-h dimer show two peaks in the same range. The two absorption peaks are from either the main chain or the side chain. In the future, we will modify the torsional angle of molecular conformation within AAMD. We will systematically explore the correlation between molecular conformation and optoelectronic properties of PBTTTV-v, PBTTTV-h, H-PBTTTV-v and H-PBTTTV-h.

碩士
國立臺灣大學
化學研究所
101
β-Sheet is a common secondary structure. The structure can be stabilized by cross strand interactions such as backbone hydrogen bonds and side chain electrostatic interactions. Ion pairing interactions can form between two oppositely charged amino acids, such as Lys, Arg, Glu, and Asp. However, some unnatural amino acids contain different number of methylene groups in the side chain are not incorporated in natural proteins. Accordingly, the ion pairing interaction involving Asp-Lys, Asp-Orn, and AspDab were investigated in a β-hairpin system. The 2D-NMR spectra including TOCSY, ROESY, and COSY were acquired for the peptides. The peptide β-hairpin structure as confirmed by chemical shift deviations, 3JNHα coupling constants, and NOE connectivities. The β-hairpin population and stability were determined by comparing the chemical shifts with the reference peptides. The peptide stability followed the trend HPTAspLys ~ HPTAspOrn > HPTAspDab. The ion pairing interactions were derived from double mutant cycles. The corresponding ion pairing interactions followed the trend Asp-Lys ~ Asp-Orn ~ Asp-Dab. Calmodulin (CaM) is a highly conserved and abundant protein in eukaryotic cells. Calmodulin participates in many physiological processes, such as muscle contraction, insulin and pituitary secretion, and neurotransmission. CaM can bind to basic amphiphilic α-helical peptides. To control the 3D-arrangement of side chains and minimize proteolytic degradation, β-amino acids were incorporated into peptides. β-Amino acids are unnatural amino acids containing one extra methylene group in the backbone compared to natural α-amino acids. In this study, the side chain sequences of peptides were the same as the basic amphiphilic α-helical peptide, but the backbone patterns were varied by mixing α- and β-amino acids, including αβ, ααβ, αααβ, and ααβαααβ. The binding affinities were determined by CD spectroscopy and fluorescence anisotropy. The proteolytic susceptibilities were tested against trypsin.

碩士
國立臺灣大學
化學研究所
101
Ion pairing interactions play important roles in protein stability and RNA recognition. Ion pairs are formed between a pair of oppositely charged amino acids. Interestingly, natural charged amino acids have different number of hydrophobic methylenes on their side chains. For negatively charged residues, Asp has one methylene and Glu has two methylenes. The analogous non-encoded negatively charged amino acid, Aad, contains three methylenes. To study the effect of negatively charged amino acid side chain length on cross strand ion pairs in β-sheets stability, a basic β-hairpin model HPTZbbArg was designed. Zbb denotes the negatively charged residues. The hairpin structure for peptides HPTAspArg, HPTGluArg, and HPTAadArg were confirmed by NMR methods. The fraction folded of the peptides was determined using chemical shift data involving the fully unfolded and the fully folded reference peptides. The interaction free energy followed the trend: Aad-Arg > Glu-Arg ≈ AspArg. Apparently, the longer the negatively charged residue side chain length, the stronger the ion pairing interaction. HIV-1 Tat protein contains an arginine-rich sequence (Tat49-57), which binds specifically to the trans-activating responsive (TAR) element and plays an important role in nuclear localization. The binding of HIV-1 Tat protein and TAR RNA is essential for HIV-1 virus genome replication. To study the effect of arginine dimethylation on RNA recognition and cellular uptake, each arginine residue in Tat49-57 was replaced with a dimethylated arginine including ADMA and SDMA, the asymmetric and symmetric dimethylated forms, respectively. The dissociation constant for the Tat derived peptide-TAR RNA complexes was determined by gel shift assay. The cellular uptake efficiency of these Tat derived peptides into Jurkat cells was assessed by flow cytometry.

碩士
中山醫學大學
生化暨生物科技研究所
101
Oxacillinas (OXA) is a class D b-lactamase, represents an emerging antibiotic resistance mechanism encountered among the most opportunistic Gram-negative bacterial pathogens, especially Acinetobacter baumannii. At present, A. baumannii OXAs mainly has four groups: OXA-23 like group, OXA-40/24 like group, OXA-51 like group and OXA-58 like group. Among them, OXA-66, group of OXA-51 like, is naturally occurring in A. baumannii. The recently solved crystal structure of OXA-24 suggests the tunnel-like entrance to the active site. Comparison of the homology model of OXA-66, the position I129 of OXA-66 is on the tunnel-like entrance and interact with active site S80 and N-carboxylated K83. Our laboratory constructed serveral mutants at position I129 with aliphatic side chain L/V/A/G by site-directed mutagensis, in order to investigate how variants affect the ability of hydrolyzing substrate impenem and N-carboxylated K83 by enzyme kinetics analysis. Finally, we simulated interactions between I129 with N-carboxylated K83 by software Swiss pdb viewer . Our data shows (i) Km (uM) ranked 13.3 (L), 13.2 (I), 10.3(V), 9.2 (A), 22.6 (G). It estimated the IMP affinity decreased as molecular size of position 129 side chain, but Gly. (ii) relative Vmax ranked 100% (I)、381% (L)、115% (V)、155% (A)、124% (G). It showed position 129 affects the reaction velocity. Furthermore, we measured CO2 affinity: (iii) Km (mM) ranked 9.06 (I), 2.89 (L), 7.82 (G) is tending with distance between side chain of position 129 and N-carboxylated K83. We suggest the side chain at position 129 affect CO2 binding to K83 by creating hydrophobic environment. Our data suggest that position 129 of OXA-66 not only affects the affinity with substrate IMP, but also affects CO2 binding to K83 by creating hydrophobic environment.

碩士
明志科技大學
材料工程系碩士班
105
In the first part of this study, we know that the conjugated side chain has been regonized as a good way to change the energy levels of conjugated polymers. Here, we found four indacenodithiophene (IDT) based side chain conjugated donor-acceptor alternating polymers. Various acceptors units (difluorobenzothiadizole: PIDTHT-FBT, difluoroquinoxaline: PIDTHT-QF, dicyanoquinoxaline PIDTHT-QCN, diketopyrrolopyrrole : PIDTHT-DPP) were introduced to investigate the effect of conjugated side chains on their optoelectronic (absorption spectra, energy levels, space charge limited current (SCLC) hole mobility,) and organic photovoltaic (OPV) properties. We observed the deeper highest occupied molecular orbital (HOMO) energy levels of polymers when incorporated the alkyl−thiophene side chain. We observed the best power conversion efficiency(PCE) of 5.2% for this type of PIDTHT-QF based device. Our findings suggest that side chain conjugated (or called 2−Diminsional) IDT polymers with suitable electron-withdrawing groups are promising photovoltaic materials. For the second part of this study, we have found that interfacial layers (IFLs) based on Jeffamines (industrial polyetheramine derivatives) can improve the performance of organic photovoltaics (OPVs). We evaluated four different Jeffamines (average molecular weight: 2000 g mol–1)—M2005, M2070, D2000, and ED-2003—having either a monoamine or diamine structure and various ratios of propylene oxide (PO) and ethylene oxide (EO) for their suitability as IF materials for OPV applications. The presence of the Jeffamine altered the work function of ZnO and improved the electron transport, thereby causing the ZnO layers to function more efficiently as electron-selective electrodes. The power conversion efficiencies (PCEs) of inverted devices having the layered configuration glass/indium tin oxide (ITO)/ZnO (with or without the Jeffamine)/PTB7:PC71BM/MoO3/Ag increased from 8.1 ± 0.49 to 8.6 ± 0.32% when containing the Jeffamine-D2000 under illumination with AM 1.5G solar light (1000 W m–2), the result of a significantly increased fill factor (FF). The greatest OPV performance was that of the device incorporating Jeffamine-D2000—a PCE of 9.1% and a remarkable FF of 74.2%.

碩士
中山醫學大學
生化暨生物科技研究所
101
Clinical use of carbapenem antibiotics Imipenem, Meropenem, etc. to deal with Oxacillinase infectious isolates. Acinetobacter baumannii bacteria OXA-66 belongs to OXA-51 like, are found in some Acinetobacter baumannii bacteria genes. OXA-66 amino acid position 129 Ile substrates and enzyme catalysis in space and in the spatial distribution and activation center Ser80 and Lys83 adjacent. 129 locations literature that will reduce the hydrophobic residues Lys83 the pKa value so that the release of a proton acceptor -NH2 for CO2. Lys83 carboxylation extent will affect the Class D beta-lactamases hydrolyze beta-lactam capabilities. Past of our laboratory found that when OXA-66 I129 point was mutated to Leu, the decomposition of the MER activity increased 5.5-fold. Speculate OXA-66 I129 addition to affecting the enzymatic hydrolysis of substrate also affect the catalytic capabilities of carboxylation capacity K83. OXA-66 I129 in order to clarify the role of the experiment, gene cloning and mutation to obtain OXA-66 and its location I129 mutated to hydrophobic amino acids L, V, A, G recombinant proteins. Observation of these recombinant proteins for substrates MER activity, an enzyme kinetic theory analysis. The result showed that Km in order were 59.7 (L), 74.7 (A), 87.9 (I), 98.9 (V), I129L observed affinity of the enzyme for the best substrates, I129V weak. Therefore Corollary 129 amino acid side chain structure position affects enzymes and substrates affinity; while descending Vmax relative value compared to 224% (L), 104% (A), 100% (I), 80.14% (V), can be observed up to a multiple of the highest I129L, but I129V be lower, suggesting that changes in amino acid position 129 of the enzyme affinity substrates affect the enzymatic hydrolysis catalyzed by a qualitative capability. In I129G mutant recombinant protein substrates meropenem for active experiments found that Bi-phasic phenomenon may be due to the 129 position affects the positioning of acetylated water molecules, or affect Lys83 carboxylation capacity. In order to clarify the position of OXA-66 129 amino acids would not affect Lys83 carboxylation capacity, adding NaHCO3, and conduct active measurements and analysis, the results wild type activity was increased 91-fold, I129L increased 30-fold, and the wild type enzyme hydrolysis of substrates with I129L activity almost identical, suggesting that the carboxylation Lys substrates for the enzyme catalytic amino acid side chain is greater than the impact caused by the spatial impact. I129G meropenem hydrolysis of substrate added when a sufficient amount of CO2 that the original bi-phase shift for the mono-phase, probably because of a weak hydrophobic nature Glysine assist Lys83 be carboxylase deficiency. Therefore, we prepared I129D recombinant protein, discovered that adding a sufficient amount of CO2 that Oxa66-I129D can not have any activity for meropenem. Therefore, by inference OXA66 enzymatic hydrolysis of the active substance meropenem relies on 129 position amino group of hydrophobic capability. To verify the position 129 for a hydrophobic group of Lys83 of carboxylation, for analysis of enzyme kinetics of enzymatic hydrolysis of substrate merpenem CO2 reaction shown Km (mM) Ascending were I (3.64), L (5.55) , V (6.14), A (9.97), G (35.93), Corollary 129 position amino group of hydrophobic ability to influence the course of the enzymatic hydrolysis of substrate affinity for CO2, CO2 is not added when the enzymes are affected by a qualitative enzyme kinetics experiments, L Km less than I, CO2 substrates for enzymes of the enzyme kinetic experiments also showed that L is smaller than the Km I. Vmax of the respectively I (100%), L (104%), G (16%), as I, L the Vmax value is not significantly different, as I, L, V, A are of hydrophobic Amino Acid, so the Vmax and no significant difference in comparison, the above results suggest that the hydrophobic amino acid position 129 affects Lys83 for carboxylation catalyst substrates thereby affecting the activity of the enzyme, and the better the hydrophobic amino acids groups such as I and L such that the enzymatic hydrolysis of substrate activity of meropenem slightly.

碩士
國立臺灣大學
化學研究所
104
Ion pairing interactions play important roles in protein structure stability. Stabilizing ion pairing interactions are formed between two oppositely charged residues such as Arg/Lys and Asp/Glu. To gain insight into ion pairing interactions and their potential roles in protein structure, we have designed a β-hairpin peptide system, allowing the measurement of the stability effects of individual charged residues and ion pairing interactions. Herein, we study the effect of side chain length on cross-strand diagonal ion pairing interactions. Peptides were synthesized by solid phase methods and purified by reverse phase HPLC. The sequence specific assignments were obtained based on TOCSY, ROESY, and DQF-COSY spectra. The β-hairpin structures were confirmed by chemical shift deviation, 3JHNα coupling constants, and NOE signals. The fraction folded and ΔGfold of the peptides were derived by comparing the chemical shifts with the folded and unfolded reference peptides. The stability of the peptides followed the trend : HPDAadDab ~ HPDAadDap > HPDGluDab ~ HPDGluDap > HPDAspDab ~ HPDAspDap. The results indicate that pairing the longer side chains provides the most stable β-hairpin. Coiled coil is a common motif found in nature. These motifs are ideal models for the study of protein secondary and teriary inteactions because the relationship between sequence and stability are well-understood. Incorporation of fluorinated amino acid residues into coiled coil peptides can stabilize coiled coils. This stabilization has been referred to as the fluoro-stabilization effect. To further understand the fluoro-stabilization effect in proteins, peptides based on the leucine zipper region of the yeast transcription factor GCN4 was designed and fluorinated amino acids were incorporated at the hydrophobic positions.

碩士
國立臺灣大學
化學研究所
101
There are many factors that contribute to protein folding and structure stability: intrinsic propensity of amino acids, side chain ion pairing interaction, hydrophobic effect, hydrogen bonding, van der Waals interaction. In this study, we focused on the effect of lysine side chain length on sheet propensity at a non-hydrogen bonded strand position in β-hairpin. The β-hairpin peptides HPTAlaXaa (Xaa= Dap, Dab, Orn, Lys) were designed with the side chain of Lys9 systematically shortened to investigate the effect of Lys side chain length on sheet propensity. The peptides were synthesized by solid phase peptide synthesis using Fmoc-based chemistry. All peptides were purified to 95% purity and were analyzed by 2D NMR experiments. Sequence specific assignment was performed. The hairpin structures were confirmed by chemical shift deviation, 3JHNα coupling constants,and NOE signals.The fraction folded and ΔG of peptides were derived by comparing the chemical shifts with the fully folded and unfolded reference peptides. The percent folding of HPTAlaXaa peptides with Lys analogs at the guest position followed the trend: HPTAlaDap ~ HPTAlaDab < HPTAlaOrn ~ HPTAlaLys, showing that the longer the Lys analogue side chain, the more stable the β-haiprin structure. The HIV Rev protein binds RRE RNA to regulate the transport of unspliced and spliced mRNA from the nucleus to the cytoplasm posttranscriptionally. The Rev peptide is a random-coil. However, the conformation of the Rev peptide changes to an α-helix while binding to RRE RNA. Hydrogen bond surrogate (HBS) is one of the several cross-linking systems for stabilizing an α-helix, using the covalent bond C=C-C-N to substitute the C=O…H-N (i, i+4) hydrogen bond in a short helix. In order to synthesize an HBS peptide, strategy for synthesis of dipeptides that contained an allyl group on the amino group was designed and refined. Two wild type Rev peptides were synthesized by solid phase peptide synthesis using Fmoc-based chemistry. The secondary structure of the two peptides was random-coil analyzed by circular dichroism spectroscopy. The binding specificity of the Rev peptides was determined by gel shift assay. The dissociation constants of the Rev peptides were similar to previous studies.

碩士
國立臺灣大學
化學研究所
93
A series of banana-shaped organic molecules which have a central aromatic ring (C ring) modified by different substituents and four side aromatic rings linked by ester bonds were synthesized and characterized in our earlier work. In this research, we aim toward the modification of terminal side chains on the molecules. Results show that the modification of chain length will alter the mesophases due to different molecule geometry. In addition, we modified the molecules with several different linkages but maintain the same carbon chain length. Results show that molecules with ester linkages prefer a larger mesophase temperature range and higher transition temperature between liquid crystal mesophase and isotropic phase comparing to ether linkages. Molecules with pure alkyl side chains are unfavorable to form liquid crystal mesophases. On the other hand, the addition of substitents on side ring B will diminish the appearance of liquid crystal mesophases except fluorine. Also, the replacement of central benzene ring (C ring) with a pyridine ring results in the disappearance of liquid crystal mesophases as well.

Semi-crystalline polymers have shown increased crystalline order and size when confined in multilayered films by coextrusion1. The resulting large crystals lead to dramatic improvements in gas barrier properties. Ordered polymers whose characteristics are between that of the liquid phase and the crystalline phase are known as liquid crystalline polymers. The highly ordered mesogens in liquid crystalline polymers contribute to their exceptional bulk properties. In this research, side-chain liquid crystalline polymers were confined in multilayered films, made by either multilayer coextrusion or spin coating, with a non-liquid crystalline polymer in an attempt to improve the ordering of the liquid crystalline mesogens. The liquid crystalline behavior and morphology was studied to understand the correlation between the confinement size and the properties of the multilayer films. Commercial main chain liquid crystalline polymers and hydrogen bonded liquid crystalline polymers were also explored in this research for their use in multilayer coextrusion.
text

碩士
國立臺灣大學
高分子科學與工程學研究所
107
Over the past decade, the polymer/fullerene-based organic solar cell has rapidly developed. In addition to the increase of power conversion efficiency (PCE) by adding additives or synthesizing new structure, the improvement of stability has also been a key issue for the organic solar cell. In this study, we synthesized poly(3-2-methylpentylthiophene) (P3MPT), a polythiophene with branched side chain and studied the morphology, thermal properties, and photovoltaic performance of P3MPT blended with different fullerene derivatives. The results are compared to those of the commonly used poly(3-hexylthiopene) (P3HT) with linear side chains to investigate the effects of side chain configuration. We found that P3MPT/PC61BM solar cells not only show a higher efficiency but can maintain the high efficiency much longer than the P3HT/PC61BM solar cells. Compared to P3HT/PC61BM systems, the size of domains extracted by the small-angle X-ray scattering (SAXS) profiles implies a more stable phase separated structure in P3MPT/PC61BM blends. We suggest that the branched side chains are bulkier than the linear side chains and thus can provide a higher steric hindrance, which causes more rigid side chains and backbones to slow down the phase separation rate between P3MPT and PC61BM. The higher glass transition temperature of P3MPT than that of P3HT was confirmed by differential scanning calorimetry (DSC). In addition, DSC and Wide-angle X-ray scattering show that the crystallization ability of P3MPT is lower than that of P3HT also due to the bulkier side chains. The higher glass transition temperature and the lower crystallization ability of P3MPT contribute to the superior long-term stability of P3MPT/PC61BM system.

碩士
國立臺灣大學
材料科學與工程學研究所
104
Donor-acceptor alternating conducting copolymers are potential materials for low cost flexible electronics such as transistors, solar cells, etc. These kinds of polymers are usually rigid and difficult to process. Through side chain engineering, we can not only tune the conformation but also optical bandgap and self assembly behavior of the copolymers. From Stille coupling reactions, we synthesized four series of donor-acceptor alternating conducting copolymers. They are basis on donor of terthiophene (3T) and acceptor of thieno[3,4-c]pyrrole-4,6-dione (TPD) by varying position, type, and length of side chain. They are named P3T(RiN)TPD(R), P3T(RiN)TPD(E), P3T(RoN)TPD(R), and P3T(RoN)TPD(E), where R is alkyl side chain and E is oligoether side chain, i represents the two R located on 3,3” position of 3T, o represents the two R located on 4,4” position of 3T, and N is the length of R. The bandgap of each copolymer is studied by the UV-Vis spectroscopy and cyclic voltammetry. The self assembly behaviors of copolymers are studied by grazing incident wide angle X-ray scattering (GIWAXS) and atomic force microscopy (AFM). It is noteworthy that the donor-acceptor conducting copolymer with Ro chemical structure performs lamellar structure. In contrast, the copolymer with Ri exhibits hexagonal cylinder structure and lower bandgap. Ro chemical structure has a more planar 3T building block structure as compared with Ri and thus provides stronger π-π interaction between the macromolecular chains, which results in easier production of continuous stacking and forming of laminates. Meanwhile, for the copolymer with Ri chemical structure, the stacking with short-range order forms macromolecular bundles with the aid of the side chain, afterwards long-range order hexagonal cylinder structure appeared due to the self assembly of macromolecular bundles with close packing. The macromolecular bundles have the effects of extending the length of the main chain, therefore increasing the effective conjugating length and obtaining a lower bandgap. According to the results of GIWAXS, the effect of phase separation leads to a higher degree of ordering in diffraction peak (√21) of hexagonal cylinder structure. This is mainly due to the advantage of replacing R with E on the TPD, which equips copolymer with amphiphilic characteristic. In solution, due to the donating effect of long alkyl side chain toward the main chain, the λmaxsol of copolymers is shifted to longer wavelength with increasing side chain length regardless the main chain structure of copolymers. In film, the extent of red shift for copolymer containing Ro structure is larger than that containing Ri structure. By tuning the side chains on the donor-acceptor alternating conducting copolymers, we can not only tune the bandgap but also observe rare case of highly ordered hexagonal cylinder structure. All of these copolymers have self assembly structure without thermal annealing, and have the potential to be applied in the fabrication of flexible electronic devices.

碩士
國立臺灣師範大學
化學系
100
SRC kinase plays a significant role in signal transduction. Its activity level is associated with cell proliferation and the migration of cancer cells. Virtual Screening is one of widely used computational tools in reducing research cost to develop drugs. Our aim is to develop computational protocols for improving the Virtual Screening of SRC kinase by side chain flexibility and hydrogen bonds constraint(s) in docking computation. First, we used DUD database to benchmark these effects, and later applied the protocols to one larger database, ZINC database. In the first place, we used three SRC Kinase crystal structures (PDB codes: 2SRC, 1Y57, and 1FMK) for docking computations and allowed all side chains within 10 Å centered at a selected point of the active site to move. Although there is no common residue’s side chain movement that can improve EF value among the examined three structures, individual effect of each examined side chain located at hinge, gatekeeper segments, and activation loop on calculated EF values are reported. After that, we applied two different kinds of hydrogen bond constraints in docking against SRC kinase. They are called Type A and B. Type A is that the ligands having hydrogen bonds with two residues of SRC kinase, and Type B is just connecting with one residue on the hinge segment. The results show that Type B hydrogen bond constraint approximately doubles the average EF value for those three crystal structures. Subsequently, we combined both side chain flexibility and hydrogen bond constraint and found that Type B hydrogen bond constraint with Asp404 side chain flexibility enhance the average EF value approximately in three-fold. Finally, we applied the above optimized conditions to the ZINC database. The calculated results are similar to the results above, and are analyzed and discussed.

碩士
國立交通大學
材料科學與工程學系所
106
In this study, in order to explore extended side chain structure effects on two dimensional conjugated polymer, a series of donor－acceptor (D－A) conjugated polymers: P2(PBDTOEHBO)、P3(PBDTTEHBO)、P4(PBDTBTEHBO)、P5(PBDTTPEHBO)、P6(PBDTTTEHBO) were synthesized. In the polymer, several different structures of two dimensional -BDT were used as donor building block, and a new structure of acceptor building block was designed. The physical, chemical, photovoltaic, structural packing, and morphological properties of polymers were characterized in this research. Among these polymers, P5、P6 exhibit wider UV−vis absorption range. This result clearly indicates that the light-harvesting properties of the parent conjugated polymers could be improved by introducing chromophoric side chains to broaden its absorption range and maximize overlap with the solar emission spectrum. The organic solar cell open circuit voltage (Voc) of P5、P6 are 0.88V and 0.79V respectively, and the shortcut current (Jsc) are 11.04 mA/cm2 and 11.56 mA/cm2 respectively. The power conversion efficiency (PCE) of P5 achieves 4.3%, P6 achieves 4.8%. The power conversion efficiency can be further improved through designing other structures of acceptor, selecting suitable solvent to enhance polymer solubility, and increasing crystallinity by thermal annealing.

碩士
國立臺灣大學
化學系研究所
85
Four series of (-diketonate complexes were prepared by modified process. The mesomorphiz behavior and physical properties of metal complexes were studied from the variation of metal ions, and numbers and structure of alkony side-chains in the liquid.From the experimentalresults., the following conclusions could be drawn.The number of side-chain should be six or more, the length of different side-chains in the same liquid should be similar and the metal ion should be high electron-density. The metal complexes are thermally stable, but the mesophase range is always narrow and may not be detected by DSC. Among the three types of studied, the palladium(II) complexes were found to have highest isotropic point, and oxovadium(IV) complexes the lowest. It is likely due to the strong force of coordination between molecules caused by the high electronic destiny. Polarized optical microsopy indicates four of the Pd(II) complexes and out one of Cu (II) complexes are liquid of crystal of Dhd type.To ear knowledge, this are the first complexes of metal complexliquidcrystal containing secondary alkony side-chain in the (-diketonate liquid.

博士
國立陽明大學
臨床醫學研究所
96
Background: Urinary Tamm-Horsfall glycoprotein (THP) is a pleotropic binding ligand of various proteins and a potent stimulator for immunocompetent cells. It is still unclear whether protein core or glycomoieties play an essential role in stimulating immune functions. In addition, whether the sugar side chains are modified in pathological state such as in allograft transplantation is also unknown. Methods: THP molecules were purified from urine of normal individuals (N-THG) and allograft renal transplant patients (R-THP). The various THP molecules were treated with carbohydrate-, protein-, and glycoprotein-degrading enzymes and then tested for the effects on their biological/immunological activities. Results: N-THP molecule contained high amount of Sia��(2,3)Gal/GalNAc, moderate amount of β(1,4)GlcNAc oligomers/GlcNAc/branched mannose, and low amount of mannose residues, but no Sia��(2,6)Gal/GalNAc, in the side chains. It could bind very efficiently to human tumor necrosis factor (TNF)-��, immunoglobulin G (IgG), complement (C1q) and bovine serum albumin (BSA), moderate-efficiently to human interleukin - 8 (IL-8), and less efficiently to human IL-6 and interferon (IFN)-��. These purified molecules were further enzyme-digested with neuraminidase (Nase), β-galactosidase (Gase), protein-specific V8 protease (V8), proteinase K (PaseK), carboxypeptidase Y (Case), or O-sialoglycoprotein endo- peptidase (Oase). N-THP molecules digested by V8, Oase, and PaseK, significantly ameliorated in their protein-binding, mononuclear cell proliferating-, and polymorphonuclear neutrophil (PMN) phagocytosis-enhancing capacities. Compared to N-THP, R-THP contained lesser amounts of Sia��(2,3)Gal/GalNAc, mannose residues, and ��(1,4)GlcNAc, but not GlcNAc/branched mannose. The binding capacity of R-THG to C1q and TNF-���nwas also decreased. In addition, R-THG exhibited less mononuclear cell-stimulating and PMN phagocytosis-enhancing activities than N-THG. The defective mononuclear cell-stimulation by R-THP was due to impaired NF-�羠 p52 translocation from the cytoplasm to the nucleus. The cell-stimulating effects of N- and R-THP could be abolished by treatment with ��-galactosidase and neuraminidase. It is quite interesting that a potent apoptosis-inducing activity of R-THP on mononuclear cells and PMN was observed. Conclusions: These results suggest that the intact protein core structure, but not carbohydrate side chains, is essential for pleotropic biological/immunological activities of normal THP molecule. On the other hand, in patients undergoing allograft renal transplantation, THP is not only modified in carbohydrate compositions but also capable of inducing mononuclear cells and PMN apoptosis, leading to an impaired immune status in vivo. Taken together, protein core of THP molecule is more important than sugar side chains in normal physiologic condition. Carbohydrate side chain alterations may occur in various pathologic states including renal allograft transplantation.

The thesis deals with possibilities of an application of system dynamics methodics for an understanding and teaching the project management. A dynamic simulation model has been created for this purpose by using Vensim. A web simulator for the project management, which is based on the simulation model, has been created in the next part of the thesis. The benefit of the simulator over the model is its user- friendliness and its self-explanatory graphic interface, which makes it possible to use the simulation model for purposes of teaching and further reaserch in the field of project management. Powered by TCPDF (www.tcpdf.org)