臺灣博碩士論文加值系統

本篇論文包含兩部份研究：第一部分：研究penicillinic acid (Peni) 與clavulanic aicd (Clav) 在鹼性溶液中的化學反應差異性之理論計算。第二部分：鋅金屬離子在蛋白質結構中的統計研究調查與歸納。
為何盤尼西林(penicillin-G)會被-lactamase酵素抑制而Clav 卻具有反抑制-lactamase酵素的功能，為瞭解這些生化過程的細節，我們在這裡選用了Clav及Peni作為模板分子，並利用ab initio與continuum dielectric methods等理論計算方法來計算來決定其反應機構，以瞭解控制這類水解反應的關鍵性因素。另外，一系列的內醯氨環（lactam ring）分子及Peni與Clav中的五員環相對於酵素活性的反應速率決定步驟（rate-limiting step）是否有影響，也將有理論計算作進一步輔助瞭解。Clav 的分子結構與盤尼西林主要差異在第一、第二及第六位置；Peni在分子結構上，除了第六位置無龐大之氨基酸類取代基外，其餘主結構相似於盤尼西林，因此利用當作本次研究盤尼西林的簡化模型；Peni-db除第一位置為硫原子，其餘結構相同於Clav。在此，理論預測的產物分佈、速率決定步驟及鹼性溶液的相對反應速率均有實際實驗值做輔佐。在鹼性溶液水解反應中，Peni，Clav與Peni-db的速率決定步驟均為帶負電之氫氧化物攻擊陰離子反應物而造成四面體中間物（tetrahedral intermediate）的形成。因Clav在第二位置的官能基可促進碳二碳三鍵的旋轉，且氧原子抓銨氫較硫原子更為快速，因此Clav較Peni更有利於形成穩定的中間產物。另外，Clav的第二官能基為拉電子基，在五員環裂解反應中可增加速率決定過度態中碳七的正電荷進而提高利於與氫氧離子靜電作用力（但不是在基態中）。而在Clav中第一位置的氧原子因反應速率過渡態相較於本身的基態有較大的溶媒穩定性，因此對加速反應也有貢獻。在第二級內醯氨環（-lactam）中其固有的四員環與五員環張力對第二級內醯氨分子，如Peni或Clav，並未幫助加速其水解，此理論結果與實驗觀察相符合，因為在速率決定步驟中並未引發四員環第二級內醯氨環或五員環thiazolidine/oxazolidine的裂解。
鋅金屬離子不但在Class B -lactamase扮演酵素催化反應的角色；在高等生物內，是含量最多的過渡態二價金屬。在第三章中，我們從蛋白質結構庫中，選出高解析度的含鋅蛋白質，來做金屬鍵結位置的結構分析。其中，鋅金屬離子分為『具結構』功能及『具催化』功能兩部份，進行第一層鍵結體（1st-shell ligand）及第二層鍵結體（2nd-shell ligand）的整合統計分析。根據蛋白質結構庫調查的結果顯示，具結構功能的鋅金屬離子與具催化功能的在第一層與第一層鍵結體上有明顯的差異。第一層鍵結體分析顯示，Cys對具結構功能的鋅離子而言是出現最多的氨基酸殘基；對具催化功能的鋅離子而言是His。其中，對具結構功能鋅離子而言，第一層Cys與第一層His其外層（也就是鋅金屬的第二層鍵結體）最常出現的是胜肰的骨幹（peptide backbone group）；對具催化功能鋅離子而言，第一層His其外層最常出現的是carboxylate Asp/Glu，且第一層的水分子其外層大多有帶負電的carboxylate Asp/Glu。綜合上述所言，在具結構功能的鋅鍵結位置中，第一層的Cys/His會與第二層的胜肰骨幹形成【Cys/His】：【BKB】作用力；而在具催化功能的鋅鍵結位置中，第一層的His會與第二層的Asp/Glu及BKB形成【His】：【Asp/Glu ,BKB】作用力。經由蛋白質結構庫的調查，這些結果將可當做未來理論計算的實驗依據。

To help elucidate why penicillin-G is inhibited by certain bacterial -lactamase enzymes, whereas clavulanic acid (Clav, which is similar to penicillin-G except at positions 1, 2 and 6) relieves this inhibition, the intrinsic chemical reactivity of these two antibiotics were assessed in this work. Ab initio and continuum dielectric methods were used to map out the gas-phase and solution-phase free energy profiles for the alkaline hydrolyses of Clav and penicillanic acid (Peni, which is similar to penicillin-G except at position 6) as well as a fictitious hybrid compound, Peni-db, which is similar to Clav and Peni except at position 1 and 2, respectively. Furthermore, ring strain energies of various lactam rings and the five-membered ring of Peni and Clav as well as their respective rate-limiting transition states were computed to assess the contribution of four- and five-membered ring strain to the antibiotic’s activity. The predicted product distribution, rate-limiting step, and relative reaction rates for the alkaline hydrolysis of Peni and Clav are in accord with experiment. The rate-limiting step in the alkaline hydrolysis of Peni, Clav or Peni-db is the approach of the negatively charged hydroxide ion toward the anionic reactant to form a tetrahedral intermediate. Alkaline hydrolysis of Clav generates more stable products than that of Peni because the hydroxyethylidene group in Clav facilitates rotation about the C2C3 bond to yield an intermediate where the amide proton is close to the O1 atom, which can abstract it easier than the less polar S1. Clav undergoes basic hydrolysis faster than Peni mainly because its hydroxyethylidene group increases the positive charge on the carbonyl C7 atom in the rate-limiting transition state (but not in the ground state), therefore enhancing favorable electrostatic interactions with the incoming hydroxide anion. To a lesser extent, the oxygen at position 1 in Clav also contributes to the rate acceleration due to greater solvent stabilization of the oxygen-containing transition state as compared to the respective ground state. Inherent strain of the four-membered -lactam ring or five-membered ring does not enhance the alkaline hydrolyses of -lactam molecules such as Peni or Clav, consistent with the observation that the rate-limiting step does not involve breakdown of the four-membered -lactam ring or five-membered thiazolidine/oxazolidine ring.
The geometrical properties of zinc-binding sites in high quality protein X-ray structures deposited in the Protein Data Bank have been examined to identify differences between zinc sites that are directly involved in catalysis (catalytic zinc sites) and those that play only a structural role (structural zinc sites). Ligands in appearing in both structural and catalytic zinc ions are also statistically including. To this end, trends in the 1st- and 2nd-coordination shell were obtained separately for structural and catalytic zinc ions in PDB structures. As expected, the Zn2+ PDB survey shows significant differences between structural and catalytic zinc sites. For structural zinc ion the most common 1st-shell ligand is Cys, whereas for catalytic zinc ions the most abundant zinc-bound ligand is His. The partners for 1st-shell His also differ according to the role/function of zinc. For structural zinc sites, the most abundant His partner is the backbone carbonyl oxygen, whereas for catalytic zinc sites it is the Asp/Glu carboxylate sidechain. For the 1st-shell Cys in structural zinc sites, its most frequent partner in the outer layer is the backbone peptide group. Altogether, for structural zinc sites, the backbone peptide groups dominate the 2nd-shell coordination layer, and [Cys/His]:[BKB] hydrogen bonds could stabilize zinc cores. For catalytic zinc sites, [His]:[Asp/Glu] hydrogen bonds are ubiquitous, indicating a possible role of His in catalysis.

Cahpter 1: Introduction of Antibiotics
Chapter 2: Factors Governing Intrinsic Chemical Reactivity
Differences Between Clavulanic And Penicillanic Acid
Chapter 3: Zinc PDB Survey: Analyses of Zinc Binding Sites in
Protein Crystal Structures
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