Can molecular dynamics and QM/MM solve the penicillin binding protein protonation puzzle?
Can molecular dynamics and QM/MM solve the penicillin binding protein protonation puzzle?
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DOI：
10.1021/ci5000517
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发表时间：
2014-05-27
影响因子：
5.6
通讯作者：
Woodcock HL
中科院分区：
文献类型：
--
作者：
Hargis JC;White JK;Chen Y;Woodcock HL
苄青霉素是β-内酰胺类抗生素的一员，自1947年以来一直被广泛用于对抗细菌感染。一般机制是众所周知的：丝氨酸蛋白酶（即，DD-肽酶）与抗生素的内酰胺环形成持久的中间体，称为酰化，有效地阻止细菌细胞壁的生物合成。尽管有这种总体的机制理解，但结合和催化的许多细节尚不清楚。具体而言，有正在进行的辩论活性位点质子化状态和一般的酸/碱在反应中的作用。在这里，一个独特的组合MD模拟，QM/MM最小化，和QM/MM轨道分析相结合的活性位点残基质子化状态的系统变化。检查使结合的抑制剂的稳定性最大化的关键相互作用并将其用作度量。通过检测头孢西丁与大肠杆菌CTX-M β-内酰胺酶的相互作用，验证了该方法的有效性。大肠杆菌，并与超高分辨率（0.88 μ m）晶体结构进行了比较。在确认所使用的方法后，进行了预酰化的链霉菌R61活性位点与结合的苄青霉素的研究，改变了His 298和Lys 65的质子化状态。我们的结论是质子化的His 298和去质子化的Lys 65最有可能存在于R61活性位点。
Benzylpenicillin, a member of the β-lactam antibiotic class, has been widely used to combat bacterial infections since 1947. The general mechanism is well-known: a serine protease enzyme (i.e., DD-peptidase) forms a long lasting intermediate with the lactam ring of the antibiotic known as acylation, effectively preventing biosynthesis of the bacterial cell wall. Despite this overall mechanistic understanding, many details of binding and catalysis are unclear. Specifically, there is ongoing debate about active site protonation states and the role of general acids/bases in the reaction. Herein, a unique combination of MD simulations, QM/MM minimizations, and QM/MM orbital analyses is combined with systematic variation of active site residue protonation states. Critical interactions that maximize the stability of the bound inhibitor are examined and used as metrics. This approach was validated by examining cefoxitin interactions in the CTX-M β-lactamase from E. coli and compared to an ultra high-resolution (0.88 Å) crystal structure. Upon confirming the approach used, an investigation of the preacylated Streptomyces R61 active site with bound benzylpenicillin was performed, varying the protonation states of His298 and Lys65. We concluded that protonated His298 and deprotonated Lys65 are most likely to exist in the R61 active site.
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影响因子：
4.8
作者：
Golemi-Kotra, D;Meroueh, SO;Mobashery, S
通讯作者：
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DOI：
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发表时间：
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影响因子：
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作者：
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