Department of Chemical Sciences, Istituto Officina dei Materiali del Consiglio Nazionale delle Ricerche, UOS SLACS, Italy.
Biophys J. 2012 Mar 7;102(5):1039-48. doi: 10.1016/j.bpj.2012.01.048. Epub 2012 Mar 6.
The novel antimicrobial peptide with a dimeric dendrimer scaffold, SB056, was empirically optimized by high-throughput screening. This procedure produced an intriguing primary sequence whose structure-function analysis is described here. The alternating pattern of hydrophilic and hydrophobic amino acids suggests the possibility that SB056 is a membrane-active peptide that forms amphiphilic β-strands in a lipid environment. Circular dichroism confirmed that the cationic SB056 folds as β-sheets in the presence of anionic vesicles. Lipid monolayer surface pressure experiments revealed unusual kinetics of monolayer penetration, which suggest lipid-induced aggregation as a membranolytic mechanism. NMR analyses of the linear monomer and the dendrimeric SB056 in water and in 30% trifluoroethanol, on the other hand, yielded essentially unstructured conformations, supporting the excellent solubility and storage properties of this compound. However, simulated annealing showed that many residues lie in the β-region of the Ramachandran plot, and molecular-dynamics simulations confirmed the propensity of this peptide to fold as a β-type conformation. The excellent solubility in water and the lipid-induced oligomerization characteristics of this peptide thus shed light on its mechanism of antimicrobial action, which may also be relevant for systems that can form toxic β-amyloid fibrils when in contact with cellular membranes. Functionally, SB056 showed high activity against Gram-negative bacteria and some limited activity against Gram-positive bacteria. Its potency against Gram-negative strains was comparable (on a molar basis) to that of colistin and polymyxin B, with an even broader spectrum of activity than numerous other reference compounds.
新型抗菌肽具有二聚树突状支架结构，SB056 通过高通量筛选得到经验优化。该方法产生了一种有趣的原始序列，其结构-功能分析在此描述。亲水和疏水氨基酸的交替模式表明，SB056 可能是一种膜活性肽，在脂质环境中形成两亲性 β-折叠。圆二色性（CD）确证了阳离子 SB056 在阴离子囊泡存在下折叠成 β-折叠。脂质单层表面压力实验揭示了异常的单层穿透动力学，这表明脂质诱导聚集是一种溶膜机制。另一方面，NMR 分析线性单体和树突状 SB056 在水和 30%三氟乙醇中的结构，得到的基本上是无结构的构象，这支持了该化合物的出色溶解性和储存稳定性。然而，模拟退火表明许多残基位于 Ramachandran 图谱的 β-区域，分子动力学模拟证实了该肽折叠成 β-型构象的趋势。该肽在水中的出色溶解性和脂质诱导的寡聚化特性阐明了其抗菌作用机制，这可能也与接触细胞膜时能形成毒性β-淀粉样纤维的系统有关。在功能上，SB056 对革兰氏阴性菌表现出高活性，对革兰氏阳性菌也有一定的活性。其对革兰氏阴性菌株的效力（以摩尔为基础）与粘菌素和多粘菌素 B 相当，活性谱比许多其他参考化合物更广泛。
