基于分子动力学模拟研究pH对抗菌肽LL-37结构的影响
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摘要
目的研究溶液p H变化对抗菌肽LL-37结构的影响。方法利用分子动力学模拟方法,采用GROMACS软件包和OPLS-AA力场,分别在中性和强碱性条件下对LL-37进行模拟,总模拟时间达1微秒,最后对模拟轨迹进行分析处理。结果LL-37在中性环境下具有部分螺旋结构存在,特别是N端部分残基,结构具有较大柔性;在强碱性环境下,螺旋含量增多,抗菌核心区域残基形成螺旋结构的几率明显增大,结构稳定性增强。结论 p H值的增大会促进LL-37螺旋结构的形成,螺旋结构的形成和与膜结合是协同的。N端残基易形成螺旋,然后是抗菌核心区域。LL-37在中性环境下的结构特征与其行使多功能的角色相一致。该研究首次分析了LL-37在中性环境下的结构特征及p H的影响,有助于认识其抗菌机制及新药设计。
Objective To study the effect of solution p H on structure characteristics of antibacterial peptide LL-37. Methods Based on molecular dynamics simulations, LL-37 had been simulated with GROMACS software package, OPLS-AA force fi eld and TIP4 P water model under neutral solution and strong alkaline solution, respectively. The simulation time was up to 1 microsecond and the simulation trajectories were analyzed. The conformational characteristics were pictured by the probability of secondary structure formation, root mean square fluctuation of atoms and contact between residues. Results LL-37, especially its N-terminal resi dues of LL-37 formed helical structures under neutral environment, and the structures had high flexibility. Under strong alkaline condition, the helical content increased and the possibility for residues located at antibacterial core region to form helical structure was signifi cantly increased. At the same time, the structure stability was also enhanced. Conclusion For LL-37, the increase of p H value can promote the formation of LL-37 helical structure. The formation of LL-37 helical structure and membrane binding is collaborative. The r esidues located at N terminal are more prone to form a helical structure than others and followed by the residues located at antibacterial core region. The structure characteristics of LL-37 under neutral solution are consistent with its multifunctional role. This work discusses thestructure characteristics in neutral environment and the effect of p H value on structure of LL-37, which is important for understanding the antimicrobial mechanism of LL-37 and new drug design.
Objective To study the effect of solution p H on structure characteristics of antibacterial peptide LL-37. Methods Based on molecular dynamics simulations, LL-37 had been simulated with GROMACS software package, OPLS-AA force fi eld and TIP4 P water model under neutral solution and strong alkaline solution, respectively. The simulation time was up to 1 microsecond and the simulation trajectories were analyzed. The conformational characteristics were pictured by the probability of secondary structure formation, root mean square fluctuation of atoms and contact between residues. Results LL-37, especially its N-terminal resi dues of LL-37 formed helical structures under neutral environment, and the structures had high flexibility. Under strong alkaline condition, the helical content increased and the possibility for residues located at antibacterial core region to form helical structure was signifi cantly increased. At the same time, the structure stability was also enhanced. Conclusion For LL-37, the increase of p H value can promote the formation of LL-37 helical structure. The formation of LL-37 helical structure and membrane binding is collaborative. The r esidues located at N terminal are more prone to form a helical structure than others and followed by the residues located at antibacterial core region. The structure characteristics of LL-37 under neutral solution are consistent with its multifunctional role. This work discusses thestructure characteristics in neutral environment and the effect of p H value on structure of LL-37, which is important for understanding the antimicrobial mechanism of LL-37 and new drug design.
引文
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[23]Wang G,Watson K M,Buckh eit R W,Jr.Anti-human immunodeficiency virus type 1 activities of antimicrobial peptides derived from human and bovine cathelicidins[J].Antimicrob Agents Chemother,2008,52(9):3438-3440.
[24]Li X,Li Y,Han H,et al.Solution structures of human LL-37 fragments and NMR-based identification of a minimal membrane-targeting antimicrobial and anticancer region[J].J Am Chem Soc,2006,128(17):5776-5785.
[25]Oren Z,Lerman J C,Gudmundss on G H,et al.Structure and organization of the human antimicrobial peptide LL-37 in phospholipid membranes:relevance to the molecular basis for its non-cell-selective activity[J].Biochem J,1999,341(Pt 3):501-513.
[26]Glaser R W,Sachse C,Durr U H,et al.Concentrationdependent realignment of the antimicrobial peptide PGLa in lipid membranes observed by solid-state 19F-NMR[J].Biophys J,2005,88(5):3392-3397.
[27]Zhao C,Nguyen T,Boo L M,et al.RL-37,an alpha-helical antimicrobial peptide of the rhesus monkey[J].Antimicrob Agents Chemother,2001,45(10):2695-2702.
[28]赵立岭,王吉华,窦相华,等.蛋白质折叠速度与其拓扑结构关系的研究[J].生物数学学报,2005,20(3):332-338.
[2]Noore J,Noore A,Li B.Cationic antimicrobial peptide LL-37 is effective against both extra-and intracellular Staphylococcus aureus[J].Antimicrob Agents Chemother,2013,57(3):1283-1290.
[3]刘娃,纪森林,宋玉竹.细菌对抗菌肽的耐受机制[J].生命科学,2013,25(10):1008-1014.
[4]Vandamme D,Landuyt B,Luyten W,et al.A comprehensive summary of LL-37,the factotum human cathelicidin peptide[J].Cell Immunol,2012,280(1):22-35.
[5]Tripathi S,Tecle T,Verma A,et al.The human cathelicidin LL-37 inhibits influenza A viruses through a mechanism distinct from that of surfactant protein D or defensins[J].J Gen Virol,2013,94(Pt 1):40-49.
[6]Singh D,Qi R,Jordan J L,et al.The human antimicrobial peptide LL-37,but not the mouse ortholog,m CRAMP,can stimulate signaling by poly(I:C)through a FPRL1-dependent pathway[J].J Biol Chem,2013,288(12):8258-8268.
[7]Salvado M D,Di Gennaro A,Lindbom L,et al.Cathelicidin LL-37 induces angiogenesis via PGE2-EP3 signaling in endothelial cells,in vivo inhibition by Aspirin[J].Arterioscler Thromb Vasc Biol,2013,33(8):1965-1972.
[8]Rivas-Santiago B,Rivas Santiago C E,Castaneda-Delgado J E,et al.Activity of LL-37,CRAMP and antimicrobial peptide-derived compounds E2,E6 and CP26 against Mycobacterium tuberculosis[J].Int J Antimicrob Agents,2013,41(2):143-148.
[9]Rico-Mata R,De Leon-Rodriguez L M,Avila E E.Effect of antimicrobial peptides derived from human cathelicidin LL-37 on Entamoeba histolytica trophozoites[J].Exp Parasitol,2013,133(3):300-306.
[10]P inheiro da Silva F,Medeiros M C,Santos A B,et al.Neutrophils LL-37 migrate to the nucleus during overwhelming infection[J].Tissue Cell,2013,45(5):318-320.
[11]Zasloff M.Antimicrobial peptides of multicellular organisms[J].Nature,2002,415(6870):389-395.
[12]Si ckmeier M,Hamilton J A,Le Gall T,et al.Dis Prot:the database of disordered proteins[J].Nucleic Acids Res,2007,35(suppl 1):D786-793.
[13]Porc elli F,Verardi R,Shi L,et al.NMR structure of the cathelicidin-derived human antimicrobial peptide LL-37 in dodecylphosphocholine micelles[J].Biochemistry,2008,47(20):5565-5572.
[14]Wang G.Structures of human host defense cathelicidin LL-37 and its smallest antimicrobial peptide KR-12 in lipid micelles[J].J Biol Chem,2008,283(47):32637-32643.
[15]Johansso n J,Gudmundsson G H,Rottenberg M E,et al.Conformation-dependent antibacterial activity of the naturally occurring human peptide LL-37[J].J Biol Chem,1998,273(6):3718-3724.
[16]Van Der Sp oel D,Lindahl E,Hess B,et al.GROMACS:fast,flexible,and free[J].J Comput Chem,2005,26(16):1701-1718.
[17]Jorgensen W L,Maxwell D S,Tirado Rives J.Development and testing of the OPLS all-atom force fi eld on conformational energetics and properties of organic liquids[J].J Am Chem Soc,1996,118(45):11225-11236.
[18]Zielkiewicz J.Structural properties of water:comparison of the SPC,SPCE,TIP4P,and TIP5P models of water[J].J Chem Phys,2005,123(10):104501.
[19]Bussi G,Donadio D,Parrinello M.Canonical sampling through velocity rescaling[J].J Chem Phys,2007,126(1):014101.
[20]Berendsen H J,Post ma J P M,van Gunsteren W F,et al.Molecular dynamics with coupling to an external bath[J].J Chem Phys,1984,81(8):3684-3690.
[21]Ryckaert J P,Ciccott i G,Berendsen H J.Numerical integration of the cartesian equations of motion of a system with constraints:molecular dynamics of n-alkanes[J].J Comput Phys,1977,23(3):327-341.
[22]Heinig M,Frishman D.S TRIDE:a web server for secondary structure assignment from known atomic coordinates of proteins[J].Nucleic Acids Res,2004,32(suppl 2):W500-502.
[23]Wang G,Watson K M,Buckh eit R W,Jr.Anti-human immunodeficiency virus type 1 activities of antimicrobial peptides derived from human and bovine cathelicidins[J].Antimicrob Agents Chemother,2008,52(9):3438-3440.
[24]Li X,Li Y,Han H,et al.Solution structures of human LL-37 fragments and NMR-based identification of a minimal membrane-targeting antimicrobial and anticancer region[J].J Am Chem Soc,2006,128(17):5776-5785.
[25]Oren Z,Lerman J C,Gudmundss on G H,et al.Structure and organization of the human antimicrobial peptide LL-37 in phospholipid membranes:relevance to the molecular basis for its non-cell-selective activity[J].Biochem J,1999,341(Pt 3):501-513.
[26]Glaser R W,Sachse C,Durr U H,et al.Concentrationdependent realignment of the antimicrobial peptide PGLa in lipid membranes observed by solid-state 19F-NMR[J].Biophys J,2005,88(5):3392-3397.
[27]Zhao C,Nguyen T,Boo L M,et al.RL-37,an alpha-helical antimicrobial peptide of the rhesus monkey[J].Antimicrob Agents Chemother,2001,45(10):2695-2702.
[28]赵立岭,王吉华,窦相华,等.蛋白质折叠速度与其拓扑结构关系的研究[J].生物数学学报,2005,20(3):332-338.