Caerin的二维HP折叠结构
2-Dimensional HP Folding Structures of Caerin
DOI: 10.12677/hjcb.2012.24004, PDF, HTML,    科研立项经费支持
作者: 王何健, 严少敏, 吴光#：广西科学院非粮生物质国家重点实验室
关键词: Caerin；折叠结构；HP模型；疏水性指标；最小能量；Caerin; Folding Structure; HP Model; Hydrophobicity Index; Minimal Energy
摘要: 采用标准化氨基酸疏水性指数将7种Caerins的氨基酸序列转换为28种疏水性(H)或极性(P)的序列，通过二维疏水性–极性(HP)模型分析其全部可能的折叠结构。结果显示Caerins有许多具有相同最小能量的天然形态，这些形态有各种各样对称的折叠结构，而且这些天然形态可以根据标准化的氨基酸疏水性指标进一步从数值上加以区分。这项研究从疏水性–极性角度揭示了Caerin折叠结构的多样性，有助于理解蛋白质的折叠过程，并提示通过工程学方法修改抗菌肽的可能途径。
Abstract: The amino acid sequences of 7 Caerins were converted into 28 hydrophobic (H) or polar (P) sequences according to the normalized amino acid hydrophobicity index, and all of their possible folding structures were analyzed using 2D hydrophobic-polar (HP) model. The results showed that Caerins have many native states with the same mini- mal energy, which consist of various symmetric folding structures, and that the normalized amino acid hydrophobicity index can help furthermore distinguish native states numerically. The study demonstrates the diversity of Caerin folding structures from hydrophobic-polar (HP) angle, which can shed light on understanding folding process of protein and implying possible ways to modify antimicrobial peptides through engineering.
文章引用：王何健, 严少敏, 吴光. Caerin的二维HP折叠结构[J]. 计算生物学, 2012, 2(4): 34-41. http://dx.doi.org/10.12677/hjcb.2012.24004

参考文献

[1] D. Bilusich, R. J. Jackway, I. F. Musgrave, et al. The host-de- fence skin peptide profiles of Peron’s tree frog Litoria peronii in winter and summer. Sequence determination by electrospray mass spectrometry and activities of the peptides. Rapid Com- munications in Mass Spectrometry, 2009, 23(17): 2628-2636.
[2] C. S. Chia, Y. Gong, J. H. Bowie, et al. Membrane binding and perturbation studies of the antimicrobial peptides Caerin, citro- pin, and maculatin. Biopolymers, 2011, 96(2): 147-157.
[3] R. Chen, A. E. Mark. The effect of membrane curvature on the conformation of antimicrobial peptides: impli-cations for binding and the mechanism of action. European Biophysics Journal with Biophysics Letters, 2011, 40(4): 545-553.
[4] T. Wang, H. J. Andreazza, T. L. Pukala, et al. His-tidine-contain- ing host-defence skin peptides of anurans bind Cu2+. An electro- spray ionisation mass spectrometry and computational model- ling study. Rapid Communications in Mass Spectrometry, 2011, 25(9): 1209-1221.
[5] P. J. Sherman, R. J. Jackway, E. Nicholson, et al. Activities of seasonably variable caerulein and rothein skin peptides from the tree frogs Litoria splendida and Litoria rothii. Toxicon, 2009, 54(6): 828-835.
[6] K. F. Lau, K. A. Dill. A lattice statistical mechanics model of the conformation and sequence spaces of proteins. Macromolecules, 1989, 22(10): 3986-3997.
[7] B. Berger, T. Leight. Protein folding in the hydrophobic-hydro- philic (HP) model is NP-complete. Journal of Computational Biology, 1998, 5(1): 27-40.
[8] Wikimedia Foundation Inc. Wikipedia, the free encyclopedia, 2012. http://en.wikipedia.org/wiki/Millennium_Prize_Problems
[9] A. Shmygelska, H. H. Hoons. An ant colony optimisation algo- rithm for the 2D and 3D hydrophobic polar protein folding problem. BMC Bioinformatics, 2005, 6: 30.
[10] R. B. Lyngsø, C. N. Pedersen. RNA pseudoknot prediction in energy-based models. Journal of Computational Biology, 2000, 7(3-4): 409-427.
[11] G. Wang, X. Li and Z. Wang. APD2: The updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Research, 2009, 37(Database issue): D933-D937.
[12] The UniProt Consortium. The universal protein resource (UniProt) in 2010. Nucleic Acids Research, 2010, 38(Database Issue): D142-D148.
[13] Sigma-Aldrich Co. LLC. Hydrophobicity index for common amino acids, 2012. http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/amino-acid-reference-chart.html
[14] S. Govindarajan, R. A. Goldstein. On the thermodynamic hypo- thesis of protein folding. Proceedings of the National Academy of Sciences of the United States of America, 1998, 95(10): 5545- 5549.
[15] T. L. Pukala, T. Urathamakul, S. J. Watt, et al. Binding studies of nNOS-active amphibian peptides and Ca2+ calmodulin, using negative ion electrospray ionisation mass spectrometry. Rapid Communications in Mass Spectrometry, 2008, 22(22): 3501- 3509.
[16] S. Yan, G. Wu. Analysis on folding of misgurin using 2-dimen- sional HP model. Proteins: Structure, Function, and Bioinforma- tics, 2012, 80(3): 764-773.
[17] S. Yan, G. Wu. Detailed folding structures of M-lycotoxin-Hc1a and its mutageneses using 2-dimensional HP model. Molecular Simulation, 2012, 38(10): 809-822.
[18] S. Yan, G. Wu. Detailed folding structures of Kappa-conotoxin RIIIJ and its mutageneses obtained from 2-dimensional HP model. Protein and Peptide Letters, 2012, 19(5): 567-572.

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