Insight into the urea binding and K166R mutation stabilizing mechanism of TlpB: Molecular dynamics and principal component analysis study

Abstract

Chemoreceptor TlpB(Tlp=transducer-like protein), which has been demonstrated to respond to pH sensing function, is crucial for the survival of Helicobacter pylori(H. pylori) in host stomach. Urea was proposed to be essential for TlpB’s pH sensing function via binding with the Per-ARNT-Sim(PAS) domain of TlpB. Additionally, K166R mutation of the TlpB protein has also been proven to have a similar effect on TlpB pH sensing as urea binding. Although X-ray crystallographic studies have been carried out for urea-bound TlpB, the molecular mechanism for the stabilization of TlpB induced by urea binding and K166R mutation remains to be elucidated. In this study, molecular dynamics simulations combined with principal component analysis(PCA) for the simulation results were used to gain an insight into the molecular mechanism of the stabilization of urea on TlpB protein. The formed H-bonds and salt-bridges surrounding Asp114, which were induced by both urea binding and K166R mutation of TlpB, were important to the stabilization of TlpB by urea. The similarity between the urea binding and K166R mutation as well as their differences in effect has been explicitly demonstrated with computer simulations at atomic-level. The findings may pave the way for the further researches of TlpB.

Keywords

TlpB / Per-ARNT-Sim(PAS) domain / Molecular dynamics simulation / Principal component analysis

References

[1] Blaser M J. EMBO Reports, 2006, 7: 956.

[2] Suerbaum S, Josenhans C. Nature Reviews Microbiology, 2007, 5: 441.

[3] Brown L M. Epidemiologic Reviews, 2000, 22: 283.

[4] Croxen M A, Sisson G, Melano R, Hoffman P S. Journal of Bacteriology, 2006, 188: 2656.

[5] Schreiber S, Konradt M, Groll C, Scheid P, Hanauer G, Werling H O, Josenhans C, Suerbaum S. Proceedings of the National Academy of Sciences of the United States of America, 2004, 101: 5024.

[6] Goers Sweeney E, Henderson J N, Goers J, Wreden C, Hicks K G, Foster J K, Parthasarathy R, Remington S J, Guillemin K. Structure, 2012, 20: 1177.

[7] Desforges J F, Peterson W L. New England Journal of Medicine, 1991, 324: 1043.

[8] Gisbert J P, Khorrami S, Carballo F, Calvet X, Gené E. Cochrane Database of Systematic Reviews, 2004, 2.

[9] Ernst P B, Gold B D. Annual Reviews in Microbiology, 2000, 54: 615.

[10] Fuccio L, Zagari R M, Eusebi L H, Laterza L, Cennamo V, Ceroni L, Grilli D, Bazzoli F. Annals of Internal Medicine, 2009, 151: 121.

[11] El-Omar E M, Carrington M, Chow W H, McColl K E, Bream J H, Young H A, Herrera J, Lissowska J, Yuan C C, Rothman N. Nature, 2000, 404: 398.

[12] Coussens L M, Werb Z. Nature, 2002, 420: 860.

[13] Graham D Y, Lu H, Yamaoka Y. Helicobacter, 2007, 12: 275.

[14] Fischbach L, Evans E. Alimentary Pharmacology & Therapeutics, 2007, 26: 343.

[15] Chey W D, Wong B C. The American Journal of Gastroenterology, 2007, 102: 1808.

[16] Graham D Y. Clinical Gastroenterology and Hepatology, 2009, 7: 145.

[17] Pittman M S, Goodwin M, Kelly D J. Microbiology, 2001, 147: 2493.

[18] Foynes S, Dorrell N, Ward S J, Stabler R A, McColm A A, Rycroft A N, Wren B W. Infection and Immunity, 2000, 68: 2016.

[19] Lowenthal A C, Simon C, Fair A S, Mehmood K, Terry K, Anastasia S, Ottemann K M. Microbiology, 2009, 155: 1181.

[20] Cerda O, Rivas A, Toledo H. FEMS Microbiology Letters, 2003, 224: 175.

[21] Schweinitzer T, Mizote T, Ishikawa N, Dudnik A, Inatsu S, Schreiber S, Suerbaum S, Aizawa S I, Josenhans C. Journal of Bacteriology, 2008, 190: 3244.

[22] Rader B A, Wreden C, Hicks K G, Sweeney E G, Ottemann K M, Guillemin K. Microbiology, 2011, 157: 2445.

[23] Jolliffe I. Principal Component Analysis, 2005, New York: Wiley Online Library.

[24] Discovery Studio, Version 2.5, Accelrys Inc., San Diego, CA, 2009

[25] Hess B, Kutzner C, van der Spoel D, Lindahl E. Journal of Chemical Theory and Computation, 2008, 4: 435.

[26] Oostenbrink C, Villa A, Mark A E, van Gunsteren W F. Journal of Computational Chemistry, 2004, 25: 1656.

[27] Schuttelkopf A W, van Aalten D M. Acta Crystallographica Section D: Biological Crystallography, 2004, 60: 1355.

[28] Darden T, York D, Pedersen L. J. Chem. Phys., 1993, 98: 10089.

[29] Hoover W G. Physical Review A, 1985, 31: 1695.

[30] Hess B, Bekker H, Berendsen H J, Fraaije J G. J. Comput. Chem., 1997, 18: 1463.

[31] Xu Y, Cui Y L, Zheng Q C, Zhang H X, Sun J Z. Chem. J. Chinese Universities, 2013, 34(5): 1226.

[32] Mezei M. J. Comput. Chem., 2010, 31: 2658.

[33] Humphrey W, Dalke A, Schulten K. Journal of Molecular Graphics, 1996, 14: 33.

[34] Pettersen E F, Goddard T D, Huang C C, Couch G S, Greenblatt D M, Meng E C, Ferrin T E. J. Comput. Chem., 2004, 25: 1605.

[35] Amadei A, Linssen A, Berendsen H J. Proteins: Structure, Function and Bioinformatics, 1993, 17: 412.

[36] Garcia A E. Physical Review Letters, 1992, 68: 2696.

[37] Zhou L, Siegelbaum S A. Structure, 2007, 15: 655.