Nhiều vai trò của histidine trong tương tác protein
Tóm tắt
Trong số 20 axit amin tự nhiên, histidine là thành viên hoạt động và linh hoạt nhất, đóng nhiều vai trò trong các tương tác protein, thường là dư lượng chủ chốt trong các phản ứng xúc tác enzyme. Một nghiên cứu lý thuyết và toàn diện về các đặc trưng cấu trúc và tính chất tương tác của histidine chắc chắn sẽ hữu ích.
Bốn loại tương tác của histidine được tính toán một cách định lượng, bao gồm: (1) Tương tác cation-π, trong đó histidine đóng vai trò như là motif π thơm ở dạng trung tính (His), hoặc đóng vai trò cation trong dạng proton hóa (His+); (2) Tương tác xếp chồng π-π giữa histidine và các axit amin thơm khác; (3) Tương tác hydro-π giữa histidine và các axit amin thơm khác; (4) Tương tác phối hợp giữa histidine và các cation kim loại. Năng lượng của các tương tác xếp chồng π-π và hydro-π được tính toán bằng phương pháp CCSD/6-31+G(d,p). Năng lượng của các tương tác cation-π và tương tác phối hợp được tính toán bằng phương pháp B3LYP/6-31+G(d,p) và điều chỉnh bằng phương pháp thực nghiệm cho năng lượng phân tán.
Các tương tác phối hợp giữa histidine và các cation kim loại là mạnh nhất và hoạt động trong một phạm vi rộng, tiếp theo là các tương tác cation-π, hydro-π, và xếp chồng π-π. Khi histidine ở dạng trung tính, các tương tác cation-π có tính hấp dẫn; khi nó bị proton hóa (His+), các tương tác chuyển thành đẩy. Hai dạng proton hóa (và giá trị pKa) của histidine được chuyển đổi một cách thuận nghịch bởi các tương tác cation-π hấp dẫn và đẩy. Trong protein, tương tác xếp chồng π-π giữa histidine trung tính và các axit amin thơm (Phe, Tyr, Trp) nằm trong khoảng từ -3.0 đến -4.0 kcal/mol, lớn hơn đáng kể so với năng lượng van der Waals.
Từ khóa
Tài liệu tham khảo
Martínez A: Evidence for a functionally important histidine residue in human tyrosine hydroxylase. Amino Acids. 1995, 9: 285-292. 10.1007/BF00805959.
Uchida K: Histidine and lysine as targets of oxidative modification. Amino Acids. 2003, 25: 249-257. 10.1007/s00726-003-0015-y.
Remko M, Fitz D, Rode BM: Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+ and Zn2+) and water coordination on the structure and properties of l-histidine and zwitterionic l-histidine. Amino Acids. 2010, 39: 1309-1319. 10.1007/s00726-010-0573-8.
Li F, Fitz D, Fraser DG, Rode BM: Catalytic effects of histidine enantiomers and glycine on the formation of dileucine and dimethionine in the salt-induced peptide formation reaction. Amino Acids. 2010, 38: 287-294. 10.1007/s00726-009-0249-4.
Agnieszka M, Janina KW, Katarzyna KK: Five-membered heterocycles. Part III. Aromaticity of 1,3-imidazole in 5+n hetero-bicyclic molecules. J Mol Struc. 2003, 655: 397-403. 10.1016/S0022-2860(03)00282-5.
Doğan A, Özel AD, Kılıç E: The protonation equilibria of selected glycine dipeptides in ethanol–water mixture: solvent composition effect. Amino Acids. 2009, 36: 373-379. 10.1007/s00726-008-0054-5.
Priyakumar UD, Punnagai M, Krishna Mohan GP, Sastry GN: A computational study of cation-π interactions in polycyclic systems: exploring the dependence on the curvature and electronic factors. Tetrahedron. 2004, 60: 3037-3043. 10.1016/j.tet.2004.01.086.
Reddy AS, Sastry GN: Cation [M = H+, Li+, Na+, K+, Ca2+, Mg2+, NH4+, and NMe4+] interactions with the aromatic motifs of naturally occurring amino acids: A theoretical study. J Phys Chem A. 2005, 109: 8893-8903. 10.1021/jp0525179.
Engerer LK, Hanusa TP: Geometric Effects in Olefinic Cation−π Interactions with Alkali Metals: A Computational Study. J Org Chem. 2011, 76: 42-49. 10.1021/jo101307z.
Hunter CA, Lawson KR, Perkins J, Urch CJ: Aromatic interactions. J Chem Soc Perkin Trans. 2001, 2: 651-669.
Crowley PB, Golovin A: Cation–π interactions in protein–protein interfaces. Proteins. 2005, 59: 231-239. 10.1002/prot.20417.
Vijay D, Sastry GN: Exploring the size dependence of cyclic and acyclic π-systems on cation-π binding. Phys Chem Chem Phys. 2008, 10: 582-590. 10.1039/b713703f.
Matsumura H, Yamamoto T, Leow TC, Mori T, Salleh AB, Basri M, Inoue T, Kai Y, Zaliha RN, Rahman RA: Novel cation-π interaction revealed by crystal structure of thermoalkalophilic lipase. Proteins. 2008, 70: 592-598.
Reddy AS, Zipse H, Sastry GN: Cation-π Interactions of Bare and Coordinatively Saturated Metal Ions: Contrasting Structural and Energetic Characteristics. J Phys Chem B. 2007, 111: 11546-11553. 10.1021/jp075768l.
Schottel BL, Chifotides HT, Dunbar KR: Anion-π interactions.Chem Soc Rev. 2008, 37: 68-83. 10.1039/b614208g.
Burley SK, Petsko GA: Amino-aromatic interactions in proteins. FEBS Lett. 1986, 203: 139-143. 10.1016/0014-5793(86)80730-X.
Stefan G: Do special noncovalent π-π stacking interactions really exist?. Angew Chem Int Ed. 2008, 47: 3430-3434. 10.1002/anie.200705157.
Mignon P, Loverix S, Steyaert J, Geerlings P: Influence of the π–π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases. Nucl Acids Res. 2005, 33: 1779-1789. 10.1093/nar/gki317.
Petitjean A, Khoury RG, Kyritsakas N, Lehn JM: Dynamic devices, shape switching and substrate binding in ion-controlled nanomechanical molecular tweezers. J Am Chem Soc. 2004, 126: 6637-6647. 10.1021/ja031915r.
Sygula A, Fronczek FR, Sygula R, Rabideau PW, Olmstead MM: A Double Concave Hydrocarbon Buckycatcher. J Am Chem Soc. 2007, 129: 3842-3843. 10.1021/ja070616p.
Janiak C: A critical account on π-π stacking in metal complexes with aromatic nitrogen-containing ligands. J Chem Soc Dalton Trans. 2000, 3885-3896.
Meyer EA, Castellano RK, Diederich F: Interactions with aromatic rings in chemical and biological recognition. Angew Chem Int Ed. 2003, 42: 1210-1250. 10.1002/anie.200390319.
Hughes RM, Waters ML: Effects of lysine acylation in a β-hairpin peptide: comparison of an amide-π and a cation-π interaction. J Am Chem Soc. 2006, 128: 13586-13591. 10.1021/ja0648460.
Kang SO, Hossain MA, Bowman-James K: Influence of dimensionality and charge on anion binding in amide-based macrocyclic receptors. Coord Chem Rev. 2000, 250: 3038-3052.
Miessler GL, Tarr DA: Inorganic Chemistry. 2003, Upper Saddle River, NJ: Pearson Prentice Hall, 3
Smith MB, March J: March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure. 2007, New York: Wiley-Interscience, 6
Jackson WG, Josephine AM, Silvia C: Alfred Werner's inorganic counterparts of racemic and mesomeric tartaric acid: A milestone revisited. Inorg Chem. 2004, 43: 6249-6254. 10.1021/ic040042e.
Sirois SW, Proynov EI, Truchon JF, Tsoukas CM, Salahub DR: A density functional study of the hydrogen-bond network within the HIV-1 protease catalytic site cleft. J Comput Chem. 2003, 24: 1110-1119. 10.1002/jcc.10176.
Du QS, Li DP, Liu PJ, Huang RB: Molecular potential energies in dodecahedron cell of methane hydrate and dispersion correction for DFT. J Mol Graph Model. 2008, 27: 140-146. 10.1016/j.jmgm.2008.03.008.
Henry M: Thermodynamics of hydrogen bond patterns in supramolecular assemblies of water molecules. Chem Phys Chem. 2002, 3: 607-616. 10.1002/1439-7641(20020715)3:7<607::AID-CPHC607>3.0.CO;2-A.
Henry M: Nonempirical quantification of molecular interactions in supramolecular assemblies. Chem Phys Chem. 2002, 3: 561-569. 10.1002/1439-7641(20020715)3:7<561::AID-CPHC561>3.0.CO;2-E.
Andrews LJ, Keefer RM: Molecular complexes in organic chemistry. 1964, San Francisco: Holden-Day
Mezey PG: Macromolecular density matrices and electron densities with adjustable nuclear geometries. J Math Chem. 1995, 18: 141-168. 10.1007/BF01164655.
Mezey PG: Quantum similarity measures and Löwdin's transform for approximate density matrices and macromolecular forces. Int J Quantum Chem. 1997, 63: 39-48. 10.1002/(SICI)1097-461X(1997)63:1<39::AID-QUA8>3.0.CO;2-3.
Sayyed FB, Suresh CH: Accurate prediction of cation−π interaction energy using substituent effects. J Phys Chem A. 2012, 116: 5723-5732. 10.1021/jp3034193.
Mohan N, Vijayalalakshmi KP, Koga N, Suresh CH: Comparison of aromatic NH…π, OH…π, and CH…π interactions of alanine using MP2, CCSD, and DFT methods. J Comput Chem. 2010, 31: 2874-2882.
Gresh N, Kafafi SA, Truchon JF, Salahub DR: Intramolecular interaction energies in model alanine and glycine tetrapeptides. Evaluation of anisotropy, polarization, and correlation effects. A parallel ab initio HF/MP2, DFT, and polarizable molecular mechanics study. J Compt Chem. 2004, 25: 823-834. 10.1002/jcc.20012.
Jurecka P, Cerný J, Hobza P, Salahub DR: Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations. J Comput Chem. 2007, 28: 555-569. 10.1002/jcc.20570.
Van Mourik T, Gdanitz RJ: A critical note on density functional theory studies on rare-gas dimers. J Chem Phys. 2002, 116: 9620-9623. 10.1063/1.1476010.
Morgado C, Vincent MA, Hillier IH, Shan X: Can the DFT-D method describe the full range of noncovalent interactions found in large biomolecules?. Phys Chem Chem Phys. 2007, 9: 448-451. 10.1039/b615263e.
Von Lilienfeld OA, Tavernelli I, Rothlisberger U, Sebastiani D: Optimization of effective atom centered potentials for London dispersion forces in density functional theory. Phys Rev Lett. 2004, 93: 153004-153007.
Du Q-S, Liu P-J, Deng J: Empirical correction to molecular interaction energies in density functional theory (DFT) for methane hydrate simulation. J Chem Theory Comput. 2007, 3: 1665-1672. 10.1021/ct700026d.
Purvis GD, Bartlett RJ: A full coupled-cluster singles and doubles model: The inclusion of disconnected triples. J Chem Phys. 1982, 76: 1910-1919. 10.1063/1.443164.
Lee TJ, Rice JE: An efficient closed-shell singles and doubles coupled-cluster method. Chem Phys Lett. 1988, 23: 406-415.
Scuseria GE, Schaefer HF: Is coupled cluster singles and doubles (CCSD) more computationally intensive than quadratic configuration interaction (QCISD)?. J Chem Phys. 1989, 90: 3700-3703. 10.1063/1.455827.
Scuseria GE, Janssen CL, Schaefer HF: An efficient reformulation of the closed-shell coupled cluster single and double excitation (CCSD) equations. J Chem Phys. 1988, 89: 7382-7388. 10.1063/1.455269.
Grimme S: Semiempirical hybrid density functional with perturbative second-order correlation. J Chem Phys. 2006, 124: 034108-10.1063/1.2148954.
Zimmerli U, Parrinello M, Koumoutsakos P: Dispersion corrections to density functionals for water aromatic interactions. J Chem Phys. 2004, 120: 2693-2699. 10.1063/1.1637034.
Grimme S: Accurate description of van der Waals complexes by density functional theory including empirical corrections. J Comput Chem. 2004, 25: 1463-1473. 10.1002/jcc.20078.
Miertus S, Scrocco E, Tomasi J: Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects. Chem Phys. 1981, 55: 117-129. 10.1016/0301-0104(81)85090-2.
Amovilli C, Barone V, Cammi R, Cances E, Cossi M, Mennucci B, Pomelli CS, Tomasi J: Recent advances in the description of solvent effects with the polarizable continuum model. Adv Quant Chem. 1998, 32: 227-262.
Cossi M, Barone V: Analytical second derivatives of the free energy in solution by polarizable continuum models. J Chem Phys. 1998, 109: 6246-6254. 10.1063/1.477265.
Foresman JB, Keith TA, Wiberg KB, Snoonian J, Frisch MJ: Solvent effects. 5. influence of cavity shape, truncation of electrostatics, and electron correlation on ab initio reaction field calculations. J Phys Chem. 1996, 100: 16098-16104. 10.1021/jp960488j.
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA: Gaussian 09, Revision B,01. 2010, Wallingford CT: Gaussian Inc
Zielkiewicz J: Structural properties of water: Comparison of the SPC, SPCE, TIP4P, and TIP5P models of water. J Chem Phys. 2005, 123: 104501-10.1063/1.2018637.
Markovitch O, Agmon N: Structure and energetics of the hydronium hydration shells. J Phys Chem A. 2007, 111: 2253-2256. 10.1021/jp068960g.
Du QS, Long SY, Meng JZ, Huang RB: Empirical formulation and parameterization of cation-π interactions for protein modeling. J Compt Chem. 2012, 33: 153-162. 10.1002/jcc.21951.
Du QS, Liao SM, Meng JZ, Huang RB: Energies and Physicochemical Properties of Cation-π Interactions in Biology Structures. J Mol Graph Model. 2012, 34: 38-45.
Olsson MHM, Søndergaard CR, Rostkowski M, Jensen JH: PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions. J Chem Theory Comput. 2011, 7: 525-537. 10.1021/ct100578z.
Huang RB, Du QS, Wang CH, Liao SM, Chou KC: A fast and accurate method for predicting pKa of residues in proteins. Protein Eeng Des Sel. 2010, 23: 35-42. 10.1093/protein/gzp067.
Ottiger P, Pfaffen C, Leist R, Leutwyler S, Bachorz RA, Klopper W: Strong N−H···π Hydrogen Bonding in Amide−Benzene Interactions. J Phys Chem B. 2009, 113: 2937-2943. 10.1021/jp8110474.
Steiner T, Koellner G: Hydrogen bonds with pi-acceptors in proteins: frequencies and role in stabilizing local 3D structures. J Mol Biol. 2001, 305: 535-557. 10.1006/jmbi.2000.4301.
Trakhanov S, Quiocho FA: Influence of divalent cations in protein crystallization. Protein Sci. 1995, 4: 1914-1919. 10.1002/pro.5560040925.
Fischer M, Pleiss J: The Lipase Engineering Database: a navigation and analysis tool for protein families. Nucleic Acids Res. 2003, 31: 319-321. 10.1093/nar/gkg015.
Bas DC, Rogers DM, Jensen JH: Very fast prediction and rationalization of pKa values for protein-ligand complexes. Proteins. 2008, 73: 765-783. 10.1002/prot.22102.
Li H, Robertson AD, Jensen JH: Very fast empirical prediction and rationalization of protein pKa values. Proteins. 2005, 6: 704-721.
Badger MR, Price GD: The role of carbonic anhydrase in photosynthesis. Annu Rev Plant Physio Plant Mol Bio. 1994, 45: 369-392. 10.1146/annurev.pp.45.060194.002101.
Lindskog S: Structure and mechanism of carbonic anhydrase. Pharmacol Ther. 1997, 74: 1-20. 10.1016/S0163-7258(96)00198-2.
Biot C, Buisine E, Rooman M: Free-energy calculations of protein-ligand cation-π and amino-π interactions: From vacuum to protein-like environments. J Am Chem Soc. 2003, 125: 13988-13994. 10.1021/ja035223e.