Understanding structure-based dynamic interactions of antihypertensive peptides extracted from food sources

References

• Antunes, D. A., Moll, M., Devaurs, D., Jackson, K. R., Lizée, G., & Kavraki, L. E. (2017). DINC 2.0: A new protein–peptide docking webserver using an incremental approach. Cancer Research, 77(21), e55–e57. doi:10.1158/0008-5472.CAN-17-0511
   PubMed Web of Science ®Google Scholar
• Assaran Darban, R., Shareghi, B., Asoodeh, A., & Chamani, J. (2017). Multi-spectroscopic and molecular modeling studies of interaction between two different angiotensin I converting enzyme inhibitory peptides from gluten hydrolysate and human serum albumin. Journal of Biomolecular Structure and Dynamics, 35(16), 3648–3662. doi:10.1080/07391102.2016.1264892
   PubMed Web of Science ®Google Scholar
• Bhattacharya, S., Bhattacharya, S., Gachhui, R., Hazra, S., & Mukherjee, J. (2019). U32 collagenase from Pseudoalteromonas agarivorans NW4327: Activity, structure, substrate interactions and molecular dynamics simulations. International Journal of Biological Macromolecules, 124, 635–650. doi:10.1016/j.ijbiomac.2018.11.206
   PubMed Web of Science ®Google Scholar
• Brunner, H. R., Gavras, H., Waeber, B., Kershaw, G. R., Turini, G. A., Vukovich, R. A., … Gavras, I. (1979). Oral angiotensin-converting enzyme inhibitor in long-term treatment of hypertensive patients. Annals of Internal Medicine, 90(1), 19–23. doi:10.7326/0003-4819-90-1-19
   PubMed Web of Science ®Google Scholar
• Chakrabarti, S., Guha, S., & Majumder, K. (2018). Food-derived bioactive peptides in human health: Challenges and opportunities. Nutrients, 10(11), 1738. doi:10.3390/nu10111738
   PubMed Web of Science ®Google Scholar
• Cushman, D. W., & Cheung, H. S. (1971). Spectrophotometric assay and properties of the angiotensin-converting enzyme of rabbit lung. Biochemical Pharmacology, 20(7), 1637–1648. doi:10.1016/0006-2952(71)90292-9
   PubMed Web of Science ®Google Scholar
• Darden, T., Perera, L., Li, L., & Pedersen, L. (1999). New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure, 7(3), R55–R60. doi:10.1016/S0969-2126(99)80033-1
   PubMed Web of Science ®Google Scholar
• DeLeon, K. Y., Patel, A. P., Kuczera, K., Johnson, C. K., & Jas, G. S. (2012). Structure and reorientational dynamics of angiotensin I and II: A microscopic physical insight. Journal of Biomolecular Structure and Dynamics, 29(6), 1175–1194. doi:10.1080/07391102.2011.672631
   Web of Science ®Google Scholar
• Ehlers, M. R. W., & Riordan, J. F. (1989). Angiotensin-converting enzyme: New concepts concerning its biological role. Biochemistry, 28(13), 5311–5318. doi:10.1021/bi00439a001
   PubMed Web of Science ®Google Scholar
• FitzGerald, R. J., & Meisel, H. (2000). Milk protein-derived peptide inhibitors of angiotensin-I-converting enzyme. British Journal of Nutrition, 84(S1), 33–37. doi:10.1017/S0007114500002221
   PubMed Web of Science ®Google Scholar
• Fujita, H., & Yoshikawa, M. (1999). LKPNM: A prodrug-type ACE-inhibitory peptide derived from fish protein. Immunopharmacology, 44(1-2), 123–127. doi:10.1016/S0162-3109(99)00118-6
   PubMed Web of Science ®Google Scholar
• Guan, S., Han, W., Zhang, H., Wang, S., & Shan, Y. (2016). Insight into the interactive residues between two domains of human somatic Angiotensin-converting enzyme and Angiotensin II by MM-PBSA calculation and steered molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 34(1), 15–28. doi:10.1080/07391102.2015.1007167
   PubMed Web of Science ®Google Scholar
• Halgren, T. A. (1996). Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. Journal of Computational Chemistry, 17(5-6), 490–519. doi:10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P
   Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Hooper, N. M. (1991). Angiotensin converting enzyme: Implications from molecular biology for its physiological functions. International Journal of Biochemistry, 23(7-8), 641–647. doi:10.1016/0020-711X(91)90032-I
   PubMedGoogle Scholar
• Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65(3), 712–725. doi:10.1002/prot.21123
   PubMed Web of Science ®Google Scholar
• Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in Science & Engineering, 9(3), 90–95. doi:10.1109/MCSE.2007.55
   Web of Science ®Google Scholar
• Iroyukifujita, H., Eiichiyokoyama, K., & Yoshikawa, M. (2000). Classification and antihypertensive activity of angiotensin I-converting enzyme inhibitory peptides derived from food proteins. Journal of Food Science, 65(4), 564–569. doi:10.1111/j.1365-2621.2000.tb16049.x
   Web of Science ®Google Scholar
• Jalkute, C. B., Barage, S. H., Dhanavade, M. J., & Sonawane, K. D. (2015). Identification of angiotensin converting enzyme inhibitor: An in silico perspective. International Journal of Peptide Research and Therapeutics, 21(1), 107–115. doi:10.1007/s10989-014-9434-8
   Web of Science ®Google Scholar
• Jmol. (2008). Jmol: An open-source Java viewer for chemical structures in 3D. Jmol Web Page. Retrieved from http://www.jmol.org/
   Google Scholar
• Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22(12), 2577–2637. doi:10.1002/bip.360221211
   PubMed Web of Science ®Google Scholar
• Kalyan, G., Junghare, V., Chattopadhyay, A., Mitra, P., & Hazra, S. (2019). Parsers, data structures and algorithms for Macromolecular Analysis Toolkit (MAT): Design and implementation. BioRxiv, 605907.
   Google Scholar
• Karplus, M., & Kushick, J. N. (1981). Method for estimating the configurational entropy of macromolecules. Macromolecules, 14(2), 325–332. doi:10.1021/ma50003a019
   Web of Science ®Google Scholar
• Kecel-Gündüz, S., Budama-Kilinc, Y., Cakir Koc, R., Kökcü, Y., Bicak, B., Aslan, B., & Özel, A. E. (2018). Computational design of Phe-Tyr dipeptide and preparation, characterization, cytotoxicity studies of Phe-Tyr dipeptide loaded PLGA nanoparticles for the treatment of hypertension. Journal of Biomolecular Structure and Dynamics, 36(11), 2893–2907. doi:10.1080/07391102.2017.1371644
   PubMed Web of Science ®Google Scholar
• Kohmura, M., Nio, N., Kubo, K., Minoshima, Y., Munekata, E., & Ariyoshi, Y. (1989). Inhibition of angiotensin-converting enzyme by synthetic peptides of human $β$-casein. Agricultural and Biological Chemistry, 53(8), 2107–2114. doi:10.1080/00021369.1989.10869621
   Web of Science ®Google Scholar
• Kuhn, B., & Kollman, P. A. (2000). Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. Journal of Medicinal Chemistry, 43(20), 3786–3791. doi:10.1021/jm000241h
   PubMed Web of Science ®Google Scholar
• Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6), 1547–1549. doi:10.1093/molbev/msy096
   PubMed Web of Science ®Google Scholar
• Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., … Higgins, D. G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23(21), 2947–2948. doi:10.1093/bioinformatics/btm404
   PubMed Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. doi:10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Majumder, K., & Wu, J. (2011). Purification and characterisation of angiotensin I converting enzyme (ACE) inhibitory peptides derived from enzymatic hydrolysate of ovotransferrin. Food Chemistry, 126(4), 1614–1619. doi:10.1016/j.foodchem.2010.12.039
   PubMed Web of Science ®Google Scholar
• Maro, D. D., Scarselli, M., Bernini, A., Cresti, S., Rossolini, G. M., Lozzi, L., … Niccolai, N. (1999). On the structural stability of a small bioactive peptide of potential use in biotechnology. Journal of Biomolecular Structure and Dynamics, 16(5), 1053–1059. doi:10.1080/07391102.1999.10508314
   PubMed Web of Science ®Google Scholar
• Masuyer, G., Schwager, S. L. U., Sturrock, E. D., Isaac, R. E., & Acharya, K. R. (2012). Molecular recognition and regulation of human angiotensin-I converting enzyme (ACE) activity by natural inhibitory peptides. Scientific Reports, 2 (1), 717. doi:10.1038/srep00717
   PubMed Web of Science ®Google Scholar
• Matsufuji, H., Matsui, T., Seki, E., Osajima, K., Nakashima, M., & Osajima, Y. (1994). Angiotensin I-converting enzyme inhibitory peptides in an alkaline protease hydrolyzate derived from sardine muscle. Bioscience, Biotechnology, and Biochemistry, 58(12), 2244–2245. doi:10.1271/bbb.58.2244
   PubMed Web of Science ®Google Scholar
• Miyamoto, S., & Kollman, P. A. (1992). Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 13(8), 952–962. doi:10.1002/jcc.540130805
   Web of Science ®Google Scholar
• O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. doi:10.1186/1758-2946-3-33
   PubMed Web of Science ®Google Scholar
• Pall, S., Abraham, M. J., Kutzner, C., Hess, B., & Lindahl, E. (2014). Tackling exascale software challenges in molecular dynamics simulations with GROMACS. International Conference on Exascale Applications and Software, 3–27.
   Google Scholar
• Paul, M., Hazra, M., Barman, A., & Hazra, S. (2014). Comparative molecular dynamics simulation studies for determining factors contributing to the thermostability of chemotaxis protein “CheY”. Journal of Biomolecular Structure and Dynamics, 32(6), 928–949. doi:10.1080/07391102.2013.799438
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. doi:10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Rastelli, G., Rio, A., Degliesposti, G., & Sgobba, M. (2010). Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. Journal of Computational Chemistry, 31(4), 797–810. doi:10.1002/jcc.21372
   PubMed Web of Science ®Google Scholar
• Schrödinger LLC. (2015). The {PyMOL} Molecular Graphics System, Version∼1.8.
   Google Scholar
• Swanson, J. M. J., Henchman, R. H., & McCammon, J. A. (2004). Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophysical Journal, 86(1), 67–74. doi:10.1016/S0006-3495(04)74084-9
   PubMed Web of Science ®Google Scholar
• Tanzadehpanah, H., Asoodeh, A., Saidijam, M., Chamani, J., & Mahaki, H. (2018). Improving efficiency of an angiotensin converting enzyme inhibitory peptide as multifunctional peptides. Journal of Biomolecular Structure and Dynamics, 36(14), 3803–3818. doi:10.1080/07391102.2017.1401001
   PubMed Web of Science ®Google Scholar
• Tian, W., Chen, C., Lei, X., Zhao, J., & Liang, J. (2018). CASTp 3.0: Computed atlas of surface topography of proteins. Nucleic Acids Research, 46(W1), W363–W367. doi:10.1093/nar/gky473
   PubMed Web of Science ®Google Scholar
• Touw, W. G., Baakman, C., Black, J., Te Beek, T. A. H., Krieger, E., Joosten, R. P., & Vriend, G. (2015). A series of PDB-related databanks for everyday needs. Nucleic Acids Research, 43(D1), D364–D368. doi:10.1093/nar/gku1028
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. doi:10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Vaught, A. (1996). Graphing with Gnuplot and Xmgr: Two graphing packages available under linux. Linux Journal, 1996(28es), 7.
   Google Scholar
• Vermeirssen, V., Van Camp, J., & Verstraete, W. (2004). Bioavailability of angiotensin I converting enzyme inhibitory peptides. British Journal of Nutrition, 92(3), 357–366. doi:10.1079/BJN20041189
   PubMed Web of Science ®Google Scholar
• Wanasundara, P. K. J. P. D., Ross, A. R. S., Amarowicz, R., Ambrose, S. J., Pegg, R. B., & Shand, P. J. (2002). Peptides with angiotensin I-converting enzyme (ACE) inhibitory activity from defibrinated, hydrolyzed bovine plasma. Journal of Agricultural and Food Chemistry, 50(24), 6981–6988. doi:10.1021/jf025592e
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. doi:10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Wang, W., McKinnie, S. M. K., Farhan, M., Paul, M., McDonald, T., McLean, B., … Oudit, G. Y. (2016). Angiotensin-converting enzyme 2 metabolizes and partially inactivates Pyr-Apelin-13 and Apelin-17Novelty and significance. Hypertension, 68(2), 365–377. doi:10.1161/HYPERTENSIONAHA.115.06892
   PubMed Web of Science ®Google Scholar
• Weber, W., Hünenberger, P. H., & McCammon, J. A. (2000). Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation. The Journal of Physical Chemistry B, 104(15), 3668–3675. doi:10.1021/jp9937757
   Web of Science ®Google Scholar
• Wisnasari, S., Rohman, M. S., & Lukitasari, M. (2016). In silico binding affinity study of lisinopril and captopril to I/D intron 16 variant of angiotensin converting enzyme protein. International Journal of Pharmaceutical and Clinical Research, 8(8), 1132–1134.
   Google Scholar
• Yang, W., Riley, B. T., Lei, X., Porebski, B. T., Kass, I., Buckle, A. M., & McGowan, S. (2018). Generation of AMBER force field parameters for zinc centres of M1 and M17 family aminopeptidases. Journal of Biomolecular Structure and Dynamics, 36(10), 2595–2604. doi:10.1080/07391102.2017.1364669
   PubMed Web of Science ®Google Scholar
• Yokoyama, K., Chiba, H., & Yoshikawa, M. (1992). Peptide inhibitors for angiotensin I-converting enzyme from thermolysin digest of dried bonito. Bioscience, Biotechnology, and Biochemistry, 56(10), 1541–1545. doi:10.1271/bbb.56.1541
   PubMed Web of Science ®Google Scholar