Re-visiting lactate dehydrogenase from a different dimension: a model bioinformatics study for wrestling

Re-visiting lactate dehydrogenase from a different dimension: a model bioinformatics study for wrestling

Sports bioinformatics is of great importance in the understanding of sports performance from different perspectives. Accumulated bio-sequences in databases provide considerable contributions to compare proteins in different organisms. In Kingdom of Animalia, some animals have experienced evolution for excellent athletic performances in nature. The present paper exhibits a model in silico approach for the evaluation of sports performance by comparing lactate dehydrogenases (LDH) in humans (Homo sapiens) and saltwater crocodiles (Crocodylus porosus). The results show that a high sequence similarity is observed between the LDHs from H. sapiens and C. porosus with minor modifications. The stability and grand averages of hydrophobicity index values for studied LDHs were found as 24.79–25.18 and -0.006 –0.020 in H. sapiens and C. porosus, respectively. In conclusion, the identification of amino acid modifications in important enzymes of specific animals that are related to sports physiology are lessons we learn from from nature, which can open a new gate for the development of sports performance and talent selection.

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  • Alam, M. T., Olin-Sandoval, V., Stincone, A., Keller, M. A., Zelezniak, A., Luisi, B. F., & Ralser, M. (2017). The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization. Nature Communications, 8(1), 1-13. https://doi.org/10.1038/ncomms16018
  • Baldwin J., Seymour R. S., Webb G. J. W. (1995). Scaling of anaerobic metabolism during exercise in the estuarine crocodile (Crocodylus porosus). Comparative Biochemistry and Physiolology A, 112, 285-293. https://doi.org/10.1016/0300-9629(95)00100-X
  • Barranco, T., Tvarijonaviciute, A., Tecles, F., Carrillo, J. M., Sánchez-Resalt, C., Jimenez-Reyes, P., Rubio M., García-Balletbó M., Cerón J. J., & Cugat, R. (2017). Changes in creatine kinase, lactate dehydrogenase and aspartate aminotransferase in saliva samples after an intense exercise: a pilot study. The Journal of Sports Medicine and Physical Fitness, 58(6), 910-916. https://doi.org/10.23736/S0022-4707.17.07214-0
  • Bennett A. F., Seymour R. S., Bradford D. F., Webb G. J. W. (1985). Mass-dependence of anaerobic metabolism and acid-base disturbance during activity in the salt-water crocodile, Crocodylus porosus. Journal of Experimental Biology, 118, 161-171. https://doi.org/10.1242/jeb.118.1.161
  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235-242. https://doi.org/10.1093/nar/28.1.235
  • Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., & Schwede, T. (2017). Modeling protein quaternary structure of homo-and hetero-oligomers beyond binary interactions by homology. Scientific Reports, 7(1), 1-15. https://doi.org/10.1038/s41598-017-09654-8
  • Bian, Y., Song, C., Cheng, K., Dong, M., Wang, F., Huang, J., Sun D., Wang L., Ye M., & Zou, H. (2014). An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. Journal of Proteomics, 96, 253-262. https://doi.org/10.1016/j.jprot.2013.11.014
  • Bienert, S., Waterhouse, A., de Beer, T. A., Tauriello, G., Studer, G., Bordoli, L., & Schwede, T. (2017). The SWISS-MODEL Repository-new features and functionality. Nucleic Acids Research, 45(D1), D313-D319. https://doi.org/10.1093/nar/gkw1132
  • Bienvenut, W. V., Sumpton, D., Martinez, A., Lilla, S., Espagne, C., Meinnel, T., & Giglione, C. (2012). Comparative large scale characterization of plant versus mammal proteins reveals similar and idiosyncratic N-α-acetylation features. Molecular & Cellular Proteomics, 11(6), M111.015131. https://doi.org/10.1074/mcp.M111.015131
  • Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C., Olsen J. V., & Mann, M. (2009). Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science, 325(5942), 834-840. https://doi.org/10.1126/science.1175371
  • Fish FE, Bostic SA, Nicastro AJ, Beneski JT. (2007). Death roll of the alligator: mechanics of twist feeding in water. The Journal of Experimental Biology, 210, 2811–2818. https://doi.org/10.1242/jeb.004267.
  • Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. Protein Identification and Analysis Tools on the ExPASy Server; (In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005). pp. 571-607.
  • Gauci, S., Helbig, A. O., Slijper, M., Krijgsveld, J., Heck, A. J., & Mohammed, S. (2009). Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. Analytical Chemistry, 81(11), 4493-4501. https://doi.org/10.1021/ac9004309
  • Hendriks, I. A., Lyon, D., Young, C., Jensen, L. J., Vertegaal, A. C., & Nielsen, M. L. (2017). Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. Nature Structural & Molecular Biology, 24(3), 325-336. https://doi.org/10.1038/nsmb.3366
  • Hoff, M. L. M., Fabrizius, A., Folkow, L. P., & Burmester, T. (2016). An atypical distribution of lactate dehydrogenase isoenzymes in the hooded seal (Cystophora cristata) brain may reflect a biochemical adaptation to diving. Journal of Comparative Physiology B, 186(3), 373-386. https://doi.org/10.1007/s00360-015-0956-y
  • Huang, N., Li, F., Zhang, M., Zhou, H., Chen, Z., Ma, X., Yang, L., Wu, X., Zhong, J., Xiao, F., Yang, X., Zhao, K., Li, X., Xia, X., Liu, Z., Gao, S., & Zhang, N. (2021). An Upstream Open Reading Frame in Phosphatase and Tensin Homolog Encodes a Circuit Breaker of Lactate Metabolism. Cell Metabolism, 33(1), 128-144. https://doi.org/10.1016/j.cmet.2020.12.008
  • Mayya, V., Lundgren, D. H., Hwang, S. I., Rezaul, K., Wu, L., Eng, J. K., Rodionov, V., & Han, D. K. (2009). Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. Science Signaling, 2(84), ra46-ra46. https://doi.org/10.1126/scisignal.2000007
  • Owerkowicz, T., Baudinette, R. V. (2008). Exercise training enhances aerobic capacity in juvenile estuarine crocodiles (Crocodylus porosus). Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 150(2), 211-216. https://doi.org/10.1016/j.cbpa.2008.04.594
  • Read, J. A., Winter, V. J., Eszes, C. M., Sessions, R. B., & Brady, R. L. (2001). Structural basis for altered activity of M‐and H‐isozyme forms of human lactate dehydrogenase. Proteins: Structure, Function, and Bioinformatics, 43(2), 175-185. https://doi.org/10.1002/10970134(20010501)43:2<175::aid-prot1029>3.0.co;2-#
  • Rodrigues, B. M., Dantas, E., de Salles, B. F., Miranda, H., Koch, A. J., Willardson, J. M., & Simão, R. (2010). Creatine kinase and lactate dehydrogenase responses after upper-body resistance exercise with different rest intervals. The Journal of Strength & Conditioning Research, 24(6), 1657-1662. https://doi.org/10.1519/JSC.0b013e3181d8e6b1
  • Rumley, A. G., Pettigrew, A. R., Colgan, M. E., Taylor, R., Grant, S., Manzie, A., Findlay, I., Dargie, H., & Elliott, A. (1985). Serum lactate dehydrogenase and creatine kinase during marathon training. British Journal of Sports Medicine, 19(3), 152-155. https://doi.org/10.1136/bjsm.19.3.152
  • Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding J., Thompson, J. D., & Higgins, D. G. (2011). Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7(1), 539. https://doi.org/10.1038/msb.2011.75
  • Studer, G., Rempfer, C., Waterhouse, A. M., Gumienny, R., Haas, J., & Schwede, T. (2020). QMEANDisCo-distance constraints applied on model quality estimation. Bioinformatics, 36(6), 1765-1771. https://doi.org/10.1093/bioinformatics/btz828
  • Studer, G., Tauriello, G., Bienert, S., Biasini, M., Johner, N., & Schwede, T. (2021). ProMod3-A versatile homology modelling toolbox. PLoS Computational Biology, 17(1), e1008667. https://doi.org/10.1371/journal.pcbi.1008667
  • The Uni Prot Consortium, the universal protein knowledgebase in 2021. Nucleic Acids Research, 2021, 49.D1: D480-D489. https://doi.org/10.1093/nar/gkaa1100
  • Voet D., Voet J. G., (2004). Biochemistry, 3rd Edition, John Wiley Sons. USA.
  • Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., De Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296-W303. https://doi.org/10.1093/nar/gky427
  • Yard, E. E., & Comstock, R. D. (2008). A comparison of pediatric freestyle and Greco‐Roman wrestling injuries sustained during a 2006 US national tournament. Scandinavian Journal of Medicine & Science in Sports, 18(4), 491-497. https://doi.org/10.1111/j.1600-0838.2007.00716.x
  • Zhou, H., Di Palma, S., Preisinger, C., Peng, M., Polat, A. N., Heck, A. J., & Mohammed, S. (2013). Toward a comprehensive characterization of a human cancer cell phosphoproteome. Journal of Proteome Research, 12(1), 260-271. https://doi.org/10.1021/pr300630k