RNA codons govern the mechanism of protein folding through the shape memory effect
DOI:
https://doi.org/10.51200/bijb.v2i.2955Keywords:
protein folding, shape memory effect, RNA codons, native structureAbstract
The complex protein folding mechanism had been researched during the past half-century, given its potential to offer cures for illnesses caused by viruses and protein misfolding. However, to date, the work remains inadequately successful and mastered, provoking the question of whether researchers are looking at the wrong place for the answer. Specifically, can RNA codons define the protein folding mechanism? This review will first present existing mechanisms for protein folding and their limitations. Then, the logic and evidence supporting the use of a protein folding mechanism governed by RNA codons will be presented. This paper explains protein folding as a shape-memory phenomenon wherein the protein chain memorises the native folded structure. Under the right chemical environment, the protein chain will fold back into its native memorised structure. The RNA codon is the imprint for the natively folded protein shape memory, responsible for programming the native folded structure shape memory onto the protein chain.
References
Adhikari, B., Bhattacharya, D., Cao, R., & Cheng, J. (2015). CONFOLD: Residue-residue contact guided ab initio protein folding. Proteins: Structure, Function, and Bioinformatics, 83 (8), 1436 – 1449. https://doi.org/10.1002/prot.24829
Alm, E. & Baker, D. (1999). Matching theory and experiment in protein folding. Current Opinion in Structural Biology, 9 (2), 189--196. https://doi.org/10.1016/S0959-440X(99)80027-X
Anfinsen, C. B., Haber, E., Sela, M., & White, F. H., Jr (1961). The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proceedings of the National Academy of Sciences of the United States of America, 47 (9), 1309 – 1314. https://doi.org/10.1073/pnas.47.9.1309
Anfinsen, C. B. (1973). Principles that govern the folding of protein chains. Science, 181 (4096), 223 – 230. https://doi.org/10.1126/science.181.4096.223
Baker, D. (2000). A surprising simplicity to protein folding. Nature, 405, 39 – 42. https://doi.org/10.1038/35011000
Ben-Naim, A. (2012). Levinthal’s paradox revisited, and dismissed. Open Journal of Biophysics, 2 (2), 23 – 32. https://doi.org/10.4236/ojbiphy.2012.22004
Braselmann, E., Chaney, J. L., & Clark, P. L. (2013). Folding the proteome. Trends in Biochemical Sciences, 38 (7), 337 – 344. https://doi.org/10.1016/j.tibs.2013.05.001
Carter, C. W., & Wolfenden, R. (2015). tRNA acceptor stem and anticodon bases form independent codes related to protein folding. Biophysics and Computational Biology, 112 (24), 7489– 7494. https://doi.org/10.1073/pnas.1507569112
Chiti, F., & Dobson, C. M. (2017). Protein misfolding, amyloid formation, and human disease: A summary of progress over the last decade. Annual Review of Biochemistry, 86, 27 – 68. https://doi.org/10.1146/annurev-biochem-061516-045115
Díaz-Villanueva, J. F., Díaz-Molina, R., & García-González, V. (2015). Protein folding and mechanisms of proteostasis. International Journal of Molecular Sciences, 16 (8), 17193 – 17230. https://doi.org/10.3390%2Fijms160817193
Dill, K. A., Bromberg, S., Yue, K., Chan, H. S., Ftebig, K. M., Yee, David P., & Thomas, P. D. (1995). Principles of protein folding—a perspective from simple exact models. Protein Science, 4 (4), 561 – 602. https://doi.org/10.1002/pro.5560040401
Dobson, C. M. (2004). Principles of protein folding, misfolding and aggregation. Seminars in Cell and Developmental Biology, 15 (1), 3 – 16. https://doi.org/10.1016/j.semcdb.2003.12.008
Dobson, C. M. (2003). Protein folding and misfolding. Nature, 426, 884 – 890. https://doi.org/10.1038/nature02261
Dykeman, E. C., Stockley, P. G., & Twarock, R. (2014). Solving a Levinthal’s paradox for virus assembly identifies a unique antiviral strategy. Biological Sciences, 111 (14), 5361 – 5366. https://doi.org/10.1073/pnas.1319479111
Englander, S. W., & Mayne, L. (2017). The case for defined protein folding pathways. Biophysics and Computational Biology, 114 (31), 8253 – 8258. https://doi.org/10.1073/pnas.1706196114
Englander, S. W., & Mayne, L. (2014). The nature of protein folding pathways. Biophysics and Computational Biology, 111 (31), 15873 – 15880. https://doi.org/10.1073/pnas.1411798111
Faure, G., Ogurtsov, A. Y., Shabalina, S. A., & Koonin, E. V. (2016). Role of mRNA structure in the
control of protein folding. Nucleic Acids Research, 44 (22), 10898 – 10911. https://doi.org/10.1093/nar/gkw671
Finkelstein, A. V., Badretdin, A. J., Galzitskaya, O. V., Ivankov, D. N., Bogatyreva, N. S., Garbuzynskiy, S. O. (2017). There and back again: Two views on the protein folding puzzle. Physics of Life Reviews, 21, 56 – 71. https://doi.org/10.1016/j.plrev.2017.01.025
Finkelstein, A. V., & Garbuzynskiy, S. O. (2016). Solution of Levinthal’s paradox is possible at the level of the formation and assembly of protein secondary structures. Biophysics, 61, 1 – 5. https://doi.org/10.1134/S0006350916010085
Frankel, A. D., & Smith, C. A. (1998). Induced folding in RNA – protein recognition: More than a simple molecular handshake. Cell, 92 (2), 149 – 151. https://doi.org/10.1016/S0092-8674(00)80908-3
Gō, N. (1983). Theoretical studies of protein folding. Annual Review of Biophysics and Bioengineering, 12, 183 – 210. https://doi.org/10.1146/annurev.bb.12.060183.001151
Hartl, F. U., Bracher, A., & Hayer-Hartl, M. (2011). Molecular chaperones in protein folding and proteostasis. Nature, 475, 324 – 332. https://doi.org/10.1038/nature10317
Honig, B. (1999). Protein folding: from the levinthal paradox to structure prediction. Journal of Molecular Biology, 293 (2), 283 – 293. https://doi.org/10.1006/jmbi.1999.3006
Jacobson, G. N., & Clark, P. L. (2016). Quality over quantity: Optimizing co-translational protein
folding with non-‘optimal’synonymous codons. Current Opinion in Structural Biology,
, 102 – 110. https://doi.org/10.1016/j.sbi.2016.06.002
Jerath, G., Hazam, P. K., Shekhar, S., & Ramakrishnan, V. (2016). Mapping the geometric evolution of protein folding motor. PloS One, 11 (10), e0163993. https://doi.org/10.1371/journal. pone.0163993
Karplus, M. (1997). The Levinthal paradox: Yesterday and today. Folding and Design, 2 (Suppl 1), S69 – S75. https://doi.org/10.1016/S1359-0278(97)00067-9
Komar, A. A., Lesnik, T., & Reiss, C. (1999). Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation. FEBS Letters, 462 (3), 387 – 391. https://doi.org/10.1016/S0014-5793(99)01566-5
Kubelka, J., & Hofrichter, J., & Eaton, W. A. (2004). The protein folding ‘speed limit’. Current Opinion in Structural Biology, 14 (1), 76 – 88. https://doi.org/10.1016/j.sbi.2004.01.013
Levinthal, C. (1968). Are there pathways for protein folding? J. Chim. Phys., 65, 44 – 45. https://doi.org/10.1051/jcp/1968650044
Levinthal, C. (1969). How to fold graciously. Mossbaun Spectroscopy in Biological Systems Proceedings, 67 (41), 22 – 24.
Meng, H., & Li, G. (2013). A review of stimuli-responsive shape memory polymer composites. Polymer, 54 (9), 2199 – 2221. https://doi.org/10.1016/j.polymer.2013.02.023
Nirenberg, M., Caskey, T., Marshall, R., Brimacombe, R., Kellogg, D., Doctor, B., Hatfield, D., Levin, J., Rottman, F., Pestka, S., Wilcox, M., & Anderson, F. (1966). The RNA code and protein synthesis. Cold Spring Harbor Symposia on Quantitative Biology, 31, 11 – 24. https://doi.org/10.1101/SQB.1966.031.01.008
Onuchic, J. N., & Wolynes, P. G. (2004). Theory of protein folding. Current Opinion in Structural Biology, 14 (1), 70 – 75. https://doi.org/10.1016/j.sbi.2004.01.009
Portman, J. J., &Takada, S. (2001). Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics. The Journal of Chemical Physics, 114, 5082 – 5096. https://doi.org/10.1063/1.1334663
Rodnina, M. V. (2016). The ribosome in action: Tuning of translational efficiency and protein folding. Protein Science, 25 (8), 1390 – 1406. https://doi.org/10.1002/pro.2950
Samanta, D., Mukhopadhyay, D., Chowdhury, S., Ghosh, J., Pal, S., Basu, A., Bhattacharya, A., Das, A., Das, D., & DasGupta, C. (2008). Protein folding by domain V of Escherichia coli 23S rRNA: Specificity of RNA-protein interactions. Journal of Bacteriology, 190 (9), 3344 – 3352. https://doi.org/10.1128/JB.01800-07
Sander, I. M., Chaney, J. L., & Clark, P. L. (2014). Expanding Anfinsen’s principle: Contributions of synonymous codon selection to rational protein design. Journal of the American Chemical Society, 136 (3), 85 – 861. https://doi.org/10.1021/ja411302m
Schuler, B., & Eaton, W. A. (2008). Protein folding studied by single-molecule FRET. Current Opinion in Structural Biology, 18 (1), 16 – 26. https://doi.org/10.1016/j.sbi.2007.12.003
Thirumalai, D., & Hyeon, C. (2005). RNA and protein folding: common themes and variations. Biochemistry, 44 (13), 4957 – 4970. https://doi.org/10.1021/bi047314+
Thommen, M., Holtkamp, W., & Rodnina, M. V. (2017). Co-translational protein folding: Progress and methods. Current Opinion in Structural Biology, 42, 83 – 89. https://doi.org/10.1016/j.sbi.2016.11.020
Tompa, P., & Rose, G. D. (2011). The Levinthal paradox of the interactome. Protein Science, 20 (12), 2074 – 2079. https://doi.org/10.1002/pro.747
Vos, T., Allen, C., Arora, M., Barber, R. M., Bhutta, Z. A., Brown, A., Carter, A., Casey, D. C., Charlson, F. J., Chen, A. Z., Coggeshall, M., Cornaby, L., Dandona, L., Dicker, D. J., Dilegge, T., Erskine, H. E., Ferrari, A. J., Fitzmaurice, C., Flemming, T., … Tura, A. K. (2016). Global, regional, and national incidence, prevalence, and years lived with disability for 310 diseases and injuries, 1990 – 2015: A systematic analysis for the Global Burden of Disease Study 2015. The Lancet, 388, 1545 – 1602. https://doi.org/10.1016/S0140-6736(16)31678-6
Waudby, C. A., Dobson, C. M., & Christodoulou, J. (2019). Nature and regulation of protein folding on the ribosome. Trends in Biochemical Sciences, 44 (11), 914 – 926. https://doi.org/10.1016/j.tibs.2019.06.008
Wolynes, P. G. (2006). Recent successes of the energy landscape theory of protein folding and function. Quarterly Reviews of Biophysics, 38 (4), 405. https://doi.org/10.1017/S0033583505004075
Young, J. C., Moarefi, I., & Hartl, F. U. (2001). Hsp90: A specialized but essential protein-folding tool. Journal of Cell Biology, 154 (2), 267 – 274. https://doi.org/10.1083/jcb.200104079
Yu, C. H., Dang, Y., Zhou, Z., Wu, C., Zhao, F., Sachs, M. S., & Liu, Y. (2015). Codon usage influences the local rate of translation elongation to regulate co-translational protein folding. Molecular Cell, 59 (5), 744 – 754. https://doi.org/10.1016/j.molcel.2015.07.018
Zhou, M., Tao, W., Fu, J., Xiao, G., & Liu, Y. (2015). Nonoptimal codon usage influences protein structure in intrinsically disordered regions. Molecular Microbiology, 97 (5), 974 – 987. https://doi.org/10.1111/mmi.13079
Zwanzig, R., Szabo, A., & Bagchi, B. (1992). Levinthal’s paradox. Proceedings of the National Academy of Sciences, 89 (1), 20 – 22. https://doi.org/10.1073/pnas.89.1.20