Abstract
The sequence-structure-function paradigm for proteins has been well accepted in the scientific community. However, with the emergence of the ensemble view of proteins, it has become clear that this fails to incorporate the importance of protein dynamics, which we now understand govern the underlying function of proteins. Here, we introduce two tools—the dynamic flexibility index (DFI) and the dynamic coupling index (DCI) which can quantify structural flexibility and dynamic coupling at a site-specific, single amino acid level. We show that it is possible to relate evolutionary conservation to amino acid flexibility and that disease-associated protein variants coincide with mutations at rigid positions within a protein. In combination with experimental data, we also capture important changes in structural conformation that coincide with the evolution of protein function through changes in structural dynamics. Finally, we discuss how nature can modulate change through allosteric mutations which alter the internal interaction network of proteins, and how changes in allosteric regulation can result in disease phenotypes.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bhabha G, Lee J, Ekiert DC, Gam J, Wilson IA, Dyson HJ, Benkovic SJ, Wright PE (2011) A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis. Science 332:234–238. https://doi.org/10.1126/science.1198542
Bhabha G, Ekiert DC, Jennewein M, Zmasek CM, Tuttle LM, Kroon G, Dyson HJ, Godzik A, Wilson IA, Wright PE (2013) Divergent evolution of protein conformational dynamics in dihydrofolate reductase. Nat Struct Mol Biol 20:1243–1249. https://doi.org/10.1038/nsmb.2676
Campbell E, Kaltenbach M, Correy GJ, Carr PD, Porebski BT, Livingstone EK, Afriat-Jurnou L, Buckle AM, Weik M, Hollfelder F, Tokuriki N, Jackson CJ (2016) The role of protein dynamics in the evolution of new enzyme function. Nat Chem Biol 12:944 EP. https://doi.org/10.1038/nchembio.2175
Campbell EC, Correy GJ, Mabbitt PD, Buckle AM, Tokuriki N, Jackson CJ (2018) Laboratory evolution of protein conformational dynamics. Curr Opin Struct Biol 50:49–57. https://doi.org/10.1016/j.sbi.2017.09.005
Campitelli P, Guo J, Zhou H-X, Ozkan SB (2018) Hinge-shift mechanism modulates allosteric regulations in human pin1. J Phys Chem B 122:5623–5629. https://doi.org/10.1021/acs.jpcb.7b11971
Culyba MJ, Mo CY, Kohli RM (2015) Targets for combating the evolution of acquired antibiotic resistance. Biochemistry 54:3573–3582. https://doi.org/10.1021/acs.biochem.5b00109
Eisenmesser EZ, Millet O, Labeikovsky W, Korzhnev DM, Wolf-Watz M, Bosco DA, Skalicky JJ, Kay LE, Kern D (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438:117–121. https://doi.org/10.1038/nature04105
Eisenmesser EZ, Bosco DA, Akke M, Kern D (2002) Enzyme dynamics during catalysis. Science 295:1520–1523. https://doi.org/10.1126/science.1066176
Gerek ZN, Ozkan SB (2011) Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning. PLoS Comput Biol, vol 7. https://doi.org/10.1371/journal.pcbi.1002154
Haliloglu T, Bahar I (2015) Adaptability of protein structures to enable functional interactions and evolutionary implications. Curr Opin Struct Biol 35:17–23. https://doi.org/10.1016/j.sbi.2015.07.007
Jackson CJ, Foo J-L, Tokuriki N, Afriat L, Carr PD, Kim H-K, Schenk G, Tawfik DS, Ollis DL (2009) Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase. Proc Natl Acad Sci USA 106:21631–21636. https://doi.org/10.1073/pnas.0907548106
Kim H, Zou T, Modi C, Dörner K, Grunkemeyer TJ, Chen L, Fromme R, Matz MV, Ozkan SB, Wachter RM (2015) A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins. Structure 23:34–43. https://doi.org/10.1016/j.str.2014.11.011
Knudsen M, Wiuf C (2010) The CATH database. Hum Genomics 4:207–212. https://doi.org/10.1186/1479-7364-4-3-207
Kumar A, Glembo TJ, Ozkan SB (2015) The role of conformational dynamics and allostery in the disease development of human ferritin. Biophys J 109:1273–1281. https://doi.org/10.1016/j.bpj.2015.06.060
Larrimore KE, Kazan IC, Kannan L, Kendle RP, Jamal T, Barcus M, Bolia A, Brimijoin S, Zhan C-G, Ozkan SB, Mor TS (2017) Plant-expressed cocaine hydrolase variants of butyrylcholinesterase exhibit altered allosteric effects of cholinesterase activity and increased inhibitor sensitivity. Scientific Reports 7:10419. https://doi.org/10.1038/s41598-017-10571-z
Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning APJ, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S (2012) The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci 21:769–785. https://doi.org/10.1002/pro.2071
Liu Y, Bahar I (2012) Sequence evolution correlates with structural dynamics. Mol Biol Evol 29:2253–2263. https://doi.org/10.1093/molbev/mss097
Liu Y, Gierasch LM, Bahar I (2010) Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs. PLoS Comput Biol, vol 6. https://doi.org/10.1371/journal.pcbi.1000931
Maguid S, Fernández-Alberti S, Parisi G, Echave J (2006) Evolutionary conservation of protein backbone flexibility. J Mol Evol 63:448–457. https://doi.org/10.1007/s00239-005-0209-x
Maguid S, Fernandez-Alberti S, Echave J (2008) Evolutionary conservation of protein vibrational dynamics. Gene 422:7–13. https://doi.org/10.1016/j.gene.2008.06.002
Modi T, Huihui J, Ghosh K, Ozkan SB (2018) Ancient thioredoxins evolved to modern-day stability-function requirement by altering native state ensemble. Philos Trans R Soc Lond, B, Biol Sci 373. https://doi.org/10.1098/rstb.2017.0184
Nevin Gerek Z, Kumar S, Banu Ozkan S (2013) Structural dynamics flexibility informs function and evolution at a proteome scale. Evol Appl 6:423–433. https://doi.org/10.1111/eva.12052
Swint-Kruse L (2016) Using evolution to guide protein engineering: the devil is in the details. Biophys J 111:10–18. https://doi.org/10.1016/j.bpj.2016.05.030
Tang GW, Altman RB (2011) Remote thioredoxin recognition using evolutionary conservation and structural dynamics. Structure 19:461–470. https://doi.org/10.1016/j.str.2011.02.007
Tokuriki N, Tawfik DS (2009) Protein dynamism and evolvability. Science 324:203–207. https://doi.org/10.1126/science.1169375
Tomaras AP, Dunman PM (2015) In the midst of the antimicrobial discovery conundrum: an overview. Curr Opin Microbiol 27:103–107. https://doi.org/10.1016/j.mib.2015.08.005
Wang Y, Rader AJ, Bahar I, Jernigan RL (2004) Global ribosome motions revealed with elastic network model. J Struct Biol 147:302–314. https://doi.org/10.1016/j.jsb.2004.01.005
Wilke MS, Lovering AL, Strynadka NCJ (2005) Beta-lactam antibiotic resistance: a current structural perspective. Curr Opin Microbiol 8:525–533. https://doi.org/10.1016/j.mib.2005.08.016
Zheng W, Brooks BR, d. Thirumalai (2006) Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc Natl Acad Sci USA 103:7664–7669. https://doi.org/10.1073/pnas.0510426103
Zheng W, Brooks BR, d. Thirumalai (2007) Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys J 93:2289–2299. https://doi.org/10.1529/biophysj.107.105270
Zou T, Risso VA, Gavira JA, Sanchez-Ruiz JM, Ozkan SB (2015) Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme. Mol Biol Evol 32:132–143. https://doi.org/10.1093/molbev/msu281
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Campitelli, P., Ozkan, S.B. (2019). Allostery and Structural Dynamics in Protein Evolution. In: Pontarotti, P. (eds) Evolution, Origin of Life, Concepts and Methods. Springer, Cham. https://doi.org/10.1007/978-3-030-30363-1_9
Download citation
DOI: https://doi.org/10.1007/978-3-030-30363-1_9
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-30362-4
Online ISBN: 978-3-030-30363-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)