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Remote loop evolution reveals a complex biological function for chitinase enzymes beyond the active site

BiochemistryRemote loop evolution reveals a complex biological function for chitinase enzymes beyond the active site


  • Arnold, F. H. Innovation by evolution: bringing new chemistry to life (nobel lecture). Angew. Chem. Int. Ed. 58, 14420–14426 (2019).

    Article 
    CAS 

    Google Scholar 

  • Tawfik, D. S. Biochemistry. Loop grafting and the origins of enzyme species. Science 311, 475–476 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Burroughs, A. M., Allen, K. N., Dunaway-Mariano, D. & Aravind, L. Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. J. Mol. Biol. 361, 1003–1034 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Akiva, E., Copp, J. N., Tokuriki, N. & Babbitt, P. C. Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily. Proc. Natl Acad. Sci. USA 114, E9549–E9558 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Monzingo, A. F., Marcotte, E. M., Hart, P. J. & Robertus, J. D. Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core. Nat. Struct. Biol. 3, 133–140 (1996).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Park, H.-S. et al. Design and evolution of new catalytic activity with an existing protein scaffold. Science 311, 535–538 (2006).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Afriat-Jurnou, L., Jackson, C. J. & Tawfik, D. S. Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling. Biochemistry 51, 6047–6055 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Miton, C. M. & Tokuriki, N. Insertions and deletions (indels): a missing piece of the protein engineering jigsaw. Biochemistry 62, 148–157 (2023).

    Article 
    PubMed 

    Google Scholar 

  • Brejc, K. et al. Crystal structure of an ACh-binding protein reveals the ligand-binding domain of nicotinic receptors. Nature 411, 269–276 (2001).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Huse, M. & Kuriyan, J. The conformational plasticity of protein kinases. Cell 109, 275–282 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Fushinobu, S., Nishimasu, H., Hattori, D., Song, H.-J. & Wakagi, T. Structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase. Nature 478, 538–541 (2011).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Hoque, M. A. et al. Stepwise loop insertion strategy for active site remodeling to generate novel enzyme functions. ACS Chem. Biol. 12, 1188–1193 (2017).

    Article 
    MathSciNet 
    CAS 
    PubMed 

    Google Scholar 

  • Dodani, S. C. et al. Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models. Nat. Chem. 8, 419–425 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hedstrom, L., Szilagyi, L. & Rutter, W. J. Converting trypsin to chymotrypsin: the role of surface loops. Science 255, 1249–1253 (1992).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Ma, W., Tang, C. & Lai, L. Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant. Biophys. J. 89, 1183–1193 (2005).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Gunasekaran, K., Ma, B. & Nussinov, R. Triggering loops and enzyme function: identification of loops that trigger and modulate movements. J. Mol. Biol. 332, 143–159 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Colombo, G. Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design. Curr. Opin. Struct. Biol. 83, 102702 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Schlumbaum, A., Mauch, F., Vögeli, U. & Boller, T. Plant chitinases are potent inhibitors of fungal growth. Nature 324, 365–367 (1986).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Taira, T. et al. Cloning and characterization of a small family 19 chitinase from moss (Bryum coronatum). Glycobiology 21, 644–654 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Fukamizo, T. et al. A flexible loop controlling the enzymatic activity and specificity in a glycosyl hydrolase family 19 endochitinase from barley seeds (Hordeum vulgare L.). Biochim. Biophys. Acta 1794, 1159–1167 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Tanaka, J., Fukamizo, T. & Ohnuma, T. Enzymatic properties of a GH19 chitinase isolated from rice lacking a major loop structure involved in chitin binding. Glycobiology 27, 477–485 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Takenaka, S., Ohnuma, T. & Fukamizo, T. Insertion of a loop structure into the “loopless” GH19 chitinase from Bryum coronatum. J. Appl. Glycosci. 64, 39–42 (2017).

    Article 
    CAS 

    Google Scholar 

  • Kawamoto, D., Takashima, T., Fukamizo, T., Numata, T. & Ohnuma, T. A conserved loop structure of GH19 chitinases assists the enzyme function from behind the core-functional region. Glycobiology 32, 356–364 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Mizuno, R. et al. Role of the loop structure of the catalytic domain in rice class I chitinase. J. Biochem. 143, 487–495 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Sljoka, A. Probing allosteric mechanism with long-range rigidity transmission across protein networks. Methods Mol. Biol. 2253, 61–75 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Whiteley, W. Counting out to the flexibility of molecules. Phys. Biol. 2, S116–S126 (2005).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Sljoka, A. Structural and functional analysis of proteins using rigidity theory. in Sublinear Computation Paradigm: Algorithmic Revolution in the Big Data Era (eds. Katoh, N. et al.) 337–367 (Springer Singapore, 2022). https://doi.org/10.1007/978-981-16-4095-7_14.

  • Huang, S. K. et al. Delineating the conformational landscape of the adenosine A2A receptor during G protein coupling. Cell 184, 1884–1894.e14 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mehrabi, P. et al. Substrate-based allosteric regulation of a homodimeric enzyme. J. Am. Chem. Soc. 141, 11540–11556 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Baksh, K. A., Augustine, J., Sljoka, A., Prosser, R. S. & Zamble, D. B. Mechanistic insights into the nickel-dependent allosteric response of the Helicobacter pylori NikR transcription factor. J. Biol. Chem. 102785. https://doi.org/10.1016/j.jbc.2022.102785 (2022).

  • Ye, L. et al. Mechanistic insights into allosteric regulation of the A2A adenosine G protein-coupled receptor by physiological cations. Nat. Commun. 9, 1372 (2018).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jacobs, D. J., Rader, A. J., Kuhn, L. A. & Thorpe, M. F. Protein flexibility predictions using graph theory. Proteins 44, 150–165 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Yamagami, T. & Funatsu, G. Identification of the tryptophan residue located at the substrate-binding site of rye seed chitinase-c. Biosci. Biotechnol. Biochem. 59, 1076–1081 (1995).

    Article 
    CAS 

    Google Scholar 

  • Chothia, C., Gough, J., Vogel, C. & Teichmann, S. A. Evolution of the protein repertoire. Science 300, 1701–1703 (2003).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Rockah-Shmuel, L. et al. Correlated occurrence and bypass of frame-shifting insertion-deletions (InDels) to give functional proteins. PLoS Genet. 9, e1003882 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Emond, S. et al. Accessing unexplored regions of sequence space in directed enzyme evolution via insertion/deletion mutagenesis. Nat. Commun. 11, 3469 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Schenkmayerova, A. et al. Engineering the protein dynamics of an ancestral luciferase. Nat. Commun. 12, 3616 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ross, C. M., Foley, G., Boden, M. & Gillam, E. M. J. Using the evolutionary history of proteins to engineer insertion-deletion mutants from robust, ancestral templates using graphical representation of ancestral sequence predictions (GRASP). Methods Mol. Biol. 2397, 85–110 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Macdonald, C. B. et al. DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology. Genome Biol. 24, 36 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Campbell, E. et al. The role of protein dynamics in the evolution of new enzyme function. Nat. Chem. Biol. 12, 944–950 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Liu, J., Tan, H. & Rost, B. Loopy proteins appear conserved in evolution. J. Mol. Biol. 322, 53–64 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Tóth-Petróczy, A. & Tawfik, D. S. Protein insertions and deletions enabled by neutral roaming in sequence space. Mol. Biol. Evol. 30, 761–771 (2013).

    Article 
    PubMed 

    Google Scholar 

  • Tokuriki, N. et al. Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme. Nat. Commun. 3, 1257 (2012).

    Article 
    ADS 
    PubMed 

    Google Scholar 

  • Noda-Garcia, L. & Tawfik, D. S. Enzyme evolution in natural products biosynthesis: target- or diversity-oriented? Curr. Opin. Chem. Biol. 59, 147–154 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kaltenbach, M., Emond, S., Hollfelder, F. & Tokuriki, N. Functional trade-offs in promiscuous enzymes cannot be explained by intrinsic mutational robustness of the native activity. PLoS Genet. 12, e1006305 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Arantes, V. & Saddler, J. N. Cellulose accessibility limits the effectiveness of minimum cellulase loading on the efficient hydrolysis of pretreated lignocellulosic substrates. Biotechnol. Biofuels 4, 3 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • UniProt Consortium. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 49, D480–D489 (2021).

    Article 

    Google Scholar 

  • Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Larsson, A. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30, 3276–3278 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Nozaki, S. & Niki, H. Exonuclease III (XthA) enforces in vivo DNA cloning of Escherichia coli to create cohesive ends. J. Bacteriol. 201, e00660-e718, (2019).

    Article 

    Google Scholar 

  • Imoto, T. & Yagishita, K. A simple activity measurement of lysozyme. Agric. Biol. Chem. 35, 1154–1156 (1971).

    Article 
    CAS 

    Google Scholar 

  • Hirata, K. et al. ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography. Acta Crystallogr. D Struct. Biol. 75, 138–150 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yamashita, K., Hirata, K. & Yamamoto, M. KAMO: towards automated data processing for microcrystals. Acta Crystallogr. D Struct. Biol. 74, 441–449 (2018).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kabsch, W. XDS. in International Tables for Crystallography: Crystallography of Biological Macromolecules (eds. Arnold, E., Himmel, D. M. & Rossmann, M. G.) vol. F304–310 (International Union of Crystallography, 2012).

  • Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26, 795–800 (1993).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242 (2011).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D Biol. Crystallogr. 68, 352–367 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article 
    ADS 
    PubMed 

    Google Scholar 

  • Páll, S. et al. Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS. J. Chem. Phys. 153, 134110 (2020).

    Article 
    ADS 
    PubMed 

    Google Scholar 

  • Huang, J. & MacKerell, A. D. CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J. Comput. Chem. 34, 2135–2145 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Izadi, S., Anandakrishnan, R. & Onufriev, A. V. Building water models: a different approach. J. Phys. Chem. Lett. 5, 3863–3871 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys. 126, 014101 (2007).

    Article 
    ADS 
    PubMed 

    Google Scholar 

  • Parrinello, M. Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys. 52, 7182 (1981).

    Article 
    ADS 
    CAS 

    Google Scholar 

  • Jacobs, D. J. & Hendrickson, B. An algorithm for two-dimensional rigidity percolation: the pebble game. J. Comput. Phys. 137, 346–365 (1997).

    Article 
    ADS 
    MathSciNet 

    Google Scholar 

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