Biophysical study of the tubulin code: From lattice mechanics and detyrosination to transport sorting and disease

Mao Hinomori; Sho Ito; Tatsuya Nishino; Mao Hinomori; Sho Ito; Tatsuya Nishino

doi:10.3934/biophy.2026018

AIMS Biophysics

2026, Volume 13, Issue 3: 302-327. doi: 10.3934/biophy.2026018

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Review

Biophysical study of the tubulin code: From lattice mechanics and detyrosination to transport sorting and disease

Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan

Received: 15 July 2026 Revised: 17 August 2026 Accepted: 21 August 2026 Published: 27 August 2026

Microtubules are dynamic biophysical polymers whose function is encoded by a combinatorial regulatory framework, the “tubulin code”, in which α/β-tubulin isotype composition, post-translational modifications (PTMs), and lattice conformation collectively determine effector recruitment and cellular behavior. Among these PTMs, α-tubulin detyrosination has become a particularly tractable model for biophysical investigation following the identification of its enzymatic machinery. In this review, we summarized progress across six thematic areas: Methodological advances enabling causal investigation of the tubulin code; the conceptual framework of isotype-PTM epistasis; the molecular mechanism and spatial regulation of detyrosination by the vasohibin-SVBP (VASH/SVBP) complex and MATCAP/TMCP family; microtubule lattice mechanics and plus-end dynamics; effector-mediated transport sorting; and pathophysiological consequences in neurological disease, cardiac dysfunction, and cancer. A central insight was that microtubule lattice conformation, expanded (GTP-like) versus compacted (GDP), constitutes a previously unrecognized third axis of the tubulin code. Lattice expansion enhances α-tubulin C-terminal tail (CTT) accessibility and selectively promotes VASH1/SVBP catalytic activity, mechanically gating detyrosination. This state-gated mechanism couples polymer biophysics to downstream transport selectivity, with consequences for axonal differentiation, chromosome segregation, ciliary organization, and cardiac mechanics. Neuronal axonal microtubules maintaining a GTP-like expanded lattice despite being GDP-bound further illustrates lattice conformation as an independent regulatory variable. Nevertheless, no single experimental system has demonstrated this complete causal cascade, from isotype composition through lattice mechanical state and PTM enzyme accessibility to reader recruitment, in an integrated manner. Establishing a unified reconstitution and imaging workflow to validate this cascade, and defining how its breakdown drives disease, stands as the central experimental challenge for tubulin biophysics. Microtubules are not merely structural scaffolds but a dynamic information-processing system whose biophysical logic is only beginning to be deciphered.
- tubulin code,
- microtubule lattice conformation,
- α-tubulin detyrosination,
- vasohibin,
- post-translational modification
Citation: Mao Hinomori, Sho Ito, Tatsuya Nishino. Biophysical study of the tubulin code: From lattice mechanics and detyrosination to transport sorting and disease[J]. AIMS Biophysics, 2026, 13(3): 302-327. doi: 10.3934/biophy.2026018

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Abstract

Microtubules are dynamic biophysical polymers whose function is encoded by a combinatorial regulatory framework, the “tubulin code”, in which α/β-tubulin isotype composition, post-translational modifications (PTMs), and lattice conformation collectively determine effector recruitment and cellular behavior. Among these PTMs, α-tubulin detyrosination has become a particularly tractable model for biophysical investigation following the identification of its enzymatic machinery. In this review, we summarized progress across six thematic areas: Methodological advances enabling causal investigation of the tubulin code; the conceptual framework of isotype-PTM epistasis; the molecular mechanism and spatial regulation of detyrosination by the vasohibin-SVBP (VASH/SVBP) complex and MATCAP/TMCP family; microtubule lattice mechanics and plus-end dynamics; effector-mediated transport sorting; and pathophysiological consequences in neurological disease, cardiac dysfunction, and cancer. A central insight was that microtubule lattice conformation, expanded (GTP-like) versus compacted (GDP), constitutes a previously unrecognized third axis of the tubulin code. Lattice expansion enhances α-tubulin C-terminal tail (CTT) accessibility and selectively promotes VASH1/SVBP catalytic activity, mechanically gating detyrosination. This state-gated mechanism couples polymer biophysics to downstream transport selectivity, with consequences for axonal differentiation, chromosome segregation, ciliary organization, and cardiac mechanics. Neuronal axonal microtubules maintaining a GTP-like expanded lattice despite being GDP-bound further illustrates lattice conformation as an independent regulatory variable. Nevertheless, no single experimental system has demonstrated this complete causal cascade, from isotype composition through lattice mechanical state and PTM enzyme accessibility to reader recruitment, in an integrated manner. Establishing a unified reconstitution and imaging workflow to validate this cascade, and defining how its breakdown drives disease, stands as the central experimental challenge for tubulin biophysics. Microtubules are not merely structural scaffolds but a dynamic information-processing system whose biophysical logic is only beginning to be deciphered.

Abbreviations

APC

adenomatous polyposis coli

CCP

cytosolic carboxypeptidase

CNS

central nervous system

CTT

C-terminal tail

cryo-EM

cryo electron microscopy

cryo-ET

cryo electron tomography

EHT

engineered heart tissue

FRET

fluorescence resonance energy transfer

H-ABC

hypomyelination with atrophy of the basal ganglia and cerebellum

HAP1

human haploid cell line 1

HS-AFM

high-speed atomic force microscopy

IDR

intrinsically disordered region

IFT

intraflagellar transport

iPSC

induced pluripotent stem cell

MAP

microtubule-associated protein

MATCAP

microtubule-associated tyrosine carboxypeptidase

MCAK

mitotic centromere-associated kinesin

molecular dynamics

MEF

mouse embryonic fibroblast

PTM

post-translational modification

RGC

retinal ganglion cell

SVBP

small vasohibin-binding protein

TCP

tubulin carboxypeptidase

TIRF

total internal reflection fluorescence

TMCP

tubulin metallocarboxypeptidase

TOG

tumor overexpressed gene

TTL

tubulin tyrosine ligase

TTLL

tubulin tyrosine ligase-like

VASH

vasohibin

Acknowledgments

The literature on the tubulin code has grown rapidly in recent years, and despite our efforts to provide a comprehensive synthesis, space and scope constraints prevented us from citing many additional valuable studies relevant to this field. We apologize to the authors of those works and thank the broader research community for their contributions.
This work was supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI Grant Number 23K05671.

Conflict of interest

All authors declare no conflicts of interest in this paper.

Author contributions

Conceptualization, supervision, and project administration: T.N.; Investigation, literature review, and writing – original draft: M.H.; Writing – review and editing: S.I. and T.N. All authors have read and approved the final version of the manuscript for publication.

References

[1]	Brouhard GJ, Rice LM (2018) Microtubule dynamics: an interplay of biochemistry and mechanics. Nat Rev Mol Cell Biol 19: 451-463. https://doi.org/10.1038/s41580-018-0009-y
[2]	Alushin GM, Lander GC, Kellogg EH, et al. (2014) High-resolution microtubule structures reveal the structural transitions in αβ-tubulin upon GTP hydrolysis. Cell 157: 1117-1129. https://doi.org/10.1016/j.cell.2014.03.053
[3]	Vemu A, Atherton J, Spector JO, et al. (2017) Tubulin isoform composition tunes microtubule dynamics. Mol Biol Cell 28: 3564-3572. https://doi.org/10.1091/mbc.E17-02-0124
[4]	Aillaud C, Bosc C, Peris L, et al. (2017) Vasohibins/SVBP are tubulin carboxypeptidases (TCPs) that regulate neuron differentiation. Science 358: 1448-1453. https://doi.org/10.1126/science.aao4165
[5]	Nieuwenhuis J, Adamopoulos A, Bleijerveld OB, et al. (2017) Vasohibins encode tubulin detyrosinating activity. Science 358: 1453-1456. https://doi.org/10.1126/science.aao5676
[6]	Roll-Mecak A (2020) The tubulin code in microtubule dynamics and information encoding. Dev Cell 54: 7-20. https://doi.org/10.1016/j.devcel.2020.06.008
[7]	Janke C, Magiera MM (2020) The tubulin code and its role in controlling microtubule properties and functions. Nat Rev Mol Cell Biol 21: 307-326. https://doi.org/10.1038/s41580-020-0214-3
[8]	McKenna ED, Sarbanes SL, Cummings SW, et al. (2023) The tubulin code, from molecules to health and disease. Annu Rev Cell Dev Biol 39: 331-361. https://doi.org/10.1146/annurev-cellbio-030123-032748
[9]	Yue Y, Hotta T, Higaki T, et al. (2023) Microtubule detyrosination by VASH1: SVBP is regulated by the conformational state of tubulin in the lattice. Curr Biol 33: 4111-4123.e7. https://doi.org/10.1016/j.cub.2023.07.062
[10]	Li F, Li Y, Ye X, et al. (2020) Cryo-EM structure of VASH1-SVBP bound to microtubules. eLife 9: e58157. https://doi.org/10.7554/eLife.58157
[11]	Hotta T, Pimm ML, Thomas EC, et al. (2026) Accessibility of the unstructured α-tubulin C-terminal tail is controlled by microtubule lattice conformation. eLife 14: RP109308. https://doi.org/10.7554/eLife.109308.3
[12]	Vemu A, Atherton J, Spector JO, et al. (2016) Structure and dynamics of single-isoform recombinant neuronal human tubulin. J Biol Chem 291: 12907-12915. https://doi.org/10.1074/jbc.C116.731133
[13]	Ramirez-Rios S, Liao S, Dumont E, et al. (2023) VASH1-SVBP and VASH2-SVBP generate different detyrosination profiles on microtubules. J Cell Biol 222: e202205096. https://doi.org/10.1083/jcb.202205096
[14]	Kalutskii M, Grubmüller H, Volkov VA, et al. (2025) Microtubule dynamics are defined by conformations and stability of clustered protofilaments. Proc Natl Acad Sci USA 122: e2424263122. https://doi.org/10.1073/pnas.2424263122
[15]	Colonna G (2025) Protein biophysics: current limitations and prospects. AIMS Biophys 12: 333-374. https://doi.org/10.3934/biophy.2025018
[16]	Chen J, Kholina E, Szyk A, et al. (2021) α-tubulin tail modifications regulate microtubule stability through selective effector recruitment, not changes in intrinsic polymer dynamics. Dev Cell 56: 2016-2028.e4. https://doi.org/10.1016/j.devcel.2021.05.005
[17]	Chhatre A, Stepanek L, Nievergelt AP, et al. (2025) Tubulin tyrosination/detyrosination regulate the affinity and sorting of intraflagellar transport trains on axonemal microtubule doublets. Nat Commun 16: 1055. https://doi.org/10.1038/s41467-025-56098-0
[18]	Janke C, Rogowski K, Wloga D, et al. (2005) Tubulin polyglutamylase enzymes are members of the TTL domain protein family. Science 308: 1758-1762. https://doi.org/10.1126/science.1113010
[19]	Lacroix B, van Dijk J, Gold ND, et al. (2010) Tubulin polyglutamylation stimulates spastin-mediated microtubule severing. J Cell Biol 189: 945-954. https://doi.org/10.1083/jcb.201001024
[20]	Bodakuntla S, Yuan X, Genova M, et al. (2021) Distinct roles of α- and β-tubulin polyglutamylation in controlling axonal transport and in neurodegeneration. EMBO J 40: e108498. https://doi.org/10.15252/embj.2021108498
[21]	Jaramillo-Restrepo C, Piazza V, Hernandez-Morales I, et al. (2026) H-ABC tubulinopathy exhibits a cytoskeletal defect associated with microtubule stability. Neurobiol Dis 224: 107420. https://doi.org/10.1016/j.nbd.2026.107420
[22]	Watanabe K, Hasegawa Y, Yamashita H, et al. (2004) Vasohibin as an endothelium-derived negative feedback regulator of angiogenesis. J Clin Invest 114: 898-907. https://doi.org/10.1172/JCI21152
[23]	Sato Y, Sonoda H (2007) The vasohibin family: a negative regulatory system of angiogenesis genetically programmed in endothelial cells. Arterioscler Thromb Vasc Biol 27: 37-41. https://doi.org/10.1161/01.ATV.0000252062.48280.61
[24]	Du H, Zhao J, Hai L, et al. (2017) The roles of vasohibin and its family members: beyond angiogenesis modulators. Cancer Biol Ther 18: 827-832. https://doi.org/10.1080/15384047.2017.1373217
[25]	Liao S, Rajendraprasad G, Wang N, et al. (2019) Molecular basis of vasohibins-mediated detyrosination and its impact on spindle function and mitosis. Cell Res 29: 533-547. https://doi.org/10.1038/s41422-019-0187-y
[26]	Wang N, Bosc C, Choi SR, et al. (2019) Structural basis of tubulin detyrosination by the vasohibin–SVBP enzyme complex. Nat Struct Mol Biol 26: 571-582. https://doi.org/10.1038/s41594-019-0241-y
[27]	Zhou C, Bhatt TK, Bharat TAM, et al. (2019) Structural basis of tubulin detyrosination by VASH2/SVBP heterodimer. Nat Commun 10: 3212. https://doi.org/10.1038/s41467-019-11277-8
[28]	Ikeda A, Urata S, Ando T, et al. (2020) The crystal structure of the tetrameric human vasohibin-1–SVBP complex reveals a variable arm region within the structural core. Acta Crystallogr D Struct Biol 76: 993-1000. https://doi.org/10.1107/S2059798320011298
[29]	Yue Y, Hotta T, Ohi R, et al. (2026) MATCAP1 preferentially binds an expanded tubulin conformation to generate detyrosinated and ΔC2 α-tubulin. EMBO J 45: 4257-4282. https://doi.org/10.1038/s44318-026-00772-6
[30]	Zehr EA, Sun S, Sarbanes SL, et al. (2026) Microtubules in the axon are GDP bound but adopt a stable GTP-like expanded state. Nat Struct Mol Biol 33: 631-640. https://doi.org/10.1038/s41594-026-01787-7
[31]	Tang Q, Sangha AK, Bharat TAM, et al. (2023) Interplay between stochastic enzyme activity and microtubule stability drives detyrosination enrichment on microtubule subsets. Curr Biol 33: 5334-5347. https://doi.org/10.1016/j.cub.2023.10.068
[32]	Landskron L, Bak J, Adamopoulos A, et al. (2022) Posttranslational modification of microtubules by the MATCAP detyrosinase. Science 376: eabn6020. https://doi.org/10.1126/science.abn6020
[33]	Nicot S, Gillard G, Impheng H, et al. (2023) A family of carboxypeptidases catalyzing α- and β-tubulin tail processing and deglutamylation. Sci Adv 9: eadi7838. https://doi.org/10.1126/sciadv.adi7838
[34]	Simon M, Espeut J, Juge F, et al. (2025) Real-time FRET assay for monitoring detyrosination by TMCP1 and VASH2. Protein Sci 34: e70374. https://doi.org/10.1002/pro.70374
[35]	Sanyal C, Pietsch N, Ramirez Rios S, et al. (2023) The detyrosination/re-tyrosination cycle of tubulin and its role and dysfunction in neurons and cardiomyocytes. Semin Cell Dev Biol 137: 46-62. https://doi.org/10.1016/j.semcdb.2021.12.006
[36]	Pietsch N, Chen CY, Kupsch S, et al. (2024) Chronic activation of tubulin tyrosination improves heart function. Circ Res 135: 910-932. https://doi.org/10.1161/CIRCRESAHA.124.324387
[37]	Chew YM, Cross RA (2025) Structural switching of tubulin in the microtubule lattice. Biochem Soc Trans 53: 161-171. https://doi.org/10.1042/BST20240360
[38]	Cleary JM, Kim T, Cook ASI, et al. (2022) Measurements and simulations of microtubule growth imply strong longitudinal interactions and reveal a role for GDP on the elongating end. eLife 11: e75931. https://doi.org/10.7554/eLife.75931
[39]	Estévez-Gallego J, Blum TB, Ruhnow F, et al. (2025) Hydrolysis-deficient mosaic microtubules as faithful mimics of the GTP cap. Nat Commun 16: 2396. https://doi.org/10.1038/s41467-025-57555-6
[40]	Zhou J, Wang A, Song Y, et al. (2023) Structural insights into the mechanism of GTP initiation of microtubule assembly. Nat Commun 14: 5980. https://doi.org/10.1038/s41467-023-41615-w
[41]	de Jager L, Jansen KI, Hoogebeen R, et al. (2025) StableMARK-decorated microtubules in cells have expanded lattices. J Cell Biol 224: e202206143. https://doi.org/10.1083/jcb.202206143
[42]	Girão H, Macário-Monteiro J, Figueiredo AC, et al. (2024) α-tubulin detyrosination fine-tunes kinetochore-microtubule attachments. Nat Commun 15: 9720. https://doi.org/10.1038/s41467-024-54155-8
[43]	Lavrsen K, Rajendraprasad G, Leda M, et al. (2023) Microtubule detyrosination drives symmetry breaking to polarize cells for directed cell migration. Proc Natl Acad Sci USA 120: e2300322120. https://doi.org/10.1073/pnas.2300322120
[44]	Leibinger M, Zeitler C, Paulat M, et al. (2023) Inhibition of microtubule detyrosination by parthenolide facilitates functional CNS axon regeneration. eLife 12: e88279. https://doi.org/10.7554/eLife.88279
[45]	Peris L, Parato J, Qu X, et al. (2022) Tubulin tyrosination regulates synaptic function and is disrupted in Alzheimer's disease. Brain 145: 2486-2506. https://doi.org/10.1093/brain/awab436
[46]	Chu D, Liu F (2019) Pathological changes of tau related to Alzheimer's disease. ACS Chem Neurosci 10: 931-944. https://doi.org/10.1021/acschemneuro.8b00457
[47]	Magiera MM, Bodakuntla S, Žiak J, et al. (2018) Excessive tubulin polyglutamylation causes neurodegeneration and perturbs neuronal transport. EMBO J 37: e100440. https://doi.org/10.15252/embj.2018100440
[48]	Shashi V, Magiera MM, Klein D, et al. (2018) Loss of tubulin deglutamylase CCP1 causes infantile-onset neurodegeneration. EMBO J 37: e100540. https://doi.org/10.15252/embj.2018100540
[49]	Iqbal Z, Tawamie H, Ba W, et al. (2019) Loss of function of SVBP leads to autosomal recessive intellectual disability, microcephaly, ataxia, and hypotonia. Genet Med 21: 1790-1796. https://doi.org/10.1038/s41436-018-0415-8
[50]	Launay N, Espinosa-Alcantud M, Verdura E, et al. (2025) Altered tubulin detyrosination due to SVBP malfunction induces cytokinesis failure and senescence, underlying a complex hereditary spastic paraplegia. Aging Cell 24: e14355. https://doi.org/10.1111/acel.14355
[51]	Chen CY, Caporizzo MA, Bedi K, et al. (2018) Suppression of detyrosinated microtubules improves cardiomyocyte function in human heart failure. Nat Med 24: 1225-1233. https://doi.org/10.1038/s41591-018-0046-2
[52]	Chen CY, Salomon AK, Caporizzo MA, et al. (2020) Depletion of vasohibin 1 speeds contraction and relaxation in failing human cardiomyocytes. Circ Res 127: e14-e27. https://doi.org/10.1161/CIRCRESAHA.119.315947
[53]	Lopes D, Seabra AL, Orr B, et al. (2023) α-Tubulin detyrosination links the suppression of MCAK activity with taxol cytotoxicity. J Cell Biol 222: e202205092. https://doi.org/10.1083/jcb.202205092
[54]	Koyanagi T, Saga Y, Takahashi Y, et al. (2021) Knockout of vasohibin-2 reduces tubulin carboxypeptidase activity and increases paclitaxel sensitivity in ovarian cancer. Cancer Med 10: 2732-2739. https://doi.org/10.1002/cam4.3841
[55]	Abbas G, Kirabo A, Ahmed U, et al. (2025) Vasohibins in health and disease: from angiogenesis to tumorigenesis, multiorgan dysfunction, and brain-heart remodeling. Cells 14: 767. https://doi.org/10.3390/cells14110767

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