Equilibrium Conformational Ensemble of the Intrinsically Disordered Peptide n16N: Linking Subdomain Structures and Function in Nacre
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n16 is a framework protein family associated with biogenic mineral stabilization, thought to operate at three key interfaces in nacre: protein/β-chitin, protein/protein, and protein/CaCO3. The N-terminal half of this protein, n16N, is known to be active in conferring this mineral stabilization and organization. While some details relating to the stabilization and organization of the mineral are known, the molecular mechanisms that underpin these processes are not yet established. To provide these molecular-scale details, here we explore current hypotheses regarding the possible subdomain organization of n16N, as related to these three interfaces in nacre, by combining outcomes of Replica Exchange with Solute Tempering molecular dynamics simulations with NMR experiments, to investigate the conformational ensemble of n16N in solution. We verify that n16N lacks a well-defined secondary structure, both with and without the presence of Ca(2+) ions, as identified from previous experiments. Our data support the presence of three different, functional subdomains within n16N. Our results reveal that tyrosine, chiefly located in the center of the peptide, plays a multifunctional role in stabilizing conformations of n16N, for intrapeptide and possibly interpeptide interactions. Complementary NMR spectroscopy data confirm the participation of tyrosine in this stabilization. The C-terminal half of n16N, lacking in tyrosine and highly charged, shows substantive conformational diversity and is proposed as a likely site for nucleation of calcium carbonate. Finally, dominant structures from our predicted conformational ensemble suggest the presentation of key residues thought to be critical to the selective binding to β-chitin surfaces.
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The conformational ensemble of n16N, an intrinsically disordered peptide, has dominant structures that place key residues in locations thought critical for selective binding to β-chitin surfaces, as shown by REMD combined with NMR.
“However, a combination of replica exchange molecular dynamics simulations with NMR experiments showed that in the equilibrium conformational ensemble of the intrinsically disordered peptide the dominant structures present the key residues in locations thought to be critical for selective binding to β-chitin surfaces.258”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [258]
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Zhao, W., Xu, Z., Cui, Q., & Sahai, N. (2016) · Langmuir · doi:10.1021/acs.langmuir.6b01582 · Cited by 47 · see citing works
Opposed Effects of Dityrosine Formation in Soluble and Aggregated α-Synuclein on Fibril Growth
Wördehoff, M. M., Shaykhalishahi, H., Groß, L., Gremer, L., Stoldt, M., Buell, A. K., Willbold, D., & Hoyer, W. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.09.005 · Cited by 42 · see citing works
Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions
Gong, X., Zhang, Y., & Chen, J. (2021) · Biomolecules · doi:10.3390/biom11101416 · Cited by 37 · see citing works
Study of Binding Interaction between Pif80 Protein Fragment and Aragonite
Du, Y., Chang, H.-H., Yang, S., Huang, S., Tsai, Y.-J., Huang, J. J., & Chan, J. C. C. (2016) · Scientific Reports · doi:10.1038/srep30883 · Cited by 35 · see citing works
Poudel, L., Tamerler, C., Misra, A. K., & Ching, W. Y. (2017) · The Journal of Physical Chemistry C · doi:10.1021/acs.jpcc.7b10004 · Cited by 31 · see citing works
Testing the transferability of a coarse-grained model to intrinsically disordered proteins
Rutter, G. O., Brown, A. H., Quigley, D., Walsh, T. R., & Allen, M. P. (2015) · Physical Chemistry Chemical Physics · doi:10.1039/c5cp05652g · Cited by 22 · see citing works
Self-citationHicks, A., & Zhou, H. (2018) · The Journal of Chemical Physics · doi:10.1063/1.5027409 · Cited by 21 · see citing works
Analytical methods for structural ensembles and dynamics of intrinsically disordered proteins
Schor, M., Mey, A. S. J. S., & MacPhee, C. E. (2016) · Biophysical Reviews · doi:10.1007/s12551-016-0234-6 · Cited by 20 · see citing works
Organic Matrix and Secondary Metabolites in Nacre
de Muizon, C. J., Iandolo, D., Nguyen, D. K., Al‐Mourabit, A., & Rousseau, M. (2022) · Marine Biotechnology · doi:10.1007/s10126-022-10145-9 · Cited by 16 · see citing works
Church, A. T., Hughes, Z. E., & Walsh, T. R. (2015) · RSC Advances · doi:10.1039/c5ra11268k · Cited by 15 · see citing works
Self-citationHan, M., Xu, J., & Ren, Y. (2016) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2016.12.014 · Cited by 11 · see citing works
Elucidating the influence of polymorph-dependent interfacial solvent structuring at chitin surfaces
Brown, A. H., & Walsh, T. R. (2016) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2016.05.116 · Cited by 8 · see citing works
Self-citationCeramic Genomics: Total Bond Order Density
Ching, W. Y. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-803581-8.11729-1 · Cited by 7 · see citing works
Elucidating Polymorph-Selective Bioadsorption on Chitin Surfaces
Brown, A. H., & Walsh, T. R. (2019) · ACS Biomaterials Science & Engineering · doi:10.1021/acsbiomaterials.8b01260 · Cited by 6 · see citing works
Self-citationEmergence of order in self-assembly of the intrinsically disordered biomineralisation peptide n16N
Rutter, G. O., Brown, A. H., Quigley, D., Walsh, T. R., & Allen, M. P. (2017) · Molecular Simulation · doi:10.1080/08927022.2017.1405158 · Cited by 4 · see citing works
Self-citationSequence‐Dependent Heterotypic Assemblies of Intrinsically Disordered Peptides
Qiao, Y., Chu, M., Wu, G., Liu, Z., & Xu, B. (2025) · ChemistryEurope · doi:10.1002/ceur.202500124 · Cited by 1 · see citing works
In search of shape in the unshaped: Constructing ensembles of intrinsically disordered proteins
Saha, D., Yang, W., & Zheng, W. (2026) · Biophysics Reviews · doi:10.1063/5.0307183 · Cited by 1 · see citing works
Acharya, A. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/125807
Integrative computational framework to decipher the functions of shell proteins in biomineralization
Dong, W., Xie, L., & Zhang, R. (2024) · Frontiers in Marine Science · doi:10.3389/fmars.2024.1362131
Strong, Hydrophobic, and Recyclable Materials Enabled by Nacre‐Like Multiple Interactions
Zeng, F., Xia, P., Huang, W., Peng, C., Wu, J., Huang, A., Ru, Y., Guo, Z., Qiao, J., & Wang, J. (2026) · Advanced Functional Materials · doi:10.1002/adfm.78796
- Authors
- Brown, A. H., Rodger, P. M., Evans, J. S., & Walsh, T. R.
- Affiliations
- Deakin University (AU)
- University of Warwick (GB)
- New York University (US)
- Corresponding author
- Walsh, Tiffany R.
- Venue
- Biomacromolecules
- Publisher
- American Chemical Society (ACS)
- Published
- 2014-11-20
- Volume
- 15
- Issue
- 12
- Pages
- 4467-4479
- ISSN
- 1525-7797 (ISSN-L)
- 1526-4602
- OpenAlex
- W2012016586
- Cited by
- 28
- References
- 101
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 1 · 2022: 2 · 2021: 1 · 2020: 2 · 2019: 1 · 2018: 1 · 2017: 6 · 2016: 6 · 2015: 4
- FWCI
- 2.02
- Type
- journal article
- Language
- en
- Open access
- green
- figshare.com
- Licence
- cc-by
- Locations
- Biomacromolecules (publishedVersion)
- PubMed (publishedVersion)
- Deakin Research Online (Deakin University) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Funders
- Engineering and Physical Sciences Research Council (EP/I001514/1)
- University of Warwick
- Deakin University
- Topics
- Physical Sciences › Materials Science › Biomaterials › Calcium Carbonate Crystallization and Inhibition
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Biomaterials › Diatoms and Algae Research
- Keywords
- nacre, intrinsically disordered peptides, conformational ensembles, tyrosine, calcium carbonate nucleation, biomineralization, calcium ions
- MeSH terms
- Binding Sites, Calcium Carbonate, Chitin, Magnetic Resonance Spectroscopy, Peptides, Protein Conformation, Cluster Analysis, Protein Structure, Secondary, Molecular Dynamics Simulation, Nacre, Intrinsically Disordered Proteins
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