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Rutter GO, Brown AH, Quigley D, Walsh TR, Allen MP. Emergence of order in self-assembly of the intrinsically disordered biomineralisation peptide n16N. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1405158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- G. O. Rutter
- Department of Physics, University of Warwick, Coventry, UK
| | - A. H. Brown
- Institute for Frontier Materials, Deakin University, Geelong, Australia
| | - D. Quigley
- Department of Physics, University of Warwick, Coventry, UK
| | - T. R. Walsh
- Institute for Frontier Materials, Deakin University, Geelong, Australia
| | - M. P. Allen
- Department of Physics, University of Warwick, Coventry, UK
- H. H. Wills Physics Laboratory, Bristol, UK
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2
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Rutter GO, Brown AH, Quigley D, Walsh TR, Allen MP. Testing the transferability of a coarse-grained model to intrinsically disordered proteins. Phys Chem Chem Phys 2015; 17:31741-9. [DOI: 10.1039/c5cp05652g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The coarse-grained PLUM model is shown to capture structural and dimerization behaviour of the intrinsically disordered biomineralisation peptide n16N.
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Affiliation(s)
- Gil O. Rutter
- Department of Physics
- University of Warwick
- Coventry CV4 7AL
- UK
| | - Aaron H. Brown
- Department of Chemistry and Centre for Scientific Computing
- University of Warwick
- Coventry
- UK
- Institute for Frontier Materials
| | - David Quigley
- Department of Physics and Centre for Scientific Computing
- University of Warwick
- Coventry CV4 7AL
- UK
| | - Tiffany R. Walsh
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Michael P. Allen
- Department of Physics
- University of Warwick
- Coventry CV4 7AL
- UK
- H. H. Wills Physics Laboratory
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Brown AH, Rodger PM, Evans JS, Walsh TR. Equilibrium Conformational Ensemble of the Intrinsically Disordered Peptide n16N: Linking Subdomain Structures and Function in Nacre. Biomacromolecules 2014; 15:4467-79. [DOI: 10.1021/bm501263s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Aaron H. Brown
- Institute
for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | | | - John Spencer Evans
- Department
of Craniofacial Biology and Center for Skeletal Sciences, New York University, New York, New York 10010, United States
| | - Tiffany R. Walsh
- Institute
for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
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Montagnani C, Marie B, Marin F, Belliard C, Riquet F, Tayalé A, Zanella-Cléon I, Fleury E, Gueguen Y, Piquemal D, Cochennec-Laureau N. Pmarg-pearlin is a matrix protein involved in nacre framework formation in the pearl oyster Pinctada margaritifera. Chembiochem 2011; 12:2033-43. [PMID: 21796751 DOI: 10.1002/cbic.201100216] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Indexed: 11/07/2022]
Abstract
The shell of pearl oysters is organized in multiple layers of CaCO(3) crystallites packed together in an organic matrix. Relationships between the components of the organic matrix and mechanisms of nacre formation currently constitute the main focus of research into biomineralization. In this study, we characterized the pearlin protein from the oyster Pinctada margaritifera (Pmarg); this shares structural features with other members of a matrix protein family, N14/N16/pearlin. Pmarg pearlin exhibits calcium- and chitin-binding properties. Pmarg pearlin transcripts are distinctively localized in the mineralizing tissue responsible for nacre formation. More specifically, we demonstrate that Pmarg pearlin is localized within the interlamellar matrix of nacre aragonite tablets. Our results support recent models for multidomain matrix protein involvement in nacreous layer formation. We provide evidence here for the existence of a conserved family of nacre-associated proteins in Pteriidae, and reassess the evolutionarily conserved set of biomineralization genes related to nacre formation in this taxa.
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Affiliation(s)
- C Montagnani
- Laboratoire Biotechnologie et Qualité de la Perle, Ifremer, Centre Océanologique du Pacifique, BP 7004, 98719 Taravao, Tahiti, French Polynesia.
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Metzler RA, Tribello GA, Parrinello M, Gilbert PUPA. Asprich Peptides Are Occluded in Calcite and Permanently Disorder Biomineral Crystals. J Am Chem Soc 2010; 132:11585-91. [DOI: 10.1021/ja103089r] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rebecca A. Metzler
- Department of Physics, University of Wisconsin—Madison, 1150 University Avenue, Madison, Wisconsin 53706, Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich USI-Campus, Via Giuseppe Buffi 13, C-6900 Lugano, Switzerland
| | - Gareth A. Tribello
- Department of Physics, University of Wisconsin—Madison, 1150 University Avenue, Madison, Wisconsin 53706, Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich USI-Campus, Via Giuseppe Buffi 13, C-6900 Lugano, Switzerland
| | - Michele Parrinello
- Department of Physics, University of Wisconsin—Madison, 1150 University Avenue, Madison, Wisconsin 53706, Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich USI-Campus, Via Giuseppe Buffi 13, C-6900 Lugano, Switzerland
| | - P. U. P. A. Gilbert
- Department of Physics, University of Wisconsin—Madison, 1150 University Avenue, Madison, Wisconsin 53706, Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich USI-Campus, Via Giuseppe Buffi 13, C-6900 Lugano, Switzerland
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Skelton AA, Liang T, Walsh TR. Interplay of sequence, conformation, and binding at the Peptide-titania interface as mediated by water. ACS APPLIED MATERIALS & INTERFACES 2009; 1:1482-1491. [PMID: 20355952 DOI: 10.1021/am9001666] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The initial stages of the adsorption of a hexapeptide at the aqueous titania interface are modeled using atomistic molecular dynamics simulations. This hexapeptide has been identified by experiment [Sano, K. I.; Shiba, K. J. Am. Chem. Soc. 2003, 125, 14234] to bind to Ti particles. We explore the current hypothesis presented by these authors that binding at this peptide-titania interface is the result of electrostatic interactions and find that contact with the surface appears to take place via a pair of oppositely charged groups in the peptide. Our data indicate that the peptide may initially recognize the water layers at the interface, not the titania surface itself, via these charged groups. We also report results of simulations for hexapeptide sequences with selected single-point mutations for alanine and compare these behaviors with those suggested from observed binding affinities from existing alanine scan experiments. Our results indicate that factors in addition to electrostatics also contribute, with the structural rigidity conferred by proline suggested to play a significant role. Finally, our findings suggest that intrapeptide interaction may provide mechanisms for surface detachment that could be detrimental to binding at the interface.
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Affiliation(s)
- Adam A Skelton
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, UK.
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Amos FF, Evans JS. AP7, a Partially Disordered Pseudo C-RING Protein, Is Capable of Forming Stabilized Aragonite in Vitro. Biochemistry 2009; 48:1332-9. [DOI: 10.1021/bi802148r] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fairland F. Amos
- Laboratory for Chemical Physics, New York University, 345 East 24th Street, New York, New York 10010
| | - John Spencer Evans
- Laboratory for Chemical Physics, New York University, 345 East 24th Street, New York, New York 10010
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8
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Sommerdijk NAJM, With GD. Biomimetic CaCO3 Mineralization using Designer Molecules and Interfaces. Chem Rev 2008; 108:4499-550. [DOI: 10.1021/cr078259o] [Citation(s) in RCA: 369] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nico A. J. M. Sommerdijk
- Soft-matter cryoTEM Research Unit and Laboratory of Materials and Interface Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Gijsbertus de With
- Soft-matter cryoTEM Research Unit and Laboratory of Materials and Interface Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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Collino S, Evans JS. Molecular specifications of a mineral modulation sequence derived from the aragonite-promoting protein n16. Biomacromolecules 2008; 9:1909-18. [PMID: 18558739 DOI: 10.1021/bm8001599] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In the nacre layer of the mollusk, proteins play an important role in regulating the morphology and lattice structure of calcium carbonate minerals. However, this process remains elusive due to the fact that we do not understand how protein sequences control the structure and morphology of biominerals. To take us a step further in this direction, we report the molecular structure of a 30 AA N-terminal mineral interactive sequence (n16N) of the aragonite-promoting protein, n16, and contrast these findings to those previously reported for two "calcite-blocker" nacre-associated sequences, AP7N and AP24N. We find that n16N is conformationally labile and adopts a random-coil conformation that possesses short, dispersed extended beta-strand segments that are located at the A1-Y2, K5-Y9, Y11-I14, and D21-N25 sequence blocks. Like AP7N and AP24N, Ca(II) ion interactions with n16N alter chain dynamics and local structure, and n16N is adsorbed onto calcite crystals and cannot easily be displaced via differential washing techniques. Furthermore, all three sequences have planar surface regions that could serve as putative sites for mineral interactions or ion cluster formation. However, what sets n16N apart from AP7N and AP24N are different folding propensities as well as unique molecular surface features and amino acid composition. n16N has a more condensed structure that, in the presence of TFE, folds into a beta-strand. This contrasts with the more open structures of AP7N and AP24N that are induced by TFE to fold into alpha-helices. Mapping of the n16N molecular surface reveals significant cationic regions and diffuse anionic charge, which contrasts with the small anionic "pocket" regions of AP7N/AP24N. Finally, n16N has 50% fewer sites for mineral surface- or ion cluster-associated water interactions compared to AP7N and AP24N. Overall, the structure of n16N is "tuned" to a different function within the in vitro mineralization scheme. The different features found in AP7N, AP24N, and n16N could be exploited for engineering polypeptides that recognize and bind to different surface features of inorganic crystalline solids.
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Affiliation(s)
- Sebastiano Collino
- Laboratory for Chemical Physics, Center for Biomolecular Materials Spectroscopy, New York University, 345 East 24th Street, Room 1007, New York, New York 10010, USA
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Collino S, Kim IW, Evans JS. Identification and structural characterization of an unusual RING-like sequence within an extracellular biomineralization protein, AP7. Biochemistry 2008; 47:3745-55. [PMID: 18298090 DOI: 10.1021/bi701949p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The RING or Really Interesting New Gene represents a family of eukaryotic sequences that bind Zn (II) ions and participate in intracellular processes involving protein-protein interaction. Although found in over 400 different proteins, very little is known regarding the structure-function properties of these domains because of the aggregation problems associated with RING sequences. To augment this data set, we report an unusual 36 AA C-terminal sequence of an extracellular matrix mollusk shell protein, AP7, that exhibits partial homology to the RING family. This Cys, His-containing sequence, termed AP7C, binds Zn (II) and other multivalent ions, but does not utilize a tetracoordinate complexation scheme for binding such as that found in Zn (II) finger polypeptides. Moreover, unlike Zn (II) finger and RING domains, this 36 AA can fold into a relatively stable structure in the absence of Zn (II). This folded structure consists of three short helical segments (A, B, and C), with segments A and B separated by a 4 AA type I beta-turn region and segments B and C separated by a 7 AA loop-like region. Interestingly, the putative RING-like region, -RRPFHECALCYSI-, experiences slow conformational exchange between two structural states in solution, most likely in response to imido ring interconversion at P8 and P21. Poisson-Boltzmann solvation calculations reveal that the AP7C molecular surface possesses a cationic region near its N-terminus, which lies adjacent to the 30 AA mineral modification domain in the AP7 protein. Given that the AP7C sequence does not influence mineralization, it is probable that this cationic pseudo-RING region is utilized by the AP7 protein for other tasks such as protein-protein interaction within the mollusk shell matrix.
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Affiliation(s)
- Sebastiano Collino
- Laboratory for Chemical Physics, Center for Biomolecular Materials Spectroscopy, New York University, 345 E. 24th Street, Room 1007, New York, New York 10010, USA
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