Site-specific determination of TTR-related functional peptides by using scanning tunneling microscopy
Download citation
601
Views
11
Downloads
9
Crossref
N/A
WoS
7
Scopus
0
CSCD
For the design and optimization of functional peptides, unravelling the structures of individual building blocks as well as the properties of the ensemble is paramount. TTR1, derived from human transthyretin, is a fibril-forming peptide implicated in diseases such as familial amyloid polyneuropathy and senile systemic amyloidosis. The functional peptide TTR1-RGD, based on a TTR1 scaffold, was designed to specifically interact with cells. Here, we used scanning tunneling microscopy (STM) to analyze the assembly structures of TTR1-related peptides with both the reverse sequence and the modified forward sequence. The sitespecific analyses show the following: ⅰ) The TTR1 peptide is involved in assembly, nearly covering the entire length within the ordered β-sheet structures. ⅱ) For TTR1-RGD peptide assemblies, the TTR1 motif forms the ordered β-sheet while the RGDS motif adopts a flexible conformation allowing it to promote cell adhesion. The key site is clearly identified as the linker residue Gly13. ⅲ) Close inspection of the forward and reverse peptide assemblies show that in spite of the difference in chemistry, they display similar assembling characteristics, illustrating the robust nature of these peptides. iv) Glycine linker residues are included in the β-strands, which strongly suggests that the sequence could be optimized by adding more linker residues. These garnered insights into the assembled structures of these peptides help unravel the mechanism driving peptide assemblies and instruct the rational design and optimization of sequenceprogrammed peptide architectures.
menu
Site-specific determination of TTR-related functional peptides by using scanning tunneling microscopy
Abstract
For the design and optimization of functional peptides, unravelling the structures of individual building blocks as well as the properties of the ensemble is paramount. TTR1, derived from human transthyretin, is a fibril-forming peptide implicated in diseases such as familial amyloid polyneuropathy and senile systemic amyloidosis. The functional peptide TTR1-RGD, based on a TTR1 scaffold, was designed to specifically interact with cells. Here, we used scanning tunneling microscopy (STM) to analyze the assembly structures of TTR1-related peptides with both the reverse sequence and the modified forward sequence. The sitespecific analyses show the following: ⅰ) The TTR1 peptide is involved in assembly, nearly covering the entire length within the ordered β-sheet structures. ⅱ) For TTR1-RGD peptide assemblies, the TTR1 motif forms the ordered β-sheet while the RGDS motif adopts a flexible conformation allowing it to promote cell adhesion. The key site is clearly identified as the linker residue Gly13. ⅲ) Close inspection of the forward and reverse peptide assemblies show that in spite of the difference in chemistry, they display similar assembling characteristics, illustrating the robust nature of these peptides. iv) Glycine linker residues are included in the β-strands, which strongly suggests that the sequence could be optimized by adding more linker residues. These garnered insights into the assembled structures of these peptides help unravel the mechanism driving peptide assemblies and instruct the rational design and optimization of sequenceprogrammed peptide architectures.
References(34)
Stoddart, J. F. Editorial: From supramolecular to systems chemistry: Complexity emerging out of simplicity. Angew. Chem., Int. Ed. 2012, 51, 12902-12903.
Srinivasan, S.; Praveen, V. K.; Philip, R.; Ajayaghosh, A. Bioinspired superhydrophobic coatings of carbon nanotubes and linear π systems based on the "bottom-up" self-assembly approach. Angew. Chem., Int. Ed. 2008, 47, 5750-5754.
Williams, R. J.; Smith, A. M.; Collins, R.; Hodson, N.; Das, A. K.; Ulijn, R. V. Enzyme-assisted self-assembly under thermodynamic control. Nat. Nanotechnol. 2009, 4, 19-24.
Yang, Y. L.; Khoe, U.; Wang, X. M.; Horii, A.; Yokoi, H.; Zhang, S. G. Designer self-assembling peptide nanomaterials. Nanotoday 2009, 4, 193-210.
Scanlon, S.; Aggeli, A. Self-assembling peptide nanotubes. Nanotoday 2008, 3, 22-30.
Fleming, S.; Ulijn, R. V. Design of nanostructures based on aromatic peptide amphiphiles. Chem. Soc. Rev. 2014, 43, 8150-8177.
Gustavsson, Å.; Engström, U.; Westermark, P. Normal transthyretin and synthetic transthyretin fragments from amyloid-like fibrils in vitro. Biochem. Biophys. Res. Commun. 1991, 175, 1159-1164.
Kelly, J. W. The alternative conformations of amyloidogenic proteins and their multi-step assembly pathways. Curr. Opin. Struct. Biol. 1998, 8, 101-106.
Sunde, M.; Blake, C. C. F. From the globular to the fibrous state: Protein structure and structural conversion in amyloid formation. Q. Rev. Biophys. 1998, 31, 1-39.
Jaroniec, C. P.; MacPhee, C. E.; Bajaj, V. S.; McMahon, M. T.; Dobson, C. M.; Griffin, R. G. High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy. Proc. Natl. Acad. Sci. USA 2004, 101, 711-716.
Gras, S. L.; Tickler, A. K.; Squires, A. M.; Devlin, G. L.; Horton, M. A.; Dobson, C. M.; MacPhee, C. E. Functionalised amyloid fibrils for roles in cell adhesion. Biomaterials 2008, 29, 1553-1562.
Pierschbacher, M. D.; Ruoslahti, E. Variants of the cell recognition site of fibronectin that retain attachment-promoting activity. Proc. Natl. Acad. Sci. USA 1984, 81, 5985-5988.
Hautanen, A.; Gailit, J.; Mann, D. M.; Ruoslahti, E. Effects of modifications of the RGD sequence and its context on recognition by the fibronectin receptor. J. Biol. Chem. 1989, 264, 1437-1442.
Baldwin, A. J.; Knowles, T. P. J.; Tartaglia, G. G.; Fitzpatrick, A. W.; Devlin, G. L.; Shammas, S. L.; Waudby, C. A.; Mossuto, M. F.; Meehan, S.; Gras, S. L. et al. Metastability of native proteins and the phenomenon of amyloid formation. J. Am. Chem. Soc. 2011, 133, 14160-14163.
Bongiovanni, M. N.; Puri, D.; Goldie, K. N.; Gras, S. L. Noncore residues influence the kinetics of functional TTR105-115-based amyloid fibril assembly. J. Mol. Biol. 2012, 421, 256-269.
Rodríguez-Pérez, J. C.; Hamley, I. W.; Grasb, S. L.; Squires, A. M. Local orientational disorder in peptide fibrils probed by a combination of residue-specific 13C-18O labelling, polarised infrared spectroscopy and molecular combing. Chem. Commun. 2012, 48, 11835-11837.
Liu, L.; Zhang, L.; Mao, X. B.; Niu, L.; Yang, Y. L.; Wang, C. Chaperon-mediated single molecular approach toward modulating aβ peptide aggregation. Nano Lett. 2009, 9, 4066-4072.
Ma, X. J.; Liu, L.; Mao, X. B.; Niu, L.; Deng, K.; Wu, W. H.; Li, Y. M.; Yang, Y. L.; Wang, C. Amyloid β (1-42) folding multiplicity and single-molecule binding behavior studied with STM. J. Mol. Biol. 2009, 388, 894-901.
Mao, X. B.; Guo, Y. Y.; Luo, Y.; Niu, L.; Liu, L.; Ma, X. J.; Wang, H. B.; Yang, Y. L.; Wei, G. H.; Wang, C. Sequence effects on peptide assembly characteristics observed by using scanning tunneling microscopy. J. Am. Chem. Soc. 2013, 135, 2181-2187.
Yu, L. L.; Sun, Z. Y.; Yu, Y.; Qu, F. Y.; Yang, Y. L.; Li, Y. M.; Wang, C. Molecular evidence of glycosylation effect on the peptide assemblies identified with scanning tunneling microscopy. J. Phys. Chem. C 2016, 120, 6577-6582.
Mao, X. B.; Wang, C. X.; Wu, X. K.; Ma, X. J.; Liu, L.; Zhang, L.; Niu, L.; Guo, Y. Y.; Li, D. H.; Yang, Y. L. et al. Beta structure motifs of islet amyloid polypeptides identified through surface-mediated assemblies. Proc. Natl. Acad. Sci. USA 2011, 108, 19605-19610.
Xu, M.; Zhu, L.; Liu, J. H.; Yang, Y. L.; Wu, J. Y.; Wang, C. Characterization of β-domains in C-terminal fragments of TDP-43 by scanning tunneling microscopy. J. Struct. Biol. 2013, 181, 11-16.
Caporini, M. A.; Bajaj, V. S.; Veshtort, M.; Fitzpatrick, A.; MacPhee, C. E.; Vendruscolo, M.; Dobson, C. M.; Griffin, R. G. Accurate determination of interstrand distances and alignment in amyloid fibrils by magic angle spinning nmr. J. Phys. Chem. B 2010, 114, 13555-13561.
Miyazawa, T. Perturbation treatment of the characteristic vibrations of polypeptide chains in various configurations. J. Chem. Phys. 1960, 32, 1647-1652.
Yu, Y.; Yang, Y. L.; Wang, C. Identification of core segment of amyloidal peptide mediated by chaperone molecules by using scanning tunneling microscopy. ChemPhysChem 2015, 16, 2995-2999.
Garrett., R. H.; Grisham., C. M. Biochemistry, 2nd ed; Saunders College Publishing: London, UK, 1999.
Fitzpatrick, A. W. P.; Debelouchina, G. T.; Bayro, M. J.; Clare, D. K.; Caporini, M. A.; Bajaj, V. S.; Jaroniec, C. P.; Wang, L. C.; Ladizhansky, V.; Muller, S. A. et al. Atomic structure and hierarchical assembly of a cross-β amyloid fibril. Proc. Natl. Acad. Sci. USA 2013, 110, 5468-5473.
Ma, X. J.; Shen, Y. T.; Deng, K.; Tang, H.; Lei, S. B.; Wang, C.; Yang, Y. L.; Feng, X. Z. Matrix-molecule induced chiral enhancement effect of binary supramolecular liquid crystals. J. Mater. Chem. 2007, 17, 4699-4704.
Liu, L.; Niu, L.; Xu, M.; Han, Q. S.; Duan, H. Y.; Dong, M. D.; Besenbacher, F.; Wang, C.; Yang, Y. L. Molecular tethering effect of C-terminus of amyloid peptide aβ42. ACS Nano 2014, 8, 9503-9510.
Gustavsson, Å.; Engström, U.; Westermark, P. Transthyretin (TTR)-derived amyloid fibrils: Immunoelectron microscopy of fibrils formed in vivo and in vitro from synthetic peptides and normal transthyretin. Amyloid. 1997, 4, 1-12.
Hornberg, A.; Eneqvist, T.; Olofsson, A.; Lundgren, E.; Sauer-Eriksson, A. E. A comparative analysis of 23 structures of the amyloidogenic protein transthyretin. J. Mol. Biol. 2000, 302, 649-669.
Tsuchiya-Suzuki, A.; Yazaki, M.; Kametani, F.; Sekijima, Y.; Ikeda, S. Wild-type transthyretin significantly contributes to the formation of amyloid fibrils in familial amyloid polyneuropathy patients with amyloidogenic transthyretin val30met. Hum. Pathol. 2011, 42, 236-243.
Hersel, U.; Dahmen, C.; Kessler, H. Rgd modified polymers: Biomaterials for stimulated cell adhesion and beyond. Biomaterials 2003, 24, 4385-4415.
Beer, J. H.; Springer, K. T.; Coller, B. S. Immobilized Arg-Gly-Asp (RGD) peptides of varying lengths as structural probes of the platelet glycoprotein Ⅱb/Ⅲa receptor. Blood 1992, 79, 117-128.
Publication history
Copyright
Acknowledgements
This work was supported by the National Natural Science Foundation of China (Nos. 21673055 and 21273051), the Chinese Academy of Sciences (Nos. XDA09040300, XDA09030306, and YZ201317) and The ARC Dairy Innovation Hub (No. IH120100005). Financial support from CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology are also gratefully acknowledged.
FEEDBACK 
TOP