Two-dimensional IR spectroscopy and segmental 13C labeling reveals the domain structure of human γD-crystallin amyloid fibrils

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 9, 2012, Pages 3329-3334

  Moran, Sean D ^a,b   Woys, Ann Marie ^a   Buchanan, Lauren E ^a   Bixby, Eli ^b   Decatur, Sean M ^b   Zanni, Martin T ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b OBERLIN COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID; CARBON 13; GAMMA CRYSTALLIN; GAMMAD CRYSTALLIN; MONOMER; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; CARBOXY TERMINAL SEQUENCE; HUMAN; INFRARED SPECTROSCOPY; ISOTOPE DILUTION ASSAY; ISOTOPE LABELING; MOLECULAR MODEL; PH; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN CONFORMATION; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; TWO DIMENSIONAL INFRARED SPECTROSCOPY;

AMYLOID; GAMMA-CRYSTALLINS; HUMANS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SPECTROPHOTOMETRY, INFRARED;

EID: 84857746675     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1117704109     Document Type: Article

References (36)

1. Wang Y, King JA (2010) Cataract as a protein-aggregation disease. Protein Misfolding Diseases (Wiley, New York), pp 487-515.
2. Bloemendal H, et al. (2004) Aging and vision: Structure, stability and function of lens crystallins. Prog Biophys Mol Biol 86:407-485. (Pubitemid 39081525)
3. Luca S, Yau W-M, Leapman R, Tycko R (2007) Peptide conformation and supramolecular organization in amylin fibrils: Constraints from solid-state NMR. Biochemistry 46:13505-13522. (Pubitemid 350209947)
4. Tycko R (2006) Molecular structure of amyloid fibrils: Insights from solid-state NMR. Q Rev Biophys 39:1-55.
5. Nelson R, et al. (2005) Structure of the cross-β spine of amyloid-like fibrils. Nature 435:773-778. (Pubitemid 40839722)
6. Shim S-H, et al. (2009) Two-dimensional IR spectroscopy and isotope labeling defines the pathway of amyloid formation with residue-specific resolution. Proc Natl Acad Sci USA 106:6614-6619.
7. Strasfeld DB, Ling YL, Gupta R, Raleigh DP, Zanni MT (2009) Strategies for extracting structural information from 2D IR spectroscopy of amyloid: Application to islet amyloid polypeptide. J Phys Chem B 113:15679-15691.
8. Kim YS, Liu L, Axelsen PH, Hochstrasser RM(2008) Two-dimensional infrared spectra of isotopically diluted amyloid fibrils from Aβ40. Proc Natl Acad Sci USA 105:7720-7725. (Pubitemid 351872705)
9. Smith AW, Tokmakoff A (2007) Probing local structural events in β-hairpin unfolding with transient nonlinear infrared spectroscopy. Angew Chem Int Ed 46:7984-7987. (Pubitemid 350033472)
10. Kolano C, Helbing J, Kozinski M, Sander W, Hamm P (2006) Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy. Nature 444:469-472. (Pubitemid 44809061)
11. Wang L, et al. (2011) 2D IR spectroscopy of human amylin fibrils reflects stable β-sheet structure. J Am Chem Soc 133:16062-16071.
12. Zhuang W, Abramavicius D, Voronine DV, Mukamel S (2007) Simulation of two-dimensional infrared spectroscopy of amyloid fibrils. Proc Natl Acad Sci USA 104:14233-14236. (Pubitemid 350003245)
13. Woys AM, et al. (2010) 2D IR line shapes probe ovispirin peptide conformation and depth in lipid bilayers. J Am Chem Soc 132:2832-2838.
14. Dijkstra AG, Jansen TlC, Knoester J (2011) Modeling the vibrational dynamics and nonlinear infrared spectra of coupled amide I and II modes in peptides. J Phys Chem B 115:5392-5401.
15. Hahn S, Kim S-S, Lee C, Cho M (2005) Characteristic two-dimensional IR spectroscopic features of antiparallel and parallel β-sheet polypeptides: Simulation studies. J Chem Phys 123:084905.
16. Manor J, et al. (2009) Gating mechanism of the influenza AM2 channel revealed by 1D and 2D IR spectroscopies. Structure 17:247-254.
17. Middleton CT, Woys AM, Mukherjee SS, Zanni MT (2010) Residue-specific structural kinetics of proteins through the union of isotope labeling, mid-IR pulse shaping, and coherent 2D IR spectroscopy. Methods 52:12-22.
18. Hamm P, Zanni M (2011) Concepts and Methods of 2D Infrared Spectroscopy (Cambridge University Press, New York).
19. Naraharisetty SRG, et al. (2009) C-D modes of deuterated side chain of leucine as structural reporters via dual-frequency two-dimensional infrared spectroscopy. J Phys Chem B 113:4940-4946.
20. Thielges MC, et al. (2011) Two-dimensional IR spectroscopy of protein dynamics using two vibrational labels: A site-specific genetically encoded unnatural amino acid and an active site ligand. J Phys Chem B 115:11294-11304.
21. Getahun Z, et al. (2003) Using nitrile-derivatized amino acids as infrared probes of local environment. J Am Chem Soc 125:405-411. (Pubitemid 36077861)
22. Flavell RR, Muir TW(2009) Expressed protein ligation (EPL) in the study of signal transduction, ion conduction, and chromatin biology. Acc Chem Res 42:107-116.
23. Dawson PE, Muir TW, Clark-Lewis I, Kent SB (1994) Synthesis of proteins by native chemical ligation. Science 266:776-779. (Pubitemid 24359280)
24. Su S, et al. (2011) Proteomic analysis of human age-related nuclear cataracts and normal lens nuclei. Invest Ophthalmol Visual Sci 52:4182-4191.
25. Basak A, et al. (2003) High-resolution X-ray crystal structures of human γD-crystallin (1.25 Å) and the R58H mutant (1.15 Å) associated with aculeiform cataract. J Mol Biol 328:1137-1147. (Pubitemid 36506879)
26. Das P, King JA, Zhou R (2011) Aggregation of ã-crystallins associated with human cataracts via domain swapping at the C-terminal â-strands. Proc Natl Acad Sci USA 108:10514-10519.
27. Papanikolopoulou K, et al. (2008) Formation of amyloid fibrils in vitro by human γD-crystallin and its isolated domains. Mol Vision 14:81-89.
28. Fatima U, Sharma S, Guptasarma P (2010) Structures of differently aggregated and precipitated forms of γB crystallin: An FTIR spectroscopic and EM study. Protein Pept Lett 17:1155-1162.
29. Ecroyd H, Carver JA (2009) Crystallin proteins and amyloid fibrils. Cell Mol Life Sci 66:62-81.
30. Flaugh SL, Kosinski-Collins MS, King J (2005) Interdomain side-chain interactions in human γD crystallin influencing folding and stability. Protein Sci 14:2030-2043. (Pubitemid 41132368)
31. Kosinski-Collins MS, Flaugh SL, King J (2004) Probing folding and fluorescence quenching in human γD crystallin Greek key domains using triple tryptophan mutant proteins. Protein Sci 13:2223-2235. (Pubitemid 38989625)
32. Brubaker WD, et al. (2011) Separating instability from aggregation propensity in γS-crystallin variants. Biophys J 100:498-506.
33. Sahin E, et al. (2011) Computational design and biophysical characterization of aggregation-resistant point mutations for γD crystallin illustrate a balance of conformational stability and intrinsic aggregation propensity. Biochemistry 50:628-639.
34. Kwak K, Rosenfeld DE, Fayer MD (2008) Taking apart the two-dimensional infrared vibrational echo spectra: More information and elimination of distortions. J Chem Phys 128:204505.
35. Petty SA, Decatur SM (2005) Intersheet rearrangement of polypeptides during nucleation of β-sheet aggregates. Proc Natl Acad Sci USA 102:14272-14277. (Pubitemid 41429688)
36. Lomas DA, Evans DL, Finch JT, Carrell RW (1992) The mechanism of Z-α1-antitrypsin accumulation in the liver. Nature 357:605-607.