1a7b › Citations

Engineering an intertwined form of CD2 for stability and assembly.

Murray AJ, Head JG, Barker JJ, Brady RL
Nat Struct Biol 5 778-82 (1998)
Related entries: 1a64, 1a6p

Cited: 33 times
EuropePMC logo PMID: 9731771

Abstract

The amino-terminal domain of CD2 has the remarkable ability to fold in two ways: either as a monomer or as an intertwined, metastable dimer. Here we show that it is possible to differentially stabilize either fold by engineering the CD2 sequence, mimicking random mutagenesis events that could occur during molecular evolution. Crystal structures of a hinge-deletion mutant, which is stable as an intertwined dimer, reveal domain rotations that enable the protein to further assemble to a tetramer. These results demonstrate that a variety of folds can be adopted by a single polypeptide sequence, and provide guidance for the design of proteins capable of further assembly.

Articles - 1a7b mentioned but not cited (2)

  1. An improved hydrogen bond potential: impact on medium resolution protein structures. Fabiola F, Bertram R, Korostelev A, Chapman MS. Protein Sci 11 1415-1423 (2002)
  2. Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A. Merlino A, Ceruso MA, Vitagliano L, Mazzarella L. Biophys J 88 2003-2012 (2005)


Reviews citing this publication (5)

  1. Deposition diseases and 3D domain swapping. Bennett MJ, Sawaya MR, Eisenberg D. Structure 14 811-824 (2006)
  2. Protein folding and three-dimensional domain swapping: a strained relationship? Newcomer ME. Curr Opin Struct Biol 12 48-53 (2002)
  3. Protein Assembly by Design. Zhu J, Avakyan N, Kakkis A, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Chem Rev 121 13701-13796 (2021)
  4. Understanding protein domain-swapping using structure-based models of protein folding. Mascarenhas NM, Gosavi S. Prog Biophys Mol Biol 128 113-120 (2017)
  5. The micro-mechanics of single molecules studied with atomic force microscopy. Fisher TE, Marszalek PE, Oberhauser AF, Carrion-Vazquez M, Fernandez JM. J Physiol 520 Pt 1 5-14 (1999)

Articles citing this publication (26)

  1. TM-align: a protein structure alignment algorithm based on the TM-score. Zhang Y, Skolnick J. Nucleic Acids Res 33 2302-2309 (2005)
  2. Three-dimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues. Rousseau F, Schymkowitz JW, Wilkinson HR, Itzhaki LS. Proc Natl Acad Sci U S A 98 5596-5601 (2001)
  3. Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins. Vendome J, Posy S, Jin X, Bahna F, Ahlsen G, Shapiro L, Honig B. Nat Struct Mol Biol 18 693-700 (2011)
  4. Metamorphic proteins mediate evolutionary transitions of structure. Yadid I, Kirshenbaum N, Sharon M, Dym O, Tawfik DS. Proc Natl Acad Sci U S A 107 7287-7292 (2010)
  5. Topological determinants of protein domain swapping. Ding F, Prutzman KC, Campbell SL, Dokholyan NV. Structure 14 5-14 (2006)
  6. Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface? Posy S, Shapiro L, Honig B. J Mol Biol 378 954-968 (2008)
  7. Domain swapping proceeds via complete unfolding: a 19F- and 1H-NMR study of the Cyanovirin-N protein. Liu L, Byeon IJ, Bahar I, Gronenborn AM. J Am Chem Soc 134 4229-4235 (2012)
  8. Effect of pH and salt bridges on structural assembly: molecular structures of the monomer and intertwined dimer of the Eps8 SH3 domain. Kishan KV, Newcomer ME, Rhodes TH, Guilliot SD. Protein Sci 10 1046-1055 (2001)
  9. Identification and structure of the nerve growth factor binding site on TrkA. Robertson AG, Banfield MJ, Allen SJ, Dando JA, Mason GG, Tyler SJ, Bennett GS, Brain SD, Clarke AR, Naylor RL, Wilcock GK, Brady RL, Dawbarn D. Biochem Biophys Res Commun 282 131-141 (2001)
  10. Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations. Launay G, Simonson T. BMC Bioinformatics 9 427 (2008)
  11. Engineered Domain Swapping as an On/Off Switch for Protein Function. Ha JH, Karchin JM, Walker-Kopp N, Castañeda CA, Loh SN. Chem Biol 22 1384-1393 (2015)
  12. 3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. Shameer K, Shingate PN, Manjunath SC, Karthika M, Pugalenthi G, Sowdhamini R. Database (Oxford) 2011 bar042 (2011)
  13. A five-residue motif for the design of domain swapping in proteins. Nandwani N, Surana P, Negi H, Mascarenhas NM, Udgaonkar JB, Das R, Gosavi S. Nat Commun 10 452 (2019)
  14. Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach. Shameer K, Pugalenthi G, Kandaswamy KK, Suganthan PN, Archunan G, Sowdhamini R. Bioinform Biol Insights 4 33-42 (2010)
  15. The enigma of the near-symmetry of proteins: Domain swapping. Bonjack-Shterengartz M, Avnir D. PLoS One 12 e0180030 (2017)
  16. Crystal structures of designed armadillo repeat proteins: implications of construct design and crystallization conditions on overall structure. Reichen C, Madhurantakam C, Plückthun A, Mittl PR. Protein Sci 23 1572-1583 (2014)
  17. Efficient folding of the FcepsilonRI alpha-chain membrane-proximal domain D2 depends on the presence of the N-terminal domain D1. Vangelista L, Cesco-Gaspere M, Lamba D, Burrone O. J Mol Biol 322 815-825 (2002)
  18. Backbone resonance assignment and order tensor estimation using residual dipolar couplings. Shealy P, Liu Y, Simin M, Valafar H. J Biomol NMR 50 357-369 (2011)
  19. Stability of structurally entangled protein dimers. Zhao Y, Cieplak M. Proteins 86 945-955 (2018)
  20. Two independently folding units of Plasmodium profilin suggest evolution via gene fusion. Bhargav SP, Vahokoski J, Kallio JP, Torda AE, Kursula P, Kursula I. Cell Mol Life Sci 72 4193-4203 (2015)
  21. HORI: a web server to compute Higher Order Residue Interactions in protein structures. Sundaramurthy P, Shameer K, Sreenivasan R, Gakkhar S, Sowdhamini R. BMC Bioinformatics 11 Suppl 1 S24 (2010)
  22. Topological and Structural Plasticity of the Single Ig Fold and the Double Ig Fold Present in CD19. Youkharibache P. Biomolecules 11 1290 (2021)
  23. Amino-acid composition after loop deletion drives domain swapping. Nandwani N, Surana P, Udgaonkar JB, Das R, Gosavi S. Protein Sci 26 1994-2002 (2017)
  24. Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA. Fahim A, Mukhopadhyay R, Yandle R, Prestegard JH, Valafar H. Molecules 18 10162-10188 (2013)
  25. EnCPdock: a web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations. Biswas G, Mukherjee D, Dutta N, Ghosh P, Basu S. J Mol Model 29 239 (2023)
  26. Monothiol and dithiol glutaredoxin-1 from Clostridium oremlandii: identification of domain-swapped structures by NMR, X-ray crystallography and HDX mass spectrometry. Lee K, Yeo KJ, Choi SH, Lee EH, Kim BK, Kim S, Cheong HK, Lee WK, Kim HY, Hwang E, Woo JR, Lee SJ, Hwang KY. IUCrJ 7 1019-1027 (2020)


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