Single-molecule protein interaction conformational dynamics

Current Pharmaceutical Biotechnology

Volumn 10, Issue 5, 2009, Pages 522-531

  Lu, H Peter ^a  

^a BOWLING GREEN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALMODULIN; DNA;

AMINO TERMINAL SEQUENCE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; CELL METABOLISM; CELL SURFACE; DNA REPAIR; DYNAMICS; ENZYME SUBSTRATE; FLUORESCENCE POLARIZATION; GENE EXPRESSION; GENETIC TRANSFORMATION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; SIGNAL TRANSDUCTION; SINGLE MOLECULE SPECTROSCOPY; SPECTROSCOPY; ALGORITHM; CELL COMMUNICATION; CHEMISTRY; DNA DAMAGE; FLUORESCENCE RESONANCE ENERGY TRANSFER; SPECTROFLUOROMETRY;

ALGORITHMS; CALMODULIN; CELL COMMUNICATION; DNA; DNA DAMAGE; FLUORESCENCE RESONANCE ENERGY TRANSFER; PROTEIN CONFORMATION; SIGNAL TRANSDUCTION; SPECTROMETRY, FLUORESCENCE;

EID: 70350482712     PISSN: 13892010     EISSN: 18734316     Source Type: Journal    
DOI: 10.2174/138920109788922119     Document Type: Review

References (51)

1. Koshland, D. E. (1958). Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA, 44, 98.
2. (a) Frueh, D.P.; Arthanari, H.; Koglin, A.; Vosburg, D.A.; Bennett, A.E.; Walsh, C.T. and Wagner, G. (2008) Dynamic thiolation-thioesterase structure of a non-ribosomal peptide synthetase. Nature, 454, 903-906
3. (b) Koglin, A.; Löhr, F.; Bernhard, F.; Rogov, V.V.; Frueh, D.P.; Strieter, E.R.; Mofid, M.R; Güntert, P.; Wagner, G.; Walsh, C.T.; Marahiel, M.A. and Dötsch, V. (2008) Structural basis for the selectivity of the external thioesterase of the surfactin synthetase. Nature, 454, 907-911
4. (c) Ma, B. ; Kumar, S. ; Tsai, C. J. and Nussinov, R. (1999) Folding funnels and binding mechanism. Protein Eng. Des. Sel., 12, 713
5. (d) Lange, O. F. ; Lakomek, N. A. ; Farès, C. ; Schröder, G. F. ; Walter, K. F. ; Becker, S. ; Meiler, J. ; Grubmüller, H. ; Griesinger, C. and de Groot, B. L. (2008) Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science, 320, 1471. (Pubitemid 351929422)
6. (a) Berger, C. et al., (1999) Antigen recognition by conformational selection. FEBS Lett., 450, 149
7. (b) Foote, J. and Milstein, C. (1994) Conformational isomerism and the diversity of antibodies Proc. Natl. Acad. Sci. USA, 91, 10370 (Pubitemid 24328998)
8. (c) James, L. C.; Roversi, P. and Tawfik, D. S. (2003) Antibody multispecificity mediated by conformational diversity. Science, 299, 1362. (Pubitemid 36254643)
9. Liu, R.; Hu, D.; Tan, X. and Lu, H. P. (2006) Revealing two-state protein-protein interactions of calmodulin by single-molecule spectroscopy. J. Am. Chem. Soc., 128, 10034-10042
10. (b) Lu, P. H. (2005) Single-molecule study of protein-protein and protein-DNA interaction dynamics," an invited book chapter in Protein-Ligand Interactions, (Uli N., Eds.), The Humana Press Inc., New York, NY.
11. Tan, X.; Hu, D.; Squier C. T.; and. Lu, P. H (2004) Probing nano-second protein motions of calmodulin by single-molecule fluorescence anisotropy. Appl. Phys. Lett., 85, 2420-2422.
12. Lu, P. H.; Iakoucheva, L. M. and Ackerman, E. J. (2001) Single-molecule conformational dynamics of fluctuating noncovalent protein- DNA interactions in DNA damage recogntion. J. Am. Chem. Soc., 123, 1984-1985.
13. Rigler, R.; Orrit, M. and Basche, T. (2003) Single Molecule Spectroscopy: Nobel conference lectures. Springer-Verlag: Berlin
14. Zwanzig,R. (1990) Rate-processes with dynamic disorder. Acc. Chem. Res., 23, 148-152.
15. Frauenfelder, H.; Sligar, S. G. and Wolynes, P. G. (1991) The energy landscapes and motions of proteins. Science, 254, 1598-1603.
16. Chin, D. and Means, A. R. (2000) Calmodulin: a prototypical calcium sensor. Trends Cell Biol., 10 (8), 322-328.
17. James, P.; Vorherr, T. and Carafoli, E. (1995) Calmodulin-binding domains: just two faced or multi-faceted? Trends Biochem. Sci., 20 (1), 38-42.
18. Babu, Y. S.; Sack, J. S.; Greenhough, T. J.; Bugg, C. E.; Means, A. R. and Cook, W. J. (1985) 3-dimensional structure of calmodulin. Nature, 315, 37-40.
19. Chattopadhyaya, R.; Meadorl, W. E.; Means, A. R. and Quiocho, F. A. (1992) Calmodulin structure refined at 1.7 angstrom resolution. J. Mol. Biol., 228 (4), 1177-1192.
20. Kuboniwa, H.; Tjandra, N.; Grzesiek, S.; Ren, H.; Klee, C. B. and Bax, A. (1995) Solution structure of calcium-free calmodulin. Nat. Struct. Biol., 2 (9), 768-776.
21. Vetter, S. W. and Leclerc, E. (2003) Novel aspects of calmodulin target recognition and activation. Eur. J. Biochem., 270, 404-414.
22. Meador, W. E.; Means, A. R. and Quiocho, F. A. (1992) Target enzyme recognition by calmodulin - 2.4-angstrom structure of calmodulin-peptide complex. Science, 257, 1251-1255.
23. Chen, B.; Mayer, M. U.; Markillie, L. M.; Stenoien, D. L. and Squier, T. C. (2005) Dynamic motion of helix A in the amino-terminal domain of calmodulin is stabilized upon calcium activation. Biochemistry, 44, 905-914.
24. Yao, Y.; Schöneich, C. and Squier, T. C. (1994) Resolution of structural -changes associated with calcium activation of calmodulin using frequency-domain fluorescence spectroscopy. Biochemistry, 33, 7797-7810. (Pubitemid 24223798)
25. 2+ pump. Biochemistry, 29, 355-365.
26. Kranz, J. K.; Flynn, P. F.; Fuentes, E. J. and Wand, A. J. (2002) Dissection of the pathway of molecular recognition by calmodulin. Biochemistry, 41, 2599-2608.
27. Adams, S. R.; Campbell, R. E.; Gross, L. A.; Martin, B. R.; Walkup, G. K.; Yao, Y.; Llopis, J. and Tsien, R. Y. (2002) New biarsenical Ligands and tetracysteine motifs for protein labeling in vitro and in vivo: Synthesis and biological applications. J. Am. Chem. Soc., 124 (21), 6063-6076. (Pubitemid 34552852)
28. Sun, H. and Squier, T. C. (2000) Ordered and cooperative binding of opposing globular domains of calmodulin to the plasma membrane Ca-ATPase. J. Biol. Chem., 275 (3), 1731-1738. (Pubitemid 30060793)
29. Crivici, A. and Ikura, M. (1995) Molecular and structural basis of target recognition by calmodulin. Ann. Rev. Biophys. Biomol. Struct., 24 (1), 85-116.
30. Hu, D. and Lu, H. P. (2003) Single-molecule nanosecond anisotropy dynamics of tethered protein motions. J. Phys. Chem. B, 107, 618.
31. Tan, X.; Nalbant, P.; Toutchkine, A.; Hu, D.; Vorpagel, R. E.; Hahn, M. K. and Lu, H. P. (2004) Single-molecule study of protein- protein interaction dynamics in a cell signaling system. J. Phys. Chem. B, 108, 737.
32. (a) Weiss, S. (1999) Fluorescence spectroscopy of single biomolecules. Science, 283, 1676-1683
33. (b) Iqbal, A.; Arslan, S.; Okumus, B.; Wilson, T. J.; Giraud, G.; Norman, D. G.; Ha, T. and Lilley, D. M.J. (2008) Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to doublestranded nucleic acids. Proc. Natl. Acad. Sci. USA, 105(32), 11176-11181.
34. Bartko, A. P.; Xu, K. and Dickson, R. M. (2002) Three-dimensional single molecule rotational diffusion in glassy state polymer films. Phys. Rev. Lett., 89 (2), 026101-026104. (Pubitemid 34799555)
35. Adachi, K.; Yasuda, R.; Noji, H.; Itoh, H.; Harada, Y.; Yoshida, M. and Kinosita, K. J. (2000) Stepping rotation of F-1-ATPase visualized through angle-resolved single-fluorophore imaging. Proc. Natl. Acad. Sci. USA, 97 (13), 7243-7247. (Pubitemid 30431448)
36. Slaughter, B. D.; Allen, M. W.; Unruh, J. R.; Urbauer, R. J. B. and Johnson, C. K. (2004) Single-molecule resonance energy transfer and fluorescence correlation spectroscopy of calmodulin in solution. J. Phys. Chem. B, 108, 10388-10397.
37. Tang, J.; Mei, E.; Green, C.; Kaplan, J.; DeGrado, W. F.; Amos, B.; Smith, I. and Hochstrasser, R. M. (2004) Probing structural dynamics of individual calmodulin : Peptide complexes in hydrogels by single-molecule confocal microscopy. J. Phys. Chem. B, 108, 15910-15918.
38. Lu, H.P. (2005) Invited review article. Probing single-molecule protein conformational dynamics. Acc. Chem. Res., 38, 557-565.
39. Chang, S.-L.; Szabo, A. and Tjandra, N. (2003) Temperature dependence of domain motions of calmodulin probed by NMR relaxation at multiple fields. J. Am. Chem. Soc., 125 (37), 11379-11384. (Pubitemid 37108075)
40. Yasuda, R.; Noji, H.; Kinosita, K. Jr. and Yoshida, M. (1998) F-1- ATPase is a highly efficient molecular motor that rotates with discrete 120 degrees steps. Cell, 93 (7), 1117-1124.
41. 2+-calmodulin reveals flexible hand-like properties of its domains. Nat. Struct. Biol., 8 (11), 990-997.
42. 2+-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticit. J. Mol. Biol., 301, 1237-1256.
43. Finn, B. E.; Evenäs, J.; Drakenberg, T.; Waltho, J. P.; Thulin, E. and Forsén, S. (1995) Calcium-induced structural-changes and domain autonomy in calmodulin. Nat. Struct. Biol., 2 (9), 777-783.
44. (a) Tan, X.; Nalbant, P.; Toutchkine, A.; Hu, D.; Vorpagel, R. E.;. Hahn, M. K. and Lu, H. P. (2004) Single-molecule study of protein- protein interaction dynamics in a cell signaling system. J. Phys. Chem. B, 108, 737
45. (b) Lu, Q.; Lu, H, P. and Wang, J. (2007) Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics. Phys. Rev. Lett., 98, 128105
46. (c) Wang, J.; Lu, Q. and Lu, H.P. (2006) Single-molecule dynamics reveals cooperative binding-folding in protein recognition. PLoS Computat. Biol., 2, 842-852. (Pubitemid 44147392)
47. Buchko, G. W.; Ni, S.; Thrall, B. D. and Kennedy, M. A. (1998) Structural features of the minimal DNA binding domain (M98- F219) of human nucleotide excision repair protein XPA. Nucleic Acids Res., 26, 2779-2788.
48. Iakoucheva, L. M. and Dunker, A. K. (2003) Order, disorder, and flexibility: prediction from protein sequence. Structure, 11, 1316-1317. (Pubitemid 37412413)
49. Lindahl, T. and Wood, R. D. (1999) Quality control by DNA repair. Science, 286, 1897-1905.
50. Richter, P. H. and Eigen, M. (1974) Diffusion controlled reaction rates in spheroidal geometry. Application to repressor-operator association and membrane bound enzymes. Biophys. Chem., 2, 255-263.
51. Shoemaker, B. A.; Portman, J.J. and Wolynes, P. G. (2000) Speeding molecular recognition by using the folding funnel: The flycasting mechanism. Proc. Natl. Acad. Sci. USA, 97, 8868-8873.