Systematic control of protein interaction using a modular ER/K α-helix linker

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

Volumn 108, Issue 51, 2011, Pages 20467-20472

  Sivaramakrishnan, Sivaraj ^a   Spudich, James A ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Cell signaling; Modulation; Systematic protein affinity strength

Indexed keywords

ARGININE; CALMODULIN; GLUTAMIC ACID; LYSINE;

ALPHA HELIX; ARTICLE; BINDING AFFINITY; DISSOCIATION CONSTANT; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; SENSOR;

AMINO ACID MOTIFS; ARGININE; BIOSENSING TECHNIQUES; CLONING, MOLECULAR; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMANS; KINETICS; LYSINE; MODELS, GENETIC; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SIGNAL TRANSDUCTION;

EID: 84855513111     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1116066108     Document Type: Article

References (31)

1. Geiger B, Spatz JP, Bershadsky AD (2009) Environmental sensing through focal adhesions. Nat Rev Mol Cell Biol 10:21-33.
2. Steitz TA (2008) A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol 9:242-253.
3. Brown MD, Sacks DB (2009) Protein scaffolds in MAP kinase signalling. Cell Signal 21:462-469.
4. Pufall MA, Graves BJ (2002) Autoinhibitory domains: Modular effectors of cellular regulation. Annu Rev Cell Dev Biol 18:421-462. (Pubitemid 35387357)
5. Chothia C (1992) Proteins. One thousand families for the molecular biologist. Nature 357:543-544.
6. Aloy P, Russell RB (2004) Ten thousand interactions for the molecular biologist. Nat Biotechnol 22:1317-1321. (Pubitemid 39336787)
7. Shoemaker BA, Panchenko AR (2007) Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol 3:e43.
8. Shoemaker BA, Panchenko AR (2007) Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput Biol 3:e42.
9. Gunasekaran K, Ma B, Nussinov R (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins 57:433-443. (Pubitemid 39390799)
10. Sivaramakrishnan S, Spink BJ, Sim AY, Doniach S, Spudich JA (2008) Dynamic charge interactions create surprising rigidity in the ER/K alpha-helical protein motif. Proc Natl Acad Sci USA 105:13356-13361.
11. Sivaramakrishnan S, et al. (2009) Combining single-molecule optical trapping and small-angle X-ray scattering measurements to compute the persistence length of a protein ER/K alpha-helix. Biophys J 97:2993-2999.
12. Mehraeen S, Sudhanshu B, Koslover E, Spakowitz A (2008) End-to-end distribution for a wormlike chain in arbitrary dimensions. Phys Rev E Nonlin Soft Matter Phys 77:061803.
13. Baldwin RL (2007) Energetics of protein folding. J Mol Biol 371:283-301.
14. Chin D, Means AR (2000) Calmodulin: A prototypical calcium sensor. Trends Cell Biol 10:322-328. (Pubitemid 30445239)
15. O'Neil KT, DeGrado WF (1990) How calmodulin binds its targets: Sequence independent recognition of amphiphilic alpha-helices. Trends Biochem Sci 15:59-64. (Pubitemid 20036857)
16. Sample V, Newman RH, Zhang J (2009) The structure and function of fluorescent proteins. Chem Soc Rev 38:2852-2864.
17. Kenworthy AK (2001) Imaging protein-protein interactions using fluorescence resonance energy transfer microscopy. Methods 24:289-296.
18. Zhang J, Allen MD (2007) FRET-based biosensors for protein kinases: Illuminating the kinome. Mol Biosyst 3:759-765. (Pubitemid 47587185)
19. Howard J (2001) Mechanics of Motor Proteins and the Cytoskeleton (Sinauer, Sunderland, MA), Chap 6.
20. Siegel RM, et al. (2000) Measurement of molecular interactions in living cells by fluorescence resonance energy transfer between variants of the green fluorescent protein. Sci STKE 2000:lp1.
21. Vorherr T, et al. (1990) Interaction of calmodulin with the calmodulin binding domain of the plasma membrane Ca2+ pump. Biochemistry 29:355-365. (Pubitemid 20037640)
22. Zettner A (1973) Principles of competitive binding assays (saturation analysis). 1. Equilibrium techniques. Clin Chem 19:699-705.
23. Malencik DA, Anderson SR (1983) Binding of hormones and neuropeptides by calmodulin. Biochemistry 22:1995-2001. (Pubitemid 13093465)
24. Sung J, Sivaramakrishnan S, Dunn AR, Spudich JA (2010) Single-molecule dual-beam optical trap analysis of protein structure and function. Methods Enzymol 475:321-375.
25. Rock RS, et al. (2001) Myosin VI is a processive motor with a large step size. Proc Natl Acad Sci USA 98:13655-13659. (Pubitemid 33115953)
26. 2+ based on green fluorescent proteins and calmodulin. Nature 388:882-887.
27. Kiyokawa E, Aoki K, Nakamura T, Matsuda M (2011) Spatiotemporal regulation of small GTPases as revealed by probes based on the principle of Forster Resonance Energy Transfer (FRET): Implications for signaling and pharmacology. Annu Rev Pharmacol Toxicol 51:337-358.
28. Violin JD, Zhang J, Tsien RY, Newton AC (2003) A genetically encoded fluorescent reporter reveals oscillatory phosphorylation by protein kinase C. J Cell Biol 161:899-909. (Pubitemid 36718423)
29. Miyawaki A, Tsien RY (2000) Monitoring protein conformations and interactions by fluorescence resonance energy transfer between mutants of green fluorescent protein. Methods Enzymol 327:472-500. (Pubitemid 34193328)
30. Baird GS, Zacharias DA, Tsien RY (1999) Circular permutation and receptor insertion within green fluorescent proteins. Proc Natl Acad Sci USA 96:11241-11246. (Pubitemid 29487365)
31. Spink BJ, Sivaramakrishnan S, Lipfert J, Doniach S, Spudich JA (2008) Long single alpha-helical tail domains bridge the gap between structure and function of myosin VI. Nat Struct Mol Biol 15:591-597. (Pubitemid 351799136)