How not to do kinetics: Examples involving GTPases and guanine nucleotide exchange factors

FEBS Journal

Volumn 281, Issue 2, 2014, Pages 593-600

  Goody, Roger S ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PHYSIOLOGY   (Germany)

Author keywords

exchange factors; GTPases; kinetics; rate constants; rates

Indexed keywords

BACTERIAL PROTEIN; BODIPY FL GUANOSINE 5' O (3 THIOTRIPHOSPHATE); FLUORESCENT DYE; GUANINE NUCLEOTIDE DISSOCIATION INHIBITOR; GUANINE NUCLEOTIDE EXCHANGE FACTOR; GUANOSINE DIPHOSPHATE; GUANOSINE TRIPHOSPHATASE; GUANOSINE TRIPHOSPHATE; PROTEIN CDC42; PROTEIN YIP3; RAB PROTEIN; RAS PROTEIN; UNCLASSIFIED DRUG;

ENZYME ANALYSIS; ENZYME KINETICS; ENZYME RELEASE; ENZYME STRUCTURE; EQUILIBRIUM CONSTANT; LEGIONELLA PNEUMOPHILA; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; REVIEW; SIGNAL TRANSDUCTION;

EUKARYOTA; LEGIONELLA PNEUMOPHILA;

EXCHANGE FACTORS; GTPASES; KINETICS; RATE CONSTANTS; RATES;

BACTERIAL PROTEINS; ENZYME ASSAYS; GTP PHOSPHOHYDROLASES; GUANINE NUCLEOTIDE EXCHANGE FACTORS; KINETICS; PROTEIN BINDING; RESEARCH DESIGN;

EID: 84892808486     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/febs.12551     Document Type: Review

References (17)

1. Klebe C, Prinz H, Wittinghofer A, &, Goody RS, (1995) The kinetic mechanism of Ran-nucleotide exchange catalyzed by RCC1. Biochemistry 34, 12543-12552.
2. Goody RS, &, Hofmann-Goody W, (2002) Exchange factors, effectors, GAPs and motor proteins: common thermodynamic and kinetic principles for different functions. Eur Biophys J 31, 268-274.
3. Cherfils J, &, Zeghouf M, (2013) Regulation of small GTPases by GEFs, GAPs, and GDIs. Physiol Rev 93, 269-309.
4. Michaelis L, &, Menten ML, (1913) The kinetics of the inversion effect. Biochem Z 49, 333-369.
5. Zhang B, Zhang Y, Shacter E, &, Zheng Y, (2005) Mechanism of the guanine nucleotide exchange reaction of Ras GTPase-evidence for a GTP/GDP displacement model. Biochemistry 44, 2566-2576.
6. Guo Z, Ahmadian MR, &, Goody RS, (2005) Guanine nucleotide exchange factors operate by a simple allosteric competitive mechanism. Biochemistry 44, 15423-15429.
7. Goody RS, Frech M, &, Wittinghofer A, (1991) Affinity of guanine-nucleotide binding-proteins for their ligands-facts and artifacts. Trends Biochem Sci 16, 327-328.
8. John J, Sohmen R, Feuerstein J, Linke R, Wittinghofer A, &, Goody RS, (1990) Kinetics of interaction of nucleotides with nucleotide-free H-Ras P21. Biochemistry 29, 6058-6065.
9. Korlach J, Baird DW, Heikal AA, Gee KR, Hoffman GR, &, Webb WW, (2004) Spontaneous nucleotide exchange in low molecular weight GTPases by fluorescently labeled gamma-phosphate-linked GTP analogs. Proc Natl Acad Sci USA 101, 2800-2805.
10. Rudolph MG, Weise C, Mirold S, Hillenbrand B, Bader B, Wittinghofer A, &, Hardt WD, (1999) Biochemical analysis of SopE from Salmonella typhimurium, a highly efficient guanosine nucleotide exchange factor for RhoGTPases. J Biol Chem 274, 30501-30509.
11. Eberth A, Dvorsky R, Becker CF, Beste A, Goody RS, &, Ahmadian MR, (2005) Monitoring the real-time kinetics of the hydrolysis reaction of guanine nucleotide-binding proteins. Biol Chem 386, 1105-1114.
12. Wu YW, Tan KT, Waldmann H, Goody RS, &, Alexandrov K, (2007) Interaction analysis of prenylated Rab GTPase with Rab escort protein and GDP dissociation inhibitor explains the need for both regulators. Proc Natl Acad Sci USA 104, 12294-12299.
13. Wu YW, Oesterlin LK, Tan KT, Waldmann H, Alexandrov K, &, Goody RS, (2010) Membrane targeting mechanism of Rab GTPases elucidated by semisynthetic protein probes. Nat Chem Biol 6, 534-540.
14. Sivars U, Aivazian D, &, Pfeffer SR, (2003) Yip3 catalyses the dissociation of endosomal Rab-GDI complexes. Nature 425, 856-859.
15. Ingmundson A, Delprato A, Lambright DG, &, Roy CR, (2007) Legionella pneumophila proteins that regulate Rab1 membrane cycling. Nature 450, 365-369.
16. Machner MP, &, Isberg RR, (2007) A bifunctional bacterial protein links GDI displacement to Rab1 activation. Science 318, 974-977.
17. Schoebel S, Oesterlin LK, Blankenfeldt W, Goody RS, &, Itzen A, (2009) RabGDI displacement by DrrA from Legionella is a consequence of its guanine nucleotide exchange activity. Mol Cell 36, 1060-1072.