From owner-btk-mca@hgmp.mrc.ac.uk Sat Aug 11 14:38:41 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 08F0A17AC6 for ; Sat, 11 Aug 2001 14:38:39 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 6A26017ACA; Sat, 11 Aug 2001 14:38:35 +0100 (BST) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B386F17AC6; Sat, 11 Aug 2001 14:38:31 +0100 (BST) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id OAA25930; Sat, 11 Aug 2001 14:23:34 +0100 (BST) X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f From: pkuzmic@biokin.com (Petr Kuzmic) X-Newsgroups: bionet.molbio.methds-reagnts,bionet.metabolic-reg Subject: Re: fitting with dynafit? Date: 11 Aug 2001 06:23:31 -0700 Organization: http://groups.google.com/ Lines: 485 Message-ID: <77754d4.0108110523.10680ca2@posting.google.com> References: <7fcc7.34584$jA2.2726200@news20.bellglobal.com> Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Complaints-To: groups-abuse@google.com To: btk-mca@hgmp.mrc.ac.uk.methods@hgmp.mrc.ac.uk Sender: owner-btk-mca@hgmp.mrc.ac.uk Precedence: bulk "ricnews" wrote in message news:<7fcc7.34584$jA2.2726200@news20.bellglobal.com>... > Hi, > > I'm wondering if anyone successfully used dynafit to fit their data to a > model? I tried but even with a simple test I couldn't get it to fit unless I > gave it starting values that were basically the answer. Using starting > values that converge easily in sigmaplot or excel dynafit still couldn't get > the answer. Hi, I am the author of DynaFit [P. Kuzmic (1996) Anal. Biochem. 237, 260]. If the program seems to be failing, most likely there is an error in your DynaFit script file. If you send me the script and the data to 'pkuzmic@biokin.com', I'll set it up correctly and you can take it from there. FYI, attached below is a list of recent journal articles published by people who "successfully used DynaFit to fit their data". It may not be a complete list, but these are the papers I know of. Regards, - Petr ------------------------------------------------------- P e t r K u z m i c, Ph. D. * BioKin Ltd. 1652 S. Grand Ave. * Suite 337 * Pullman, WA 99163 509.334.4131 * 509.332.3493 fax * http://www.biokin.com ________________________________________________________ 1. "High enzymatic activity and chaperone function are mechanistically related features of the dimeric E-coli peptidyl-prolyl-isomerase FkpA" Ramm, K; Pluckthun, A (2001) J. Mol. Biol. 310(2), 485-498. 2. "Reduction of aflatoxin B-1 dialdehyde by rat and human aldo- keto reductases" Guengerich, FP; Cai, HL; McMahon, M; Hayes, JD; Sutter, TR; Groopman, JD; Deng, ZW; Harris, TM (2001) Chem. Res. Toxicol. 14(6), 727-737. 3. "The mechanism of DNA cytosine-5 methylation - Kinetic and mutational dissection of HhaI methyltransferase" Vilkaitis, G; Merkiene, E; Serva, S; Weinhold, E; Klimasauskas, S (2001) J. Biol. Chem. 276(24), 20924-20934. 4. "Binding and oxidation of alkyl 4-nitrophenyl ethers by rabbit cytochrome P450 1A2: Evidence for two binding sites" Miller, GP; Guengerich, FP (2001) Biochemistry 40(24), 7262-7272. 5. "Examination of donor substrate conversion in yeast transketolase" Fiedler, E; Golbik, R; Schneider, G; Tittmann, K; Neef, H; Konig, S; Hubner, G (2001) J. Biol. Chem. 276(19), 16051-16058. 6. "Kinetic analysis of three activated phenylalanyl intermediates generated by the initiation module PheATE of gramicidin S synthetase" Luo, LS; Walsh, CT (2001) Biochemistry 40(18), 5329-5337. 7. "Characterization of glycine sarcosine N-methyltransferase and sarcosine dimethylglycine N-methyltransferase" Nyyssola, A; Reinikainen, T; Leisola, M (2001) Appl. Environ. Microbiol. 67(5), 2044-2050. 8. "Mechanism of reaction of acyl phosph(on)ates with the beta- lactamase of Enterobacter cloacae P99" Kaur, K; Pratt, RF (2001) Biochemistry 40(15), 4610-4621. 9. "Spectroscopic properties of the metalloregulatory Cd(II) and Pb(II) sites of S. aureus pI258 CadC" Busenlehner, LS; Cosper, NJ; Scott, RA; Rosen, BP; Wong, MD; Giedroc, DP (2001) Biochemistry 40(14), 4426-4436. 10. "Oxidations of p-alkoxyacylanilides catalyzed by human cytochrome P450 1A2: Structure-activity relationships and simulation of rate constants of individual steps in catalysis" Yun, CH; Miller, GP; Guengerich, FP (2001) Biochemistry 40(14), 4521-4530. 11. "Acetohydroxyacid synthase: A proposed structure for regulatory subunits supported by evidence from mutagenesis" Mendel, S; Elkayam, T; Sella, C; Vinogradov, V; Vyazmensky, M; Chipman, DM; Barak, Z (2001) J. Mol. Biol. 307(1), 465-477. 12. "Chain length-dependent affinity of helical foldamers for a rodlike guest" Tanatani, A; Mio, MJ; Moore, JS (2001) J. Am. Chem. Soc. 123(8), 1792-1793. 13. "Thermostable and site-specific DNA binding of the gene product ORF56 from the Sulfolobus islandicus plasmid pRN1, a putative archael plasmid copy control protein" Lipps, G; Stegert, M; Krauss, G (2001) Nucleic Acids Res. 29(4), 904-913. 14. "Kinetic studies of Fos center dot Jun center dot DNA complex formation: DNA binding prior to dimerization" Kohler, JJ; Schepartz, A (2001) Biochemistry 40(1), 130-142. 15. "The N-terminal region of cystatin A (stefin A) binds to papain subsequent to the two hairpin loops of the inhibitor. Demonstration of two-step binding by rapid-kinetic studies of cystatin A labeled at the N-terminus with a fluorescent reporter group" Estrada, S; Olson, ST; Raub-Segall, E; Bjork, I (2000) Protein Sci. 9(11), 2218-2224. 16. "Degradation of chlortoluron in water disinfection processes: a kinetic study" Losito, H; Zambonin, CG; Palmisano, F (2000) J. Environ. Monit. 2(6), 582-586. 17. "Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase" Vilkaitis, G; Dong, AP; Weinhold, E; Cheng, XD; Klimasauskas, S (2000) J. Biol. Chem. 275(49), 38722-38730. 18. "Characterization of enzymatic processes by rapid mix-quench mass spectrometry: The case of dTDP-glucose 4,6-dehydratase" Gross, JW; Hegeman, AD; Vestling, MM; Frey, PA (2000) Biochemistry 39(45), 13633-13640. 19. "X-ray structures of five renin inhibitors bound to saccharopepsin: Exploration of active-site specificity" Cronin, NB; Badasso, MO; Tickle, IJ; Dreyer, T; Hoover, DJ; Rosati, RL; Humblet, CC; Lunney, EA; Cooper, JB (2000) J. Mol. Biol. 303(5), 745-760. 20. "The zinc metalloregulatory protein Synechococcus PCC7942 SmtB binds a single zinc ion per monomer with high affinity in a tetrahedral coordination geometry" VanZile, ML; Cosper, NJ; Scott, RA; Giedroc, DP (2000) Biochemistry 39(38), 11818-11829. 21. "Mechanism of elementary catalytic steps of pyruvate oxidase from Lactobacillus plantarum" Tittmann, K; Golbik, R; Ghisla, S; Hubner, G (2000) Biochemistry 39(35), 10747-10754. 22. "Dynamic hemicarcerands and hemicarceplexes" Ro, S; Rowan, SJ; Pease, AR; Cram, DJ; Stoddart, JF (2000) Org. Lett. 2(16), 2411-2414. 23. "Interactions of GroEL/GroES with a heterodimeric intermediate during alpha(2)beta(2) assembly of mitochondrial branched-chain alpha-ketoacid dehydrogenase - cis capping of the native-like 86-kDa intermediate by GroES" Song, JL; Wynn, RM; Chuang, DT (2000) J. Biol. Chem. 275(29), 22305-22312. 24. "Alkaline proteinase inhibitor of Pseudomonas aeruginosa - Interaction of native and N-terminally truncated inhibitor proteins with Pseudomonas metalloproteinases" Feltzer, RE; Gray, RD; Dean, WL; Pierce, WM (2000) J. Biol. Chem. 275(28), 21002-21009. 25. "Degradation of phytochrome A and the high irradiance response in Arabidopsis: a kinetic analysis" Hennig, L; Buche, C; Schafer, E (2000) Plant Cell Environ. 23(7), 727-734. 26. "Characteristics of L-ornithine: 2-oxoacid aminotransferase and potential prenatal diagnosis of gyrate atrophy of the choroid and retina by first trimester chorionic villus sampling" Roschinger, W; Endres, W; Shin, YS (2000) Clin. Chim. Acta 296(1-2), 91-100. 27. "Dissecting the nucleotide binding properties of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase with fluorescent 3 '(2)'-o-anthraniloyladenosine 5 '-triphosphate" Shi, GB; Gong, YC; Savchenko, A; Zeikus, JG; Xiao, B; Ji, XH; Yan, HG (2000) Biochim. Biophys. Acta-Protein Struct. Molec. Enzym. 1478(2), 289-299. 28. "Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1 as determined by fluorescence and NMR spectroscopy" Lacourciere, KA; Stivers, JT; Marino, JP (2000) Biochemistry 39(19), 5630-5641. 29. "Transient kinetics of ligand binding and role of the C-terminus in the dUTPase from equine infectious anemia virus" Nord, J; Kiefer, M; Adolph, HW; Zeppezauer, MM; Nyman, PO (2000) FEBS Lett. 472(2-3), 312-316. 30. "A novel approach to serine protease inhibition: Kinetic characterization of inhibitors whose potencies and selectivities are dramatically enhanced by zinc(II)" Janc, JW; Clark, JM; Warne, RL; Elrod, KC; Katz, BA; Moore, WR (2000) Biochemistry 39(16), 4792-4800. 31. "Structural basis for selectivity of a small molecule, S1- binding, submicromolar inhibitor of urokinase-type plasminogen activator" Katz, BA; Mackman, R; Luong, C; Radika, K; Martelli, A; Sprengeler, PA; Wang, J; Chan, HD; Wong, L (2000) Chem. Biol. 7(4), 299-312. 32. "Osmotic pressure effects on EcoRV cleavage and binding" Wenner, JR; Bloomfield, VA (1999) J. Biomol. Struct. Dyn. 17(3), 461-471. 33. "GroEL/GroES promote dissociation/reassociation cycles of a heterodimeric intermediate during alpha(2)beta(2) protein assembly - Iterative annealing at the quaternary structure level" Wynn, RM; Song, JL; Chuang, DT (2000) J. Biol. Chem. 275(4), 2786-2794. 34. "Hydrophilic residues at the apical domain of GroEL contribute to GroES finding but attenuate polypeptide binding" Motojima, F; Makio, T; Aoki, K; Makino, Y; Kuwajima, K; Yoshida, M (2000) Biochem. Biophys. Res. Commun. 267(3), 842-849. 35. "Kinetic modelling in food science: a case study on chlorophyll degradation in olives" van Boekel, MAJS (2000) J. Sci. Food Agric. 80(1), 3-9. 36. "Microcomputer applications in biochemistry" Tsai, CS (2000) J. Chem. Educ. 77(2), 219-221. 37. "Crowding effects on EcoRV kinetics and binding" Wenner, JR; Bloomfield, VA (1999) Biophys. J. 77(6), 3234-3241. 38. "Selective antibody-catalyzed solvolysis of endo-2-norbornyl mesylate" Ma, LF; Sweet, EH; Schultz, PG (1999) J. Am. Chem. Soc. 121(43), 10227-10228. 39. "Substrate channeling" Spivey, HO; Ovadi, J (1999) Methods 19(2), 306-321. 40. "Testing of kinetic models: usefulness of the multiresponse approach as applied to chlorophyll degradation in foods" van Boekel, MAJS (1999) Food Res. Int. 32(4), 261-269. 41. "Role of electrophilic and general base catalysis in the mechanism of Escherichia coli uracil DNA glycosylase" Drohat, AC; Jagadeesh, J; Ferguson, E; Stivers, JT (1999) Biochemistry 38(37), 11866-11875. 42. "Rate determination in phosphorylation of shark rectal Na,K- ATPase by ATP: Temperature sensitivity and effects of ADP" Cornelius, F (1999) Biophys. J. 77(2), 934-942. 43. "Adenylosuccinate synthase from Saccharomyces cerevisiae: homologous overexpression, purification and characterization of the recombinant protein" Lipps, G; Krauss, G (1999) Biochem. J. 341(Pt. 3), 537-543. 44. "Synthesis and biochemical evaluation of bis(6,7-dimethyl-8-D- ribityllumazines) as potential bisubstrate analogue inhibitors of riboflavin synthase" Cushman, M; Mavandadi, F; Yang, DL; Kugelbrey, K; Kis, K; Bacher, A (1999) J. Org. Chem. 64(13), 4635-4642. 45. "The propeptides of the vitamin K-dependent proteins possess different affinities for the vitamin K-dependent carboxylase" Stanley, TB; Jin, DY; Lin, PJ; Stafford, DW (1999) J. Biol. Chem. 274(24), 16940-16944. 46. "Design, synthesis, and biological evaluation of homologous phosphonic acids and sulfonic acids as inhibitors of lumazine synthase" Cushman, M; Mihalic, JT; Kis, K; Bacher, A (1999) J. Org. Chem. 64(11), 3838-3845. 47. "Reactions of prostaglandin endoperoxide synthase with hydroperoxide and reducing substrates under single turnover conditions" Koshkin, V; Dunford, HB (1999) Biochim. Biophys. Acta-Protein Struct. Molec. Enzym. 1431(1), 47-52. 48. "RXP 407, a phosphinic peptide, is a potent inhibitor of angiotensin I converting enzyme able to differentiate between its two active sites" Dive, V; Cotton, J; Yiotakis, A; Michaud, A; Vassiliou, S; Jiracek, J; Vazeux, G; Chauvet, MT; Cuniasse, P; Corvol, P (1999) Proc. Natl. Acad. Sci. U. S. A. 96(8), 4330-4335. 49. "Coupling of the peroxidase and cyclooxygenase reactions of prostaglandin H synthase" Koshkin, V; Dunford, HB (1999) Biochim. Biophys. Acta-Protein Struct. Molec. Enzym. 1430(2), 341-348. 50. "Buffer effects on EcoRV kinetics as measured by fluorescent staining and digital imaging of plasmid cleavage" Wenner, JR; Bloomfield, VA (1999) Anal. Biochem. 268(2), 201-212. 51. "Superoxide free radical generation by Amadori compounds: The role of acyclic forms and metal ions" Mossine, VV; Linetsky, M; Glinsky, GV; Ortwerth, BJ; Feather, MS (1999) Chem. Res. Toxicol. 12(3), 230-236. 52. "Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: Structure and glycosylase mechanism revisited" Xiao, GY; Tordova, M; Jagadeesh, J; Drohat, AC; Stivers, JT; Gilliland, GL (1999) Proteins 35(1), 13-24. 53. "Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase" Stivers, JT; Pankiewicz, KW; Watanabe, KA (1999) Biochemistry 38(3), 952-963. 54. "Studies on the catalysis of carbon-cobalt bond homolysis by ribonucleoside triphosphate reductase: Evidence for concerted carbon-cobalt bond homolysis and thiyl radical formation" Licht, SS; Booker, S; Stubbe, JA (1999) Biochemistry 38(4), 1221-1233. 55. "General numerical treatment of competitive binding kinetics: Application to thrombin-dehydrothrombin-hirudin" Kuzmic, P (1999) Anal. Biochem. 267(1), 17-23. 56. "Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation" Mendes, P; Kell, DB (1998) Bioinformatics 14(10), 869-883. 57. "E2P phosphoforms of Na,K-ATPase. II. Interaction of substrate and cation-binding sites in P-i phosphorylation of Na,K-ATPase" Cornelius, F; Fedosova, NU; Klodos, I (1998) Biochemistry 37(47), 16686-16696. 58. "Stability of recombinant yeast protoporphyrinogen oxidase: Effects of diphenyl ether-type herbicides and diphenyleneiodonium" Arnould, S; Takahashi, M; Camadro, JM (1998) Biochemistry 37(37), 12818-12828. 59. "Spectroscopic characterization of intermediates in the urate oxidase reaction" Kahn, K; Tipton, PA (1998) Biochemistry 37(33), 11651-11659. 60. "Antibody catalysis of peptidyl-prolyl cis-trans isomerization in the folding of RNase T1" Ma, LF; Hsieh-Wilson, LC; Schultz, PG (1998) Proc. Natl. Acad. Sci. U. S. A. 95(13), 7251-7256. 61. "Kinetic determinations and some kinetic aspects of analytical chemistry" Crouch, SR; Cullen, TF; Scheeline, A; Kirkor, ES (1998) Anal. Chem. 70(12), 53R-106R. 62. "Fixed-point methods for computing the equilibrium composition of complex biochemical mixtures" Kuzmic, P (1998) Biochem. J. 331(Pt. 2), 571-575. 63. "Regulation of extrinsic pathway factor Xa formation by tissue factor pathway inhibitor" Baugh, RJ; Broze, GJ; Krishnaswamy, S (1998) J. Biol. Chem. 273(8), 4378-4386. 64. "Design of potent selective zinc-mediated serine protease inhibitors" Katz, BA; Clark, JM; Finer-Moore, JS; Jenkins, TE; Johnson, CR; Ross, MJ; Luong, C; Moore, WR; Stroud, RM (1998) Nature 391(6667), 608-612. 65. "Structure-based thermodynamic design of peptide ligands: Application to peptide inhibitors of the aspartic protease endothiapepsin" Luque, I; Gomez, J; Semo, N; Freire, E (1998) Proteins 30(1), 74-85. --------------------------------------- COUNT JOURNAL 17 Biochemistry 8 J. Biol. Chem. 3 J. Mol. Biol. 3 Biochim. Biophys. Acta-Protein Struct. Molec. Enzym. 2 Anal. Biochem. 2 Proc. Natl. Acad. Sci. U. S. A. 2 Proteins 2 J. Am. Chem. Soc. 2 Chem. Res. Toxicol. 2 Biochem. J. 2 Biophys. J. 2 J. Org. Chem. 1 Org. Lett. 1 Protein Sci. 1 Anal. Chem. 1 Nature 1 Plant Cell Environ. 1 Bioinformatics 1 J. Environ. Monit. 1 J. Sci. Food Agric. 1 Chem. Biol. 1 FEBS Lett. 1 J. Chem. Educ. 1 Food Res. Int. 1 Methods 1 J. Biomol. Struct. Dyn. 1 Biochem. Biophys. Res. Commun. 1 Nucleic Acids Res. 1 Clin. Chim. Acta 1 Appl. Environ. Microbiol. --------------------------------------- .