fitting with dynafit?

Petr Kuzmic pkuzmic at
Sat Aug 11 08:23:31 EST 2001

"ricnews" <ricnews at> wrote in message news:<7fcc7.34584$jA2.2726200 at>...
> 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.


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 at', 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.


    - 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 *


"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.

"Reduction of aflatoxin B-1 dialdehyde by rat and human aldo- keto
Guengerich, FP; Cai, HL; McMahon, M; Hayes, JD; Sutter, TR; Groopman,
JD; Deng, ZW; Harris, TM (2001)
Chem. Res. Toxicol. 14(6), 727-737.

"The mechanism of DNA cytosine-5 methylation - Kinetic and mutational
dissection of HhaI methyltransferase"
Vilkaitis, G; Merkiene, E; Serva, S; Weinhold, E; Klimasauskas, S
J. Biol. Chem. 276(24), 20924-20934.

"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.

"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.

"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.

"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.

"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.

"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.

"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.

"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.

"Chain length-dependent affinity of helical foldamers for a rodlike
Tanatani, A; Mio, MJ; Moore, JS (2001) 
J. Am. Chem. Soc. 123(8), 1792-1793.

"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.

"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.

"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.

"Degradation of chlortoluron in water disinfection processes: a
kinetic study"
Losito, H; Zambonin, CG; Palmisano, F (2000) 
J. Environ. Monit. 2(6), 582-586.

"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.

"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.

"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.

"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.

"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.

"Dynamic hemicarcerands and hemicarceplexes"
Ro, S; Rowan, SJ; Pease, AR; Cram, DJ; Stoddart, JF (2000) 
Org. Lett. 2(16), 2411-2414.

"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.

"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.

"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.

"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.

"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
Biochim. Biophys. Acta-Protein Struct. Molec. Enzym. 1478(2), 289-299.

"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.

"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.

"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.

"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.

"Osmotic pressure effects on EcoRV cleavage and binding"
Wenner, JR; Bloomfield, VA (1999) 
J. Biomol. Struct. Dyn. 17(3), 461-471.

"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.

"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
Biochem. Biophys. Res. Commun. 267(3), 842-849.

"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.

"Microcomputer applications in biochemistry"
Tsai, CS (2000) 
J. Chem. Educ. 77(2), 219-221.

"Crowding effects on EcoRV kinetics and binding"
Wenner, JR; Bloomfield, VA (1999) 
Biophys. J. 77(6), 3234-3241.

"Selective antibody-catalyzed solvolysis of endo-2-norbornyl mesylate"
Ma, LF; Sweet, EH; Schultz, PG (1999) 
J. Am. Chem. Soc. 121(43), 10227-10228.

"Substrate channeling"
Spivey, HO; Ovadi, J (1999) 
Methods 19(2), 306-321.

"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.

"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.

"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.

"Adenylosuccinate synthase from Saccharomyces cerevisiae: homologous
overexpression, purification and characterization of the recombinant
Lipps, G; Krauss, G (1999) 
Biochem. J. 341(Pt. 3), 537-543.

"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
J. Org. Chem. 64(13), 4635-4642.

"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.

"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.

"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.

"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.

"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.

"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.

"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
Chem. Res. Toxicol. 12(3), 230-236.

"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.

"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.

"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.

"General numerical treatment of competitive binding kinetics:
Application to thrombin-dehydrothrombin-hirudin"
Kuzmic, P (1999) 
Anal. Biochem. 267(1), 17-23.

"Non-linear optimization of biochemical pathways: applications to
metabolic engineering and parameter estimation"
Mendes, P; Kell, DB (1998) 
Bioinformatics 14(10), 869-883.

"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.

"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.

"Spectroscopic characterization of intermediates in the urate oxidase
Kahn, K; Tipton, PA (1998) 
Biochemistry 37(33), 11651-11659.

"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.

"Kinetic determinations and some kinetic aspects of analytical
Crouch, SR; Cullen, TF; Scheeline, A; Kirkor, ES (1998) 
Anal. Chem. 70(12), 53R-106R.

"Fixed-point methods for computing the equilibrium composition of
complex biochemical mixtures"
Kuzmic, P (1998) 
Biochem. J. 331(Pt. 2), 571-575.

"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.

"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.

"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.


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.

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