References: Program DynaFit for kinetics and equilibria

Petr Kuzmic pkuzmic at
Mon Apr 9 14:25:04 EST 2001

Program DynaFit [P. Kuzmic (1996) Anal. Biochem. 237, 260-273] is
useful in the analysis of complex reaction mechanism, for which
traditional (algebraic) kinetic equations cannot be derived.

Attached below is a bibliography containing 54 journal articles
that cited DynaFit over the last three years. Most citations are
from articles in the journal Biochemistry, followed by the Journal
of Biological Chemistry, and Biochimica & Biophysica Acta.

The main application of DynaFit seems to be in figuring out
biochemical reaction mechanisms from kinetic and/or equilibrium
data.  However, the program has been used in many different areas,
such as environmental chemistry, food chemistry, guest-host
interactions, and structure-activity studies.

The program is available free of charge to academic researchers:

Home page:
User manual:

Please contact me if you have any questions about installing or
running the program.

Best Regards,

    - P.K.

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 *

-----	--------------------------------
12	Biochemistry
6	J. Biol. Chem.
3	Biochim. Biophys. Acta-Protein Struct. Molec. Enzym.
2	J. Am. Chem. Soc.
2	Biophys. J.
2	Proteins
2	Proc. Natl. Acad. Sci. U. S. A.
2	Anal. Biochem.
2	J. Org. Chem.
2	Biochem. J.
1	J. Chem. Educ.
1	Biochem. Biophys. Res. Commun.
1	FEBS Lett.
1	Chem. Res. Toxicol.
1	J. Mol. Biol.
1	Methods
1	J. Biomol. Struct. Dyn.
1	Anal. Chem.
1	Plant Cell Environ.
1	Protein Sci.
1	Bioinformatics
1	Nature
1	Food Res. Int.
1	J. Environ. Monit.
1	Clin. Chim. Acta
1	J. Sci. Food Agric.
1	Org. Lett.
1	Nucleic Acids Res.
1	Chem. Biol.


"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.

"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
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
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 (2000) 
Biochim. Biophys. Acta-Protein Struct. Molec. Enzym. 1478(2),

"Mechanism of neomycin and Rev peptide binding to the Rev
responsive element of HIV-1 as determined by fluorescence and NMR
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
Biochemistry 39(16), 4792-4800.

"Structural basis for selectivity of a small molecule, S1-
binding, submicromolar inhibitor of urokinase-type plasminogen
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
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 protein"
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 (1999) 
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
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
Koshkin, V; Dunford, HB (1999) 
Biochim. Biophys. Acta-Protein Struct. Molec. Enzym. 1431(1),

"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),

"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 reaction"
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
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
Luque, I; Gomez, J; Semo, N; Freire, E (1998) 
Proteins 30(1), 74-85.

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