Third-domain ovomucoid

Fujinaga, M., et al. Crystal and molecular structures of the complex of a-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 A resolution. 

The discrete protonation states methods have been tested in pKa calculations for several small molecules and peptides, including succinic acid [4, 25], acetic acid [93], a heptapeptide derived from ovomucoid third domain [27], and decalysine [61], However, these methods have sofar been tested on only one protein, the hen egg lysozyme [16, 61, 71], While the method using explicit solvent for both MD and MC sampling did not give quantitative agreement with experiment due to convergence difficulty [16], the results using a GB model [71] and the mixed PB/explicit... 

Dlugosz M, Antosiewicz JM, Robertson AD (2004) Constant-pH molecular dynamics study of protonation-structure relationship in a heptapeptide derived from ovomucoid third domain. Phys RevE 69 021915. 

Mine, Y., Sasaki, E., Zhang, J.W. 2003. Reduction of antigenicity and allergenicity of genetically modified egg white allergen, ovomucoid third domain. Biochem Biophys Res Commun 302 133-137. 

Protein-Protein Interaction The Binding of Ovomucoid Third Domain to Elastase. 

Lu W, Qasim MA, Kent SBH. Comparative total syntheses of turkey ovomucoid third domain by both stepwise solid phase peptide synthesis and native chemical ligation. J. Am. Chem. Soc. 1996 118 8518-8523. 

Fujinaga, M., Sielecki, A. R., Read, R. J., Ardelt, W., Laskowski, M., Jr., and James, M. N. (1987). Crystal and molecular structures of the complex of alpha-chymotrypsin with its inhibitor turkey ovomucoid third domain at 1.8 A resolution. J. Mol. Biol. 195, 397-418. 

Baker, B., and Murphy, K. (1997). Dissecting the Energetics of a Protein-protein Interaction The Binding of Ovomucoid Third Domain to Elastase, J. Mol. Biol. 268 557-569. 

In another interesting application of the TCI cycle, Li et al. [128] examined the pK of proteins. This paper represents the first attempt at predicting proteins pK values using an ab initio QM/MM description of the protein in combination with a polarizable continuum model for the solvent. Briefly, the ionizable residue of the protein is treated quanto-mechanically while the rest of the structure is represented by an MM force field. This QM/MM representation of the proteins is combined with a linearized Poisson-Boltmann equation (LPBE) description of bulk solvation. By using this procedure, the authors predicted pK of Glu 43 (4.4 units) and Lys 55 (11.3 units) in Turkey Ovomucoid third domain that are in very good agreement with the experimental values of 4.8 and 11.1 units, respectively. 

Table 9.2. Amino acid sequences of ovomucoid third domains from 153 species of birds...

Apostol, I., Giletto, A., Komiyama, T., Zhatig, W.-L Laskowski, M. (1993). Amirto acid sequences of ovomucoid third domains from 27 additional species of birds. J. Prot. Chem., 12, 419-33. 

Empie, M.W. Laskowski, M. (1982). Thermodynamics and kinetics of single residue replacements in avian ovomucoid third domains effect on inhibitor interactions with serine proteinases. Biodtemistry, 21, 2274--84. 

Komiyama, T., Bigler, T.L., Yoshida, N., Noda, K. Laskowski, M. (1991). Replacement of Pi Leul8 by Glul8 in the reactive site of turkey ovomucoid third domain converts it into a strong inhibitor of glu-specific Streptomyces-griseus proteinase (GLUSGP). ]. Biol. Chem., 266, 10727-30. 

Laskowski, M., Apostol, 1., Ardelt, W. et al. (1990). Amino acid sequences of ovomucoid third domain from 25 additional species of birds. ]. Prot. Chem., 9, 715-26. 

C. M. MacDermald and G. A. Kaminski. Electrostatic polarization is crucial for reproducing pKa shifts of carboxylic residues in turkey ovomucoid third domain./ Phys. Chem. B, lll(30] 9036-9044, 2007. 

H. Li, A.D. Robertson, and J.H. Jensen, The determinants of carboxyl pK values in Turkey ovomucoid third domain. Proteins Struct. Funct. Bioinform. 55 (2004), pp. 689-704. 

M. Fujinaga, A. R. Sielecki, R. J. Read, W. Ardelt, M. Laskowski, and M. N. G. James, /. MoL Biol., 195, 397 (1987). Crystal and Molecular Structures of the Conmiexed of a-Chymotrypsin with Its Inhibitor Turkey Ovomucoid Third Domain at 1.8 Angstroms Resolution. 

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