1. Conformational preferences of X-Pro sequences: Ala-Pro and Aib-Pro motifs
Byung Jin Byun, Il Keun Song, Yong Je Chung, Keun Ho Ryu, Young Kee Kang J Phys Chem B. 2010 Nov 11;114(44):14077-86. doi: 10.1021/jp107200f.
Conformational preferences and prolyl cis-trans isomerizations of the X-Pro motifs (Ac-X-Pro-NHMe, X = Ala and Aib) are explored using the meta-hybrid functional M06-2X and the double-hybrid functional B2PLYP-D with empirical dispersion corrections in the gas phase and in water, where solvation free energies were calculated using the implicit SMD model. Ac-Ala-Pro-NHMe favors the type VI β-turns in the gas phase and the open conformations in water. The populations of type VI β-turns decrease from 71% in the gas phase to 21% in water, which is reasonably consistent with IR and NMR experimental results on tBoc-Ala-Pro-NHMe. However, Ac-Aib-Pro-NHMe prefers the type I β-turns with α-helical structures for both residues in the gas phase and in water, whose populations are estimated to be 66% in both phases. These calculated results may rationalize why most of the peptaibiotics containing the Aib-Pro sequence have a regular α-helical conformation at the N- or C-terminus but a kinked α-helical structure in the middle of the helix. The cis-trans isomerizations of the Ala-Pro and Aib-Pro peptide bonds proceed via the clockwise rotation with the different backbone conformations. The rotational barriers to cis-to-trans isomerization are estimated to be 19.73 kcal/mol for the Ala-Pro tripeptide and 16.64 kcal/mol for the Aib-Pro tripeptide in water, which indicates that the rotational barrier becomes lower by ~3 kcal/mol for the Aib-Pro peptide bond. The calculated rotational barrier for Ac-Ala-Pro-NHMe is consistent with the observed value of 19.3 kcal/mol for Suc-Ala-Ala-Pro-Phe-pNA from NMR experiments in a buffered solution.
2. Cleavage specificity of cucumisin, a plant serine protease
T Uchikoba, H Yonezawa, M Kaneda J Biochem. 1995 May;117(5):1126-30. doi: 10.1093/oxfordjournals.jbchem.a124817.
Cucumisin was isolated from prince melon sarcocarp by means of a simple purification procedure. Serine protease inhibitors such as soybean trypsin inhibitor, ovomucoid, and aprotinin had no effect on the enzyme activity. alpha 2-Macroglobulin showed 38% inhibition of the original caseinolytic activity of cucumisin. The favorable synthetic substrates for cucumisin were Glt-Ala-Ala-Pro-Leu-pNA and Suc-Ala-Ala-Pro-Phe-pNA. The constant (kcat/Km) for Suc-Ala-Pro-Ala-pNA was found to be 30 times greater than that for Suc-Ala-Ala-Ala-pNA. The substrate specificity of cucumisin for oligopeptides and proteins was shown to be broad.
3. Extracellular expression of keratinase Ker P from Pseudomonas aeruginosa in E. coli
Richa Sharma, Rani Gupta Biotechnol Lett. 2010 Dec;32(12):1863-8. doi: 10.1007/s10529-010-0361-2. Epub 2010 Jul 31.
Keratinase from Pseudomonas aeruginosa KS-1 was expressed constitutively as an extracellular protein in Escherichia coli with high specific activity of 3.7 kU/mg. It was purified fourfold as a 33 kDa monomeric protein by Q-Sepharose ion exchange chromatography with a recovery of 95%. It is a serine protease with optimal activity at pH 9 and 50°C. It was stable from pH 4 to 12 for 1 h with a t(1/2) of 12 min at 70°C. It hydrolyzed haemoglobin > fibrin > feather keratin > azo-casein > casein > meat protein > gelatin. Among synthetic substrates, it efficiently hydrolyzed N-Suc-ala-ala-pro-phe-pNA, N-Suc-ala-ala-ala-pNA, N-Suc-ala-ala-pro-leu-pNA and also plasmin substrate, D: -Val-Leu-Lys-pNA.
