Structure of hydrophobic core in plant carboxylesterase

• Autorzy: Banach M. , Konieczny L. , Wiśniowski Z. , Roterman I.

Identyfikatory

DOI

10.1515/bams-2017-0001

• Języki publikacji: EN

Abstrakty

EN

The fuzzy oil drop model was applied to characterize the hydrophobic core structure in plant carboxylesterase. The characteristics revealed the status of β-sheets in the central part of the molecule as discordant as opposed to the expected hydrophobicity distribution. Particularly, the β-strands and helices in close proximity to the enzymatic residues recognized as discordant with respect to the ideal hydrophobicity distribution of hydrophobic core are of high importance. It is assumed that this local irregularity is the form of coding the specificity of enzymes. The protein under consideration appears to be the next example proving this assumption.

Słowa kluczowe

EN

carboxylesterase; fuzzy oil drop model; hydrolase; hydrophobicity

• Wydawca: Uniwersytet Jagielloński - Collegium Medicum ; Index Copernicus Sp. z o.o.
• Czasopismo: Bio-Algorithms and Med-Systems
• Rocznik: 2017
• Tom: Vol. 13, no. 1
• Strony: 13--16
• Opis fizyczny: Bibliogr. 11 poz., rys., wykr.

Twórcy

autor

Banach M.

• Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Krakow, Poland

autor

Konieczny L.

• Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Krakow, Poland

autor

Wiśniowski Z.

• Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Krakow, Poland

autor

Roterman I.

• Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Lazarza 16, 31-530 Krakow, Poland

Bibliografia

• 1. Ileperuma NR, Marshall SD, Squire CJ, Baker HM, Oakeshott JG, Russell RJ, et al. High-resolution crystal structure of plant carboxylesterase AeCXE1, from Actinidia eriantha, and its complex with a high-affinity inhibitor paraoxon. Biochemistry 2007;46:1851–9.
• 2. Sillitoe I, Lewis TE, Cuff AL, Das S, Ashford P, Dawson NL, et al. CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res 2015;43:D376–81.
• 3. Kalinowska B, Banach M, Konieczny L, Roterman I. Application of divergence entropy to characterize the structure of the hydrophobic core in DNA interacting proteins. Entropy 2015;17:1477–507.
• 4. Kullback S, Leibler RA. On information and sufficiency. Ann Math Stat 1951;22:79–86.
• 5. Levitt M, Levitt MA. A simplified representation of protein conformations for rapid simulation of protein holding. J Mol Biol 1976;104:59–107.
• 6. Prymula K, Jadczyk T, Roterman I. Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction. J Comput Aided Mol Des 2011;25:117–33.
• 7. Banach M, Konieczny L, Roterman I. Ligand-binding-site recognition. In: Roterman-Konieczna I, editor. Protein folding in silico. Oxford/Cambridge/Philadelphia/New Delhi: Woodhead Publishing, 2012:78–94.
• 8. Alejster P, Banach M, Jurkowski W, Marchewka D, Roterman, I. Comparative analysis of techniques oriented on the recognition of ligand binding area in proteins. In: Roterman-Konieczna I, editor. Protein folding in silico. Oxford/Cambridge/Philadelphia/New Delhi: Woodhead Publishing, 2012:55–86.
• 9. Kalinowska B, Banach M, Wiśniowski Z, Konieczny L, Roterman I. Impact of mutations on the hydrophobic core structure in lysozymes – analysis of factors triggering loss of enzymatic activity. Submitted for publication.
• 10. Souleyre EJ, Marshall SD, Oakeshott JG, Russell RJ, Plummer KM, Newcomb RD. Biochemical characterisation of MdCXE1, a carboxylesterase from apple that is expressed during fruit ripening. Phytochemistry 2011;72:564–71.
• 11. Crowhurst RN, Gleave AP, MacRae EA, Ampomah-Dwamena C, Atkinson RG, Beuning LL, et al. Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. BMC Genomics 2008;9:351.

Uwagi

Opracowanie ze środków MNiSW w ramach umowy 812/P-DUN/2016 na działalność upowszechniającą naukę (zadania 2017)