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Structure of hydrophobic core in plant carboxylesterase

Structure of hydrophobic core in plant carboxylesterase The fuzzy oil drop model was applied to characterize the hydrophobic core structure in plant carboxylesterase. The characteristics revealed the status of -sheets in the central part of the molecule as discordant as opposed to the expected hydrophobicity distribution. Particularly, the -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. Keywords: carboxylesterase; fuzzy oil drop model; hydrolase; hydrophobicity. The aim of this work is to recognize the relation between the hydrophobic core structure and its local discrepancies, which are usually present in enzymes. The fuzzy oil drop model is able to identify and evaluate quantitatively the local discordance versus the ideal hydrophobicity distribution. Materials and methods The protein structure taken as the object of analysis is the 2O7R (PDB [1]). The fuzzy oil drop model is presented in detail in Ref. [3]. The main point of this model is the assumption that the ideal structure of hydrophobic core in proteins can be described by the 3D Gauss function. The maximum of this function is placed in the center of an ellipsoid with values decreasing as the distance versus the center increases, reaching zero values in the distance of 3 in each direction. The protein molecule encapsulated by such ellipsoid with appropriate parameters ( is the Gauss function parameter that expresses the size and shape of the ellipsoid) is assumed to represent the hydrophobicity distribution in accordance with the 3D Gauss function. It appears that some fragments of the polypeptide chain in proteins represent local discordance. The local excess of hydrophobicity (especially on the protein surface) is assumed to represent the potential area for protein-protein complexation. The local deficiency of hydrophobicity is related to the cavity that usually is the place for ligand (substrate) binding. The local discrepancies versus the ideal hydrophobicity distribution can be measured quantitatively by applying the Kullback-Leibler entropy [4]. This quantity expresses the distance between two distributions: the observed versus the target. The observed hydrophobicity distribution is calculated using Levitt's function for hydrophobic interaction (interresidual) [5]. The value of divergence entropy cannot be interpreted immediately (common characteristics of entropy). This is why the second reference distribution is introduced: the unified one. This distribution assumes equal hydrophobicity for each residue. This is the case of no hydrophobicity concentration in any point of the protein body. It means Introduction Carboxylesterases ­ to this group belongs the protein under consideration ­ are widely distributed in plants. Their probable role is in the development processes, plant defense, and participation in secondary metabolism. The structure of hydrolase [2O7R Protein Data Bank (PDB) ID] [1] is characterized by the centrally located -sheet surrounded by helices. This structure belongs to the class 3.40.50.1820-/ three-layer (aba) sandwich according to CATH classification [2]. The structure represents the enzyme with the inhibitor bound covalently. The detailed analysis of this complex shows no differences in comparison to free enzyme [1]. Due to its very characteristic type of fold, the protein is also classified as representing the /-hydrolase fold superfamily. *Corresponding author: Irena Roterman, Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Lazarza 16, 31-530 Krakow, Poland, E-mail: myroterm@cyf-kr.edu.pl Mateusz Banach, Leszek Konieczny and Zdzislaw Winiowski: Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Krakow, Poland 14Banach et al.: Structure of hydrophobic core in plant carboxylesterase Table 1:RD parameters that characterize the status of hydrophobic core in 2O7R. 2O7R Secondary form -sheet I -sheet II No E Protein BI BI Loop B II Loop B II H B II Loop H B II Loop H H B II H H B II Loop B II Loop H Loop H B II H B II H H Fragment 25­27 31­33 34­51 52­61 62­65 66­74 75­79 83­89 90­100 101­116 118­123 124­132 133­148 151­157 158­168 169­184 185­190 193­201 202­209 210­216 217­222 223­235 236­255 256­265 266­274 278­292 295­301 307­311 312­328 RD complete molecule 0.502 0.462 0.034 0.775 0.500 0.741 0.376 0.531 0.709 0.796 0.498 0.574 0.450 0.249 0.241 0.513 0.554 0.172 0.415 0.359 0.684 0.631 0.505 0.507 0.236 0.588 0.330 0.347 0.913 0.210 0.436 0.624 0.499 RD 18­53 absent 0.475 E 169 Ser E 276 Asp E 304 His Figure 1:3D structure of 2O7R with fragments of status that are different in comparison to the ideal distribution shown in red (helical and -strands). Green fragments, irregular loops; yellow residues, residues engaged in enzymatic activity in hydrolase under consideration. The calculation of O/T and O/R can be performed for selected polypeptide chain fragments in particular fragments of defined secondary structure. To avoid dealing with two parameters (O/T and O/R), the relative distance (RD) parameter is introduced. RD = O/T . O/T+O/R Left column: E denotes the position of enzymatic residues. Symbols B I and B II distinguish the two -sheets present in the protein molecule. H is helical fragment. that it expresses the status of no hydrophobic core present in the protein molecule. The distance between observed and theoretical distributions (O/T) compared to the distance between observed and unified distributions (O/R) allows the classification of hydrophobic core status. The values O/T<O/R are interpreted to describe that the status of hydrophobic core in accordance with the assumed one is present in the protein molecule. If the relation is opposite, the hydrophobicity distribution in the particular protein is disordered. This quantity expresses the RD versus the theoretical distribution, taking the unified distribution as the reference form of hydrophobic core. RD<0.5 is interpreted as the presence of regularly ordered hydrophobic core in protein. RD expresses the relative proximity of the position of observed distribution versus the theoretical one and the unified one. RD<0.5 means that the position of observed distribution is closer to the theoretical one than the unified one. The RD value can be also calculated for polypeptide chain with some residues eliminated. In our case, there are residues engaged in enzymatic activity. The decrease of RD values after the elimination of certain residues suggests the position requiring the local irregularity of Banach et al.: Structure of hydrophobic core in plant carboxylesterase15 0.01 Hydrophobicity 0.008 0.006 0.004 0.002 0 0 50 100 150 2O7R T O B L H E 200 Residue 250 300 350 Figure 2:Profiles of hydrophobicity distribution (T for theoretical and O for observed). On the horizontal axis: yellow, -strands; turquoise, loops; violet, helices. Only fragments of the status RD>0.5 are distinguished on the horizontal axis. Top line: positions of enzymatic residues (E). hydrophobic core. Such status of selected residues suggests also the intentional local irregularity, which seems to be necessary for biological activity. This paper discusses the enzyme to check the status of enzymatic residues in carboxylesterase in a wider context of the entire molecule, including also the close neighborhood of the active site. Conclusions The discordant status versus the ideal one in enzymes appears quite frequently [6­8]. It seems that it is intentional. It was also observed in lysozyme [9]. Usually, the area in close proximity with respect to the active site appears discordant [6­8]. The presented results are the introductory step in the recognition of biological function of the discussed protein, which is recognized as responsible for the apple flavor due to the hydrolysis of relevant flavor esters in the ripe apple fruit [10, 11]. The identification of the active site is performed for a larger set of enzymes of different activities in Ref. [6]. Acknowledgments: Many thanks to Anna Zarembamietaska for technical support. Author contributions: The authors have accepted responsibility for the entire content of this submitted manuscript and approved submission. Research funding: The work was financially supported by the Jagiellonian University Medical College (grant K/ ZDS/006363). Employment or leadership: None declared. Honorarium: None declared. Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication. Results The characteristics of hydrolase under consideration are given in Table 1. The values in bold distinguish the fragments of status RD>0.5 ­ it means the fragments representing different than expected status of hydrophobicity distribution. The RD parameters are calculated for two forms of hydrolase under consideration: the complete one and the molecule with the fragment 18­35 eliminated. This fragment represents a quite exposed loop, which stands out regarding the main body of protein. The spatial representation of the mutual orientation of fragments characterized by RD>0.5 are shown in Figure 1. The profiles of theoretical and observed hydrophobicities in 2O7R shown in Figure 2 reveal the localization of fragments with discordant hydrophobicity distribution. The positions of the active site appear to be in close proximity versus the fragments of discordant status. The interpretation of two compared profiles based on Kullback-Leibler entropy identifies the polypeptide chain fragments in terms of differences in distributions. Visually recognized differences (as about position 200 in polypeptide) do not appear as significantly different due to sequential changes that are similar in both profiles. The local maximum in this position is of two-local maxima form in both profiles. This is why it is not categorized as different. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bio-Algorithms and Med-Systems de Gruyter

Structure of hydrophobic core in plant carboxylesterase

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de Gruyter
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1895-9091
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1896-530X
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10.1515/bams-2017-0001
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Abstract

The fuzzy oil drop model was applied to characterize the hydrophobic core structure in plant carboxylesterase. The characteristics revealed the status of -sheets in the central part of the molecule as discordant as opposed to the expected hydrophobicity distribution. Particularly, the -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. Keywords: carboxylesterase; fuzzy oil drop model; hydrolase; hydrophobicity. The aim of this work is to recognize the relation between the hydrophobic core structure and its local discrepancies, which are usually present in enzymes. The fuzzy oil drop model is able to identify and evaluate quantitatively the local discordance versus the ideal hydrophobicity distribution. Materials and methods The protein structure taken as the object of analysis is the 2O7R (PDB [1]). The fuzzy oil drop model is presented in detail in Ref. [3]. The main point of this model is the assumption that the ideal structure of hydrophobic core in proteins can be described by the 3D Gauss function. The maximum of this function is placed in the center of an ellipsoid with values decreasing as the distance versus the center increases, reaching zero values in the distance of 3 in each direction. The protein molecule encapsulated by such ellipsoid with appropriate parameters ( is the Gauss function parameter that expresses the size and shape of the ellipsoid) is assumed to represent the hydrophobicity distribution in accordance with the 3D Gauss function. It appears that some fragments of the polypeptide chain in proteins represent local discordance. The local excess of hydrophobicity (especially on the protein surface) is assumed to represent the potential area for protein-protein complexation. The local deficiency of hydrophobicity is related to the cavity that usually is the place for ligand (substrate) binding. The local discrepancies versus the ideal hydrophobicity distribution can be measured quantitatively by applying the Kullback-Leibler entropy [4]. This quantity expresses the distance between two distributions: the observed versus the target. The observed hydrophobicity distribution is calculated using Levitt's function for hydrophobic interaction (interresidual) [5]. The value of divergence entropy cannot be interpreted immediately (common characteristics of entropy). This is why the second reference distribution is introduced: the unified one. This distribution assumes equal hydrophobicity for each residue. This is the case of no hydrophobicity concentration in any point of the protein body. It means Introduction Carboxylesterases ­ to this group belongs the protein under consideration ­ are widely distributed in plants. Their probable role is in the development processes, plant defense, and participation in secondary metabolism. The structure of hydrolase [2O7R Protein Data Bank (PDB) ID] [1] is characterized by the centrally located -sheet surrounded by helices. This structure belongs to the class 3.40.50.1820-/ three-layer (aba) sandwich according to CATH classification [2]. The structure represents the enzyme with the inhibitor bound covalently. The detailed analysis of this complex shows no differences in comparison to free enzyme [1]. Due to its very characteristic type of fold, the protein is also classified as representing the /-hydrolase fold superfamily. *Corresponding author: Irena Roterman, Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Lazarza 16, 31-530 Krakow, Poland, E-mail: myroterm@cyf-kr.edu.pl Mateusz Banach, Leszek Konieczny and Zdzislaw Winiowski: Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Krakow, Poland 14Banach et al.: Structure of hydrophobic core in plant carboxylesterase Table 1:RD parameters that characterize the status of hydrophobic core in 2O7R. 2O7R Secondary form -sheet I -sheet II No E Protein BI BI Loop B II Loop B II H B II Loop H B II Loop H H B II H H B II Loop B II Loop H Loop H B II H B II H H Fragment 25­27 31­33 34­51 52­61 62­65 66­74 75­79 83­89 90­100 101­116 118­123 124­132 133­148 151­157 158­168 169­184 185­190 193­201 202­209 210­216 217­222 223­235 236­255 256­265 266­274 278­292 295­301 307­311 312­328 RD complete molecule 0.502 0.462 0.034 0.775 0.500 0.741 0.376 0.531 0.709 0.796 0.498 0.574 0.450 0.249 0.241 0.513 0.554 0.172 0.415 0.359 0.684 0.631 0.505 0.507 0.236 0.588 0.330 0.347 0.913 0.210 0.436 0.624 0.499 RD 18­53 absent 0.475 E 169 Ser E 276 Asp E 304 His Figure 1:3D structure of 2O7R with fragments of status that are different in comparison to the ideal distribution shown in red (helical and -strands). Green fragments, irregular loops; yellow residues, residues engaged in enzymatic activity in hydrolase under consideration. The calculation of O/T and O/R can be performed for selected polypeptide chain fragments in particular fragments of defined secondary structure. To avoid dealing with two parameters (O/T and O/R), the relative distance (RD) parameter is introduced. RD = O/T . O/T+O/R Left column: E denotes the position of enzymatic residues. Symbols B I and B II distinguish the two -sheets present in the protein molecule. H is helical fragment. that it expresses the status of no hydrophobic core present in the protein molecule. The distance between observed and theoretical distributions (O/T) compared to the distance between observed and unified distributions (O/R) allows the classification of hydrophobic core status. The values O/T<O/R are interpreted to describe that the status of hydrophobic core in accordance with the assumed one is present in the protein molecule. If the relation is opposite, the hydrophobicity distribution in the particular protein is disordered. This quantity expresses the RD versus the theoretical distribution, taking the unified distribution as the reference form of hydrophobic core. RD<0.5 is interpreted as the presence of regularly ordered hydrophobic core in protein. RD expresses the relative proximity of the position of observed distribution versus the theoretical one and the unified one. RD<0.5 means that the position of observed distribution is closer to the theoretical one than the unified one. The RD value can be also calculated for polypeptide chain with some residues eliminated. In our case, there are residues engaged in enzymatic activity. The decrease of RD values after the elimination of certain residues suggests the position requiring the local irregularity of Banach et al.: Structure of hydrophobic core in plant carboxylesterase15 0.01 Hydrophobicity 0.008 0.006 0.004 0.002 0 0 50 100 150 2O7R T O B L H E 200 Residue 250 300 350 Figure 2:Profiles of hydrophobicity distribution (T for theoretical and O for observed). On the horizontal axis: yellow, -strands; turquoise, loops; violet, helices. Only fragments of the status RD>0.5 are distinguished on the horizontal axis. Top line: positions of enzymatic residues (E). hydrophobic core. Such status of selected residues suggests also the intentional local irregularity, which seems to be necessary for biological activity. This paper discusses the enzyme to check the status of enzymatic residues in carboxylesterase in a wider context of the entire molecule, including also the close neighborhood of the active site. Conclusions The discordant status versus the ideal one in enzymes appears quite frequently [6­8]. It seems that it is intentional. It was also observed in lysozyme [9]. Usually, the area in close proximity with respect to the active site appears discordant [6­8]. The presented results are the introductory step in the recognition of biological function of the discussed protein, which is recognized as responsible for the apple flavor due to the hydrolysis of relevant flavor esters in the ripe apple fruit [10, 11]. The identification of the active site is performed for a larger set of enzymes of different activities in Ref. [6]. Acknowledgments: Many thanks to Anna Zarembamietaska for technical support. Author contributions: The authors have accepted responsibility for the entire content of this submitted manuscript and approved submission. Research funding: The work was financially supported by the Jagiellonian University Medical College (grant K/ ZDS/006363). Employment or leadership: None declared. Honorarium: None declared. Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication. Results The characteristics of hydrolase under consideration are given in Table 1. The values in bold distinguish the fragments of status RD>0.5 ­ it means the fragments representing different than expected status of hydrophobicity distribution. The RD parameters are calculated for two forms of hydrolase under consideration: the complete one and the molecule with the fragment 18­35 eliminated. This fragment represents a quite exposed loop, which stands out regarding the main body of protein. The spatial representation of the mutual orientation of fragments characterized by RD>0.5 are shown in Figure 1. The profiles of theoretical and observed hydrophobicities in 2O7R shown in Figure 2 reveal the localization of fragments with discordant hydrophobicity distribution. The positions of the active site appear to be in close proximity versus the fragments of discordant status. The interpretation of two compared profiles based on Kullback-Leibler entropy identifies the polypeptide chain fragments in terms of differences in distributions. Visually recognized differences (as about position 200 in polypeptide) do not appear as significantly different due to sequential changes that are similar in both profiles. The local maximum in this position is of two-local maxima form in both profiles. This is why it is not categorized as different.

Journal

Bio-Algorithms and Med-Systems – de Gruyter

Published: Mar 1, 2017

References

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  • High-resolution crystal structure of plant carboxylesterase AeCXE1, from Actinidia eriantha, and its complex with a high-affinity inhibitor paraoxon
  • Biochemical characterisation of MdCXE1, a carboxylesterase from apple that is expressed during fruit ripening
  • CATH: comprehensive structural and functional annotations for genome sequences
  • A simplified representation of protein conformations for rapid simulation of protein holding
  • On information and sufficiency
  • Application of divergence entropy to characterize the structure of the hydrophobic core in DNA interacting proteins
  • 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