scholarly journals Uncovering of cytochrome P450 anatomy by SecStrAnnotator

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Adam Midlik ◽  
Veronika Navrátilová ◽  
Taraka Ramji Moturu ◽  
Jaroslav Koča ◽  
Radka Svobodová ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Cytochromes P450 ◽  
Substrate Recognition ◽  
Specific Protein ◽  
Homologous Proteins ◽  
Biotransformation Enzymes ◽  
Recognition Sites ◽  
The Family ◽  
Typical Length ◽  
Model Family

AbstractProtein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, always assigning the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs provides an overview of the studied family and enriches the analysis of any particular protein at hand. We developed a workflow for the analysis of the secondary structure anatomy of a protein family. We applied this analysis to the model family of cytochromes P450 (CYPs)—a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, the conservation/variability of these properties and relationship to the substrate recognition sites. We also suggest a generic residue numbering scheme for the CYP family. Comparing the bacterial and eukaryotic part of the family highlights the significant differences and reveals a well-known anomalous group of bacterial CYPs with some typically eukaryotic features. Our workflow for SSE annotation for CYP and other families can be freely used at address https://sestra.ncbr.muni.cz.

scholarly journals Uncovering of Cytochrome P450 Anatomy by SecStrAnnotator

2020 ◽  
Author(s):  
Adam Midlik ◽  
Veronika Navrátilová ◽  
Taraka Ramji Moturu ◽  
Jaroslav Koča ◽  
Radka Svobodová ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Cytochromes P450 ◽  
Specific Protein ◽  
Protein Family ◽  
Homologous Proteins ◽  
Functional Relationships ◽  
Biotransformation Enzymes ◽  
The Family ◽  
Family Based ◽  
Typical Length

AbstractMotivationProtein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of homologous structures and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, assigning always the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs and their variability provides an overview of the studied protein family and can be used to enrich the analysis of a particular protein at hand.ResultsWe developed a workflow for analysis of the secondary structure anatomy of a protein family, based on SSE annotation tool SecStrAnnotator. We applied this analysis to the model family of cytochromes P450 (CYPs) – a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, as well as the conservation/variability of these properties. We also suggest a generic residue numbering scheme for the CYP family. The comparison between the bacterial and eukaryotic part of the family highlights the major differences and reveals an anomalous group of bacterial CYPs with some typically eukaryotic features. This hints at possible evolutionary and functional relationships.AvailabilityThe software and data are available at https://webchem.ncbr.muni.cz/Wiki/[email protected], [email protected]

scholarly journals Evolution of substrate recognition sites (SRSs) in cytochromes P450 from Apiaceae exemplified by the CYP71AJ subfamily

2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Bjørn Dueholm ◽  
Célia Krieger ◽  
Damian Drew ◽  
Alexandre Olry ◽  
Tsunashi Kamo ◽  
...  
Keyword(s):  
Cytochromes P450 ◽  
Substrate Recognition ◽  
Recognition Sites

Intergenerational Family Relations in Luxembourg

2013 ◽  
Vol 18 (1) ◽  
pp. 59-69 ◽  
Author(s):  
Isabelle Albert ◽  
Dieter Ferring ◽  
Tom Michels
Keyword(s):  
Family Relations ◽  
Family Values ◽  
Generation Gap ◽  
Intergenerational Solidarity ◽  
Acculturation Gap ◽  
Family Obligations ◽  
Mothers And Daughters ◽  
The Family ◽  
The Relationship ◽  
Model Family

According to the intergenerational solidarity model, family members who share similar values about family obligations should have a closer relationship and support each other more than families with a lower value consensus. The present study first describes similarities and differences between two family generations (mothers and daughters) with respect to their adherence to family values and, second, examines patterns of relations between intergenerational consensus on family values, affectual solidarity, and functional solidarity in a sample of 51 mother-daughter dyads comprising N = 102 participants from Luxembourgish and Portuguese immigrant families living in the Grand Duchy of Luxembourg. Results showed a small generation gap in values of hierarchical gender roles, but an acculturation gap was found in Portuguese mother-daughter dyads regarding obligations toward the family. A higher mother-daughter value consensus was related to higher affectual solidarity of daughters toward their mothers but not vice versa. Whereas affection and value consensus both predicted support provided by daughters to their mothers, affection mediated the relationship between consensual solidarity and received maternal support. With regard to mothers, only affection predicted provided support for daughters, whereas mothers’ perception of received support from their daughters was predicted by value consensus and, in the case of Luxembourgish mothers, by affection toward daughters.

RNA secondary structure dependence in METTL3–METTL14 mRNA methylation is modulated by the N-terminal domain of METTL3

2020 ◽  
Vol 402 (1) ◽  
pp. 89-98
Author(s):  
Nathalie Meiser ◽  
Nicole Mench ◽  
Martin Hengesbach
Keyword(s):  
Secondary Structure ◽  
Rna Binding ◽  
Specific Protein ◽  
Structure Dependence ◽  
Terminal Domain ◽  
Methylation Assay ◽  
A Site ◽  
Methylation Activity

AbstractN6-methyladenosine (m6A) is the most abundant modification in mRNA. The core of the human N6-methyltransferase complex (MTC) is formed by a heterodimer consisting of METTL3 and METTL14, which specifically catalyzes m6A formation within an RRACH sequence context. Using recombinant proteins in a site-specific methylation assay that allows determination of quantitative methylation yields, our results show that this complex methylates its target RNAs not only sequence but also secondary structure dependent. Furthermore, we demonstrate the role of specific protein domains on both RNA binding and substrate turnover, focusing on postulated RNA binding elements. Our results show that one zinc finger motif within the complex is sufficient to bind RNA, however, both zinc fingers are required for methylation activity. We show that the N-terminal domain of METTL3 alters the secondary structure dependence of methylation yields. Our results demonstrate that a cooperative effect of all RNA-binding elements in the METTL3–METTL14 complex is required for efficient catalysis, and that binding of further proteins affecting the NTD of METTL3 may regulate substrate specificity.

scholarly journals An automated protocol for modelling peptide substrates to proteases

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Rodrigo Ochoa ◽  
Mikhail Magnitov ◽  
Roman A. Laskowski ◽  
Pilar Cossio ◽  
Janet M. Thornton
Keyword(s):  
Substrate Recognition ◽  
Accessible Surface Area ◽  
Conformational Sampling ◽  
Structural Determinants ◽  
Peptide Substrates ◽  
The Family ◽  
Protease Substrate ◽  
Peptide Complexes ◽  
Accessible Surface ◽  
Automated Protocol

Abstract Background Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promiscuity which can also be essential. Databases compiling specificity matrices derived from experimental assays have provided valuable insights into protease substrate recognition. Despite this, there are still gaps in our knowledge of the structural determinants. Here, we compile a set of protease crystal structures with bound peptide-like ligands to create a protocol for modelling substrates bound to protease structures, and for studying observables associated to the binding recognition. Results As an application, we modelled a subset of protease–peptide complexes for which experimental cleavage data are available to compare with informational entropies obtained from protease–specificity matrices. The modelled complexes were subjected to conformational sampling using the Backrub method in Rosetta, and multiple observables from the simulations were calculated and compared per peptide position. We found that some of the calculated structural observables, such as the relative accessible surface area and the interaction energy, can help characterize a protease’s substrate recognition, giving insights for the potential prediction of novel substrates by combining additional approaches. Conclusion Overall, our approach provides a repository of protease structures with annotated data, and an open source computational protocol to reproduce the modelling and dynamic analysis of the protease–peptide complexes.

scholarly journals Characterization of porcine osteonectin extracted from foetal calvariae

1988 ◽  
Vol 253 (1) ◽  
pp. 139-151 ◽  
Author(s):  
C Domenicucci ◽  
H A Goldberg ◽  
T Hofmann ◽  
D Isenman ◽  
S Wasi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
Type I Collagen ◽  
Culture Shock ◽  
Gel Filtration ◽  
Alpha Helix ◽  
Type I ◽  
Homologous Proteins ◽  
Compact Structure ◽  
Significant Difference

Osteonectin, extracted from foetal porcine calvariae with 0.5 M-EDTA, was purified to homogeneity by using gel filtration and polyanion anion-exchange fast protein liquid chromatography under dissociative conditions without the need of reducing agents. The purified protein migrated with an Mr of 40,300 on SDS/polyacrylamide gels and was similar to bovine osteonectin in both amino acid composition and in its ability to bind to hydroxyapatite in the presence of 4 M-guanidinium hydrochloride (GdmCl). However, unlike the bovine protein, porcine osteonectin did not bind selectively to hydroxyapatite when EDTA tissue extracts were used. In addition, purified porcine osteonectin did not show any apparent affinity for either native or denatured type I collagen, but did bind to serum albumin. Primary sequence analysis revealed an N-terminal alanine residue, with approximately one-half of the subsequent 35 residues identified as small hydrophobic amino acids and one-quarter as acidic amino acids. The only significant difference between the N-terminal sequences of the bovine and porcine proteins was the deletion of the tripeptide Val-Ala-Glu in porcine osteonectin. In contrast with bovine osteonectin, far-u.v.c.d. of porcine osteonectin revealed considerable secondary structure, of which 27% was alpha-helix and 39% was beta-sheet. Cleavage of the molecule with CNBr under non-reducing conditions generated five fragments, of which two major fragments (Mr 27,900 and 12,400) stained blue with Stains All, a reagent that stains sialic-acid-rich proteins/phosphate-containing proteins and/or Ca2+-binding proteins blue while staining other proteins pink. The 12,400-Mr fragment bound 45Ca2+ selectively, indicating a Ca2+-binding site in this part of the molecule. The 27,900-Mr fragment did not bind Ca2+, and since biosynthetic studies with 32PO4(3-) did not show phosphorylation of porcine osteonectin, this fragment is likely to be highly acidic. The incomplete cleavage of the molecule with CNBr and the ability of the molecule to regain its secondary structure after exposure to 7 M-urea are features consistent with the molecule having a compact structure that is stabilized by numerous disulphide bridges. The chemical and binding properties of porcine osteonectin are closely similar to the recently described ‘culture shock’, SPARC and BM-40 proteins, indicating that these are homologous proteins.

The yeast UME5 gene regulates the stability of meiotic mRNAs in response to glucose

1994 ◽  
Vol 14 (5) ◽  
pp. 3446-3458
Author(s):  
R T Surosky ◽  
R Strich ◽  
R E Esposito
Keyword(s):  
Vegetative Growth ◽  
Signal Transduction Pathway ◽  
Kinase Domain ◽  
Specific Protein ◽  
Transcript Stability ◽  
The Family ◽  
Two Factors ◽  
Genetic Epistasis ◽  
The Stability ◽  
Acetate Medium

We reported previously that early meiotic transcripts are highly unstable. These mRNAs exhibit half-lives of approximately 3 min when expressed during vegetative growth in glucose medium and are stabilized twofold during sporulation in acetate medium. Two genes, UME2 and UME5, that regulate the stability of meiosis-specific transcripts have been identified. The wild-type UME5 gene, which has been analyzed in detail, decreases the stability of all meiotic mRNAs tested approximately twofold when expressed during vegetative growth but has no effect on the half-lives of a number of vegetative mRNAs examined. The UME5 gene is dispensable for mitotic and meiotic development. Cells in which the entire UME5 gene has been deleted are viable, although the generation time is slightly longer and sporulation is less efficient. The UME5 transcript is constitutively expressed, and its stability is not autoregulated. The UME5 gene encodes a predicted 63-kDa protein with homology to the family of CDC28 serine/threonine-specific protein kinases. The kinase activity appears to be central to the function of the UME5 protein, since alteration of a highly conserved amino acid in the kinase domain results in a phenotype identical to that of a ume5 deletion. Genetic epistasis studies suggest that the UME2 and UME5 gene products act in the same pathway to regulate meiotic transcript stability. This pathway is independent of deadenylation and translation, two factors known to be important in regulating mRNA turnover. Significantly, the UME5-mediated destabilization of meiotic mRNAs occurs in glucose- but not in acetate-containing medium. Thus, the UME5 gene appears to participate in a glucose signal transduction pathway governing message stability.

Differential Contribution of Active Site Residues in Substrate Recognition Sites 1 and 5 to Cytochrome P450 2C8 Substrate Selectivity and Regioselectivity†

Biochemistry ◽  
2004 ◽  
Vol 43 (24) ◽  
pp. 7834-7842 ◽  
Author(s):  
Oranun Kerdpin ◽  
David J. Elliot ◽  
Sanford L. Boye ◽  
Donald J. Birkett ◽  
Krongtong Yoovathaworn ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Active Site ◽  
Substrate Recognition ◽  
Substrate Selectivity ◽  
Active Site Residues ◽  
Recognition Sites ◽  
Cytochrome P450 2C8 ◽  
Differential Contribution

Methylene chain ruler for evaluating the regioselectivity of a substrate-recognising oxidation catalyst

2019 ◽  
Vol 55 (58) ◽  
pp. 8378-8381
Author(s):  
Shota Teramae ◽  
Akane Kito ◽  
Tomoteru Shingaki ◽  
Yu Hamaguchi ◽  
Yuuki Yano ◽  
...  
Keyword(s):  
Substrate Recognition ◽  
Major Product ◽  
Oxidation Catalyst ◽  
Central Position ◽  
Recognition Sites ◽  
Methylene Chain ◽  
Catalysed Oxidation

We designed and synthesised Ru porphyrin 1a as an oxidation catalyst with substrate recognition sites. The 1a catalysed oxidation of substrate 7 selectively oxidised the central position of the methylene chain, affording ketone 8 as the major product.

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