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Dyzma A, Wielgus-Kutrowska B, Girstun A, Matošević ZJ, Staroń K, Bertoša B, Trylska J, Bzowska A. Trimeric Architecture Ensures the Stability and Biological Activity of the Calf Purine Nucleoside Phosphorylase: In Silico and In Vitro Studies of Monomeric and Trimeric Forms of the Enzyme. Int J Mol Sci 2023; 24:ijms24032157. [PMID: 36768477 PMCID: PMC9916683 DOI: 10.3390/ijms24032157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
Mammalian purine nucleoside phosphorylase (PNP) is biologically active as a homotrimer, in which each monomer catalyzes a reaction independently of the others. To answer the question of why the native PNP forms a trimeric structure, we constructed, in silico and in vitro, the monomeric form of the enzyme. Molecular dynamics simulations showed different geometries of the active site in the non-mutated trimeric and monomeric PNP forms, which suggested that the active site in the isolated monomer could be non-functional. To confirm this hypothesis, six amino acids located at the interface of the subunits were selected and mutated to alanines to disrupt the trimer and obtain a monomer (6Ala PNP). The effects of these mutations on the enzyme structure, stability, conformational dynamics, and activity were examined. The solution experiments confirmed that the 6Ala PNP mutant occurs mainly as a monomer, with a secondary structure almost identical to the wild type, WT PNP, and importantly, it shows no enzymatic activity. Simulations confirmed that, although the secondary structure of the 6Ala monomer is similar to the WT PNP, the positions of the amino acids building the 6Ala PNP active site significantly differ. These data suggest that a trimeric structure is necessary to stabilize the geometry of the active site of this enzyme.
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Affiliation(s)
- Alicja Dyzma
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
- Correspondence: (B.W.-K.); (A.B.)
| | - Agnieszka Girstun
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Zoe Jelić Matošević
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Krzysztof Staroń
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
- Correspondence: (B.W.-K.); (A.B.)
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Wielgus-Kutrowska B, Grycuk T, Bzowska A. Part-of-the-sites binding and reactivity in the homooligomeric enzymes - facts and artifacts. Arch Biochem Biophys 2018; 642:31-45. [PMID: 29408402 DOI: 10.1016/j.abb.2018.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/13/2018] [Accepted: 01/17/2018] [Indexed: 01/18/2023]
Abstract
For a number of enzymes composed of several subunits with the same amino acid sequence, it was documented, or suggested, that binding of a ligand, or catalysis, is carried out by a single subunit. This phenomenon may be the result of a pre-existent asymmetry of subunits or a limiting case of the negative cooperativity, and is sometimes called "half-of-the-sites binding (or reactivity)" for dimers and could be called "part-of-the-sites binding (or reactivity)" for higher oligomers. In this article, we discuss molecular mechanisms that may result in "part-of-the-sites binding (and reactivity)", offer possible explanations why it may have a beneficial role in enzyme function, and point to experimental problems in documenting this behaviour. We describe some cases, for which such a mechanism was first reported and later disproved. We also give several examples of enzymes, for which this mechanism seems to be well documented, and profitable. A majority of enzymes identified in this study as half-of-the-sites binding (or reactive) use it in the flip-flop version, in which "half-of-the-sites" refers to a particular moment in time. In general, the various variants of the mechanism seems to be employed often by oligomeric enzymes for allosteric regulation to enhance the efficiency of enzymatic reactions in many key metabolic pathways.
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Affiliation(s)
- Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland.
| | - Tomasz Grycuk
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland.
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Yokomatsu T. Development of Biologically Active Compounds on the Basis of Phosphonic and Phosphinic Acid Functionalities. YAKUGAKU ZASSHI 2017; 137:1051-1086. [PMID: 28867694 DOI: 10.1248/yakushi.17-00110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phosphonic and phosphinic acids, especially α-heteroatom-substituted ones, possess unique structural and physical features which enable them to act as hydrotically stable analogs to biological phosphates in biological processes. They also act as mimetics in the transition state of the protease-induced hydrolysis of dipeptides. The first half of this review focuses on selected new synthetic methods developed by our research group for the stereoselective synthesis of α-heteroatom-substituted phosphonic and phosphinic acid derivatives, including modified nucleotide analogs and phosphinyl dipeptide isosteres. In the latter half, this review summarizes the utility of difluoromethylenephosphonic acids and phosphonic acid esters in the development of enzyme inhibitors against protein tyrosine phosphatases, sphingomyelinases, purine nucleoside phosphorylases and thrombin. The enzyme inhibitors developed were used as probes to elucidate signal transductions and the mechanisms of enzyme actions. The findings of the studies are briefly described.
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Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
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Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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Purine nucleoside phosphorylase activity decline is linked to the decay of the trimeric form of the enzyme. Arch Biochem Biophys 2014; 549:40-8. [DOI: 10.1016/j.abb.2014.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 03/17/2014] [Accepted: 03/19/2014] [Indexed: 10/25/2022]
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Baszczyňski O, Janeba Z. Medicinal Chemistry of Fluorinated Cyclic and Acyclic Nucleoside Phosphonates. Med Res Rev 2013; 33:1304-44. [DOI: 10.1002/med.21296] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i. Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i. Flemingovo nám. 2 16610 Prague 6 Czech Republic
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Wielgus-Kutrowska B, Breer K, Hashimoto M, Hikishima S, Yokomatsu T, Narczyk M, Dyzma A, Girstun A, Staroń K, Bzowska A. Trimeric purine nucleoside phosphorylase: Exploring postulated one-third-of-the-sites binding in the transition state. Bioorg Med Chem 2012; 20:6758-69. [DOI: 10.1016/j.bmc.2012.08.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 08/24/2012] [Indexed: 11/28/2022]
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Lefurgy ST, Leyh TS. Analytical expressions for the homotropic binding of ligand to protein dimers and trimers. Anal Biochem 2011; 421:433-8. [PMID: 22230282 DOI: 10.1016/j.ab.2011.12.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 11/28/2011] [Accepted: 12/05/2011] [Indexed: 11/16/2022]
Abstract
Cooperative binding of a ligand to multiple subsites on a protein is a common theme among enzymes and receptors. The analysis of cooperative binding data (either positive or negative) often relies on the assumption that free ligand concentration, L, can be approximated by the total ligand concentration, L(T). When this approximation does not hold, such analyses result in inaccurate estimates of dissociation constants. Presented here are exact analytical expressions for equilibrium concentrations of all enzyme and ligand species (in terms of K(d) values and total concentrations of protein and ligand) for homotropic dimeric and trimeric protein-ligand systems. These equations circumvent the need to approximate L and are provided in Excel worksheets suitable for simulation and least-squares fitting. The equations and worksheets are expanded to treat cases where binding signals vary with distinct site occupancy.
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Affiliation(s)
- Scott T Lefurgy
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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