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Smith IN, Briggs JM. Structural mutation analysis of PTEN and its genotype-phenotype correlations in endometriosis and cancer. Proteins 2016; 84:1625-1643. [PMID: 27481051 DOI: 10.1002/prot.25105] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/17/2016] [Accepted: 07/05/2016] [Indexed: 12/19/2022]
Abstract
The phosphatase and tensin homolog deleted on chromosome ten (PTEN) gene encodes a tumor suppressor phosphatase that has recently been found to be frequently mutated in patients with endometriosis, endometrial cancer and ovarian cancer. Here, we present the first computational analysis of 13 somatic missense PTEN mutations associated with these phenotypes. We found that a majority of the mutations are associated in conserved positions within the active site and are clustered within the signature motif, which contain residues that play a crucial role in loop conformation and are essential for catalysis. In silico analyses were utilized to identify the putative effects of these mutations. In addition, coarse-grained models of both wild-type (WT) PTEN and mutants were constructed using elastic network models to explore the interplay of the structural and global dynamic effects that the mutations have on the relationship between genotype and phenotype. The effects of the mutations reveal that the local structure and interactions affect polarity, protein structure stability, electrostatic surface potential, and global dynamics of the protein. Our results offer new insight into the role in which PTEN missense mutations contribute to the molecular mechanism and genotypic-phenotypic correlation of endometriosis, endometrial cancer, and ovarian cancer. Proteins 2016; 84:1625-1643. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Iris N Smith
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, 77204-5001
| | - James M Briggs
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, 77204-5001.
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2
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Sobieraj M, Krzyśko KA, Jarmuła A, Kalinowski MW, Lesyng B, Prokopowicz M, Cieśla J, Gojdź A, Kierdaszuk B. A QM-MD simulation approach to the analysis of FRET processes in (bio)molecular systems. A case study: complexes of E. coli purine nucleoside phosphorylase and its mutants with formycin A. J Mol Model 2015; 21:75. [PMID: 25754135 PMCID: PMC4353879 DOI: 10.1007/s00894-015-2602-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/01/2015] [Indexed: 11/25/2022]
Abstract
Predicting FRET pathways in proteins using computer simulation techniques is very important for reliable interpretation of experimental data. A novel and relatively simple methodology has been developed and applied to purine nucleoside phosphorylase (PNP) complexed with a fluorescent ligand - formycin A (FA). FRET occurs between an excited Tyr residue (D*) and FA (A). This study aims to interpret experimental data that, among others, suggests the absence of FRET for the PNPF159A mutant in complex with FA, based on novel theoretical methodology. MD simulations for the protein molecule containing D*, and complexed with A, are carried out. Interactions of D* with its molecular environment are accounted by including changes of the ESP charges in S1, compared to S0, and computed at the SCF-CI level. FRET probability W F depends on the inverse six-power of the D*-A distance, R da . The orientational factor 0 < k(2) < 4 between D* and A is computed and included in the analysis. Finally W F is time-averaged over the MD trajectories resulting in its mean value. The red-shift of the tyrosinate anion emission and thus lack of spectral overlap integral and thermal energy dissipation are the reasons for the FRET absence in the studied mutants at pH 7 and above. The presence of the tyrosinate anion results in a competitive energy dissipation channel and red-shifted emission, thus in consequence in the absence of FRET. These studies also indicate an important role of the phenyl ring of Phe159 for FRET in the wild-type PNP, which does not exist in the Ala159 mutant, and for the effective association of PNP with FA. In a more general context, our observations point out very interesting and biologically important properties of the tyrosine residue in its excited state, which may undergo spontaneous deprotonation in the biomolecular systems, resulting further in unexpected physical and/or biological phenomena. Until now, this observation has not been widely discussed in the literature.
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Affiliation(s)
- M. Sobieraj
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - K. A. Krzyśko
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
- Bioinformatics Laboratory, Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - A. Jarmuła
- Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - M. W. Kalinowski
- Bioinformatics Laboratory, Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - B. Lesyng
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
- Bioinformatics Laboratory, Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - M. Prokopowicz
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - J. Cieśla
- Department of Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
| | - A. Gojdź
- Department of Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland
| | - B. Kierdaszuk
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
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Gerlits O, Waltman MJ, Taylor S, Langan P, Kovalevsky A. Insights into the phosphoryl transfer catalyzed by cAMP-dependent protein kinase: an X-ray crystallographic study of complexes with various metals and peptide substrate SP20. Biochemistry 2013; 52:3721-7. [PMID: 23672593 PMCID: PMC3666212 DOI: 10.1021/bi400066a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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X-ray
structures of several ternary substrate and product complexes
of the catalytic subunit of cAMP-dependent protein kinase (PKAc) have
been determined with different bound metal ions. In the PKAc complexes,
Mg2+, Ca2+, Sr2+, and Ba2+ metal ions could bind to the active site and facilitate the phosphoryl
transfer reaction. ATP and a substrate peptide (SP20) were modified,
and the reaction products ADP and the phosphorylated peptide were
found trapped in the enzyme active site. Finally, we determined the
structure of a pseudo-Michaelis complex containing Mg2+, nonhydrolyzable AMP-PCP (β,γ-methyleneadenosine 5′-triphosphate)
and SP20. The product structures together with the pseudo-Michaelis
complex provide snapshots of different stages of the phosphorylation
reaction. Comparison of these structures reveals conformational, coordination,
and hydrogen bonding changes that might occur during the reaction
and shed new light on its mechanism, roles of metals, and active site
residues.
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Affiliation(s)
- Oksana Gerlits
- Bioscience Division, Los Alamos National Laboratory , Los Alamos, New Mexico 87544, United States
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Kovalevsky AY, Johnson H, Hanson BL, Waltman MJ, Fisher SZ, Taylor S, Langan P. Low- and room-temperature X-ray structures of protein kinase A ternary complexes shed new light on its activity. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:854-60. [PMID: 22751671 DOI: 10.1107/s0907444912014886] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 04/04/2012] [Indexed: 11/10/2022]
Abstract
Post-translational protein phosphorylation by protein kinase A (PKA) is a ubiquitous signalling mechanism which regulates many cellular processes. A low-temperature X-ray structure of the ternary complex of the PKA catalytic subunit (PKAc) with ATP and a 20-residue peptidic inhibitor (IP20) at the physiological Mg(2+) concentration of ∼0.5 mM (LT PKA-MgATP-IP20) revealed a single metal ion in the active site. The lack of a second metal in LT PKA-MgATP-IP20 renders the β- and γ-phosphoryl groups of ATP very flexible, with high thermal B factors. Thus, the second metal is crucial for tight positioning of the terminal phosphoryl group for transfer to a substrate, as demonstrated by comparison of the former structure with that of the LT PKA-Mg(2)ATP-IP20 complex obtained at high Mg(2+) concentration. In addition to its kinase activity, PKAc is also able to slowly catalyze the hydrolysis of ATP using a water molecule as a substrate. It was found that ATP can be readily and completely hydrolyzed to ADP and a free phosphate ion in the crystals of the ternary complex PKA-Mg(2)ATP-IP20 by X-ray irradiation at room temperature. The cleavage of ATP may be aided by X-ray-generated free hydroxyl radicals, a very reactive chemical species, which move rapidly through the crystal at room temperature. The phosphate anion is clearly visible in the electron-density maps; it remains in the active site but slides about 2 Å from its position in ATP towards Ala21 of IP20, which mimics the phosphorylation site. The phosphate thus pushes the peptidic inhibitor away from the product ADP, while resulting in dramatic conformational changes of the terminal residues 24 and 25 of IP20. X-ray structures of PKAc in complex with the nonhydrolysable ATP analogue AMP-PNP at both room and low temperature demonstrated no temperature effects on the conformation and position of IP20.
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Affiliation(s)
- Andrey Y Kovalevsky
- Bioscience Division, Los Alamos National Laboratory, PO Box 1663, MS M888, Los Alamos, NM 87545, USA.
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Montenegro M, Garcia-Viloca M, González-Lafont À, Lluch JM. Comparative study of the prereactive protein kinase A Michaelis complex with Kemptide substrate. J Comput Aided Mol Des 2007; 21:603-15. [DOI: 10.1007/s10822-007-9143-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 10/23/2007] [Indexed: 12/01/2022]
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Puig E, Garcia-Viloca M, Gonzalez-Lafont A, Lluch JM, Field MJ. New insights into the reaction mechanism catalyzed by the glutamate racemase enzyme: pH titration curves and classical molecular dynamics simulations. J Phys Chem B 2007; 111:2385-97. [PMID: 17286428 DOI: 10.1021/jp066350a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of the reactions catalyzed by the pyridoxal-phosphate-independent amino acid racemases and epimerases faces the difficult task of deprotonating a relatively low acidicity proton, the amino acid's alpha-hydrogen, with a relatively poor base, a cysteine. In this work, we propose a mechanism for one of these enzymes, glutamate racemase (MurI), about which many controversies exist, and the roles that its active site residues may play. The titration curves and the pK1/2 values of all of the ionizable residues for different structures leading from reactants to products have been analyzed. From these results a concerted mechanism has been proposed in which the Cys70 residue would deprotonate the alpha-hydrogen of the substrate while, at the same time, being deprotonated by the Asp7 residue. To study the consistency of this mechanism classical molecular dynamics (MD) simulations have been carried out along with pK1/2 calculations on the MD-generated structures.
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Affiliation(s)
- Eduard Puig
- Departament de Química and Institut de Biotecnologia i de Biomedicina, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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Wojciechowski M, Grycuk T, Antosiewicz JM, Lesyng B. Prediction of secondary ionization of the phosphate group in phosphotyrosine peptides. Biophys J 2003; 84:750-6. [PMID: 12547759 PMCID: PMC1302655 DOI: 10.1016/s0006-3495(03)74894-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2002] [Accepted: 08/29/2002] [Indexed: 11/16/2022] Open
Abstract
A computational approach, based on a continuum molecular electrostatics model, for the calculation of the pK(a) values of secondary ionization of the phosphate group in phenyl phosphate derivatives is described. The method uses the ESP atomic charges of the mono-anionic and di-anionic forms of the ionizable phosphate group, computed with the use of the density functional method, and applies a new concept of the model group, being the reference state for the pK(a) calculations. Both conformational flexibility and tautomeric degrees of freedom are taken into account in the calculations. The method was parameterized using experimentally available pK(a) values of four derivatives of phenyl phosphates, and phosphotyrosine. Subsequently this parameterization was used to predict pK(a) of the phosphate group in a short peptide Gly-Gly-Tyr(P)-Ala, and in a longer peptide consisting of 12 residues, the latter in water, and in a complex with a protein-phospholipase. The agreement between the computed and the experimental pK(a) values is better than +/-0.3 pH units for the optimized solute dielectric constant of 11-13. This approach is promising and its extension to other phospho-amino acids is in progress.
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Affiliation(s)
- M Wojciechowski
- Department of Biophysics, Warsaw University, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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