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Pregled bibliografske jedinice broj: 772494

New insights into active site conformation dynamics of E. coli PNP revealed by combined H/D exchange approach and molecular dynamics simulations


Kazazić, Saša; Bertoša, Branimir; Luić, Marija; Mikleušević, Goran; Tarnowski, Krzysztof; Dadlez, Michal; Narczyk, Marta; Bzowska, Agnieszka
New insights into active site conformation dynamics of E. coli PNP revealed by combined H/D exchange approach and molecular dynamics simulations // Journal of the American Society for Mass Spectrometry, 27 (2016), 1; 73-82 doi:10.1007/s13361-015-1239-2 (međunarodna recenzija, članak, znanstveni)


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Naslov
New insights into active site conformation dynamics of E. coli PNP revealed by combined H/D exchange approach and molecular dynamics simulations

Autori
Kazazić, Saša ; Bertoša, Branimir ; Luić, Marija ; Mikleušević, Goran ; Tarnowski, Krzysztof ; Dadlez, Michal ; Narczyk, Marta ; Bzowska, Agnieszka

Izvornik
Journal of the American Society for Mass Spectrometry (1044-0305) 27 (2016), 1; 73-82

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
Allostery ; Negative cooperativity ; Phosphate binding site ; Purine metabolism ; Purine nucleoside phosphorylase

Sažetak
The biologically active form of purine nucleoside phosphorylase (PNP) from Escherichia coli (EC 2.4.2.1) is a homohexamer unit, assembled as a trimer of dimers. Upon binding of phosphate, neighboring monomers adopt different active site conformations, described as open and closed. To get insight into the functions of the two distinctive active site conformations, virtually inactive Arg24Ala mutant is complexed with phosphate ; all active sites are found to be in the open conformation. To understand how the sites of neighboring monomers communicate with each other, we have combined H/D exchange (H/DX) experiments with molecular dynamics (MD) simulations. Both methods point to the mobility of the enzyme, associated with a few flexible regions situated at the surface and within the dimer interface. Although H/DX provides an average extent of deuterium uptake for all six hexamer active sites, it was able to indicate the dynamic mechanism of cross-talk between monomers, allostery. Using this technique, it was found that phosphate binding to the wild type (WT) causes arrest of the molecular motion in backbone fragments that are flexible in a ligand-free state. This was not the case for the Arg24Ala mutant. Upon nucleoside substrate/inhibitor binding, some release of the phosphate-induced arrest is observed for the WT, whereas the opposite effects occur for the Arg24Ala mutant. MD simulations confirmed that phosphate is bound tightly in the closed active sites of the WT ; conversely, in the open conformation of the active site of the WT phosphate is bound loosely moving towards the exit of the active site. In Arg24Ala mutant binary complex P is bound loosely, too.

Izvorni jezik
Engleski

Znanstvena područja
Kemija, Biologija



POVEZANOST RADA


Projekti:
InnoMol-316289
IP-2013-11-7423 - Enzimi purinskog reciklirajućeg ciklusa iz Helicobacter pylori i Escherichie coli (PSPE) (Luić, Marija, HRZZ - 2013-11) ( POIROT)

Ustanove:
Institut "Ruđer Bošković", Zagreb,
Prirodoslovno-matematički fakultet, Zagreb

Poveznice na cjeloviti tekst rada:

doi link.springer.com

Citiraj ovu publikaciju:

Kazazić, Saša; Bertoša, Branimir; Luić, Marija; Mikleušević, Goran; Tarnowski, Krzysztof; Dadlez, Michal; Narczyk, Marta; Bzowska, Agnieszka
New insights into active site conformation dynamics of E. coli PNP revealed by combined H/D exchange approach and molecular dynamics simulations // Journal of the American Society for Mass Spectrometry, 27 (2016), 1; 73-82 doi:10.1007/s13361-015-1239-2 (međunarodna recenzija, članak, znanstveni)
Kazazić, S., Bertoša, B., Luić, M., Mikleušević, G., Tarnowski, K., Dadlez, M., Narczyk, M. & Bzowska, A. (2016) New insights into active site conformation dynamics of E. coli PNP revealed by combined H/D exchange approach and molecular dynamics simulations. Journal of the American Society for Mass Spectrometry, 27 (1), 73-82 doi:10.1007/s13361-015-1239-2.
@article{article, year = {2016}, pages = {73-82}, DOI = {10.1007/s13361-015-1239-2}, keywords = {Allostery, Negative cooperativity, Phosphate binding site, Purine metabolism, Purine nucleoside phosphorylase}, journal = {Journal of the American Society for Mass Spectrometry}, doi = {10.1007/s13361-015-1239-2}, volume = {27}, number = {1}, issn = {1044-0305}, title = {New insights into active site conformation dynamics of E. coli PNP revealed by combined H/D exchange approach and molecular dynamics simulations}, keyword = {Allostery, Negative cooperativity, Phosphate binding site, Purine metabolism, Purine nucleoside phosphorylase} }
@article{article, year = {2016}, pages = {73-82}, DOI = {10.1007/s13361-015-1239-2}, keywords = {Allostery, Negative cooperativity, Phosphate binding site, Purine metabolism, Purine nucleoside phosphorylase}, journal = {Journal of the American Society for Mass Spectrometry}, doi = {10.1007/s13361-015-1239-2}, volume = {27}, number = {1}, issn = {1044-0305}, title = {New insights into active site conformation dynamics of E. coli PNP revealed by combined H/D exchange approach and molecular dynamics simulations}, keyword = {Allostery, Negative cooperativity, Phosphate binding site, Purine metabolism, Purine nucleoside phosphorylase} }

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE


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