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Pregled bibliografske jedinice broj: 870938

Localization improvement of deuterium uptake in hydrogen/deuterium exchange in proteins


Babić, Darko; Smith, David M.
Localization improvement of deuterium uptake in hydrogen/deuterium exchange in proteins // Journal of chemometrics, 31 (2017), 3; e2876-1 doi:10.1002/cem.2876 (međunarodna recenzija, članak, znanstveni)


Naslov
Localization improvement of deuterium uptake in hydrogen/deuterium exchange in proteins

Autori
Babić, Darko ; Smith, David M.

Izvornik
Journal of chemometrics (0886-9383) 31 (2017), 3; E2876-1

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

Ključne riječi
Deuterium uptake localization ; hydrogen/deuterium exchange ; mass spectrometry ; proteins ; pseudoinverse

Sažetak
We present a procedure for localization of deuterium uptake from overlapping proteolytic peptides to contiguous protein parts called segments. A system of linear equations expressing experimental peptide uptakes in segments cannot be solved by ordinary methods because of insufficient rank and/or linearly dependent peptides. Solvable segments are identified, and their uptakes and associated variances are evaluated by using the Moore-Penrose pseudoinverse. The method also allows consistency check of experimental data and detection of outliers. The conditions for segment solvability are formulated in a peptide graph. From the peptide graph, it is easy to find more useful information hidden in the experimental data, like sums or differences of unsolvable segment uptakes. Expected localization gain was estimated from simulations with random peptide arrangements. The recently proposed averaging method (Keppel TR, Weis DD. J. Am. Soc. Mass Spectrom. 2015 ; 26: 547) for resolution of exchange halftimes was extended to resolution of uptakes and combined with the present approach to achieve maximum uptake localization, which is also consistent with experimental data.

Izvorni jezik
Engleski

Znanstvena područja
Kemija



POVEZANOST RADA


Projekt / tema
HRZZ-IP-2013-11-8238 - Računalna rješenja u bioznanostima: Značaj savitljivosti molekula (David Smith, )

Ustanove
Institut "Ruđer Bošković", Zagreb

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


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