Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites.

Tytuł:: Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites.
Autorzy:: Perlinska AP; College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland.; Centre of New Technologies, University of Warsaw, Warsaw, Poland.
Stasiulewicz A; Centre of New Technologies, University of Warsaw, Warsaw, Poland.; Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland.
Nawrocka EK; Centre of New Technologies, University of Warsaw, Warsaw, Poland.; Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
Kazimierczuk K; Centre of New Technologies, University of Warsaw, Warsaw, Poland.
Setny P; Centre of New Technologies, University of Warsaw, Warsaw, Poland.
Sulkowska JI; Centre of New Technologies, University of Warsaw, Warsaw, Poland.; Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
Źródło:: PLoS computational biology [PLoS Comput Biol] 2020 May 26; Vol. 16 (5), pp. e1007904. Date of Electronic Publication: 2020 May 26 (Print Publication: 2020).
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
Język:: English
Imprint Name(s):: Original Publication: San Francisco, CA : Public Library of Science, [2005]-
MeSH Terms:: Binding Sites*
Methionine Adenosyltransferase/*chemistry
S-Adenosylmethionine/*chemistry
Adenine/chemistry ; Amino Acid Motifs ; Computational Biology/methods ; Computer Simulation ; Databases, Protein ; Glycine/chemistry ; Magnetic Resonance Spectroscopy ; Molecular Dynamics Simulation ; Principal Component Analysis ; Protein Binding ; Protein Domains ; Protein Folding ; Solvents ; Temperature ; Water/chemistry ; tRNA Methyltransferases/chemistry
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Molecular Sequence:: figshare 10.6084/m9.figshare.9944423
Substance Nomenclature:: 0 (Solvents)
059QF0KO0R (Water)
7LP2MPO46S (S-Adenosylmethionine)
EC 2.1.1.- (tRNA Methyltransferases)
EC 2.5.1.6 (Methionine Adenosyltransferase)
JAC85A2161 (Adenine)
TE7660XO1C (Glycine)
Entry Date(s):: Date Created: 20200527 Date Completed: 20200807 Latest Revision: 20200807
Update Code:: 20240105
PubMed Central ID:: PMC7319350
DOI:: 10.1371/journal.pcbi.1007904
PMID:: 32453784
: Czasopismo naukowe

Pełny tekst

S-adenosylmethionine (SAM) is one of the most important enzyme substrates. It is vital for the function of various proteins, including large group of methyltransferases (MTs). Intriguingly, some bacterial and eukaryotic MTs, while catalysing the same reaction, possess significantly different topologies, with the former being a knotted one. Here, we conducted a comprehensive analysis of SAM conformational space and factors that affect its vastness. We investigated SAM in two forms: free in water (via NMR studies and explicit solvent simulations) and bound to proteins (based on all data available in the PDB and on all-atom molecular dynamics simulations in water). We identified structural descriptors-angles which show the major differences in SAM conformation between unknotted and knotted methyltransferases. Moreover, we report that this is caused mainly by a characteristic for knotted MTs compact binding site formed by the knot and the presence of adenine-binding loop. Additionally, we elucidate conformational restrictions imposed on SAM molecules by other protein groups in comparison to conformational space in water.
Competing Interests: The authors have declared that no competing interests exist.

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