Abstract:Methionine in proteins, apart from its role in the initiation of translation, is assumed to play a simple structural role in the hydrophobic core, in a similar way to other hydrophobic amino acids such as leucine, isoleucine, and valine. However, research from a number of laboratories supports the concept that methionine serves as an important cellular antioxidant, stabilizes the structure of proteins, participates in the sequence‐independent recognition of protein surfaces, and can act as a regulatory switch … Show more
“…Even though both residues are hydrophobic, an increase in backbone motion was observed. It is possible that by the replacing of the unbranched methionine side chain 111 by the branched amino acid isoleucine, the potential for local mobility is reduced, possibly leading to far-ranging compensatory effects.…”
A new coronavirus (SARS-CoV-2) is a global threat to world health
and economy. Its dimeric main protease (M
pro
), which
is required for the proteolytic cleavage of viral precursor
proteins, is a good candidate for drug development owing to its
conservation and the absence of a human homolog. Improving our
understanding of M
pro
behavior can accelerate the
discovery of effective therapies to reduce mortality. All-atom
molecular dynamics (MD) simulations (100 ns) of 50 mutant
M
pro
dimers obtained from filtered sequences
from the GISAID database were analyzed using root-mean-square
deviation, root-mean-square fluctuation,
R
g
, averaged betweenness
centrality, and geometry calculations. The results showed that
SARS-CoV-2 M
pro
essentially behaves in a similar
manner to its SAR-CoV homolog. However, we report the following
new findings from the variants: (1) Residues GLY15, VAL157, and
PRO184 have mutated more than once in SARS CoV-2; (2) the D48E
variant has lead to a novel “TSEEMLN”” loop
at the binding pocket; (3) inactive apo M
pro
does not
show signs of dissociation in 100 ns MD; (4) a non-canonical
pose for PHE140 widens the substrate binding surface; (5) dual
allosteric pockets coinciding with various stabilizing and
functional components of the substrate binding pocket were found
to display correlated compaction dynamics; (6) high betweenness
centrality values for residues 17 and 128 in all M
pro
samples suggest their high importance in dimer
stability—one such consequence has been observed for the
M17I mutation whereby one of the N-fingers was highly unstable.
(7) Independent coarse-grained Monte Carlo simulations suggest a
relationship between the rigidity/mutability and enzymatic
function. Our entire approach combining database preparation,
variant retrieval, homology modeling, dynamic residue network
(DRN), relevant conformation retrieval from 1-D kernel density
estimates from reaction coordinates to other existing approaches
of structural analysis, and data visualization within the
coronaviral M
pro
is also novel and is applicable to
other coronaviral proteins.
“…Even though both residues are hydrophobic, an increase in backbone motion was observed. It is possible that by the replacing of the unbranched methionine side chain 111 by the branched amino acid isoleucine, the potential for local mobility is reduced, possibly leading to far-ranging compensatory effects.…”
A new coronavirus (SARS-CoV-2) is a global threat to world health
and economy. Its dimeric main protease (M
pro
), which
is required for the proteolytic cleavage of viral precursor
proteins, is a good candidate for drug development owing to its
conservation and the absence of a human homolog. Improving our
understanding of M
pro
behavior can accelerate the
discovery of effective therapies to reduce mortality. All-atom
molecular dynamics (MD) simulations (100 ns) of 50 mutant
M
pro
dimers obtained from filtered sequences
from the GISAID database were analyzed using root-mean-square
deviation, root-mean-square fluctuation,
R
g
, averaged betweenness
centrality, and geometry calculations. The results showed that
SARS-CoV-2 M
pro
essentially behaves in a similar
manner to its SAR-CoV homolog. However, we report the following
new findings from the variants: (1) Residues GLY15, VAL157, and
PRO184 have mutated more than once in SARS CoV-2; (2) the D48E
variant has lead to a novel “TSEEMLN”” loop
at the binding pocket; (3) inactive apo M
pro
does not
show signs of dissociation in 100 ns MD; (4) a non-canonical
pose for PHE140 widens the substrate binding surface; (5) dual
allosteric pockets coinciding with various stabilizing and
functional components of the substrate binding pocket were found
to display correlated compaction dynamics; (6) high betweenness
centrality values for residues 17 and 128 in all M
pro
samples suggest their high importance in dimer
stability—one such consequence has been observed for the
M17I mutation whereby one of the N-fingers was highly unstable.
(7) Independent coarse-grained Monte Carlo simulations suggest a
relationship between the rigidity/mutability and enzymatic
function. Our entire approach combining database preparation,
variant retrieval, homology modeling, dynamic residue network
(DRN), relevant conformation retrieval from 1-D kernel density
estimates from reaction coordinates to other existing approaches
of structural analysis, and data visualization within the
coronaviral M
pro
is also novel and is applicable to
other coronaviral proteins.
“…Given this, we wondered whether the Arp3Bdependent actin tail phenotype depends on oxidation of Met293. To investigate this possibility, we replaced Thr293 in Arp3 and Met293 in Arp3B with glutamine to mimic the Met-SO state (27,28). In both cases, the glutamine mutants induced the formation of shorter actin tails (Fig 4A, S4A).…”
The Arp2/3 complex (Arp2, Arp3 and ARPC1-5) is essential to generate branched actin filament networks for many cellular processes. Human Arp3, ARPC1 and ARPC5 exist as two isoforms but the functional properties of Arp2/3 iso-complexes is largely unexplored. Here we show that Arp3B, but not Arp3 is subject to regulation by the methionine monooxygenase MICAL2, which is recruited to branched actin networks by coronin-1C. Although Arp3 and Arp3B iso-complexes promote actin assembly equally efficiently in vitro, they have different cellular properties. Arp3B turns over significantly faster than Arp3 within the network and upon its depletion actin turnover decreases. Substitution of Arp3B Met293 by Thr, the corresponding residue in Arp3 increases actin network stability, and conversely, replacing Arp3 Thr293 with Gln to mimic Met oxidation promotes network disassembly. Thus, MICAL2 regulates a subset of Arp2/3 complexes to control branched actin network disassembly.
“…Methionine is an essential and unique amino acid that plays a critical role in starting the protein‐synthesis process. It is also involved in the production of other sulfur‐containing molecules with important functions for the cells, such as glutathione, taurine, creatine, and perhaps most importantly, the methionine‐derived sulfonium cation S ‐adenosyl methionine (SAM), which alters DNA and RNA by adding a methyl group . In proteins methionine usually exists at a relatively low level (2 %) compared with other common amino acids; this offers the possibility of controllable functionalization at a specific location.…”
Methionine has been recognized as an ideal target for labeling proteins without disturbing their tasks. However, exploration in single post‐transcriptional modification of methionine is sluggish. In this Highlight, we summarize some of the most exciting reports on the precise control of protein function by selectively modifying methionine residues.
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