A single mutation Gln142Lys doubles the catalytic activity of VPR, a cold adapted subtilisin-like serine proteinase

Óskarsson, Kristinn Ragnar; Nygaard, Mads; Ellertsson, Brynjar Ö.; Thorbjarnardóttir, Sigrídur H.; Papaleo, Elena; Kristjánsson, Magnús M.

doi:10.1016/j.bbapap.2016.07.003

Cited by 11 publications

(7 citation statements)

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“…The first study of Brandsdal et al [ 53 ] in 1999 on trypsin collected in total 1.2 ns of trajectories and in more recent years the simulation length reached higher sampling, such as in Martinez et al on subtilisin S41 [ 54 ] with 50 ns. The longest trajectory was ran by Óskarsson et al [ 55 ] in 2016 on cold-adapted subtilase for 600 ns.…”

Section: Resultsmentioning

confidence: 99%

A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations

et al. 2017

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The psychrophilic and mesophilic endonucleases A (EndA) from Aliivibrio salmonicida (VsEndA) and Vibrio cholera (VcEndA) have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD) simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale. The only exception is a more rigid C-terminal region in VcEndA, which is ascribable to a cluster of electrostatic interactions and hydrogen bonds, as also supported by MD simulations of the VsEndA mutant variant where the cluster of interactions was introduced. Moreover, we identified three additional amino acidic substitutions through multiple sequence alignment and the analyses of MD-based protein structure networks. In particular, T120V occurs in the proximity of the catalytic residue H80 and alters the interaction with the residue Y43, which belongs to the second coordination sphere of the Mg2+ ion. This makes T120V an amenable candidate for future experimental mutagenesis.

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Section: Resultsmentioning

confidence: 99%

A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations

et al. 2017

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“…We calculated the per-residue Cα-atoms Root Mean Square Fluctuation (RMSF) as an index of flexibility. RMSF was calculated over non-overlapping time windows of 10 ns along the trajectories and then averaged, with a protocol used for other proteins [62–64].…”

Section: Methodsmentioning

confidence: 99%

Conformational gating in ammonia lyases

Lambrughi

Maršić

Sáez-Jiménez

et al. 2019

Preprint

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14Ammonia lyases (AL) are enzymes of industrial and biomedical interest. Knowledge 15 of AL structure-dynamics-function relationship would be instrumental for making use 16 of the application potential of these enzymes. We investigated, using microsecond 17 molecular dynamics, the conformational changes in the proximity of the catalytic 18 pocket of a 3-methylaspartate ammonia lyase (MAL) as a model system. In 19 particular, we identified two regulatory elements in the MAL structure, i.e., the β 5-α2 20 loop, and the helix-hairpin-loop subdomain. We showed that they undergo 21 conformational changes switching from 'occluded' to 'open' states. We observed that 22 these rearrangements are coupled to changes in the accessibility of the active site. 23 The β 5-α2 loop and the helix-hairpin-loop subdomain modulate the formation of 24 tunnels from the protein surface to the substrate binding site, making the active site 25 more accessible to the substrate when they are in an open state. We pinpointed a 26 sequential mechanism, in which the helix-hairpin-loop subdomain needs to break a 27 subset of intramolecular interactions first, to then allow the opening of the β 5-α2 loop 28 and, as a consequence, make the AL catalytic pocket accessible for the substrate.29 2 Our data suggest that protein dynamics need to be considered in the design of new 1 AL variants for protein engineering and therapeutic purposes. 2 Keywords 3 molecular dynamics simulations, conformational changes, disordered regions, 4 conformational switches, correlated motions 5 6

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Section: Protein Flexibilitymentioning

confidence: 99%

Conformational gating in ammonia lyases

Lambrughi

Maršić

Sáez-Jiménez

et al. 2020

Biochimica et Biophysica Acta (BBA) - General Subjects

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Ammonia lyases (AL) are enzymes of industrial and biomedical interest. Knowledge of AL structure-dynamics-function relationship would be instrumental for making use of the application potential of these enzymes. We investigated, using microsecond molecular dynamics, the conformational changes in the proximity of the catalytic pocket of a 3-methylaspartate ammonia lyase (MAL) as a model system. In particular, we identified two regulatory elements in the MAL structure, i.e., the Our data suggest that protein dynamics need to be considered in the design of new AL variants for protein engineering and therapeutic purposes.

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A single mutation Gln142Lys doubles the catalytic activity of VPR, a cold adapted subtilisin-like serine proteinase

Cited by 11 publications

References 57 publications

A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations

A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations

Conformational gating in ammonia lyases

Conformational gating in ammonia lyases

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