The novel coronavirus whose outbreak took place in December 2019 continues to spread at a rapid rate worldwide. In the absence of an effective vaccine, inhibitor repurposing or de novo drug design may offer longer-term strategy combat this and future infections due similar viruses. Here, we report on detailed classical mixed-solvent molecular dynamics simulations main protease (Mpro) enriched by evolutionary stability analysis protein. results were compared with those for highly severe acute...

Abstract Motivation Tunnels, pores, channels, pockets and cavities contribute to proteins architecture performance. However, analysis characteristics of transportation pathways internal binding are performed separately. We aimed provide universal tool for integral interior with access detailed information on the ligands phenomena preferences. Results AQUA-DUCT version 1.0 is a comprehensive method macromolecules from intramolecular voids perspective using small as molecular probes. This...

The identification and tracking of molecules which enter active site cavity requires screening the positions thousands single along several thousand molecular dynamic steps. To fill existing gap between tools searching for tunnels pathways advanced employed accelerated water flux investigations, we have developed AQUA-DUCT.AQUA-DUCT is an easy-to-use tool that facilitates analysis behaviour penetrate any selected region in a protein. It can be used type molecules, e.g. water, oxygen, carbon...

Abstract The novel coronavirus whose outbreak took place in December 2019 continues to spread at a rapid rate worldwide. In the absence of an effective vaccine, inhibitor repurposing or de novo drug design may offer longer-term strategy combat this and future infections due similar viruses. Here, we report on detailed classical mix-solvent molecular dynamics simulations main protease (Mpro) enriched by evolutionary stability analysis protein. results were compared with those for highly SARS...

Several different approaches are used to describe the role of protein compartments and residues in catalysis identify key suitable for modification activity or selectivity desired enzyme. In our research, we applied a combination molecular dynamics simulations water tracking approach accessible volume Solanum tuberosum epoxide hydrolase. Using as probe, were able small cavities linked with active site: (i) one made up conserved amino acids indispensable proper positioning catalytic (ii) two...

D-amino acid oxidase (DAAO) degrades acids to produce α-ketoacids, hydrogen peroxide and ammonia. DAAO has often been investigated engineered for industrial clinical applications. We combined information from literature with a detailed analysis of the structure engineer mammalian DAAOs. The structural was complemented molecular dynamics simulations characterize solvent accessibility product release mechanisms. identified non-obvious residues located on loops border between active site...

The cupin-type phosphoglucose isomerase (PfPGI) from the hyperthermophilic archaeon Pyrococcus furiosus catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate. We investigated PfPGI using protein-engineering bioinformatics tools select functionally-important residues based on correlated mutation analyses. A pair amino acids in periphery was found be dominant co-evolving mutation. position these selected non-obvious conventional protein engineering methods. designed...

The evolutionary variability of a protein’s residues is highly dependent on protein region and function. Solvent-exposed residues, excluding those at interaction interfaces, are more variable than buried whereas active site considered to be conserved. abovementioned rules apply also α/β-hydrolase fold proteins—one the oldest biggest superfamily enzymes with sites equipped tunnels linking reaction exterior. We selected soluble epoxide hydrolases as representative this family conduct first...

Different methods for tunnel identification, geometry-based and small-molecule tracking approaches, were compared to provide their benefits pitfalls. Results obtained both crystal structures molecular dynamics (MD) simulations analyzed investigate if a more computationally demanding method would be beneficial. Careful examination of the results is essential low-diameter description, assessment functionality based only on geometrical parameters challenging. We showed that approach can...

Abstract Penicillin binding proteins (PBPs) are involved in biosynthesis, remodeling and recycling of peptidoglycan (PG) bacteria. PBP-A from Thermosynechococcus elongatus belongs to a cyanobacterial family enzymes sharing close structural phylogenetic proximity class A β-lactamases. With the long-term aim converting into β-lactamase by directed evolution, we simulated what may happen when an organism like Escherichia coli acquires such new PBP observed growth defect associated with enzyme...

The utilization of tunnels and water transport within enzymes is crucial for their catalytic function as molecules can stabilize bound substrates help with unbinding processes products inhibitors. Since the choice models molecular dynamics simulations was shown to determine accuracy various calculated properties bulk solvent solvated proteins, we have investigated if what extent through enzyme depends on selection model. Here, focused simulating well-defined tunnel geometries. In a...

Enzymes with buried active sites maintain their catalytic function via a single tunnel or network. In this study we analyzed the functionality of soluble epoxide hydrolases (sEHs) network, by comparing overall enzyme structure tunnel’s shape and size. sEHs were divided into three groups based on usage. The obtained results compared known substrate preferences studied enzymes, as well reported in our other work evolutionary analyses data. network architecture corresponded lineage source...

Abstract Understanding the utilization of tunnels and water transport within enzymes is crucial for catalytic function enzymes, as molecules can stabilize bound substrates help with unbinding processes products inhibitors. Since choice models molecular dynamics simulations was shown to determine accuracy various calculated properties bulk solvent solvated proteins, we have investigated if what extent through enzyme depends on selection model. Here, focused simulating well-defined tunnel...

The pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a serious global health threat. Since no specific therapeutics are available, researchers around world screened compounds to inhibit various molecular targets SARS-CoV-2 including its main protease (Mpro) essential for viral replication. Due high urgency these discovery efforts, off-target binding, which is one major reasons drug-induced toxicity and safety-related drug attrition, was neglected. Here, we...

Congenital Disorders of Glycosylation (CDG) are multisystemic metabolic disorders showing highly heterogeneous clinical presentation, molecular etiology, and laboratory results. Here, we present different transferrin isoform patterns (obtained by isoelectric focusing) from three female patients harboring the ALG13 c.320A>G mutation. Contrary to other known variants type I CDGs, where focusing revealed notably increased asialo- disialotransferrin fractions, a normal glycosylation pattern...

AlphaFold - a game changer for accurate protein structure prediction was tested on metamorphic proteins, which display two or more distinct folds while having the same sequence. We highlighted limitations of method and suggested careful investigation obtained models.

<title>Abstract</title> Penicillin binding proteins (PBPs) are involved in biosynthesis, remodeling and recycling of peptidoglycan (PG) bacteria. PBP-A from <italic>Thermosynechococcus elongatus</italic> belongs to a cyanobacterial family enzymes sharing close structural phylogenetic proximity class A b-lactamases. With the aim converting into b-lactamase, we expressed enzyme periplasm <italic>Escherichia coli</italic> but failed directed evolution experiments observed growth defect...

Loops are the most variable and unorganized elements of secondary structure proteins. Their ability to shift their shape can play a role in binding small ligands, enzymatic catalysis, or protein–protein interactions. Due loop flexibility, positions residues solved structures show largest B-factors, worst-case scenario be unknown. Based on loops’ movements’ timeline, they divided into slow (static) fast (flexible). Although loops that missing experimental belong flexible group, computational...

AQUA-DUCT software reverses the standard approach of molecular dynamics simulations analysis macromolecules, focusing on solvent, cosolvent and small ligands considered as specific probes instead macromolecules atoms movement. In this article we present six basic tutorials instructing users in best practices for preparing, carrying out, analysing results various applications. Users are expected to already have significant experience with running any dedicated (e.g., Amber, GROMACS, NAMD),...

Abstract The evolutionary variability of a protein’s residues is highly dependent on protein region and function. Solvent-exposed residues, excluding those at interaction interfaces, are more variable than buried whereas active site considered to be conserved. abovementioned rules apply also α/β-hydrolase fold proteins - one the oldest biggest superfamily enzymes with sites equipped tunnels linking reaction exterior. We selected soluble epoxide hydrolases as representative this family...