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This Special Issue collects novel contributions from scientists in the interdisciplinary field of biomolecular evolution. Works listed here use information theoretical concepts as a core but are tightly integrated with the study of molecular processes. Applications include the analysis of phylogenetic signals to elucidate biomolecular structure and function, the study and quantification of structural dynamics and allostery, as well as models of molecular interaction specificity inspired by evolutionary cues.

Research & information: general --- Biology, life sciences --- power law --- Brownian process --- Kolmogorov complexity --- entropy --- chaos --- monofractal --- non-linear --- cumulative sum --- sequence analysis --- protein engineering --- direct coupling analysis --- evolutionary coupling analysis --- contact prediction --- phylogenetic bias --- phylogeny --- co-evolution --- coevolutionary analysis --- direct-coupling analysis --- specificity determining contacts --- sequence reweighting --- maximum entropy models --- protein contact predictions --- TEM-1 --- TOHO-1 --- PBP-A --- DD-transpeptidase --- conformational changes --- catalytic mechanism --- evolution --- epistasis --- allostery --- elastic network model --- protein conformational dynamics --- statistical inference --- mutational phenotypes --- interaction specificity --- phosphorylation --- fitness landscape --- bacterial signaling --- power law --- Brownian process --- Kolmogorov complexity --- entropy --- chaos --- monofractal --- non-linear --- cumulative sum --- sequence analysis --- protein engineering --- direct coupling analysis --- evolutionary coupling analysis --- contact prediction --- phylogenetic bias --- phylogeny --- co-evolution --- coevolutionary analysis --- direct-coupling analysis --- specificity determining contacts --- sequence reweighting --- maximum entropy models --- protein contact predictions --- TEM-1 --- TOHO-1 --- PBP-A --- DD-transpeptidase --- conformational changes --- catalytic mechanism --- evolution --- epistasis --- allostery --- elastic network model --- protein conformational dynamics --- statistical inference --- mutational phenotypes --- interaction specificity --- phosphorylation --- fitness landscape --- bacterial signaling

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G-quadruplexes (G4s) are nucleic acids secondary structures that form in DNA or RNA guanine (G)-rich strands. In recent years, the presence of G4s in microorganisms has attracted increasing interest. In prokaryotes, G4 sequences have been reported in several human pathogens. Bacterial enzymes able to process G4s have been identified. In viruses, G4s have been suggested to be involved in key steps of the viral life cycle: They have been associated with the human immunodeficiency virus (HIV), herpes simplex virus 1 (HSV-1), human papilloma virus, swine pseudorabies virus, and other viruses’ genomes. New evidence shows the presence of G4s in parasitic protozoa, such as the causative agent of malaria. G4 binding proteins and mRNA G4s have been implicated in the regulation of microorganisms’ genome replication and translation. G4 ligands have been developed and tested both as tools to study the complexity of G4-mediated mechanisms in the viral life cycle and as therapeutic agents. Moreover, new techniques to study G4 folding and their interactions with proteins have been developed. This Special Issue will focus on G4s present in microorganisms, addressing all the above aspects.

bacteria --- folding --- co-translational refolding --- RecQ helicase --- regulatory element --- conformational dynamics --- G4Hunter --- NDPK --- fluorescence --- pseudorabies virus --- Epstein-Barr virus (EBV) --- structure-activity relationship --- PhenDC3 --- eukaryotic hosts --- Herpesvirus --- translation suppression --- turn-on ligands --- co-transcriptional folding --- Herpesviridae --- G-quadruplex --- nucleoside diphosphate kinase --- nucleic acids --- nucleic acids conformation --- bioinformatics --- protein–DNA interaction --- aptamers --- deinococcus --- Alphaherpesvirinae --- EBNA1 --- G4 --- virus --- human papillomaviruses --- S. cerevisiae --- genome stability --- G-quadruplexes --- metastable structure --- genome evolution --- pyridostatin --- alphaherpesviruses --- structure --- protozoa --- genome --- G-quadruplex ligand --- NMR --- microbes --- DNA --- protein-mRNA interactions --- G-quadruplex formation --- immediate early promoters

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Applied biocatalysis and biotransformation, that is, the use of enzymes and whole-cell systems in manufacturing processes for synthetic purposes, has been experiencing a clear boom in recent years, which has led to the start of the so-called “fourth wave”. In fact, the latest advances in bioinformatics, system biology, process intensification, and, in particular, enzyme-directed evolution (encouraged by the 2018 Nobel Prize awarded to F. Arnold), are widening the range of the efficacy of biocatalysts and accelerating the rate at which new enzymes are becoming available, even for activities not previously known. European scientists have been very actively involved in different aspects of this field. Nine contributions dealing with different aspects of applied biocatalysis developed by European researchers are gathered in this Special Issue

Research & information: general --- biocatalysis --- glycosidases --- isomerases --- Pichia pastoris --- sweeteners --- rare sugars --- cheese whey --- sustainable chemistry --- penicillin acylase --- aculeacin acylase --- N-acyl-homoserine lactone acylases --- quorum quenching --- biofouling --- estolides --- castor oil --- lipase --- candida antarctica lipase A --- Arabidopsis thaliana --- hydroxynitrile lyase --- oxynitrilase --- His-tag --- immobilization --- batch --- continuous flow --- Geobacillus thermocatenolatus --- lipases --- ethanolysis --- ionic liquids --- kinetic resolution --- mandelic acid --- Aspergillus --- fermentation --- filamentous fungi --- genetic engineering --- heterologous expression --- recombinant protein --- secretion --- transcriptional regulation --- n/a --- Halohydrin dehalogenases --- conformational dynamics --- active site tunnels --- molecular dynamics simulations --- omega-3 ethyl esters --- monkfish liver oil --- COSMO-RS --- fungal resting cells --- selectivity --- ketone body ester --- asymmetric synthesis --- configuration inversion

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Applied biocatalysis and biotransformation, that is, the use of enzymes and whole-cell systems in manufacturing processes for synthetic purposes, has been experiencing a clear boom in recent years, which has led to the start of the so-called “fourth wave”. In fact, the latest advances in bioinformatics, system biology, process intensification, and, in particular, enzyme-directed evolution (encouraged by the 2018 Nobel Prize awarded to F. Arnold), are widening the range of the efficacy of biocatalysts and accelerating the rate at which new enzymes are becoming available, even for activities not previously known. European scientists have been very actively involved in different aspects of this field. Nine contributions dealing with different aspects of applied biocatalysis developed by European researchers are gathered in this Special Issue

Research & information: general --- biocatalysis --- glycosidases --- isomerases --- Pichia pastoris --- sweeteners --- rare sugars --- cheese whey --- sustainable chemistry --- penicillin acylase --- aculeacin acylase --- N-acyl-homoserine lactone acylases --- quorum quenching --- biofouling --- estolides --- castor oil --- lipase --- candida antarctica lipase A --- Arabidopsis thaliana --- hydroxynitrile lyase --- oxynitrilase --- His-tag --- immobilization --- batch --- continuous flow --- Geobacillus thermocatenolatus --- lipases --- ethanolysis --- ionic liquids --- kinetic resolution --- mandelic acid --- Aspergillus --- fermentation --- filamentous fungi --- genetic engineering --- heterologous expression --- recombinant protein --- secretion --- transcriptional regulation --- Halohydrin dehalogenases --- conformational dynamics --- active site tunnels --- molecular dynamics simulations --- omega-3 ethyl esters --- monkfish liver oil --- COSMO-RS --- fungal resting cells --- selectivity --- ketone body ester --- asymmetric synthesis --- configuration inversion --- biocatalysis --- glycosidases --- isomerases --- Pichia pastoris --- sweeteners --- rare sugars --- cheese whey --- sustainable chemistry --- penicillin acylase --- aculeacin acylase --- N-acyl-homoserine lactone acylases --- quorum quenching --- biofouling --- estolides --- castor oil --- lipase --- candida antarctica lipase A --- Arabidopsis thaliana --- hydroxynitrile lyase --- oxynitrilase --- His-tag --- immobilization --- batch --- continuous flow --- Geobacillus thermocatenolatus --- lipases --- ethanolysis --- ionic liquids --- kinetic resolution --- mandelic acid --- Aspergillus --- fermentation --- filamentous fungi --- genetic engineering --- heterologous expression --- recombinant protein --- secretion --- transcriptional regulation --- Halohydrin dehalogenases --- conformational dynamics --- active site tunnels --- molecular dynamics simulations --- omega-3 ethyl esters --- monkfish liver oil --- COSMO-RS --- fungal resting cells --- selectivity --- ketone body ester --- asymmetric synthesis --- configuration inversion