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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.

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 --- n/a

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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 --- n/a

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Iron–sulfur (FeS) centers are essential protein cofactors in all forms of life. They are involved in many key biological processes. In particular, Fe-S centers not only serve as enzyme cofactors in catalysis and electron transfer, they are also indispensable for the biosynthesis of complex metal-containing cofactors. Among these cofactors are the molybdenum (Moco) and tungsten (Wco) cofactors. Both Moco/Wco biosynthesis and Fe-S cluster assembly are highly conserved among all kingdoms of life. After formation, Fe-S clusters are transferred to carrier proteins, which insert them into recipient apo-proteins. Moco/Wco cofactors are composed of a tricyclic pterin compound, with the metal coordinated to its unique dithiolene group. Moco/Wco biosynthesis starts with an Fe-S cluster-dependent step involving radical/S-adenosylmethionine (SAM) chemistry. The current lack of knowledge of the connection of the assembly/biosynthesis of complex metal-containing cofactors is due to the sheer complexity of their synthesis with regard to both the (genetic) regulation and (chemical) metal center assembly. Studies on these metal-cofactors/cofactor-containing enzymes are important for understanding fundamental cellular processes. They will also provide a comprehensive view of the complex biosynthesis and the catalytic mechanism of metalloenzymes that underlie metal-related human diseases.

Research & information: general --- Biology, life sciences --- CO dehydrogenase --- dihydrogen --- hydrogenase --- quantum/classical modeling --- density functional theory --- metal–dithiolene --- pyranopterin molybdenum enzymes --- fold-angle --- tungsten enzymes --- electronic structure --- pseudo-Jahn–Teller effect --- thione --- molybdenum cofactor --- Moco --- mixed-valence complex --- dithiolene ligand --- tetra-nuclear nickel complex --- X-ray structure --- magnetic moment --- formate hydrogenlyase --- hydrogen metabolism --- energy conservation --- MRP (multiple resistance and pH)-type Na+/H+ antiporter --- CCCP—carbonyl cyanide m-chlorophenyl-hydrazone --- EIPA—5-(N-ethyl-N-isopropyl)-amiloride --- nicotinamide adenine dinucleotide (NADH) --- electron transfer --- enzyme kinetics --- enzyme structure --- formate dehydrogenase --- carbon assimilation --- Moco biosynthesis --- Fe-S cluster assembly --- l-cysteine desulfurase --- ISC --- SUF --- NIF --- iron --- molybdenum --- sulfur --- tungsten cofactor --- aldehyde:ferredoxin oxidoreductase --- benzoyl-CoA reductase --- acetylene hydratase --- [Fe]-hydrogenase --- FeGP cofactor --- guanylylpyridinol --- conformational changes --- X-ray crystallography --- iron-sulfur cluster --- persulfide --- metallocofactor --- frataxin --- Friedreich’s ataxia --- n/a --- metal-dithiolene --- pseudo-Jahn-Teller effect --- CCCP-carbonyl cyanide m-chlorophenyl-hydrazone --- EIPA-5-(N-ethyl-N-isopropyl)-amiloride --- Friedreich's ataxia

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Iron–sulfur (FeS) centers are essential protein cofactors in all forms of life. They are involved in many key biological processes. In particular, Fe-S centers not only serve as enzyme cofactors in catalysis and electron transfer, they are also indispensable for the biosynthesis of complex metal-containing cofactors. Among these cofactors are the molybdenum (Moco) and tungsten (Wco) cofactors. Both Moco/Wco biosynthesis and Fe-S cluster assembly are highly conserved among all kingdoms of life. After formation, Fe-S clusters are transferred to carrier proteins, which insert them into recipient apo-proteins. Moco/Wco cofactors are composed of a tricyclic pterin compound, with the metal coordinated to its unique dithiolene group. Moco/Wco biosynthesis starts with an Fe-S cluster-dependent step involving radical/S-adenosylmethionine (SAM) chemistry. The current lack of knowledge of the connection of the assembly/biosynthesis of complex metal-containing cofactors is due to the sheer complexity of their synthesis with regard to both the (genetic) regulation and (chemical) metal center assembly. Studies on these metal-cofactors/cofactor-containing enzymes are important for understanding fundamental cellular processes. They will also provide a comprehensive view of the complex biosynthesis and the catalytic mechanism of metalloenzymes that underlie metal-related human diseases.

Research & information: general --- Biology, life sciences --- CO dehydrogenase --- dihydrogen --- hydrogenase --- quantum/classical modeling --- density functional theory --- metal-dithiolene --- pyranopterin molybdenum enzymes --- fold-angle --- tungsten enzymes --- electronic structure --- pseudo-Jahn-Teller effect --- thione --- molybdenum cofactor --- Moco --- mixed-valence complex --- dithiolene ligand --- tetra-nuclear nickel complex --- X-ray structure --- magnetic moment --- formate hydrogenlyase --- hydrogen metabolism --- energy conservation --- MRP (multiple resistance and pH)-type Na+/H+ antiporter --- CCCP-carbonyl cyanide m-chlorophenyl-hydrazone --- EIPA-5-(N-ethyl-N-isopropyl)-amiloride --- nicotinamide adenine dinucleotide (NADH) --- electron transfer --- enzyme kinetics --- enzyme structure --- formate dehydrogenase --- carbon assimilation --- Moco biosynthesis --- Fe-S cluster assembly --- l-cysteine desulfurase --- ISC --- SUF --- NIF --- iron --- molybdenum --- sulfur --- tungsten cofactor --- aldehyde:ferredoxin oxidoreductase --- benzoyl-CoA reductase --- acetylene hydratase --- [Fe]-hydrogenase --- FeGP cofactor --- guanylylpyridinol --- conformational changes --- X-ray crystallography --- iron-sulfur cluster --- persulfide --- metallocofactor --- frataxin --- Friedreich's ataxia