RESUMO
Ancestral sequence reconstruction has had recent success in decoding the origins and the determinants of complex protein functions. However, phylogenetic analyses of remote homologues must handle extreme amino acid sequence diversity resulting from extended periods of evolutionary change. We exploited the wealth of protein structures to develop an evolutionary model based on protein secondary structure. The approach follows the differences between discrete secondary structure states observed in modern proteins and those hypothesized in their immediate ancestors. We implemented maximum likelihood-based phylogenetic inference to reconstruct ancestral secondary structure. The predictive accuracy from the use of the evolutionary model surpasses that of comparative modeling and sequence-based prediction; the reconstruction extracts information not available from modern structures or the ancestral sequences alone. Based on a phylogenetic analysis of a sequence-diverse protein family, we showed that the model can highlight relationships that are evolutionarily rooted in structure and not evident in amino acid-based analysis.
Assuntos
Proteínas Adaptadoras de Transporte Vesicular/química , Proteínas de Bactérias/química , Evolução Molecular , Modelos Estatísticos , Proteínas Adaptadoras de Transporte Vesicular/história , Animais , Bactérias/química , Bactérias/classificação , Bactérias/metabolismo , Proteínas de Bactérias/história , Simulação por Computador , História do Século XXI , História Antiga , Humanos , Mamíferos/classificação , Mamíferos/metabolismo , Filogenia , Plantas/química , Plantas/classificação , Plantas/metabolismo , Estrutura Secundária de ProteínaRESUMO
Use of Green Fluorescent Protein (GFP) as a marker has revolutionized biological research in the last few decades. In this brief commentary, we reflect upon the success story of GFP and highlight a few lesser-known facets about GFP that add up to its usefulness.
Assuntos
Proteínas de Bactérias/genética , Recuperação de Fluorescência Após Fotodegradação/métodos , Regulação da Expressão Gênica , Proteínas de Fluorescência Verde/genética , Proteínas Luminescentes/genética , Receptores Acoplados a Proteínas G/genética , Animais , Proteínas de Bactérias/história , Proteínas de Bactérias/metabolismo , Bibliometria , Linhagem Celular , Fluorescência , Recuperação de Fluorescência Após Fotodegradação/história , Recuperação de Fluorescência Após Fotodegradação/instrumentação , Genes Reporter , Proteínas de Fluorescência Verde/química , Proteínas de Fluorescência Verde/história , Proteínas de Fluorescência Verde/metabolismo , História do Século XIX , História do Século XX , História do Século XXI , Humanos , Proteínas Luminescentes/história , Proteínas Luminescentes/metabolismo , Modelos Moleculares , Estrutura Secundária de Proteína , Receptores Acoplados a Proteínas G/metabolismoRESUMO
Here we provide reflections of and a tribute to John M. Olson, a pioneering researcher in photosynthesis. We trace his career, which began at Wesleyan University and the University of Pennsylvania, and continued at Utrech in The Netherlands, Brookhaven National Laboratory, and Odense University in Denmark. He was the world expert on pigment organization in the green photosynthetic bacteria, and discovered and characterized the first chlorophyll-containing protein, which has come to be known as the Fenna-Matthews-Olson (FMO) protein. He also thought and wrote extensively on the origin and early evolution of photosynthesis. We include personal comments from Brian Matthews, Raymond Cox, Paolo Gerola, Beverly Pierson and Jon Olson.
Assuntos
Fotossíntese/fisiologia , Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/história , Proteínas de Bactérias/metabolismo , Botânica/história , Dinamarca , História do Século XX , Complexos de Proteínas Captadores de Luz/genética , Complexos de Proteínas Captadores de Luz/história , Complexos de Proteínas Captadores de Luz/metabolismo , Estados UnidosAssuntos
Membrana Celular/fisiologia , Parede Celular/fisiologia , Bactérias Gram-Negativas/fisiologia , Bactérias Gram-Negativas/ultraestrutura , Bactérias Gram-Positivas/fisiologia , Bactérias Gram-Positivas/ultraestrutura , Proteínas de Bactérias/genética , Proteínas de Bactérias/história , Proteínas de Bactérias/metabolismo , Regulação Bacteriana da Expressão Gênica/fisiologia , História do Século XXRESUMO
The history of research on microbial rhodopsins offers a novel perspective on the history of the molecular life sciences. Events in this history play important roles in the development of fields such as general microbiology, membrane research, bioenergetics, metagenomics and, very recently, neurobiology. New concepts, techniques, methods and fields have arisen as a result of microbial rhodopsin investigations. In addition, the history of microbial rhodopsins sheds light on the dynamic connections between basic and applied science, and hypothesis-driven and data-driven approaches. The story begins with the late nineteenth century discovery of microorganisms on salted fish and leads into ecological and taxonomical studies of halobacteria in hypersaline environments. These programmes were built on by the discovery of bacteriorhodopsin in organisms that are part of what is now known as the archaeal genus Halobacterium. The transfer of techniques from bacteriorhodopsin studies to the metagenomic discovery of proteorhodopsin in 2000 further extended the field. Microbial rhodopsins have also been used as model systems to understand membrane protein structure and function, and they have become the target of technological applications such as optogenetics and nanotechnology. Analysing the connections between these historical episodes provides a rich example of how science works over longer time periods, especially with regard to the transfer of materials, methods and concepts between different research fields.
Assuntos
Proteínas Arqueais/história , Proteínas de Bactérias/história , Disciplinas das Ciências Biológicas/história , Rodopsinas Microbianas/história , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Bactérias/genética , Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Halobacterium/genética , Halobacterium/metabolismo , História do Século XIX , História do Século XX , História do Século XXI , Rodopsinas Microbianas/genética , Rodopsinas Microbianas/metabolismoAssuntos
Bioquímica/história , Corantes Fluorescentes/história , Proteínas Luminescentes/história , Prêmio Nobel , Equorina/química , Equorina/história , Equorina/isolamento & purificação , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/história , Cristalografia por Raios X , Transferência Ressonante de Energia de Fluorescência , Corantes Fluorescentes/química , Proteínas de Fluorescência Verde/química , Proteínas de Fluorescência Verde/genética , Proteínas de Fluorescência Verde/história , História do Século XX , Proteínas Luminescentes/química , Proteínas Luminescentes/genética , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/históriaRESUMO
A brief memorial, from the ferrocentric view of science, about E.I. Stiefel's discovery of heme, maxi-ferritins in bacteria, recognition of the relationship to animal maxi-ferritins, and other reminiscences of ferritin defined as a storage battery.
Assuntos
Proteínas de Bactérias/química , Química Inorgânica/história , Grupo dos Citocromos b/química , Ferritinas/química , Proteínas de Bactérias/história , Grupo dos Citocromos b/história , Ferritinas/história , História do Século XX , Estados UnidosAssuntos
Proteínas de Bactérias/história , Proteínas de Bactérias/metabolismo , Cocos Gram-Positivos/metabolismo , Receptores de Superfície Celular/história , Receptores de Superfície Celular/metabolismo , Proteínas de Bactérias/isolamento & purificação , História do Século XX , Humanos , Receptores de Superfície Celular/isolamento & purificação , Receptores de Ativador de Plasminogênio Tipo UroquinaseAssuntos
Proteínas de Bactérias/história , Escherichia coli/genética , Mutagênese , Óperon , Serina Endopeptidases/história , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Sequência de Bases , Reparo do DNA , DNA Polimerase Dirigida por DNA , Proteínas de Escherichia coli , História do Século XX , Mutagênese/efeitos dos fármacos , Mutagênese/efeitos da radiação , Fases de Leitura , Homologia de Sequência do Ácido Nucleico , Serina Endopeptidases/genética , Raios UltravioletaRESUMO
Oxygen has always been recognized as an essential element of many life forms, initially through its role as a terminal electron acceptor for the energy-generating pathways of oxidative phosphorylation. In 1955, Hayaishi et al. [Mechanism of the pyrocatechase reaction, J. Am. Chem. Soc. 77 (1955) 5450-5451] presented the most important discovery that changed this simplistic view of how Nature uses atmospheric dioxygen. His discovery, the naming and mechanistic understanding of the first "oxygenase" enzyme, has provided a wonderful opportunity and scientific impetus for four decades of researchers. This volume provides an opportunity to recognize the breakthroughs of the "Hayaishi School." Notable have been the prolific contributions of Professor Ishimura et al. [Oxygen and life. Oxygenases, Oxidases and Lipid Mediators, International Congress Series, Elsevier, Amsterdam, 2002], a first-generation Hayaishi product, to characterization of the cytochrome P450 monooxygenases.
Assuntos
Proteínas de Bactérias/história , Cânfora 5-Mono-Oxigenase/história , Sistema Enzimático do Citocromo P-450/história , Heme Oxigenase (Desciclizante)/história , Heme/história , Peroxidases/história , Proteínas de Bactérias/química , Cânfora 5-Mono-Oxigenase/química , Catálise , Cristalografia por Raios X/história , Sistema Enzimático do Citocromo P-450/química , Espectroscopia de Ressonância de Spin Eletrônica/história , Heme/química , Heme Oxigenase (Desciclizante)/química , História do Século XX , Peroxidases/químicaRESUMO
Few proteins have had such a strong impact on a field as the lac repressor has had in Molecular Biology. Over 40 years ago, Jacob and Monod [Genetic regulatory mechanisms in the synthesis of proteins, J. Mol. Biol. 3 (1961) 318] proposed a model for gene regulation, which survives essentially unchanged in contemporary textbooks. It is a cogent depiction of how a set of 'structural' genes may be coordinately transcribed in response to environmental conditions and regulates metabolic events in the cell. In bacteria, the genes required for lactose utilization are negatively regulated when a repressor molecule binds to an upstream cis activated operator. The repressor and its operator together form a genetic switch, the lac operon. The switch functions when inducer molecules alter the conformation of the repressor in a specific manner. In the presence of a particular metabolite, the repressor undergoes a conformational change that reduces its affinity for the operator. The structures of the lac repressor and its complexes with operator DNA and effector molecules have provided a physical platform for visualizing at the molecular level the different conformations the repressor and the molecular basis for the switch. The structures of lac repressor, bound to its operator and inducer, have also been invaluable for interpreting a plethora of biochemical and genetic data.
Assuntos
Proteínas de Bactérias , Proteínas Repressoras , Sítio Alostérico , Animais , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/história , Proteínas de Bactérias/metabolismo , Sítios de Ligação , DNA/metabolismo , Dimerização , Escherichia coli/genética , Proteínas de Escherichia coli , História do Século XX , Óperon Lac , Repressores Lac , Camundongos , Modelos Moleculares , Estrutura Molecular , Mutagênese , Proteínas Repressoras/química , Proteínas Repressoras/genética , Proteínas Repressoras/história , Proteínas Repressoras/metabolismo , Relação Estrutura-AtividadeRESUMO
Following DNA damage to Escherichia coli bacteria, RecA protein is activated by binding to single stranded DNA and cleaves its own gene repressor (LexA protein). Two papers from Graham Walker's laboratory showed that several bacterial genes in addition to RecA are repressed by the LexA repressor and are inducible following DNA damage [C.J. Keyon, G.C. Walker, DNA-damaging agents stimulate gene expression at specific loci in Escherichia coli, in: Proceedings of the National Academy of Sciences of the United States of America 77, 1980, pp. 2819--2823] and predicted that one of them (UmuD) might itself be subject to activation by a further cleavage reaction involving activated RecA protein [K.L. Perry, S.J. Elledge, B.B. Mitchell, L. Marsh, G.C. Walker, umuD,C and mucA,B operans whose products are required for UV light- and chemical-induced mutagenesis: UmuD, MucA, and LexA proteins share homology, in: Proceedings of the National Academy of Sciences of the United States of America 82, 1985, pp. 4331--4335]. The processed form of UmuD, termed UmuD', later proved to be a subunit of DNA polymerase V, a key enzyme involved in translesion synthesis.