scholarly journals FAD/NADH Dependent Oxidoreductases: From Different Amino Acid Sequences to Similar Protein Shapes for Playing an Ancient Function

2019 ◽  
Vol 8 (12) ◽  
pp. 2117 ◽  
Author(s):  
Lucia Trisolini ◽  
Nicola Gambacorta ◽  
Ruggiero Gorgoglione ◽  
Michele Montaruli ◽  
Luna Laera ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Amino Acid ◽  
Pyridine Nucleotide ◽  
Amino Acid Sequences ◽  
Type Ii ◽  
Conserved Sequence ◽  
Large Protein Family ◽  
Species Specific ◽  
Apoptosis Inducing Factor ◽  
Computational Analyses

Flavoprotein oxidoreductases are members of a large protein family of specialized dehydrogenases, which include type II NADH dehydrogenase, pyridine nucleotide-disulphide oxidoreductases, ferredoxin-NAD+ reductases, NADH oxidases, and NADH peroxidases, playing a crucial role in the metabolism of several prokaryotes and eukaryotes. Although several studies have been performed on single members or protein subgroups of flavoprotein oxidoreductases, a comprehensive analysis on structure–function relationships among the different members and subgroups of this great dehydrogenase family is still missing. Here, we present a structural comparative analysis showing that the investigated flavoprotein oxidoreductases have a highly similar overall structure, although the investigated dehydrogenases are quite different in functional annotations and global amino acid composition. The different functional annotation is ascribed to their participation in species-specific metabolic pathways based on the same biochemical reaction, i.e., the oxidation of specific cofactors, like NADH and FADH2. Notably, the performed comparative analysis sheds light on conserved sequence features that reflect very similar oxidation mechanisms, conserved among flavoprotein oxidoreductases belonging to phylogenetically distant species, as the bacterial type II NADH dehydrogenases and the mammalian apoptosis-inducing factor protein, until now retained as unique protein entities in Bacteria/Fungi or Animals, respectively. Furthermore, the presented computational analyses will allow consideration of FAD/NADH oxidoreductases as a possible target of new small molecules to be used as modulators of mitochondrial respiration for patients affected by rare diseases or cancer showing mitochondrial dysfunction, or antibiotics for treating bacterial/fungal/protista infections.

Partial Proteolysis of Rice Phytochrome: Comparison with Oat Phytochrome

1989 ◽  
Vol 44 (9-10) ◽  
pp. 757-764 ◽  
Author(s):  
Rudolf Schendel ◽  
Zhe Tong ◽  
Wolfhart Rüdiger
Keyword(s):  
Signal Transduction ◽  
Oryza Sativa ◽  
Amino Acid ◽  
Spectral Data ◽  
Active Center ◽  
Oryza Sativa L ◽  
Slight Modification ◽  
Amino Acid Sequences ◽  
Rice Seedlings ◽  
Conserved Sequence

Phytochrome was isolated from etiolated rice seedlings (Oryza sativa L.) by slight modification of the procedure for oat phytochrome. Spectral data of rice phytochrome are comparable with those of oat and rye phytochrome. Controlled proteolysis with endoproteinases Lys-C and Glu-C yielded defined fragments some of which were different for Pr and Pfr. The fragments were identified by comparison with the corresponding fragments of oat phytochrome and by comparison of the amino acid sequences of rice and oat phytochrome. Regions of the peptide chain which are differently exposed in Pr and Pfr were identified. A highly conserved sequence around residues 740-750 is discussed as candidate for an ‘‘active center’’ of signal transduction.

Sequence analysis of the immunoglobulin antigen receptor of hepatitis C virus–associated non-Hodgkin lymphomas suggests that the malignant cells are derived from the rheumatoid factor–producing cells that occur mainly in type II cryoglobulinemia

Blood ◽  
2000 ◽  
Vol 96 (10) ◽  
pp. 3578-3584 ◽  
Author(s):  
Valli De Re ◽  
Salvatore De Vita ◽  
Alessandra Marzotto ◽  
Maurizio Rupolo ◽  
Annunziata Gloghini ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Amino Acid ◽  
Rheumatoid Factor ◽  
Light Chain ◽  
Mixed Cryoglobulinemia ◽  
Amino Acid Sequences ◽  
Type Ii ◽  
E2 Protein ◽  
Immunoglobulin Receptor

Analysis of the immunoglobulin receptor (IGR) variable heavy- and light-chain sequences on 17 hepatitis C virus (HCV)-associated non-Hodgkin lymphomas (NHLs) (9 patients also had type II mixed cryoglobulinemia [MC] syndrome and 8 had NHL unrelated to MC) and analysis of intraclonal diversity on 8 of them suggest that such malignant lymphoproliferations derive from an antigen-driven pathologic process, with a selective pressure for the maintenance of a functional IgR and a negative pressure for additional amino acid mutations in the framework regions (FRs). For almost all NHLs, both heavy- and light-chain complementarity-determining regions (CDR3) showed the highest similarity to antibodies with rheumatoid factor (RF) activity that have been found in the MC syndrome, thus suggesting that a common antigenic stimulus is involved in MC syndrome and in HCV-associated lymphomagenesis. Moreover, because HCV is the recognized pathologic agent of MC and the CDR3 amino acid sequences of some HCV-associated NHLs also present a high homology for antibody specific for the E2 protein of HCV, it may be reasonable to speculate that HCV E2 protein is one of the chronic antigenic stimuli involved in the lymphomagenetic process. Finally, the use of specific segments, in particular the D segment, in assembling the IgH chain of IgR seems to confer B-cell disorders with the property to produce antibody with RF activity, which may contribute to the manifestation of an overt MC syndrome.

scholarly journals Comparative Analysis of the Putative Amino Acid Sequences of Chlamydial Heat Shock Protein 60 and Escherichia coli GroEL.

2000 ◽  
Vol 62 (9) ◽  
pp. 941-945 ◽  
Author(s):  
Yoshitsugu OCHIAI ◽  
Hideto FUKUSHI ◽  
Cai YAN ◽  
Tsuyoshi YAMAGUCHI ◽  
Katsuya HIRAI
Keyword(s):  
Escherichia Coli ◽  
Comparative Analysis ◽  
Amino Acid ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Amino Acid Sequences ◽  
Heat Shock Protein 60

scholarly journals Macronuclei and micronuclei in Tetrahymena thermophila contain high-mobility-group-like chromosomal proteins containing a highly conserved eleven-amino-acid putative DNA-binding sequence.

1991 ◽  
Vol 11 (1) ◽  
pp. 166-174 ◽  
Author(s):  
I G Schulman ◽  
T Wang ◽  
M Wu ◽  
J Bowen ◽  
R G Cook ◽  
...  
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Tetrahymena Thermophila ◽  
High Mobility ◽  
Amino Acid Sequences ◽  
High Mobility Group ◽  
Binding Motif ◽  
Hmg Proteins ◽  
Chromosomal Proteins ◽  
Conserved Sequence

HMG (high-mobility-group protein) B and HMG C are abundant nonhistone chromosomal proteins isolated from Tetrahymena thermophila macronuclei with solubilities, molecular weights, and amino acid compositions like those of vertebrate HMG proteins. Genomic clones encoding each of these proteins have been sequenced. Both are single-copy genes that encode single polyadenylated messages whose amounts are 10 to 15 times greater in growing cells than in starved, nongrowing cells. The derived amino acid sequences of HMG B and HMG C contain a highly conserved sequence, the HMG 1 box, found in vertebrate HMGs 1 and 2, and we speculate that this sequence may represent a novel, previously unrecognized DNA-binding motif in this class of chromosomal proteins. Like HMGs 1 and 2, HMGs B and C contain a high percentage of aromatic amino acids. However, the Tetrahymena HMGs are small, are associated with nucleosome core particles, and can be specifically extracted from macronuclei by elutive intercalation, properties associated with vertebrate HMGs 14 and 17, not HMGs 1 and 2. Thus, it appears that these Tetrahymena proteins have features in common with both of the major subgroups of higher eucaryotic HMG proteins. Surprisingly, a linker histone found exclusively in transcriptionally inactive micronuclei also has several HMG-like characteristics, including the ability to be specifically extracted from nuclei by elutive intercalation and the presence of the HMG 1 box. This finding suggests that at least in T. thermophila, proteins with HMG-like properties are not restricted to regions of transcriptionally active chromatin.

scholarly journals Amino acid sequences of α-helical segments from S-carboxymethylkerateine-A. Complete sequence of a type-II segment

1978 ◽  
Vol 173 (2) ◽  
pp. 365-371 ◽  
Author(s):  
W G Crewther ◽  
A S Inglis ◽  
N M McKern
Keyword(s):  
Amino Acid ◽  
Coiled Coil ◽  
Complete Sequence ◽  
Amino Acid Sequences ◽  
Helical Axis ◽  
Type I ◽  
Type Ii ◽  
Coil Structure ◽  
Aqueous Urea ◽  
Alpha Keratin

1. The helical fragments obtained by partial chymotryptic digestion of S-carboxymethylkeratine-A, the low-sulphur fraction from wool, were fractionated into type-I and type-II helical segments in aqueous urea under conditions limiting carbamoylation. 2. The amino acid sequence of a 109-residue type-II segment was completed by using the sequenator. 3. When the data were incorporated into a helical model of 3.6 residues per turn the hydrophobic residues generated a band aligned at a slight angle to the helical axis. This result is in accord with the postulated coiled-coil structure of the crystalline regions of alpha-keratin.

scholarly journals Diversity of radA Genes from Cultured and UnculturedArchaea: Comparative Analysis of Putative RadA Proteins and Their Use as a Phylogenetic Marker

1999 ◽  
Vol 181 (3) ◽  
pp. 907-915 ◽  
Author(s):  
Steven J. Sandler ◽  
Philip Hugenholtz ◽  
Christa Schleper ◽  
Edward F. DeLong ◽  
Norman R. Pace ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Amino Acid ◽  
Tissue Sample ◽  
Reca Protein ◽  
Amino Acid Sequences ◽  
Sponge Tissue ◽  
Amino Acid Deletion ◽  
Archaeal Species ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Archaea-specific radA primers were used with PCR to amplify fragments of radA genes from 11 cultivated archaeal species and one marine sponge tissue sample that contained essentially an archaeal monoculture. The amino acid sequences encoded by the PCR fragments, three RadA protein sequences previously published (21), and two new complete RadA sequences were aligned with representative bacterial RecA proteins and eucaryal Rad51 and Dmc1 proteins. The alignment supported the existence of four insertions and one deletion in the archaeal and eucaryal sequences relative to the bacterial sequences. The sizes of three of the insertions were found to have taxonomic and phylogenetic significance. Comparative analysis of the RadA sequences, omitting amino acids in the insertions and deletions, shows a cladal distribution of species which mimics to a large extent that obtained by a similar analysis of archaeal 16S rRNA sequences. The PCR technique also was used to amplify fragments of 15 radA genes from uncultured natural sources. Phylogenetic analysis of the amino acid sequences encoded by these fragments reveals several clades with affinity, sometimes only distant, to the putative RadA proteins of several species ofCrenarcheota. The two most deeply branching archaealradA genes found had some amino acid deletion and insertion patterns characteristic of bacterial recA genes. Possible explanations are discussed. Finally, signature codons are presented to distinguish among RecA protein family members.

scholarly journals Genetic Determinants of Sindbis Virus Mosquito Infection Are Associated with a Highly Conserved Alphavirus and Flavivirus Envelope Sequence

2007 ◽  
Vol 82 (6) ◽  
pp. 2966-2974 ◽  
Author(s):  
Dennis J. Pierro ◽  
Erik L. Powers ◽  
Ken E. Olson
Keyword(s):  
Amino Acid ◽  
Sindbis Virus ◽  
Virus Genome ◽  
Growth Patterns ◽  
Amino Acid Sequences ◽  
Genetic Determinants ◽  
Nucleotide Substitutions ◽  
Conserved Sequence ◽  
E2 Glycoprotein ◽  
Envelope Sequence

ABSTRACT Wild-type Sindbis virus (SINV) strain MRE16 efficiently infects Aedes aegypti midgut epithelial cells (MEC), but laboratory-derived neurovirulent SINV strain TE/5′2J infects MEC poorly. SINV determinants for MEC infection have been localized to the E2 glycoprotein. The E2 amino acid sequences of MRE16 and TE/5′2J differ at 60 residue sites. To identify the genetic determinants of MEC infection of MRE16, the TE/5′2J virus genome was altered to contain either domain chimeras or more focused nucleotide substitutions of MRE16. The growth patterns of derived viruses in cell culture were determined, as were the midgut infection rates (MIR) in A. aegypti mosquitoes. The results showed that substitutions of MRE16 E2 aa 95 to 96 and 116 to 119 into the TE/5′2J virus increased MIR both independently and in combination with each other. In addition, a unique PPF/.GDS amino acid motif was located between these two sites that was found to be a highly conserved sequence among alphaviruses and flaviviruses but not other arboviruses.

scholarly journals Role of Transmembrane Domain and Cytoplasmic Tail Amino Acid Sequences of Influenza A Virus Neuraminidase in Raft Association and Virus Budding

2004 ◽  
Vol 78 (10) ◽  
pp. 5258-5269 ◽  
Author(s):  
Subrata Barman ◽  
Lopa Adhikary ◽  
Alok K. Chakrabarti ◽  
Carl Bernas ◽  
Yoshihiro Kawaoka ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Influenza A ◽  
Transmembrane Domain ◽  
Amino Acid Sequences ◽  
Type Ii ◽  
Virus Growth ◽  
Transmembrane Glycoprotein ◽  
Virus Life Cycle

ABSTRACT Influenza virus neuraminidase (NA), a type II transmembrane glycoprotein, possesses receptor-destroying activity and thereby facilitates virus release from the cell surface. Among the influenza A viruses, both the cytoplasmic tail (CT) and transmembrane domain (TMD) amino acid sequences of NA are highly conserved, yet their function(s) in virus biology remains unknown. To investigate the role of amino acid sequences of the CT and TMD on the virus life cycle, we systematically mutagenized the entire CT and TMD of NA by converting two to five contiguous amino acids to alanine. In addition, we also made two chimeric NA by replacing the CT proximal one-third amino acids of the NA TMD [NA(1T2N)NA] and the entire NA TMD (NATRNA) with that of human transferrin receptor (TR) (a type II transmembrane glycoprotein). We rescued transfectant mutant viruses by reverse genetics and examined their phenotypes. Our results show that all mutated and chimeric NAs could be rescued into transfectant viruses. Different mutants showed pleiotropic effects on virus growth and replication. Some mutants (NA2A5, NA3A7, and NA4A10) had little effect on virus growth while others (NA3A2, NA5A27, and NA5A31) produced about 50- to 100-fold-less infectious virus and still some others (NA5A14, NA4A19, and NA4A23) exhibited an intermediate phenotype. In general, mutations towards the ectodomain-proximal sequences of TMD progressively caused reduction in NA enzyme activity, affected lipid raft association, and attenuated virus growth. Electron microscopic analysis showed that these mutant viruses remained aggregated and bound to infected cell surfaces and could be released from the infected cells by bacterial NA treatment. Moreover, viruses containing mutations in the extreme N terminus of the CT (NA3A2) as well as chimeric NA containing the TMD replaced partially [NA(1T2N)NA] or fully (NATRNA) with TR TMD caused reduction in virus growth and exhibited the morphological phenotype of elongated particles. These results show that although the sequences of NA CT and TMD per se are not absolutely essential for the virus life cycle, specific amino acid sequences play a critical role in providing structural stability, enzyme activity, and lipid raft association of NA. In addition, aberrant morphogenesis including elongated particle formation of some mutant viruses indicates the involvement of NA in virus morphogenesis and budding.

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