Publications
| Title | Abstract | Year(sorted descending) Filter | PMID Filter |
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| first evidence for substrate channeling between proline catabolic enzymes: a validation of domain fusion analysis for predicting protein-protein interactions. | proline dehydrogenase (prodh) and δ(1)-pyrroline-5-carboxylate (p5c) dehydrogenase (p5cdh) catalyze the four-electron oxidation of proline to glutamate via the intermediates p5c and l-glutamate-γ-semialdehyde (gsa). in gram-negative bacteria, prodh and p5cdh are fused together in the bifunctional enzyme proline utilization a (puta) whereas in other organisms prodh and p5cdh are expressed as separate monofunctional enzymes. substrate channeling has previously been shown for bifunctional putas, bu ... | 2014 | 25492892 |
| crispr rna binding and dna target recognition by purified cascade complexes from escherichia coli. | clustered regularly interspaced short palindromic repeats (crisprs) and their associated cas proteins comprise a prokaryotic rna-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. the type i-e crispr interference complex cascade from escherichia coli is composed of five different cas proteins and a 61-nt-long guide rna (crrna). crrnas contain a unique 32-nt spacer flanked by a repeat-derived 5' handle (8 nt) and a 3' handle (21 nt). the space ... | 2014 | 25488810 |
| crispr rna binding and dna target recognition by purified cascade complexes from escherichia coli. | clustered regularly interspaced short palindromic repeats (crisprs) and their associated cas proteins comprise a prokaryotic rna-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. the type i-e crispr interference complex cascade from escherichia coli is composed of five different cas proteins and a 61-nt-long guide rna (crrna). crrnas contain a unique 32-nt spacer flanked by a repeat-derived 5' handle (8 nt) and a 3' handle (21 nt). the space ... | 2014 | 25488810 |
| the biosynthesis of thiol- and thioether-containing cofactors and secondary metabolites catalyzed by radical s-adenosylmethionine enzymes. | sulfur atoms are present as thiol and thioether functional groups in amino acids, coenzymes, cofactors, and various products of secondary metabolic pathways. the biosynthetic pathways for several sulfur-containing biomolecules require the substitution of sulfur for hydrogen at unreactive aliphatic or electron-rich aromatic carbon atoms. examples discussed in this review include biotin, lipoic acid, methylthioether modifications found in some nucleic acids and proteins, and thioether cross-links ... | 2014 | 25477512 |
| the biosynthesis of thiol- and thioether-containing cofactors and secondary metabolites catalyzed by radical s-adenosylmethionine enzymes. | sulfur atoms are present as thiol and thioether functional groups in amino acids, coenzymes, cofactors, and various products of secondary metabolic pathways. the biosynthetic pathways for several sulfur-containing biomolecules require the substitution of sulfur for hydrogen at unreactive aliphatic or electron-rich aromatic carbon atoms. examples discussed in this review include biotin, lipoic acid, methylthioether modifications found in some nucleic acids and proteins, and thioether cross-links ... | 2014 | 25477512 |
| fada5 a thiolase from mycobacterium tuberculosis: a steroid-binding pocket reveals the potential for drug development against tuberculosis. | with the exception of hiv, tuberculosis (tb) is the leading cause of mortality among infectious diseases. the urgent need to develop new antitubercular drugs is apparent due to the increasing number of drug-resistant mycobacterium tuberculosis (mtb) strains. proteins involved in cholesterol import and metabolism have recently been discovered as potent targets against tb. fada5, a thiolase from mtb, is catalyzing the last step of the β-oxidation reaction of the cholesterol side-chain degradation ... | 2014 | 25482540 |
| fada5 a thiolase from mycobacterium tuberculosis: a steroid-binding pocket reveals the potential for drug development against tuberculosis. | with the exception of hiv, tuberculosis (tb) is the leading cause of mortality among infectious diseases. the urgent need to develop new antitubercular drugs is apparent due to the increasing number of drug-resistant mycobacterium tuberculosis (mtb) strains. proteins involved in cholesterol import and metabolism have recently been discovered as potent targets against tb. fada5, a thiolase from mtb, is catalyzing the last step of the β-oxidation reaction of the cholesterol side-chain degradation ... | 2014 | 25482540 |
| essential structural and functional roles of the cmr4 subunit in rna cleavage by the cmr crispr-cas complex. | the cmr complex is the multisubunit effector complex of the type iii-b clustered regularly interspaced short palindromic repeats (crispr)-cas immune system. the cmr complex recognizes a target rna through base pairing with the integral crispr rna (crrna) and cleaves the target at multiple regularly spaced locations within the complementary region. to understand the molecular basis of the function of this complex, we have assembled information from electron microscopic and x-ray crystallographic ... | 2014 | 25482566 |
| a novel mechanism of protein thermostability: a unique n-terminal domain confers heat resistance to fe/mn-sods. | superoxide dismutases (sods), especially thermostable sods, are widely applied in medical treatments, cosmetics, food, agriculture, and other industries given their excellent antioxidant properties. a novel thermostable cambialistic sod from geobacillus thermodenitrificans ng80-2 exhibits maximum activity at 70 °c and high thermostability over a broad range of temperatures (20-80 °c). unlike other reported sods, this enzyme contains an extra repeat-containing n-terminal domain (ntd) of 244 resid ... | 2014 | 25445927 |
| a new window into the molecular physiology of membrane proteins. | integral membrane proteins comprise ∼25% of the human proteome. yet, our understanding of their molecular physiology is still in its infancy. this can be attributed to two factors: the experimental challenges that arise from the difficult chemical nature of membrane proteins, and the unclear relationship between their activity and their native environment. new approaches are therefore required to address these challenges. recent developments in mass spectrometry have shown that it is possible to ... | 2014 | 25630257 |
| a new window into the molecular physiology of membrane proteins. | integral membrane proteins comprise ∼25% of the human proteome. yet, our understanding of their molecular physiology is still in its infancy. this can be attributed to two factors: the experimental challenges that arise from the difficult chemical nature of membrane proteins, and the unclear relationship between their activity and their native environment. new approaches are therefore required to address these challenges. recent developments in mass spectrometry have shown that it is possible to ... | 2014 | 25630257 |
| interface matters: the stiffness route to stability of a thermophilic tetrameric malate dehydrogenase. | in this work we investigate by computational means the behavior of two orthologous bacterial proteins, a mesophilic and a thermophilic tetrameric malate dehydrogenase (maldh), at different temperatures. namely, we quantify how protein mechanical rigidity at different length- and time-scales correlates to protein thermophilicity as commonly believed. in particular by using a clustering analysis strategy to explore the conformational space of the folded proteins, we show that at ambient conditions ... | 2014 | 25437494 |
| substrate-specific development of thermophilic bacterial consortia by using chemically pretreated switchgrass. | microbial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. we exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (sg) biomass of various compositions. microbial communities were adapted to untreated, ammonium fiber expansion (afex)-pretreated, and ionic-liquid ( ... | 2014 | 25261509 |
| structural insights into translational recoding by frameshift suppressor trnasufj. | the three-nucleotide mrna reading frame is tightly regulated during translation to ensure accurate protein expression. translation errors that lead to aberrant protein production can result from the uncoupled movement of the trna in either the 5' or 3' direction on mrna. here, we report the biochemical and structural characterization of +1 frameshift suppressor trna(sufj), a trna known to decode four, instead of three, nucleotides. frameshift suppressor trna(sufj) contains an insertion 5' to its ... | 2014 | 25352689 |
| protein acetylation affects acetate metabolism, motility and acid stress response in escherichia coli. | although protein acetylation is widely observed, it has been associated with few specific regulatory functions making it poorly understood. to interrogate its functionality, we analyzed the acetylome in escherichia coli knockout mutants of cobb, the only known sirtuin-like deacetylase, and patz, the best-known protein acetyltransferase. for four growth conditions, more than 2,000 unique acetylated peptides, belonging to 809 proteins, were identified and differentially quantified. nearly 65% of t ... | 2014 | 25518064 |
| double-sieving-defective aminoacyl-trna synthetase causes protein mistranslation and affects cellular physiology and development. | aminoacyl-trna synthetases (aarss) constitute a family of ubiquitously expressed essential enzymes that ligate amino acids to their cognate trnas for protein synthesis. recently, aars mutations have been linked to various human diseases; however, how these mutations lead to diseases has remained unclear. in order to address the importance of aminoacylation fidelity in multicellular organisms, we generated an amino-acid double-sieving model in drosophila melanogaster using phenylalanyl-trna synth ... | 2014 | 25427601 |
| structure and transport mechanism of the sodium/proton antiporter mjnhap1. | sodium/proton antiporters are essential for sodium and ph homeostasis and play a major role in human health and disease. we determined the structures of the archaeal sodium/proton antiporter mjnhap1 in two complementary states. the inward-open state was obtained by x-ray crystallography in the presence of sodium at ph 8, where the transporter is highly active. the outward-open state was obtained by electron crystallography without sodium at ph 4, where mjnhap1 is inactive. comparison of both str ... | 2014 | 25426803 |
| structure and substrate ion binding in the sodium/proton antiporter panhap. | sodium/proton antiporters maintain intracellular ph and sodium levels. detailed structures of antiporters with bound substrate ions are essential for understanding how they work. we have resolved the substrate ion in the dimeric, electroneutral sodium/proton antiporter panhap from pyrococcus abyssi at 3.2 å, and have determined its structure in two different conformations at ph 8 and ph 4. the ion is coordinated by three acidic sidechains, a water molecule, a serine and a main-chain carbonyl in ... | 2014 | 25426802 |
| structural principles of crispr rna processing. | the cas6 superfamily, the cas5d subclass, and the host rnase iii endoribonucleases are responsible for producing small rnas (crrna) that function in the crispr-cas immunity. the three enzymes may also interact with the crrna-associated nucleic acid interference complexes. recent development in structural biology of cas6 and cas5d and their complexes with rna substrates has lent new insights on principles of crrna processing and the structural basis for linking crrna processing to interference. b ... | 2014 | 25435327 |
| structural principles of crispr rna processing. | the cas6 superfamily, the cas5d subclass, and the host rnase iii endoribonucleases are responsible for producing small rnas (crrna) that function in the crispr-cas immunity. the three enzymes may also interact with the crrna-associated nucleic acid interference complexes. recent development in structural biology of cas6 and cas5d and their complexes with rna substrates has lent new insights on principles of crrna processing and the structural basis for linking crrna processing to interference. b ... | 2014 | 25435327 |
| structure of putrescine aminotransferase from escherichia coli provides insights into the substrate specificity among class iii aminotransferases. | ygjg is a putrescine aminotransferase enzyme that transfers amino groups from compounds with terminal primary amines to compounds with an aldehyde group using pyridoxal-5'-phosphate (plp) as a cofactor. previous biochemical data show that the enzyme prefers primary diamines, such as putrescine, over ornithine as a substrate. to better understand the enzyme's substrate specificity, crystal structures of ygjg from escherichia coli were determined at 2.3 and 2.1 å resolutions for the free and putre ... | 2014 | 25423189 |
| tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by nmr, saxs, chemical crosslinking, and functional studies. | proteins containing iron-sulfur (fe-s) clusters arose early in evolution and are essential to life. organisms have evolved machinery consisting of specialized proteins that operate together to assemble fe-s clusters efficiently so as to minimize cellular exposure to their toxic constituents: iron and sulfide ions. to date, the best studied system is the iron-sulfur cluster (isc) operon of escherichia coli, and the eight isc proteins it encodes. our investigations over the past five years have id ... | 2014 | 25450980 |
| tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by nmr, saxs, chemical crosslinking, and functional studies. | proteins containing iron-sulfur (fe-s) clusters arose early in evolution and are essential to life. organisms have evolved machinery consisting of specialized proteins that operate together to assemble fe-s clusters efficiently so as to minimize cellular exposure to their toxic constituents: iron and sulfide ions. to date, the best studied system is the iron-sulfur cluster (isc) operon of escherichia coli, and the eight isc proteins it encodes. our investigations over the past five years have id ... | 2014 | 25450980 |
| recq helicase and recj nuclease provide complementary functions to resect dna for homologous recombination. | recombinational dna repair by the recf pathway of escherichia coli requires the coordinated activities of reca, recfor, recq, recj, and single-strand dna binding (ssb) proteins. these proteins facilitate formation of homologously paired joint molecules between linear double-stranded (dsdna) and supercoiled dna. repair starts with resection of the broken dsdna by recq, a 3'→5' helicase, recj, a 5'→3' exonuclease, and ssb protein. the ends of a dsdna break can be blunt-ended, or they may possess e ... | 2014 | 25411316 |
| argonaute piwi domain and microrna duplex structure regulate small rna sorting in arabidopsis. | small rnas (srnas) are loaded into argonaute (ago) proteins to induce gene silencing. in plants, the 5'-terminal nucleotide is important for srna sorting into different agos. here we show that microrna (mirna) duplex structure also contributes to mirna sorting. base pairing at the 15th nucleotide of a mirna duplex is important for mirna sorting in both arabidopsis ago1 and ago2. ago2 favours mirna duplexes with no middle mismatches, whereas ago1 tolerates, or prefers, duplexes with central misma ... | 2014 | 25406978 |
| structural and functional characterization of a ketosteroid transcriptional regulator of mycobacterium tuberculosis. | catabolism of host cholesterol is critical to the virulence of mycobacterium tuberculosis and is a potential target for novel therapeutics. kstr2, a tetr family repressor (tfr), regulates the expression of 15 genes encoding enzymes that catabolize the last half of the cholesterol molecule, represented by 3aα-h-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indane-dione (hip). binding of kstr2 to its operator sequences is relieved upon binding of hip-coa. a 1.6-å resolution crystal structure of the ks ... | 2014 | 25406313 |
| structural and functional characterization of a ketosteroid transcriptional regulator of mycobacterium tuberculosis. | catabolism of host cholesterol is critical to the virulence of mycobacterium tuberculosis and is a potential target for novel therapeutics. kstr2, a tetr family repressor (tfr), regulates the expression of 15 genes encoding enzymes that catabolize the last half of the cholesterol molecule, represented by 3aα-h-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indane-dione (hip). binding of kstr2 to its operator sequences is relieved upon binding of hip-coa. a 1.6-å resolution crystal structure of the ks ... | 2014 | 25406313 |
| movement of elongation factor g between compact and extended conformations. | previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor g (ef-g). here, we follow the movement of domain iv of ef-g relative to domain ii of ef-g using ensemble and single-molecule förster resonance energy transfer. our results indicate that ribosome-free ef-g predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain iv moves away f ... | 2014 | 25463439 |
| movement of elongation factor g between compact and extended conformations. | previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor g (ef-g). here, we follow the movement of domain iv of ef-g relative to domain ii of ef-g using ensemble and single-molecule förster resonance energy transfer. our results indicate that ribosome-free ef-g predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain iv moves away f ... | 2014 | 25463439 |
| viruses of haloarchaea. | in hypersaline environments, haloarchaea (halophilic members of the archaea) are the dominant organisms, and the viruses that infect them, haloarchaeoviruses are at least ten times more abundant. since their discovery in 1974, described haloarchaeoviruses include head-tailed, pleomorphic, spherical and spindle-shaped morphologies, representing myoviridae, siphoviridae, podoviridae, pleolipoviridae, sphaerolipoviridae and fuselloviridae families. this review overviews current knowledge of haloarc ... | 2014 | 25402735 |
| phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response. | organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. to improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersa ... | 2014 | 25393412 |
| structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the lysz·lysw complex from thermus thermophilus. | in the biosynthesis of lysine by thermus thermophilus, the metabolite α-ketoglutarate is converted to the intermediate α-aminoadipate (aaa), which is protected by the 54-amino acid acidic protein lysw. in this study, we determined the crystal structure of lysz from t. thermophilus (ttlysz), an amino acid kinase that catalyzes the second step in the aaa to lysine conversion, which was in a complex with lysw at a resolution of 1.85 å. a crystal analysis coupled with isothermal titration calorimetr ... | 2014 | 25392000 |
| structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the lysz·lysw complex from thermus thermophilus. | in the biosynthesis of lysine by thermus thermophilus, the metabolite α-ketoglutarate is converted to the intermediate α-aminoadipate (aaa), which is protected by the 54-amino acid acidic protein lysw. in this study, we determined the crystal structure of lysz from t. thermophilus (ttlysz), an amino acid kinase that catalyzes the second step in the aaa to lysine conversion, which was in a complex with lysw at a resolution of 1.85 å. a crystal analysis coupled with isothermal titration calorimetr ... | 2014 | 25392000 |
| cecafdb: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13c-fluxomics. | the central carbon metabolic flux database (cecafdb, available at http://www.cecafdb.org) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. it encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information ... | 2014 | 25392417 |
| cecafdb: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13c-fluxomics. | the central carbon metabolic flux database (cecafdb, available at http://www.cecafdb.org) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. it encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information ... | 2014 | 25392417 |
| thermodynamic system drift in protein evolution. | proteins from thermophiles are generally more thermostable than their mesophilic homologs, but little is known about the evolutionary process driving these differences. here we attempt to understand how the diverse thermostabilities of bacterial ribonuclease h1 (rnh) proteins evolved. rnh proteins from thermus thermophilus (ttrnh) and escherichia coli (ecrnh) share similar structures but differ in melting temperature (t(m)) by 20 °c. ttrnh's greater stability is caused in part by the presence of ... | 2014 | 25386647 |
| interacting cytoplasmic loops of subunits a and c of escherichia coli f1f0 atp synthase gate h+ transport to the cytoplasm. | h(+)-transporting f1f0 atp synthase catalyzes the synthesis of atp via coupled rotary motors within f0 and f1. h(+) transport at the subunit a-c interface in transmembranous f0 drives rotation of a cylindrical c10 oligomer within the membrane, which is coupled to rotation of subunit γ within the α3β3 sector of f1 to mechanically drive atp synthesis. f1f0 functions in a reversible manner, with atp hydrolysis driving h(+) transport. atp-driven h(+) transport in a select group of cysteine mutants i ... | 2014 | 25385585 |
| phenotyping the quality of complex medium components by simple online-monitored shake flask experiments. | media containing yeast extracts and other complex raw materials are widely used for the cultivation of microorganisms. however, variations in the specific nutrient composition can occur, due to differences in the complex raw material ingredients and in the production of these components. these lot-to-lot variations can affect growth rate, product yield and product quality in laboratory investigations and biopharmaceutical production processes. in the fda's process analytical technology (pat) ini ... | 2014 | 25376163 |
| the σ enigma: bacterial σ factors, archaeal tfb and eukaryotic tfiib are homologs. | structural comparisons of initiating rna polymerase complexes and structure-based amino acid sequence alignments of general transcription initiation factors (eukaryotic tfiib, archaeal tfb and bacterial σ factors) show that these proteins are homologs. tfiib and tfb each have two-five-helix cyclin-like repeats (clrs) that include a c-terminal helix-turn-helix (hth) motif (clr/hth domains). four homologous hth motifs are present in bacterial σ factors that are relics of clr/hth domains. sequence ... | 2014 | 25483602 |
| rna targeting by the type iii-a crispr-cas csm complex of thermus thermophilus. | crispr-cas is a prokaryotic adaptive immune system that provides sequence-specific defense against foreign nucleic acids. here we report the structure and function of the effector complex of the type iii-a crispr-cas system of thermus thermophilus: the csm complex (ttcsm). ttcsm is composed of five different protein subunits (csm1-csm5) with an uneven stoichiometry and a single crrna of variable size (35-53 nt). the ttcsm crrna content is similar to the type iii-b cmr complex, indicating that cr ... | 2014 | 25457165 |
| silencing by h-ns potentiated the evolution of salmonella. | the bacterial h-ns protein silences expression from sequences with higher at-content than the host genome and is believed to buffer the fitness consequences associated with foreign gene acquisition. loss of h-ns results in severe growth defects in salmonella, but the underlying reasons were unclear. an experimental evolution approach was employed to determine which secondary mutations could compensate for the loss of h-ns in salmonella. six independently derived s. typhimurium hns mutant strains ... | 2014 | 25375226 |
| multilayered polyelectrolyte microcapsules: interaction with the enzyme cytochrome c oxidase. | cell-sized polyelectrolyte capsules functionalized with a redox-driven proton pump protein were assembled for the first time. the interaction of polyelectrolyte microcapsules, fabricated by electrostatic layer-by-layer assembly, with cytochrome c oxidase molecules was investigated. we found that the cytochrome c oxidase retained its functionality, that the functionalized microcapsules interacting with cytochrome c oxidase were permeable and that the permeability characteristics of the microcapsu ... | 2014 | 25372607 |
| diversity and regulation of atp sulfurylase in photosynthetic organisms. | atp sulfurylase (atps) catalyzes the first committed step in the sulfate assimilation pathway, the activation of sulfate prior to its reduction. atps has been studied in only a few model organisms and even in these cases to a much smaller extent than the sulfate reduction and cysteine synthesis enzymes. this is possibly because the latter were considered of greater regulatory importance for sulfate assimilation. recent evidences (reported in this paper) challenge this view and suggest that atps ... | 2014 | 25414712 |
| studying the active-site loop movement of the são paolo metallo-β-lactamase-1†electronic supplementary information (esi) available: procedures for protein expression and purification, (19)f-labelling, crystallisation, data collection, and structure determination, table of crystallographic data, table of crystallographic parameters and refinement statistics, figures showing binding mode and distances, procedures for mass spectrometry measurements, differential scanning fluorimetry measurements, stopped-flow measurements and other kinetics measurements. see doi: 10.1039/c4sc01752hclick here for additional data file. | metallo-β-lactamases (mbls) catalyse the hydrolysis of almost all β-lactam antibiotics. we report biophysical and kinetic studies on the são paulo mbl (spm-1), which reveal its zn(ii) ion usage and mechanism as characteristic of the clinically important di-zn(ii) dependent b1 mbl subfamily. biophysical analyses employing crystallography, dynamic (19)f nmr and ion mobility mass spectrometry, however, reveal that spm-1 possesses loop and mobile element regions characteristic of the b2 mbls. these ... | 2014 | 25717359 |
| studying the active-site loop movement of the são paolo metallo-β-lactamase-1†electronic supplementary information (esi) available: procedures for protein expression and purification, (19)f-labelling, crystallisation, data collection, and structure determination, table of crystallographic data, table of crystallographic parameters and refinement statistics, figures showing binding mode and distances, procedures for mass spectrometry measurements, differential scanning fluorimetry measurements, stopped-flow measurements and other kinetics measurements. see doi: 10.1039/c4sc01752hclick here for additional data file. | metallo-β-lactamases (mbls) catalyse the hydrolysis of almost all β-lactam antibiotics. we report biophysical and kinetic studies on the são paulo mbl (spm-1), which reveal its zn(ii) ion usage and mechanism as characteristic of the clinically important di-zn(ii) dependent b1 mbl subfamily. biophysical analyses employing crystallography, dynamic (19)f nmr and ion mobility mass spectrometry, however, reveal that spm-1 possesses loop and mobile element regions characteristic of the b2 mbls. these ... | 2014 | 25717359 |
| structural basis for ion selectivity revealed by high-resolution crystal structure of mg2+ channel mgte. | magnesium is the most abundant divalent cation in living cells and is crucial to several biological processes. mgte is a mg(2+) channel distributed in all domains of life that contributes to the maintenance of cellular mg(2+) homeostasis. here we report the high-resolution crystal structures of the transmembrane domain of mgte, bound to mg(2+), mn(2+) and ca(2+). the high-resolution mg(2+)-bound crystal structure clearly visualized the hydrated mg(2+) ion within its selectivity filter. based on ... | 2014 | 25367295 |
| proton transfer in the k-channel analog of b-type cytochrome c oxidase from thermus thermophilus. | a key enzyme in aerobic metabolism is cytochrome c oxidase (cco), which catalyzes the reduction of molecular oxygen to water in the mitochondrial and bacterial membranes. substrate electrons and protons are taken up from different sides of the membrane and protons are pumped across the membrane, thereby generating an electrochemical gradient. the well-studied a-type cco uses two different entry channels for protons: the d-channel for all pumped and two consumed protons, and the k-channel for the ... | 2014 | 25418102 |
| molecular insights into dna interference by crispr-associated nuclease-helicase cas3. | mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (crisprs) and crispr-associated (cas) proteins. type i crispr-cas systems use a "cascade" ribonucleoprotein complex to guide rna specifically to complementary sequence in invader double-stranded dna (dsdna), a process called "interference." after target recognition by cascade, formation of an r-loop triggers recruitment of a cas3 nuclease-helicase, completing the int ... | 2014 | 25368186 |
| subnanometre-resolution electron cryomicroscopy structure of a heterodimeric abc exporter. | atp-binding cassette (abc) transporters translocate substrates across cell membranes, using energy harnessed from atp binding and hydrolysis at their nucleotide-binding domains. abc exporters are present both in prokaryotes and eukaryotes, with examples implicated in multidrug resistance of pathogens and cancer cells, as well as in many human diseases. tmrab is a heterodimeric abc exporter from the thermophilic gram-negative eubacterium thermus thermophilus; it is homologous to various multidrug ... | 2014 | 25363761 |
| subnanometre-resolution electron cryomicroscopy structure of a heterodimeric abc exporter. | atp-binding cassette (abc) transporters translocate substrates across cell membranes, using energy harnessed from atp binding and hydrolysis at their nucleotide-binding domains. abc exporters are present both in prokaryotes and eukaryotes, with examples implicated in multidrug resistance of pathogens and cancer cells, as well as in many human diseases. tmrab is a heterodimeric abc exporter from the thermophilic gram-negative eubacterium thermus thermophilus; it is homologous to various multidrug ... | 2014 | 25363761 |
| defect in the formation of 70s ribosomes caused by lack of ribosomal protein l34 can be suppressed by magnesium. | to elucidate the biological functions of the ribosomal protein l34, which is encoded by the rpmh gene, the rpmh deletion mutant of bacillus subtilis and two suppressor mutants were characterized. although the δrpmh mutant exhibited a severe slow-growth phenotype, additional mutations in the yhdp or mgte gene restored the growth rate of the δrpmh strain. either the disruption of yhdp, which is thought to be involved in the efflux of mg(2+), or overexpression of mgte, which plays a major role in t ... | 2014 | 25182490 |
| phenotypic interactions among mutations in a thermus thermophilus 16s rrna gene detected with genetic selections and experimental evolution. | during protein synthesis, the ribosome undergoes conformational transitions between functional states, requiring communication between distant structural elements of the ribosome. despite advances in ribosome structural biology, identifying the protein and rrna residues governing these transitions remains a significant challenge. such residues can potentially be identified genetically, given the predicted deleterious effects of mutations stabilizing the ribosome in discrete conformations and the ... | 2014 | 25157075 |
| dissection of the region of pseudomonas aeruginosa para that is important for dimerization and interactions with its partner parb. | pseudomonas aeruginosa para belongs to a large subfamily of walker-type atpases acting as partitioning proteins in bacteria. para has the ability to both self-associate and interact with its partner parb. analysis of the deletion mutants defined the part of the protein involved in dimerization and interactions with parb. here, a set of para alanine substitution mutants in the region between e67 and l85 was created and analysed in vivo and in vitro. all mutants impaired in dimerization (substitut ... | 2014 | 25139949 |
| target rna capture and cleavage by the cmr type iii-b crispr-cas effector complex. | the effector complex of the cmr/type iii-b crispr (clustered regularly interspaced short palindromic repeat)-cas (crispr-associated) system cleaves rnas recognized by the crispr rna (crrna) of the complex and includes six protein subunits of unknown functions. using reconstituted pyrococcus furiosus cmr complexes, we found that each of the six cmr proteins plays a critical role in either crrna interaction or target rna capture. cmr2, cmr3, cmr4, and cmr5 are all required for formation of a crrna ... | 2014 | 25367038 |
| rejection of tmrna·smpb after gtp hydrolysis by ef-tu on ribosomes stalled on intact mrna. | messenger rnas lacking a stop codon trap ribosomes at their 3' ends, depleting the pool of ribosomes available for protein synthesis. in bacteria, a remarkable quality control system rescues and recycles stalled ribosomes in a process known as trans-translation. acting as a trna, transfer-messenger rna (tmrna) is aminoacylated, delivered by ef-tu to the ribosomal a site, and accepts the nascent polypeptide. translation then resumes on a reading frame within tmrna, encoding a short peptide tag th ... | 2014 | 25246654 |
| structure and mechanism of e. coli rna 2',3'-cyclic phosphodiesterase. | 2h (two-histidine) phosphoesterase enzymes are distributed widely in all domains of life and are implicated in diverse rna and nucleotide transactions, including the transesterification and hydrolysis of cyclic phosphates. here we report a biochemical and structural characterization of the escherichia coli 2h protein yapd yadp [corrected], which was identified originally as a reversible transesterifying "nuclease/ligase" at rna 2',5'-phosphodiesters. we find that yapd yadp [corrected] is an "end ... | 2014 | 25239919 |
| rna. complete pairing not needed. | 2014 | 25359948 | |
| interplay between e. coli dnak, clpb and grpe during protein disaggregation. | the dnak/hsp70 chaperone system and clpb/hsp104 collaboratively disaggregate protein aggregates and reactivate inactive proteins. the teamwork is specific: escherichia coli dnak interacts with e. coli clpb and yeast hsp70, ssa1, interacts with yeast hsp104. this interaction is between the middle domains of hexameric clpb/hsp104 and the dnak/hsp70 nucleotide-binding domain (nbd). to identify the site on e. coli dnak that interacts with clpb, we substituted amino acid residues throughout the dnak ... | 2014 | 25451597 |
| interplay between e. coli dnak, clpb and grpe during protein disaggregation. | the dnak/hsp70 chaperone system and clpb/hsp104 collaboratively disaggregate protein aggregates and reactivate inactive proteins. the teamwork is specific: escherichia coli dnak interacts with e. coli clpb and yeast hsp70, ssa1, interacts with yeast hsp104. this interaction is between the middle domains of hexameric clpb/hsp104 and the dnak/hsp70 nucleotide-binding domain (nbd). to identify the site on e. coli dnak that interacts with clpb, we substituted amino acid residues throughout the dnak ... | 2014 | 25451597 |
| arfa recognizes the lack of mrna in the mrna channel after rf2 binding for ribosome rescue. | although trans-translation mediated by tmrna-smpb has long been known as the sole system to relieve bacterial stalled ribosomes, arfa has recently been identified as an alternative factor for ribosome rescue in escherichia coli. this process requires hydrolysis of nascent peptidyl-trna by rf2, which usually acts as a stop codon-specific peptide release factor. it poses a fascinating question of how arfa and rf2 recognize and rescue the stalled ribosome. here, we mapped the location of arfa in th ... | 2014 | 25355516 |
| the mechanism of torsin atpase activation. | torsins are membrane-associated atpases whose activity is dependent on two activating cofactors, lamina-associated polypeptide 1 (lap1) and luminal domain-like lap1 (lull1). the mechanism by which these cofactors regulate torsin activity has so far remained elusive. in this study, we identify a conserved domain in these activators that is predicted to adopt a fold resembling an aaa+ (atpase associated with a variety of cellular activities) domain. within these domains, a strictly conserved arg r ... | 2014 | 25352667 |
| structure of type ii dehydroquinase from pseudomonas aeruginosa. | pseudomonas aeruginosa causes opportunistic infections and is resistant to most antibiotics. ongoing efforts to generate much-needed new antibiotics include targeting enzymes that are vital for p. aeruginosa but are absent in mammals. one such enzyme, type ii dehydroquinase (dhqase), catalyzes the interconversion of 3-dehydroquinate and 3-dehydroshikimate, a necessary step in the shikimate pathway. this step is vital for the proper synthesis of phenylalanine, tryptophan, tyrosine and other aroma ... | 2014 | 25372814 |
| temperature-dependent radiation sensitivity and order of 70s ribosome crystals. | all evidence to date indicates that at t = 100 k all protein crystals exhibit comparable sensitivity to x-ray damage when quantified using global metrics such as change in scaling b factor or integrated intensity versus dose. this is consistent with observations in cryo-electron microscopy, and results because nearly all diffusive motions of protein and solvent, including motions induced by radiation damage, are frozen out. but how do the sensitivities of different proteins compare at room tempe ... | 2014 | 25372680 |
| trigger-helix folding pathway and si3 mediate catalysis and hairpin-stabilized pausing by escherichia coli rna polymerase. | the conformational dynamics of the polymorphous trigger loop (tl) in rna polymerase (rnap) underlie multiple steps in the nucleotide addition cycle and diverse regulatory mechanisms. these mechanisms include nascent rna hairpin-stabilized pausing, which inhibits tl folding into the trigger helices (th) required for rapid nucleotide addition. the nascent rna pause hairpin forms in the rna exit channel and promotes opening of the rnap clamp domain, which in turn stabilizes a partially folded, paus ... | 2014 | 25336618 |
| noncanonical cell-to-cell dna transfer in thermus spp. is insensitive to argonaute-mediated interference. | horizontal gene transfer drives the rapid evolution of bacterial populations. classical processes that promote the lateral flow of genetic information are conserved throughout the prokaryotic world. however, some species have nonconserved transfer mechanisms that are not well known. this is the case for the ancient extreme thermophile thermus thermophilus. in this work, we show that t. thermophilus strains are capable of exchanging large dna fragments by a novel mechanism that requires cell-to-c ... | 2014 | 25331432 |
| noncanonical cell-to-cell dna transfer in thermus spp. is insensitive to argonaute-mediated interference. | horizontal gene transfer drives the rapid evolution of bacterial populations. classical processes that promote the lateral flow of genetic information are conserved throughout the prokaryotic world. however, some species have nonconserved transfer mechanisms that are not well known. this is the case for the ancient extreme thermophile thermus thermophilus. in this work, we show that t. thermophilus strains are capable of exchanging large dna fragments by a novel mechanism that requires cell-to-c ... | 2014 | 25331432 |
| rna-protein distance patterns in ribosomes reveal the mechanism of translational attenuation. | elucidating protein translational regulation is crucial for understanding cellular function and drug development. a key molecule in protein translation is ribosome, which is a super-molecular complex extensively studied for more than a half century. the structure and dynamics of ribosome complexes were resolved recently thanks to the development of x-ray crystallography, cryo-em, and single molecule biophysics. current studies of the ribosome have shown multiple functional states, each with a un ... | 2014 | 25326828 |
| molecular dynamics simulations of the nip7 proteins from the marine deep- and shallow-water pyrococcus species. | the identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. we performed molecular dynamics (md) simulations of the nip7 protein involved in rna processing from the shallow-water (p. furiosus) and the deep-water (p. abyssi) marine hyperthermophylic archaea at different temperatures (300 and 373 k) and pressures (0.1, 50 and 100 mpa). the aim was to disclose similarities and differences between the deep- ... | 2014 | 25315147 |
| translation initiation factor 3 regulates switching between different modes of ribosomal subunit joining. | ribosomal subunit joining is a key checkpoint in the bacterial translation initiation pathway during which initiation factors (ifs) regulate association of the 30s initiation complex (ic) with the 50s subunit to control formation of a 70s ic that can enter into the elongation stage of protein synthesis. the gtp-bound form of if2 accelerates subunit joining, whereas if3 antagonizes subunit joining and plays a prominent role in maintaining translation initiation fidelity. the molecular mechanisms ... | 2014 | 25308340 |
| translation initiation factor 3 regulates switching between different modes of ribosomal subunit joining. | ribosomal subunit joining is a key checkpoint in the bacterial translation initiation pathway during which initiation factors (ifs) regulate association of the 30s initiation complex (ic) with the 50s subunit to control formation of a 70s ic that can enter into the elongation stage of protein synthesis. the gtp-bound form of if2 accelerates subunit joining, whereas if3 antagonizes subunit joining and plays a prominent role in maintaining translation initiation fidelity. the molecular mechanisms ... | 2014 | 25308340 |
| structure and mechanism of the bifunctional cina enzyme from thermus thermophilus. | cina is a widely distributed protein in gram-positive and gram-negative bacteria. it is associated with natural competence and is proposed to have a function as an enzyme participating in the pyridine nucleotide cycle, which recycles products formed by non-redox uses of nad. here we report the determination of the crystal structure of cina from thermus thermophilus, in complex with several ligands. cina was shown to have both nicotinamide mononucleotide deamidase and adp-ribose pyrophosphatase a ... | 2014 | 25313401 |
| chemical probing of rna with the hydroxyl radical at single-atom resolution. | while hydroxyl radical cleavage is widely used to map rna tertiary structure, lack of mechanistic understanding of strand break formation limits the degree of structural insight that can be obtained from this experiment. here, we determine how individual ribose hydrogens of sarcin/ricin loop rna participate in strand cleavage. we find that substituting deuterium for hydrogen at a ribose 5'-carbon produces a kinetic isotope effect on cleavage; the major cleavage product is an rna strand terminate ... | 2014 | 25313156 |
| structural characterization of the putative abc-type 2 transporter from thermotoga maritima msb8. | this study describes the structure of the putative abc-type 2 transporter tm0543 from thermotoga maritima msb8 determined at a resolution of 2.3 å. in comparative sequence-clustering analysis, tm0543 displays similarity to natab-like proteins, which are components of the abc-type na(+) efflux pump permease. however, the overall structure fold of the predicted nucleotide-binding domain reveals that it is different from any known structure of abc-type efflux transporters solved to date. the struct ... | 2014 | 25306867 |
| negamycin interferes with decoding and translocation by simultaneous interaction with rrna and trna. | negamycin (neg) is a ribosome-targeting antibiotic that exhibits clinically promising activity. its binding site and mode of action have remained unknown. we solved the structure of the thermus thermophilus ribosome bound to mrna and three trnas, in complex with neg. the drug binds to both small and large ribosomal subunits at nine independent sites. resistance mutations in the 16s rrna unequivocally identified the binding site in the vicinity of the conserved helix 34 (h34) in the small subunit ... | 2014 | 25306922 |
| amicoumacin a inhibits translation by stabilizing mrna interaction with the ribosome. | we demonstrate that the antibiotic amicoumacin a (ami) is a potent inhibitor of protein synthesis. resistance mutations in helix 24 of the 16s rrna mapped the ami binding site to the small ribosomal subunit. the crystal structure of bacterial ribosome in complex with ami solved at 2.4 å resolution revealed that the antibiotic makes contacts with universally conserved nucleotides of 16s rrna in the e site and the mrna backbone. simultaneous interactions of ami with 16s rrna and mrna and the in vi ... | 2014 | 25306919 |
| versatility of acyl-acyl carrier protein synthetases. | the acyl carrier protein (acp) requires posttranslational modification with a 4'-phosphopantetheine arm for activity, and this thiol-terminated modification carries cargo between enzymes in acp-dependent metabolic pathways. we show that acyl-acp synthetases (aasss) from different organisms are able to load even, odd, and unnatural fatty acids onto e. coli acp in vitro. vibrio harveyi aass not only shows promiscuity for the acid substrate, but also is active upon various alternate carrier protein ... | 2014 | 25308274 |
| structure of the large ribosomal subunit from human mitochondria. | human mitochondrial ribosomes are highly divergent from all other known ribosomes and are specialized to exclusively translate membrane proteins. they are linked with hereditary mitochondrial diseases and are often the unintended targets of various clinically useful antibiotics. using single-particle cryogenic electron microscopy, we have determined the structure of its large subunit to 3.4 angstrom resolution, revealing 48 proteins, 21 of which are specific to mitochondria. the structure unveil ... | 2014 | 25278503 |
| the k-turn motif in riboswitches and other rna species. | the kink turn is a widespread structure motif that introduces a tight bend into the axis of duplex rna. this generally functions to mediate tertiary interactions, and to serve as a specific protein binding site. k-turns or closely related structures are found in at least seven different riboswitch structures, where they function as key architectural elements that help generate the ligand binding pocket. this article is part of a special issue entitled: riboswitches. | 2014 | 24798078 |
| overview of cell-free protein synthesis: historic landmarks, commercial systems, and expanding applications. | during the early days of molecular biology, cell-free protein synthesis played an essential role in deciphering the genetic code and contributed to our understanding of translation of protein from messenger rna. owing to several decades of major and incremental improvements, modern cell-free systems have achieved higher protein synthesis yields at lower production costs. commercial cell-free systems are now available from a variety of material sources, ranging from "traditional" e. coli, rabbit ... | 2014 | 25271714 |
| in vivo tmrna protection by smpb and pre-ribosome binding conformation in solution. | tmrna is an abundant rna in bacteria with trna and mrna features. it is specialized in trans-translation, a translation rescuing system. we demonstrate that its partner protein smpb binds the trna-like region (tld) in vivo and chaperones the fold of the tld-h2 region. we use an original approach combining the observation of tmrna degradation pathways in a heterologous system, the analysis of the tmrna digests by ms and nmr, and co-overproduction assays of tmrna and smpb. we study the conformatio ... | 2014 | 25135523 |
| the bioconversion of red ginseng ethanol extract into compound k by saccharomyces cerevisiae hj-014. | a β-glucosidase producing yeast strain was isolated from korean traditional rice wine. based on the sequence of the ycl008c gene and analysis of the fatty acid composition, the isolate was identified as saccharomyces cerevisiae strain hj-014. s. cerevisiae hj-014 produced ginsenoside rd, f2, and compound k from the ethanol extract of red ginseng. the production was increased by shaking culture, where the bioconversion efficiency was increased 2-fold compared to standing culture. the production o ... | 2014 | 25346602 |
| identification and evaluation of improved 4'-o-(alkyl) 4,5-disubstituted 2-deoxystreptamines as next-generation aminoglycoside antibiotics. | the emerging epidemic of drug resistance places the development of efficacious and safe antibiotics in the spotlight of current research. here, we report the design of next-generation aminoglycosides. discovery efforts were driven by rational synthesis focusing on 4' alkylations of the aminoglycoside paromomycin, with the goal to alleviate the most severe and disabling side effect of aminoglycosides-irreversible hearing loss. compounds were evaluated for target activity in in vitro ribosomal tra ... | 2014 | 25271289 |
| speciation and reactivity of uranium products formed during in situ bioremediation in a shallow alluvial aquifer. | in this study, we report the results of in situ u(vi) bioreduction experiments at the integrated field research challenge site in rifle, colorado, usa. columns filled with sediments were deployed into a groundwater well at the site and, after a period of conditioning with groundwater, were amended with a mixture of groundwater, soluble u(vi), and acetate to stimulate the growth of indigenous microorganisms. individual reactors were collected as various redox regimes in the column sediments were ... | 2014 | 25265543 |
| sequence co-evolution gives 3d contacts and structures of protein complexes. | protein-protein interactions are fundamental to many biological processes. experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3d protein complexes. an alternative rich source of information about protein interactions is the evolutionary sequence record. building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in spac ... | 2014 | 25255213 |
| torque generation of enterococcus hirae v-atpase. | v-atpase (v(o)v1) converts the chemical free energy of atp into an ion-motive force across the cell membrane via mechanical rotation. this energy conversion requires proper interactions between the rotor and stator in v(o)v1 for tight coupling among chemical reaction, torque generation, and ion transport. we developed an escherichia coli expression system for enterococcus hirae v(o)v1 (ehv(o)v1) and established a single-molecule rotation assay to measure the torque generated. recombinant and nat ... | 2014 | 25258315 |
| evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule. | the molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. however, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. escherichia coli rnase h is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. we investigated this hypoth ... | 2014 | 25258414 |
| analysis of genomic rearrangements, horizontal gene transfer and role of plasmids in the evolution of industrial important thermus species. | bacteria of genus thermus inhabit both man-made and natural thermal environments. several thermus species have shown biotechnological potential such as reduction of heavy metals which is essential for eradication of heavy metal pollution; removing of organic contaminants in water; opening clogged pipes, controlling global warming among many others. enzymes from thermophilic bacteria have exhibited higher activity and stability than synthetic or enzymes from mesophilic organisms. | 2014 | 25257245 |
| inactivation and unfolding of protein tyrosine phosphatase from thermus thermophilus hb27 during urea and guanidine hydrochloride denaturation. | the effects of urea and guanidine hydrochloride (gdnhcl) on the activity, conformation and unfolding process of protein tyrosine phosphatase (ptpase), a thermostable low molecular weight protein from thermus thermophilus hb27, have been studied. enzymatic activity assays showed both urea and gdnhcl resulted in the inactivation of ptpase in a concentration and time-dependent manner. inactivation kinetics analysis suggested that the inactivation of ptpase induced by urea and gdnhcl were both monop ... | 2014 | 25255086 |
| trans-acting arginine residues in the aaa+ chaperone clpb allosterically regulate the activity through inter- and intradomain communication. | the molecular chaperone clpb/hsp104, a member of the aaa+ superfamily (atpases associated with various cellular activities), rescues proteins from the aggregated state in collaboration with the dnak/hsp70 chaperone system. clpb/hsp104 forms a hexameric, ring-shaped complex that functions as a tightly regulated, atp-powered molecular disaggregation machine. highly conserved and essential arginine residues, often called arginine fingers, are located at the subunit interfaces of the complex, which ... | 2014 | 25253689 |
| ribosome-induced tuning of gtp hydrolysis by a translational gtpase. | gtp hydrolysis by elongation factor tu (ef-tu), a translational gtpase that delivers aminoacyl-trnas to the ribosome, plays a crucial role in decoding and translational fidelity. the basic reaction mechanism and the way the ribosome contributes to catalysis are a matter of debate. here we use mutational analysis in combination with measurements of rate/ph profiles, kinetic solvent isotope effects, and ion dependence of gtp hydrolysis by ef-tu off and on the ribosome to dissect the reaction mecha ... | 2014 | 25246550 |
| severe mgadp inhibition of bacillus subtilis f1-atpase is not due to the absence of nucleotide binding to the noncatalytic nucleotide binding sites. | f1-atpase from bacillus subtilis (bf1) is severely suppressed by the mgadp inhibition. here, we have tested if this is due to the loss of nucleotide binding to the noncatalytic site that is required for the activation. measurements with a tryptophan mutant of bf1 indicated that the noncatalytic sites could bind atp normally. furthermore, the mutant bf1 that cannot bind atp to the noncatalytic sites showed much lower atpase activity. it was concluded that the cause of strong mgadp inhibition of b ... | 2014 | 25244289 |
| iron-sulfur cluster biogenesis in mammalian cells: new insights into the molecular mechanisms of cluster delivery. | iron-sulfur (fe-s) clusters are ancient, ubiquitous cofactors composed of iron and inorganic sulfur. the combination of the chemical reactivity of iron and sulfur, together with many variations of cluster composition, oxidation states and protein environments, enables fe-s clusters to participate in numerous biological processes. fe-s clusters are essential to redox catalysis in nitrogen fixation, mitochondrial respiration and photosynthesis, to regulatory sensing in key metabolic pathways (i.e. ... | 2014 | 25245479 |
| iron-sulfur cluster biogenesis in mammalian cells: new insights into the molecular mechanisms of cluster delivery. | iron-sulfur (fe-s) clusters are ancient, ubiquitous cofactors composed of iron and inorganic sulfur. the combination of the chemical reactivity of iron and sulfur, together with many variations of cluster composition, oxidation states and protein environments, enables fe-s clusters to participate in numerous biological processes. fe-s clusters are essential to redox catalysis in nitrogen fixation, mitochondrial respiration and photosynthesis, to regulatory sensing in key metabolic pathways (i.e. ... | 2014 | 25245479 |
| ribosome rescue and translation termination at non-standard stop codons by ict1 in mammalian mitochondria. | release factors (rfs) govern the termination phase of protein synthesis. human mitochondria harbor four different members of the class 1 rf family: rf1lmt/mtrf1a, rf1mt, c12orf65 and ict1. the homolog of the essential ict1 factor is widely distributed in bacteria and organelles and has the peculiar feature in human mitochondria to be part of the ribosome as a ribosomal protein of the large subunit. the factor has been suggested to rescue stalled ribosomes in a codon-independent manner. the mecha ... | 2014 | 25233460 |
| dynamics of rna modification by a multi-site-specific trna methyltransferase. | in most organisms, the widely conserved 1-methyl-adenosine58 (m1a58) trna modification is catalyzed by an s-adenosyl-l-methionine (sam)-dependent, site-specific enzyme trmi. in archaea, trmi also methylates the adjacent adenine 57, m1a57 being an obligatory intermediate of 1-methyl-inosine57 formation. to study this multi-site specificity, we used three oligoribonucleotide substrates of pyrococcus abyssi trmi (pabtrmi) containing a fluorescent 2-aminopurine (2-ap) at the two target positions and ... | 2014 | 25217588 |
| macrolide-peptide conjugates as probes of the path of travel of the nascent peptides through the ribosome. | despite decades of research on the bacterial ribosome, the ribosomal exit tunnel is still poorly understood. although it has been suggested that the exit tunnel is simply a convenient route of egress for the nascent chain, specific protein sequences serve to slow the rate of translation, suggesting some degree of interaction between the nascent peptide chain and the exit tunnel. to understand how the ribosome interacts with nascent peptide sequences, we synthesized and characterized a novel clas ... | 2014 | 25198768 |
| architecture of mammalian respiratory complex i. | complex i (nadh:ubiquinone oxidoreductase) is essential for oxidative phosphorylation in mammalian mitochondria. it couples electron transfer from nadh to ubiquinone with proton translocation across the energy-transducing inner membrane, providing electrons for respiration and driving atp synthesis. mammalian complex i contains 44 different nuclear- and mitochondrial-encoded subunits, with a combined mass of 1 mda. the 14 conserved 'core' subunits have been structurally defined in the minimal, b ... | 2014 | 25209663 |
| the evolution of respiratory o2/no reductases: an out-of-the-phylogenetic-box perspective. | complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. however, the history of o2-levels in the atmosphere is complex and prior to the great oxidation event some 2.3 billion years ago, the amount of o2 in the biosphere is considered to have been extremely low as compared with present-day values. therefore the evolutionary histories of life and of o2-levels are likely intricately intertwined. the ... | 2014 | 24968694 |
| molecular mechanics of 30s subunit head rotation. | during ribosomal translocation, a process central to the elongation phase of protein synthesis, movement of mrna and trnas requires large-scale rotation of the head domain of the small (30s) subunit of the ribosome. it has generally been accepted that the head rotates by pivoting around the neck helix (h28) of 16s rrna, its sole covalent connection to the body domain. surprisingly, we observe that the calculated axis of rotation does not coincide with the neck. instead, comparative structure ana ... | 2014 | 25187561 |
| bacterial sigma factors as targets for engineered or synthetic transcriptional control. | sigma (σ) factors are the predominant constituents of transcription regulation in bacteria. σ factors recruit the core rna polymerase to recognize promoters with specific dna sequences. recently, engineering of transcriptional regulators has become a significant tool for strain engineering. the present review summarizes the recent advances in σ factor based engineering or synthetic design. the manipulation of σ factors presents insights into the bacterial stress tolerance and metabolite producti ... | 2014 | 25232540 |