Publications

functional specialization of transcription elongation factors.	elongation factors nusg and rfah evolved from a common ancestor and utilize the same binding site on rna polymerase (rnap) to modulate transcription. however, although nusg associates with rnap transcribing most escherichia coli genes, rfah regulates just a few operons containing ops, a dna sequence that mediates rfah recruitment. here, we describe the mechanism by which this specificity is maintained. we observe that rfah action is indeed restricted to those several operons that are devoid of n ...	2009	19096362
a novel insertion mutation in streptomyces coelicolor ribosomal s12 protein results in paromomycin resistance and antibiotic overproduction.	we identified a novel paromomycin resistance-associated mutation in rpsl, caused by the insertion of a glycine residue at position 92, in streptomyces coelicolor ribosomal protein s12. this insertion mutation (gi92) resulted in a 20-fold increase in the paromomycin resistance level. in combination with another s12 mutation, k88e, the gi92 mutation markedly enhanced the production of the blue-colored polyketide antibiotic actinorhodin and the red-colored antibiotic undecylprodigiosin. the gene re ...	2009	19104019
a novel insertion mutation in streptomyces coelicolor ribosomal s12 protein results in paromomycin resistance and antibiotic overproduction.	we identified a novel paromomycin resistance-associated mutation in rpsl, caused by the insertion of a glycine residue at position 92, in streptomyces coelicolor ribosomal protein s12. this insertion mutation (gi92) resulted in a 20-fold increase in the paromomycin resistance level. in combination with another s12 mutation, k88e, the gi92 mutation markedly enhanced the production of the blue-colored polyketide antibiotic actinorhodin and the red-colored antibiotic undecylprodigiosin. the gene re ...	2009	19104019
epr evidence of cyanide binding to the mn(mg) center of cytochrome c oxidase: support for cu(a)-mg involvement in proton pumping.	we examined the anion binding behavior of the mg(mn) site in cytochrome c oxidase to test a possible role of this center in proton pumping. rhodobacter sphaeroides grown in a mn(ii)-rich medium replaces the intrinsic mg(ii) ion with an epr-detectable mn(ii) ion without change in activity. due to its close proximity and a shared ligand, oxidized cu(a) is spin-coupled to the mn(ii) ion, affecting the epr spectrum. an examination of both bovine and r.s. oxidase crystal structures reveals a hydrogen ...	2009	19108635
implementation of a flash-photolysis system for time-resolved cryo-electron microscopy.	we describe here the implementation of a flash-photolysis system for time-resolved cryo-electron microscopy. a previously designed computer-controlled cryo-plunging apparatus [white, h.d., thirumurugan, k., walker, m.l., trinick, j., 2003. a second generation apparatus for time-resolved electron cryo-microscopy using stepper motors and electrospray. j. struct. biol. 144, 246-252] was used as a hardware platform, onto which a xenon flash lamp and liquid light pipe were mounted. the irradiation in ...	2008	19114106
implementation of a flash-photolysis system for time-resolved cryo-electron microscopy.	we describe here the implementation of a flash-photolysis system for time-resolved cryo-electron microscopy. a previously designed computer-controlled cryo-plunging apparatus [white, h.d., thirumurugan, k., walker, m.l., trinick, j., 2003. a second generation apparatus for time-resolved electron cryo-microscopy using stepper motors and electrospray. j. struct. biol. 144, 246-252] was used as a hardware platform, onto which a xenon flash lamp and liquid light pipe were mounted. the irradiation in ...	2008	19114106
characterization of two novel alpha-glucosidases from bifidobacterium breve ucc2003.	two alpha-glucosidase-encoding genes (agl1 and agl2) from bifidobacterium breve ucc2003 were identified and characterized. based on their similarity to characterized carbohydrate hydrolases, the agl1 and agl2 enzymes are both assigned to a subgroup of the glycosyl hydrolase family 13, the alpha-1,6-glucosidases (ec 3.2.1.10). recombinant agl1 and agl2 into which a his(12) sequence was incorporated (agl1(his) and agl2(his), respectively) exhibited hydrolytic activity towards panose, isomaltose, i ...	2009	19114534
characterization of two novel alpha-glucosidases from bifidobacterium breve ucc2003.	two alpha-glucosidase-encoding genes (agl1 and agl2) from bifidobacterium breve ucc2003 were identified and characterized. based on their similarity to characterized carbohydrate hydrolases, the agl1 and agl2 enzymes are both assigned to a subgroup of the glycosyl hydrolase family 13, the alpha-1,6-glucosidases (ec 3.2.1.10). recombinant agl1 and agl2 into which a his(12) sequence was incorporated (agl1(his) and agl2(his), respectively) exhibited hydrolytic activity towards panose, isomaltose, i ...	2009	19114534
the eukaryotic ribosome: current status and challenges.	despite having been identified first, their greater degree of complexity has resulted in our understanding of eukaryotic ribosomes lagging behind that of their bacterial and archaeal counterparts. a much more complicated biogenesis program results in ribosomes that are structurally, biochemically, and functionally more complex. however, recent advances in molecular genetics and structural biology are helping to reveal the intricacies of the eukaryotic ribosome and to address many longstanding qu ...	2009	19117941
the crystal structure of galacto-n-biose/lacto-n-biose i phosphorylase: a large deformation of a tim barrel scaffold.	galacto-n-biose/lacto-n-biose i phosphorylase (glnbp) from bifidobacterium longum, a key enzyme for intestinal growth, phosphorolyses galacto-n-biose and lacto-n-biose i with anomeric inversion. glnbp homologues are often found in human pathogenic and commensal bacteria, and their substrate specificities potentially define the nutritional acquisition ability of these microbes in their habitat. we report the crystal structures of glnbp in five different ligand-binding forms. this is the first thr ...	2009	19124470
architectural underpinnings of the genetic code for glutamine.	structure-based mutational analysis was used to probe the architecture of the glutamine binding pocket in escherichia coli glutaminyl-trna synthetase (glnrs). crystallographic studies of several different glnrs complexes in a lattice that supports catalytic activity have shown that the glutamine amide group makes only ambiguous hydrogen-bonding interactions with a tyrosine hydroxyl and bound water molecule, rather than the highly specific hydrogen-bonding and electrostatic interactions made by t ...	2009	19128026
dihydroorotase from the hyperthermophile aquifex aeolicus is activated by stoichiometric association with aspartate transcarbamoylase and forms a one-pot reactor for pyrimidine biosynthesis.	in prokaryotes, the first three enzymes in pyrimidine biosynthesis, carbamoyl phosphate synthetase (cps), aspartate transcarbamoylase (atc), and dihydroorotase (dho), are commonly expressed separately and either function independently (escherichia coli) or associate into multifunctional complexes (aquifex aeolicus). in mammals the enzymes are expressed as a single polypeptide chain (cad) in the order cps-dho-atc and associate into a hexamer. this study presents the three-dimensional structure of ...	2009	19128030
ribosome hijacking: a role for small protein b during trans-translation.	tight recognition of codon-anticodon pairings by the ribosome ensures the accuracy and fidelity of protein synthesis. in eubacteria, translational surveillance and ribosome rescue are performed by the 'tmrna-smpb' system (transfer messenger rna-small protein b). remarkably, entry and accommodation of aminoacylated-tmrna into stalled ribosomes occur without a codon-anticodon interaction but in the presence of smpb. here, we show that within a stalled ribosome, smpb interacts with the three univer ...	2009	19132006
evolution of prokaryotic spfh proteins.	the spfh protein superfamily is a diverse family of proteins whose eukaryotic members are involved in the scaffolding of detergent-resistant microdomains. recently the origin of the spfh proteins has been questioned. instead, convergent evolution has been proposed. however, an independent, convergent evolution of three large prokaryotic and three eukaryotic families is highly unlikely, especially when other mechanisms such as lateral gene transfer which could also explain their distribution patt ...	2009	19138386
combined microspectrophotometric and crystallographic examination of chemically reduced and x-ray radiation-reduced forms of cytochrome ba3 oxidase from thermus thermophilus: structure of the reduced form of the enzyme.	three paths for obtaining crystals of reduced (ii-e4q/i-k258r) cytochrome ba(3) are described, and the structures of these are reported at approximately 2.8-3.0 a resolution. microspectrophotometry of single crystals of thermus ba(3) oxidase at 100 k was used to show that crystals of the oxidized enzyme are reduced in an intense x-ray (beam line 7-1 at the stanford synchrotron radiation laboratory), being nearly complete in 1 min. the previously reported structures of ba(3) (protein data bank en ...	2009	19140675
a conserved active site tyrosine residue of proline dehydrogenase helps enforce the preference for proline over hydroxyproline as the substrate.	proline dehydrogenase (prodh) catalyzes the oxidation of l-proline to delta-1-pyrroline-5-carboxylate. prodhs exhibit a pronounced preference for proline over hydroxyproline (trans-4-hydroxy-l-proline) as the substrate, but the basis for specificity is unknown. the goal of this study, therefore, is to gain insight into the structural determinants of substrate specificity of this class of enzyme, with a focus on understanding how prodhs discriminate between the two closely related molecules, prol ...	2009	19140736
coarse-grained modeling of large rna molecules with knowledge-based potentials and structural filters.	understanding the function of complex rna molecules depends critically on understanding their structure. however, creating three-dimensional (3d) structural models of rna remains a significant challenge. we present a protocol (the nucleic acid simulation tool [nast]) for rna modeling that uses an rna-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate plausible 3d structures. we demonstrate nast's capabilities by using only secondary structure and tertiar ...	2009	19144906
genetic and structural analysis of base substitutions in the central pseudoknot of thermus thermophilus 16s ribosomal rna.	characterization of base substitutions in rrnas has provided important insights into the mechanism of protein synthesis. knowledge of the structural effects of such alterations is limited, and could be greatly expanded with the development of a genetic system based on an organism amenable to both genetics and structural biology. here, we describe the genetic analysis of base substitutions in 16s ribosomal rna of the extreme thermophile thermus thermophilus, and an analysis of the conformational ...	2009	19144908
electronic structure of the ground and excited states of the cu(a) site by nmr spectroscopy.	the electronic properties of thermus thermophilus cu(a) in the oxidized form were studied by (1)h and (13)c nmr spectroscopy. all of the (1)h and (13)c resonances from cysteine and imidazole ligands were observed and assigned in a sequence-specific fashion. the detection of net electron spin density on a peptide moiety is attributed to the presence of a h-bond to a coordinating sulfur atom. this hydrogen bond is conserved in all natural cu(a) variants and plays an important role for maintaining ...	2009	19146411
new information content in rna base pairing deduced from quantitative analysis of high-resolution structures.	non-canonical base pairs play important roles in organizing the complex three-dimensional folding of rna. here, we outline methodology developed both to analyze the spatial patterns of interacting base pairs in known rna structures and to reconstruct models from the collective experimental information. we focus attention on the structural context and deformability of the seven pairing patterns found in greatest abundance in the helical segments in a set of well-resolved crystal structures, inclu ...	2009	19150407
proteomic analysis of protein tyrosine nitration after ischemia reperfusion injury: mitochondria as the major target.	endothelial nitric oxide synthase-derived no and its derivative, peroxynitrite (onoo(-)), suppresses oxygen consumption by nitration of mitochondrial proteins after reperfusion. however, very few nitrated proteins are identified to date. in this paper, ischemia/reperfusion (i/r) injury was induced in mouse heart by ligation and release of the left anterior descending coronary artery. western blotting showed that tyrosine nitration was higher in i/r hearts. nitrated proteins were identified by ca ...	2009	19150419
proteomic analysis of protein tyrosine nitration after ischemia reperfusion injury: mitochondria as the major target.	endothelial nitric oxide synthase-derived no and its derivative, peroxynitrite (onoo(-)), suppresses oxygen consumption by nitration of mitochondrial proteins after reperfusion. however, very few nitrated proteins are identified to date. in this paper, ischemia/reperfusion (i/r) injury was induced in mouse heart by ligation and release of the left anterior descending coronary artery. western blotting showed that tyrosine nitration was higher in i/r hearts. nitrated proteins were identified by ca ...	2009	19150419
mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at trna wobble positions.	the wobble modification in trnas, 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)u), is required for the proper decoding of nnr codons in eukaryotes. the 2-thio group confers conformational rigidity of mcm(5)s(2)u by largely fixing the c3'-endo ribose puckering, ensuring stable and accurate codon-anticodon pairing. we have identified five genes in saccharomyces cerevisiae, yil008w (urm1), yhr111w (uba4), yor251c (tum1), ynl119w (ncs2) and ygl211w (ncs6), that are required for 2-thiolation of m ...	2009	19151091
cloning, expression, crystallization and preliminary x-ray crystallographic analysis of glutamyl-trna synthetase (xoo1504) from xanthomonas oryzae pv. oryzae.	the gltx gene from xanthomonas oryzae pv. oryzae (xoo1504) encodes glutamyl-trna synthetase (glurs), one of the most important enzymes involved in bacterial blight (bb), which causes huge production losses of rice worldwide. glurs is a class i-type aminoacyl-trna synthetase (aars) that is primarily responsible for the glutamylation of trna(glu). it plays an essential role in protein synthesis, as well as the regulation of cells, in all organisms. as it represents an important target for the deve ...	2009	19153456
cloning, expression, crystallization and preliminary x-ray crystallographic analysis of glutamyl-trna synthetase (xoo1504) from xanthomonas oryzae pv. oryzae.	the gltx gene from xanthomonas oryzae pv. oryzae (xoo1504) encodes glutamyl-trna synthetase (glurs), one of the most important enzymes involved in bacterial blight (bb), which causes huge production losses of rice worldwide. glurs is a class i-type aminoacyl-trna synthetase (aars) that is primarily responsible for the glutamylation of trna(glu). it plays an essential role in protein synthesis, as well as the regulation of cells, in all organisms. as it represents an important target for the deve ...	2009	19153456
x-ray diffraction analysis of a human trna(gly) acceptor-stem microhelix isoacceptor at 1.18 a resolution.	interest has been focused on comparative x-ray structure analyses of different trna(gly) acceptor-stem helices. trna(gly)/glycyl-trna synthetase belongs to the so-called class ii system, in which the trna identity elements consist of simple and unique determinants that are located in the trna acceptor stem and the discriminator base. comparative structure investigations of trna(gly) microhelices provide insight into the role of trna identity elements. predominant differences in the structures of ...	2009	19153458
x-ray diffraction analysis of a human trna(gly) acceptor-stem microhelix isoacceptor at 1.18 a resolution.	interest has been focused on comparative x-ray structure analyses of different trna(gly) acceptor-stem helices. trna(gly)/glycyl-trna synthetase belongs to the so-called class ii system, in which the trna identity elements consist of simple and unique determinants that are located in the trna acceptor stem and the discriminator base. comparative structure investigations of trna(gly) microhelices provide insight into the role of trna identity elements. predominant differences in the structures of ...	2009	19153458
characterization of a heat-stable enzyme possessing gtp-dependent rna ligase activity from a hyperthermophilic archaeon, pyrococcus furiosus.	using an expression protein library of a hyperthermophilic archaeon, pyrococcus furiosus, we identified a gene (pf0027) that encodes a protein with heat-stable cyclic nucleotide phosphodiesterase (cpdase) activity. the pf0027 gene encoded a 21-kda protein and an amino acid sequence that showed approximately 27% identity to that of the 2'-5' trna ligase protein, ligt (20 kda), from escherichia coli. we found that the purified pf0027 protein possessed gtp-dependent rna ligase activity and that syn ...	2009	19155324
new role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase.	using fmn and a reducing agent such as nad(p)h, type 2 isopentenyl-diphosphate isomerase catalyzes isomerization between isopentenyl diphosphate and dimethylallyl diphosphate, both of which are elemental units for the biosynthesis of highly diverse isoprenoid compounds. although the flavin cofactor is expected to be integrally involved in catalysis, its exact role remains controversial. here we report the crystal structures of the substrate-free and complex forms of type 2 isopentenyl-diphosphat ...	2009	19158086
a novel bicistronic vector for overexpressing mycobacterium tuberculosis proteins in escherichia coli.	a putative dna glycosylase encoded by the rv3297 gene (mtunei2) has been identified in mycobacterium tuberculosis. our efforts to express this gene in escherichia coli either by supplementing trnas for rare codons or optimizing the gene with preferred codons for e. coli resulted in little or no expression. on the other hand, high-level expression was observed using a bicistronic expression vector in which the target gene was translationally coupled to an upstream leader sequence. further compari ...	2009	19162193
a novel bicistronic vector for overexpressing mycobacterium tuberculosis proteins in escherichia coli.	a putative dna glycosylase encoded by the rv3297 gene (mtunei2) has been identified in mycobacterium tuberculosis. our efforts to express this gene in escherichia coli either by supplementing trnas for rare codons or optimizing the gene with preferred codons for e. coli resulted in little or no expression. on the other hand, high-level expression was observed using a bicistronic expression vector in which the target gene was translationally coupled to an upstream leader sequence. further compari ...	2009	19162193
a peroxide bridge between fe and cu ions in the o2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump.	the fully oxidized form of cytochrome c oxidase, immediately after complete oxidation of the fully reduced form, pumps protons upon each of the initial 2 single-electron reduction steps, whereas protons are not pumped during single-electron reduction of the fully oxidized "as-isolated" form (the fully oxidized form without any reduction/oxidation treatment) [bloch d, et al. (2004) the catalytic cycle of cytochrome c oxidase is not the sum of its two halves. proc natl acad sci usa 101:529-533]. f ...	2009	19164527
a systematic evaluation of the function of the protein-remodeling factor hsp104 in [psi+] prion propagation in s. cerevisiae by comprehensive chromosomal mutations.	the yeast prion [psi(+)] represents an aggregated state of the translational release factor sup35 (erf3) and deprives termination complexes of functional sup35, resulting in nonsense codon suppression. protein-remodeling factor hsp104 is involved in thermotolerance and [psi(+)] propagation, however the structure-and-function relationship of hsp104 for [psi(+)] remains unclear. in this study, we engineered 58 chromosomal hsp104 mutants that affect residues considered structurally or functionally ...	2007	19164920
biosynthesis of undecaprenyl phosphate-galactosamine and undecaprenyl phosphate-glucose in francisella novicida.	lipid a of francisella tularensis subsp. novicida contains a galactosamine (galn) residue linked to its 1-phosphate group. as shown in the preceding paper, this galn unit is transferred to lipid a from the precursor undecaprenyl phosphate-beta-d-galn. a small portion of the free lipid a of francisella novicida is further modified with a glucose residue at position-6'. we now demonstrate that the two f. novicida homologues of escherichia coli arnc, designated flmf1 and flmf2, are essential for li ...	2009	19166326
characterization of oxidized guanosine 5'-triphosphate as a viable inhibitor of soluble guanylyl cyclase.	the guanine base is prone to oxidation by free radicals regardless of the cellular moiety it is bound to. however, under conditions of oxidative stress, 8-oxoguanosine triphosphate (oxo(8)gtp) formation has been shown to occur without oxidation of the guanine base in dna. in vitro studies have suggested that oxo(8)gtp could impact g-protein signaling and rna synthesis. whether increased levels of oxo(8)gtp translate into cellular malfunction is unknown. data presented herein show that oxo(8)gtp ...	2009	19167482
allosteric control of escherichia coli rrna promoter complexes by dksa.	the escherichia coli dksa protein inserts into the rna polymerase (rnap) secondary channel, modifying the transcription initiation complex so that promoters with specific kinetic characteristics are regulated by changes in the concentrations of ppgpp and ntps. we used footprinting assays to determine the specific kinetic intermediate, rp(i), on which dksa acts. genetic approaches identified substitutions in the rnap switch regions, bridge helix, and trigger loop that mimicked, reduced, or enhanc ...	2009	19171784
ribosomal translocation: one step closer to the molecular mechanism.	protein synthesis occurs in ribosomes, the targets of numerous antibiotics. how these large and complex machines read and move along mrna have proven to be challenging questions. in this review, we focus on translocation, the last step of the elongation cycle in which movement of trna and mrna is catalyzed by elongation factor g. translocation entails large-scale movements of the trnas and conformational changes in the ribosome that require numerous tertiary contacts to be disrupted and reformed ...	2009	19173642
molecular modeling and site-directed mutagenesis reveal essential residues for catalysis in a prokaryote-type aspartate aminotransferase.	we recently reported that aspartate (asp) biosynthesis in plant chloroplasts is catalyzed by two different asp aminotransferases (aat): a previously characterized eukaryote type and a prokaryote type (pt-aat) similar to bacterial and archaebacterial enzymes. the available molecular and kinetic data suggest that the eukaryote-type aat is involved in the shuttling of reducing equivalents through the plastidic membrane, whereas the pt-aat could be involved in the biosynthesis of the asp-derived ami ...	2009	19176717
a green fluorescent protein screen for identification of well-expressed membrane proteins from a cohort of extremophilic organisms.	green fluorescent protein (gfp) fusion proteins provide a potentially facile tool for identification of well expressed, properly behaved membrane proteins for biochemical and structural study. here, we present a gfp-expression survey of >300 membrane proteins from 18 bacterial and archaeal extremophiles, organisms expected to be rich sources of membrane proteins having robust biophysical properties. we find that gfp-fusion fluorescence intensity is an excellent indicator of over-expression poten ...	2009	19177357
a green fluorescent protein screen for identification of well-expressed membrane proteins from a cohort of extremophilic organisms.	green fluorescent protein (gfp) fusion proteins provide a potentially facile tool for identification of well expressed, properly behaved membrane proteins for biochemical and structural study. here, we present a gfp-expression survey of >300 membrane proteins from 18 bacterial and archaeal extremophiles, organisms expected to be rich sources of membrane proteins having robust biophysical properties. we find that gfp-fusion fluorescence intensity is an excellent indicator of over-expression poten ...	2009	19177357
constant c10 ring stoichiometry in the escherichia coli atp synthase analyzed by cross-linking.	the subunit c stoichiometry of escherichia coli atp synthase was studied by intermolecular cross-linking via oxidation of bi-cysteine-substituted subunit c (ca21c/cm65c). independent of the carbon source used for growth and independent of the presence of other fof1 subunits, an equal pattern of cross-link formation stopping at the formation of decamers was obtained.	2009	19181809
mechanistic and functional insights into fatty acid activation in mycobacterium tuberculosis.	the recent discovery of fatty acyl-amp ligases (faals) in mycobacterium tuberculosis (mtb) provided a new perspective of fatty acid activation. these proteins convert fatty acids to the corresponding adenylates, which are intermediates of acyl-coa-synthesizing fatty acyl-coa ligases (facls). presently, it is not evident how obligate pathogens such as mtb have evolved such new themes of functional versatility and whether the activation of fatty acids to acyladenylates could indeed be a general me ...	2009	19182784
effect of primer proximity to a difficult-to-sequence region on read length and sequence quality.	anecdotal and not well-established evidence implies that there could be some effect of primer proximity in relation to a difficult region on read length and sequence quality. in this paper we sequenced many different categories of difficult regions where primers were located at various distances in relation to such regions and we found that there is only weak, if any, correlation between primer proximity and read length or sequence quality. the occasional improvements observed in some studies co ...	2008	19183797
x-ray crystal structure of garr-tartronate semialdehyde reductase from salmonella typhimurium.	tartronate semialdehyde reductases (tsrs), also known as 2-hydroxy-3-oxopropionate reductases, catalyze the reduction of tartronate semialdehyde using nad as cofactor in the final stage of d-glycerate biosynthesis. these enzymes belong to family of structurally and mechanically related beta-hydroxyacid dehydrogenases which differ in substrate specificity and catalyze reactions in specific metabolic pathways. here, we present the crystal structure of garr a tsr from salmonella typhimurium determi ...	2009	19184529
mechanism of inhibition of the v-type molecular motor by tributyltin chloride.	tributyltin chloride (tbt-cl) is an endocrine disruptor found in many animal species, and it is also known to be an inhibitor for the v-atpases that are emerging as potential targets in the treatment of diseases such as osteoporosis and cancer. we demonstrated by using biochemical and single-molecular imaging techniques that tbt-cl arrests an elementary step for rotary catalysis of the v(1) motor domain. in the presence of tbt-cl, the consecutive rotation of v(1) paused for a long duration ( app ...	2009	19186155
accommodation of two diatomic molecules in cytochrome bo: insights into no reductase activity in terminal oxidases.	bacterial heme-copper terminal oxidases react quickly with no to form a heme-nitrosyl complex, which, in some of these enzymes, can further react with a second no molecule to produce n(2)o. previously, we characterized the heme a(3)-no complex formed in cytochrome ba(3) from thermus thermophilus and the product of its low-temperature illumination. we showed that the photolyzed no group binds to cu(b)(i) to form an end-on no-cu(b) or a side-on copper-nitrosyl complex, which is likely to represent ...	2009	19187032
synthesizing non-natural parts from natural genomic template.	the current knowledge of genes and proteins comes from 'naturally designed' coding and non-coding regions. it would be interesting to move beyond natural boundaries and make user-defined parts. to explore this possibility we made six non-natural proteins in e. coli. we also studied their potential tertiary structure and phenotypic outcomes.	2009	19187561
enhancement of the seed-target recognition step in rna silencing by a piwi/mid domain protein.	target recognition in rna silencing is governed by the "seed sequence" of a guide rna strand associated with the piwi/mid domain of an argonaute protein in risc. using a reconstituted in vitro target recognition system, we show that a model piwi/mid domain protein confers position-dependent tightening and loosening of guide-strand-target interactions. over the seed sequence, the interaction affinity is enhanced up to approximately 300-fold. enhancement is achieved through a reduced entropy penal ...	2009	19187762
an unexpected type of ribosomes induced by kasugamycin: a look into ancestral times of protein synthesis?	translation of leaderless mrnas, lacking ribosomal recruitment signals other than the 5'-terminal aug-initiating codon, occurs in all three domains of life. contemporary leaderless mrnas may therefore be viewed as molecular fossils resembling ancestral mrnas. here, we analyzed the phenomenon of sustained translation of a leaderless mrna in the presence of the antibiotic kasugamycin. unexpected from the known in vitro effects of the drug, kasugamycin induced the formation of stable approximately ...	2009	19187763
evolutionary basis for the coupled-domain motions in thermus thermophilus leucyl-trna synthetase.	aminoacyl-trna synthetases are multidomain proteins that catalyze the covalent attachment of amino acids to their cognate transfer rna. various domains of an aminoacyl-trna synthetase perform their specific functions in a highly coordinated manner to maintain high accuracy in protein synthesis in cells. the coordination of their function, therefore, requires communication between domains. in this study we explored the relevance of enzyme motion in domain-domain communications. specifically, we a ...	2009	19188368
critical roles of subunit nuoh (nd1) in the assembly of peripheral subunits with the membrane domain of escherichia coli ndh-1.	the bacterial proton-translocating nadh:quinone oxidoreductase (ndh-1) consists of two domains, a peripheral arm and a membrane arm. nuoh is a counterpart of nd1, which is one of seven mitochondrially encoded hydrophobic subunits, and is considered to be involved in quinone/inhibitor binding. sequence comparison in a wide range of species showed that nuoh is comprehensively conserved, particularly with charged residues in the cytoplasmic side loops. we have constructed 40 mutants of 27 conserved ...	2009	19189973
a minimized rrna-binding site for ribosomal protein s4 and its implications for 30s assembly.	primary ribosomal protein s4 is essential for 30s ribosome biogenesis in eubacteria, because it nucleates subunit assembly and helps coordinate assembly with the synthesis of its rrna and protein components. s4 binds a five-helix junction (5wj) that bridges the 5' and 3' ends of the 16s 5' domain. to delineate which nucleotides contribute to s4 recognition, sequential deletions of the 16s 5' domain were tested in competitive s4-binding assays based on electrophoretic mobility shifts. s4 binds th ...	2009	19190093
a stable hyponitrite-bridged iron porphyrin complex.	the coupling of two nitric oxide (no) molecules in heme active sites is an important contributor to the conversion of no to nitrous oxide (n(2)o) by heme-containing enzymes. several formulations for the presumed heme-fe{n(2)o(2)}(n-) intermediates have been proposed previously, however, no crystal structures of heme-fe{n(2)o(2)}(n-) systems have been reported to date. we report the first isolation and characterization of a stable bimetallic hyponitrite iron porphyrin, [(oep)fe](2)(mu-n(2)o(2)), ...	2009	19191487
delineation of alternative conformational states in escherichia coli peptide deformylase via thermodynamic studies for the binding of actinonin.	we investigated the binding of a naturally occurring antibiotic, actinonin, to the ni(2+)-reconstituted recombinant form of escherichia coli peptide deformylase (pdf(ec)) via isothermal titration microcalorimetry. the binding data conformed to both exothermic and endothermic phases with magnitudes of deltag degrees , deltah degrees , and tdeltas degrees being equal to -12, -2.7, and 9.3 kcal/mol and -8.7, 3.9, and 12.6 kcal/mol, respectively. evidently, although both phases are dominated by favo ...	2009	19191548
hgf and bmp-7 ameliorate high glucose-induced epithelial-to-mesenchymal transition of peritoneal mesothelium.	over time, peritoneal dialysis results in functional and structural alterations of the peritoneal membrane, but the underlying mechanisms and whether these changes are reversible are not completely understood. here, we studied the effects of high levels of glucose, which are found in the dialysate, on human peritoneal mesothelial cells (hpmcs). we found that high concentrations of glucose induced epithelial-to-mesenchymal transition (emt) of hpmc, suggested by decreased expression of e-cadherin ...	2009	19193779
crystallization and x-ray analysis of human cytoplasmic phenylalanyl-trna synthetase.	human cytosolic phenylalanyl-trna synthetase (hcphers) is responsible for the covalent attachment of phenylalanine to its cognate trna(phe). significant differences between the amino-acid sequences of eukaryotic and prokaryotic pherss indicate that the domain composition of hcphers differs from that of the thermus thermophilus analogue. as a consequence of the absence of the anticodon-recognizing b8 domain, the binding mode of trna(phe) to hcphers is expected to differ from that in prokaryotes. ...	2009	19193993
escherichia coli trna(arg) acceptor-stem isoacceptors: comparative crystallization and preliminary x-ray diffraction analysis.	the aminoacylation of trna is a crucial step in cellular protein biosynthesis. recognition of the cognate trna by the correct aminoacyl-trna synthetase is ensured by trna identity elements. in trna(arg), the identity elements consist of the anticodon, parts of the d-loop and the discriminator base. the minor groove of the aminoacyl stem interacts with the arginyl-trna synthetase. as a consequence of the redundancy of the genetic code, six trna(arg) isoacceptors exist. in the present work, three ...	2009	19193994
crystallization, data collection and data processing of maltose-binding protein (male) from the phytopathogen xanthomonas axonopodis pv. citri.	maltose-binding protein is the periplasmic component of the abc transporter responsible for the uptake of maltose/maltodextrins. the xanthomonas axonopodis pv. citri maltose-binding protein male has been crystallized at 293 k using the hanging-drop vapour-diffusion method. the crystal belonged to the primitive hexagonal space group p6(1)22, with unit-cell parameters a = 123.59, b = 123.59, c = 304.20 a, and contained two molecules in the asymetric unit. it diffracted to 2.24 a resolution.	2009	19193996
preliminary x-ray crystallographic analysis of ornithine acetyltransferase (rv1653) from mycobacterium tuberculosis.	the gene product of open reading frame rv1653 from mycobacterium tuberculosis is annotated as encoding a probable ornithine acetyltransferase (oatase; ec 2.3.1.35), an enzyme that catalyzes two steps in the arginine-biosynthesis pathway. it transfers an acetyl group from n-acetylornithine to l-glutamate to produce n-acetylglutamate and l-ornithine. rv1653 was crystallized using the sitting-drop vapour-diffusion method. the native crystals diffracted to a resolution of 1.7 a and belonged to space ...	2009	19194014
predicting peptide structures in native proteins from physical simulations of fragments.	it has long been proposed that much of the information encoding how a protein folds is contained locally in the peptide chain. here we present a large-scale simulation study designed to examine the extent to which conformations of peptide fragments in water predict native conformations in proteins. we perform replica exchange molecular dynamics (remd) simulations of 872 8-mer, 12-mer, and 16-mer peptide fragments from 13 proteins using the amber 96 force field and the obc implicit solvent model. ...	2009	19197352
three genomes from the phylum acidobacteria provide insight into the lifestyles of these microorganisms in soils.	the complete genomes of three strains from the phylum acidobacteria were compared. phylogenetic analysis placed them as a unique phylum. they share genomic traits with members of the proteobacteria, the cyanobacteria, and the fungi. the three strains appear to be versatile heterotrophs. genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. the genomes encode low-specificity major facilitator ...	2009	19201974
three-dimensional structure of a1a0 atp synthase from the hyperthermophilic archaeon pyrococcus furiosus by electron microscopy.	the archaeal atp synthase is a multisubunit complex that consists of a catalytic a(1) part and a transmembrane, ion translocation domain a(0). the a(1)a(0) complex from the hyperthermophile pyrococcus furiosus was isolated. mass analysis of the complex by laser-induced liquid bead ion desorption (lilbid) indicated a size of 730 +/- 10 kda. a three-dimensional map was generated by electron microscopy from negatively stained images. the map at a resolution of 2.3 nm shows the a(1) and a(0) domain, ...	2009	19203996
minimum contradiction matrices in whole genome phylogenies.	minimum contradiction matrices are a useful complement to distance-based phylogenies. a minimum contradiction matrix represents phylogenetic information under the form of an ordered distance matrix y(i) (,) (j) (n). a matrix element corresponds to the distance from a reference vertex n to the path (i, j). for an x-tree or a split network, the minimum contradiction matrix is a robinson matrix. it therefore fulfills all the inequalities defining perfect order: y(i) (,) (j) (n) >or= y(i) (,) (k) (n ...	2008	19204821
comphy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets.	with the increasing availability of whole genome sequences, it is becoming more and more important to use complete genome sequences for inferring species phylogenies. we developed a new tool comphy, 'composite distance phylogeny', based on a composite distance matrix calculated from the comparison of complete gene sets between genome pairs to produce a prokaryotic phylogeny.	2009	19208152
recurring cluster and operon assembly for phenylacetate degradation genes.	a large number of theories have been advanced to explain why genes involved in the same biochemical processes are often co-located in genomes. most of these theories have been dismissed because empirical data do not match the expectations of the models. in this work we test the hypothesis that cluster formation is most likely due to a selective pressure to gradually co-localise protein products and that operon formation is not an inevitable conclusion of the process.	2009	19208251
characterization of dna polymerase x from thermus thermophilus hb8 reveals the polxc and php domains are both required for 3'-5' exonuclease activity.	the x-family dna polymerases (polxs) comprise a highly conserved dna polymerase family found in all kingdoms. mammalian polxs are known to be involved in several dna-processing pathways including repair, but the cellular functions of bacterial polxs are less known. many bacterial polxs have a polymerase and histidinol phosphatase (php) domain at their c-termini in addition to a polx core (polxc) domain, and possess 3'-5' exonuclease activity. although both domains are highly conserved in bacteri ...	2009	19211662
limited proteolysis analysis of the ribosome is affected by subunit association.	our understanding of the structural organization of ribosome assembly intermediates, in particular those intermediates that result from misfolding leading to their eventual degradation within the cell, is limited because of the lack of methods available to characterize assembly intermediate structures. because conventional structural approaches, such as nmr, x-ray crystallography, and cryo-em, are not ideally suited to characterize the structural organization of these flexible and sometimes hete ...	2009	19213046
functional expression of a bacterial xylose isomerase in saccharomyces cerevisiae.	in industrial fermentation processes, the yeast saccharomyces cerevisiae is commonly used for ethanol production. however, it lacks the ability to ferment pentose sugars like d-xylose and l-arabinose. heterologous expression of a xylose isomerase (xi) would enable yeast cells to metabolize xylose. however, many attempts to express a prokaryotic xi with high activity in s. cerevisiae have failed so far. we have screened nucleic acid databases for sequences encoding putative xis and finally were a ...	2009	19218403
characterization of a mimivirus rna cap guanine-n2 methyltransferase.	a 2,2,7-trimethylguanosine (tmg) cap is a signature feature of eukaryal snrnas, telomerase rnas, and trans-spliced nematode mrnas. tmg and 2,7-dimethylguanosine (dmg) caps are also present on mrnas of two species of alphaviruses (positive strand rna viruses of the togaviridae family). it is presently not known how viral mrnas might acquire a hypermethylated cap. mimivirus, a giant dna virus that infects amoeba, encodes many putative enzymes and proteins implicated in rna transactions, including ...	2009	19218551
target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies.	to study the substrate specificity of enzymes, we use the amidohydrolase and enolase superfamilies as model systems; members of these superfamilies share a common tim barrel fold and catalyze a wide range of chemical reactions. here, we describe a collaboration between the enzyme specificity consortium (enspec) and the new york sgx research center for structural genomics (nysgxrc) that aims to maximize the structural coverage of the amidohydrolase and enolase superfamilies. using sequence- and s ...	2009	19219566
reduction of hydrophilic ubiquinones by the flavin in mitochondrial nadh:ubiquinone oxidoreductase (complex i) and production of reactive oxygen species.	nadh:ubiquinone oxidoreductase (complex i) from bovine heart mitochondria is a complicated, energy-transducing, membrane-bound enzyme that contains 45 different subunits, a non-covalently bound flavin mononucleotide, and eight iron-sulfur clusters. the mechanisms of nadh oxidation and intramolecular electron transfer by complex i are gradually being defined, but the mechanism linking ubiquinone reduction to proton translocation remains unknown. studies of ubiquinone reduction by isolated complex ...	2009	19220002
comparison of molecular dynamics and superfamily spaces of protein domain deformation.	it is well known the strong relationship between protein structure and flexibility, on one hand, and biological protein function, on the other hand. technically, protein flexibility exploration is an essential task in many applications, such as protein structure prediction and modeling. in this contribution we have compared two different approaches to explore the flexibility space of protein domains: i) molecular dynamics (md-space), and ii) the study of the structural changes within superfamily ...	2009	19220918
the ribosome returned.	since the mid-1990s, insights obtained from electron microscopy and x-ray crystallography have transformed our understanding of how the most important ribozyme in the cell, the ribosome, catalyzes protein synthesis. this review provides a brief account of how this structural revolution came to pass, and the impact it has had on our understanding of how the ribosome decodes messenger rnas.	2009	19222865
a genetic screen for components of the mammalian rna interference pathway in bloom-deficient mouse embryonic stem cells.	genetic screens performed in model organisms have helped identify key components of the rna interference (rnai) pathway. recessive genetic screens have recently become feasible through the use of mouse embryonic stem (es) cells that are bloom's syndrome protein (blm) deficient. here, we developed and performed a recessive genetic screen to identify components of the mammalian rnai pathway in blm-deficient es cells. genome-wide mutagenesis using a retroviral gene trap strategy resulted in the iso ...	2009	19223321
dodecin is the key player in flavin homeostasis of archaea.	flavins are employed to transform physical input into biological output signals. in this function, flavins catalyze a variety of light-induced reactions and redox processes. however, nature also provides flavoproteins with the ability to uncouple the mediation of signals. such proteins are the riboflavin-binding proteins (rfbps) with their function to store riboflavin for fast delivery of fmn and fad. here we present in vitro and in vivo data showing that the recently discovered archaeal dodecin ...	2009	19224924
idiosyncratic helix-turn-helix motif in methanosarcina barkeri seryl-trna synthetase has a critical architectural role.	all seryl-trna synthetases (serrss) are functional homodimers with a c-terminal active site domain typical for class ii aminoacyl-trna synthetases and an n-terminal domain involved in trna binding. the recently solved three-dimensional structure of methanosarcina barkeri serrs revealed the idiosyncratic features of methanogenic-type serrss; that is, an active site zinc ion, a unique trna binding domain, and an insertion of approximately 30 residues in the catalytic domain, which adopt a helix-tu ...	2009	19228694
evolution of mutation rates: phylogenomic analysis of the photolyase/cryptochrome family.	photoreactivation, one of the first dna repair pathways to evolve, is the direct reversal of premutagenic lesions caused by ultraviolet (uv) irradiation, catalyzed by photolyases in a light-dependent, single-enzyme reaction. it has been experimentally shown that photoreactivation prevents uv mutagenesis in a broad range of species. in the absence of photoreactivation, uv-induced photolesions are repaired by the more complex and much less efficient nucleotide excision repair pathway. despite thei ...	2009	19228922
gtpase activation of elongation factor ef-tu by the ribosome during decoding.	we have used single-particle reconstruction in cryo-electron microscopy to determine a structure of the thermus thermophilus ribosome in which the ternary complex of elongation factor tu (ef-tu), trna and guanine nucleotide has been trapped on the ribosome using the antibiotic kirromycin. this represents the state in the decoding process just after codon recognition by trna and the resulting gtp hydrolysis by ef-tu, but before the release of ef-tu from the ribosome. progress in sample purificati ...	2009	19229291
a molybdopterin oxidoreductase is involved in h2 oxidation in desulfovibrio desulfuricans g20.	three mutants deficient in hydrogen/formate uptake were obtained through screening of a transposon mutant library containing 5,760 mutants of desulfovibrio desulfuricans g20. mutations were in the genes encoding the type i tetraheme cytochrome c(3) (cyca), fe hydrogenase (hydb), and molybdopterin oxidoreductase (mopb). mutations did not decrease the ability of cells to produce h(2) or formate during growth. complementation of the cyca and mopb mutants with a plasmid carrying the intact cyca and/ ...	2009	19233927
stimulation of expression of a silica-induced protein (sip) in thermus thermophilus by supersaturated silicic acid.	the effects of silicic acid on the growth of thermus thermophilus tmy, an extreme thermophile isolated from a siliceous deposit formed from geothermal water at a geothermal power plant in japan, were examined at 75 degrees c. at concentrations higher than the solubility of amorphous silica (400 to 700 ppm sio(2)), a silica-induced protein (sip) was isolated from the cell envelope fraction of log-phase tmy cells grown in the presence of supersaturated silicic acid. two-dimensional sodium dodecyl ...	2009	19233950
domain architecture of the stator complex of the a1a0-atp synthase from thermoplasma acidophilum.	a key structural element in the ion translocating f-, a-, and v-atpases is the peripheral stalk, an assembly of two polypeptides that provides a structural link between the atpase and ion channel domains. previously, we have characterized the peripheral stalk forming subunits e and h of the a-atpase from thermoplasma acidophilum and demonstrated that the two polypeptides interact to form a stable heterodimer with 1:1 stoichiometry (kish-trier, e., briere, l. k., dunn, s. d., and wilkens, s. (200 ...	2009	19234304
improving the functional expression of a bacillus licheniformis laccase by random and site-directed mutagenesis.	laccases have huge potential for biotechnological applications due to their broad substrate spectrum and wide range of reactions they are able to catalyze. these include, for example, the formation and degradation of dimers, oligomers, polymers, and ring cleavage as well as oxidation of aromatic compounds. potential applications of laccases include detoxification of industrial effluents, decolorization of textile dyes and the synthesis of natural products by, for instance, dimerization of phenol ...	2009	19236694
structures of alternatively spliced isoforms of human ketohexokinase.	a molecular understanding of the unique aspects of dietary fructose metabolism may be the key to understanding and controlling the current epidemic of fructose-related obesity, diabetes and related adverse metabolic states in western populations. fructose catabolism is initiated by its phosphorylation to fructose 1-phosphate, which is performed by ketohexokinase (khk). here, the crystal structures of the two alternatively spliced isoforms of human ketohexokinase, hepatic khk-c and the peripheral ...	2009	19237742
origins and mechanisms of mirnas and sirnas.	over the last decade, approximately 20-30 nucleotide rna molecules have emerged as critical regulators in the expression and function of eukaryotic genomes. two primary categories of these small rnas--short interfering rnas (sirnas) and micrornas (mirnas)--act in both somatic and germline lineages in a broad range of eukaryotic species to regulate endogenous genes and to defend the genome from invasive nucleic acids. recent advances have revealed unexpected diversity in their biogenesis pathways ...	2009	19239886
regulation of translation initiation in eukaryotes: mechanisms and biological targets.	translational control in eukaryotic cells is critical for gene regulation during nutrient deprivation and stress, development and differentiation, nervous system function, aging, and disease. we describe recent advances in our understanding of the molecular structures and biochemical functions of the translation initiation machinery and summarize key strategies that mediate general or gene-specific translational control, particularly in mammalian systems.	2009	19239892
dna uracil repair initiated by the archaeal exoiii homologue mth212 via direct strand incision.	no genes for any of the known uracil dna glycosylases of the udg superfamily are present in the genome of methanothermobacter thermautotrophicus deltah, making it difficult to imagine how dna-u repair might be initiated in this organism. recently, mth212, the exoiii homologue of m. thermautotrophicus deltah has been characterized as a dna uridine endonuclease, which suggested the possibility of a novel endonucleolytic entry mechanism for dna uracil repair. with no system of genetic experimentati ...	2009	19240141
frequency and isostericity of rna base pairs.	most of the hairpin, internal and junction loops that appear single-stranded in standard rna secondary structures form recurrent 3d motifs, where non-watson-crick base pairs play a central role. non-watson-crick base pairs also play crucial roles in tertiary contacts in structured rna molecules. we previously classified rna base pairs geometrically so as to group together those base pairs that are structurally similar (isosteric) and therefore able to substitute for each other by mutation withou ...	2009	19240142
involvement of a carboxylated lysine in uv damage endonuclease.	uv damage endonuclease is a dna repair enzyme that can both recognize damage such as uv lesions and introduce a nick directly 5' to them. recently, the crystal structure of the enzyme from thermus thermophilus was solved. in the electron density map of this structure, unexplained density near the active site was observed at the tip of lys229. based on this finding, it was proposed that lys229 is post-translationally modified. in this article, we give evidence that this modification is a carboxyl ...	2009	19241382
allopatric speciation in ticks: genetic and reproductive divergence between geographic strains of rhipicephalus (boophilus) microplus.	the cattle tick, rhipicephalus (boophilus) microplus, economically impact cattle industry in tropical and subtropical regions of the world. the morphological and genetic differences among r. microplus strains have been documented in the literature, suggesting that biogeographical and ecological separation may have resulted in boophilid ticks from america/africa and those from australia being different species. to test the hypothesis of the presence of different boophilid species, herein we perfo ...	2009	19243585
identification of neisserial dna binding components.	neisseria meningitidis, a causative agent of meningitis and septicaemia, expresses type iv pili, a feature correlating with the uptake of exogenous dna from the environment by natural transformation. the outer membrane complex pilq, through which pili are extruded and retracted, has previously been shown to bind dna in its pore region. in order to further elucidate how dna is transported across the membranes, we searched for dna binding proteins within the meningococcal inner membrane. inner mem ...	2009	19246756
the family x dna polymerase from deinococcus radiodurans adopts a non-standard extended conformation.	deinococcus radiodurans is an extraordinarily radioresistant bacterium that is able to repair hundreds of radiation-induced double-stranded dna breaks. one of the players in this pathway is an x family dna polymerase (polx(dr)). deletion of polx(dr) has been shown to decrease the rate of repair of double-stranded dna breaks and increase cell sensitivity to gamma-rays. a 3'-->5' exonuclease activity that stops cutting close to dna loops has also been demonstrated. the present crystal structure of ...	2009	19251692
crystallization and preliminary characterization of the thermus thermophilus rna helicase hera c-terminal domain.	heat-resistant rna-dependent atpase (hera) from thermus thermophilus is a dead-box rna helicase. two constructs encompassing the second reca-like domain and the c-terminal domain of hera were overproduced in escherichia coli and purified to homogeneity. single crystals of both hera constructs were obtained in three crystal forms. a tetragonal crystal form belonged to space group p4(1)2(1)2, with unit-cell parameters a = 65.5, c = 153.0 a, and contained one molecule per asymmetric unit. two ortho ...	2009	19255475
crystallization and preliminary x-ray diffraction analysis of a putative two-domain-type laccase from a metagenome.	a putative two-domain-type laccase retrieved from a metagenome was successfully crystallized using the sitting-drop vapour-diffusion method. data were collected to a resolution of 1.7 a at 100 k using synchrotron radiation. the crystal belonged to space group p2(1)2(1)2(1), with unit-cell parameters a = 74.67, b = 100.95, c = 124.11 a. the self-rotation function showed the presence of a noncrystallographic threefold axis in the structure. the presence of one trimer in the asymmetric unit yielded ...	2009	19255479
chemically modified primers for improved multiplex polymerase chain reaction.	multiplex polymerase chain reaction (pcr), the amplification of multiple targets in a single reaction, presents a new set of challenges that further complicate more traditional pcr setups. these complications include a greater probability for nonspecific amplicon formation and for imbalanced amplification of different targets, each of which can compromise quantification and detection of multiple targets. despite these difficulties, multiplex pcr is frequently used in applications such as pathoge ...	2009	19258004
defects in transient trna translocation bypass trna synthetase quality control mechanisms.	quality control mechanisms during protein synthesis are essential to fidelity and cell survival. leucyl-trna synthetase (leurs) misactivates non-leucine amino acids including isoleucine, methionine, and norvaline. to prevent translational errors, mischarged trna products are translocated 30a from the canonical aminoacylation core to a hydrolytic editing-active site within a completely separate domain. because it is transient, the trna translocation mechanism has been difficult to isolate. we hav ...	2009	19258309
inhibition of bacterial ribosome assembly: a suitable drug target?	the assembly of bacterial ribosomes is viewed with increasing interest as a potential target for new antibiotics. the in vivo synthesis and assembly of ribosomes are briefly reviewed here, highlighting the many ways in which assembly can be perturbed. the process is compared with the model in vitro process from which much of our knowledge is derived. the coordinate synthesis of the ribosomal components is essential for their ordered and efficient assembly; antibiotics interfere with this coordin ...	2009	19258531
identification of rna molecules by specific enzyme digestion and mass spectrometry: software for and implementation of rna mass mapping.	the idea of identifying or characterizing an rna molecule based on a mass spectrum of specifically generated rna fragments has been used in various forms for well over a decade. we have developed software-named rrm for 'rna mass mapping'-which can search whole prokaryotic genomes or rna fasta sequence databases to identify the origin of a given rna based on a mass spectrum of rna fragments. as input, the program uses the masses of specific rnase cleavage of the rna under investigation. rnase t1 ...	2009	19264806
contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis.	superoxide dismutase (sod) enzymes are critical in controlling levels of reactive oxygen species (ros) that are linked to aging, cancer, and neurodegenerative disease. superoxide (o(2)(*-)) produced during respiration is removed by the product of the sod2 gene, the homotetrameric manganese superoxide dismutase (mnsod). here, we examine the structural and catalytic roles of the highly conserved active-site residue tyr34, based upon structure-function studies of mnsod enzymes with mutations at thi ...	2009	19265433
extension of the tryptophan chi2,1 dihedral angle-w3 band frequency relationship to a full rotation: correlations and caveats.	the correlation of the uvrr nuw3 mode with the tryptophan chi(2,1) dihedral angle [maruyama and takeuchi (1995) j. raman spectrosc. 26, 319; miura et al. (1989) j. raman spectrosc. 20, 667; takeuchi (2003) biopolymers 72, 305] has been extended to a full, 360 degrees rotation. the 3-fold periodicity of the relationship (cos 3chi(2,1)) over 360 degrees results in up to six dihedral angles for a given nuw3. consideration of a newman plot of dihedral angles for proteinaceous tryptophans taken from ...	2009	19267450
a novel endo-hydrogenase activity recycles hydrogen produced by nitrogen fixation.	nitrogen (n(2)) fixation also yields hydrogen (h(2)) at 1:1 stoichiometric amounts. in aerobic diazotrophic (able to grow on n(2) as sole n-source) bacteria, orthodox respiratory hupsl-encoded hydrogenase activity, associated with the cell membrane but facing the periplasm (exo-hydrogenase), has nevertheless been presumed responsible for recycling such endogenous hydrogen.	2009	19277114