Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| the folding trajectory of rnase h is dominated by its topology and not local stability: a protein engineering study of variants that fold via two-state and three-state mechanisms. | proteins can sample a variety of partially folded conformations during the transition between the unfolded and native states. some proteins never significantly populate these high-energy states and fold by an apparently two-state process. however, many proteins populate detectable, partially folded forms during the folding process. the role of such intermediates is a matter of considerable debate. a single amino acid change can convert escherichia coli ribonuclease h from a three-state folder th ... | 2009 | 19501596 |
| identification of optimal protocols for sequencing difficult templates: results of the 2008 abrf dna sequencing research group difficult template study 2008. | the 2008 abrf dna sequencing research group (dsrg) difficult template sequencing study was designed to identify a general set of guidelines that would constitute the best approaches for sequencing difficult templates. this was a continuation of previous dsrg difficult template studies performed in 1996, 1997, and 2003. the distinguishing factors in the present study were the number of dna templates used, the number of different types of difficult regions tested, and the inclusion of a follow-up ... | 2009 | 19503623 |
| toward the catalytic mechanism of a cysteine ligase (mshc) from mycobacterium smegmatis: an enzyme involved in the biosynthetic pathway of mycothiol. | mycobacterium tuberculosis and other members of the actinomycete family produce mycothiol (msh or acetylcysteine-glucosamine-inositol, accys-glcn-ins) to protect the organism against oxidative and antibiotic stress. the biosynthesis of msh proceeds via a five-step process that involves four unique enzymes, msha-d, which represent specific targets for inhibitor design. recombinant mycobacterium smegmatis mshc catalyzes the atp-dependent condensation of glucosamine-inositol (glcn-ins) and cysteine ... | 2009 | 19505149 |
| the 5' terminal uracil of let-7a is critical for the recruitment of mrna to argonaute2. | small rnas modulate gene expression by forming a ribonucleoprotein complex with argonaute proteins and directing them to specific complementary sites in target nucleic acids. however, the interactions required for the recruitment of the target nucleic acid to the ribonucleoprotein complex are poorly understood. in the present manuscript we have investigated this question by using let-7a, argonaute2 and a fully complementary mrna target. importantly, we have found that recombinant argonaute2 is s ... | 2009 | 19508234 |
| thermodynamic characterization of tandem mismatches found in naturally occurring rna. | although all sequence symmetric tandem mismatches and some sequence asymmetric tandem mismatches have been thermodynamically characterized and a model has been proposed to predict the stability of previously unmeasured sequence asymmetric tandem mismatches [christiansen,m.e. and znosko,b.m. (2008) biochemistry, 47, 4329-4336], experimental thermodynamic data for frequently occurring tandem mismatches is lacking. since experimental data is preferred over a predictive model, the thermodynamic para ... | 2009 | 19509311 |
| hsp70 structure, function, regulation and influence on yeast prions. | heat shock proteins protect cells from various conditions of stress. hsp70, the most ubiquitous and highly conserved hsp, helps proteins adopt native conformation or regain function after misfolding. various co-chaperones specify hsp70 function and broaden its substrate range. we discuss hsp70 structure and function, regulation by co-factors and influence on propagation of yeast prions. | 2009 | 19519514 |
| hsp104 and prion propagation. | high-ordered aggregates (amyloids) may disrupt cell functions, cause toxicity at certain conditions and provide a basis for self-perpetuated, protein-based infectious heritable agents (prions). heat shock proteins acting as molecular chaperones counteract protein aggregation and influence amyloid propagation. the yeast hsp104/hsp70/hsp40 chaperone complex plays a crucial role in interactions with both ordered and unordered aggregates. the main focus of this review will be on the hsp104 chaperone ... | 2009 | 19519517 |
| insights into trna-dependent amidotransferase evolution and catalysis from the structure of the aquifex aeolicus enzyme. | many bacteria form gln-trna(gln) and asn-trna(asn) by conversion of the misacylated glu-trna(gln) and asp-trna(asn) species catalyzed by the gatcab amidotransferase in the presence of atp and an amide donor (glutamine or asparagine). here, we report the crystal structures of gatcab from the hyperthermophilic bacterium aquifex aeolicus, complexed with glutamine, asparagine, aspartate, adp, or atp. in contrast to the staphylococcus aureus gatcab, the a. aeolicus enzyme formed acyl-enzyme intermedi ... | 2009 | 19520089 |
| insights into the role of val45 and gln182 of escherichia coli muty in dna substrate binding and specificity. | escherichia coli muty (ecmuty) reduces mutagenesis by removing adenines paired with guanines or 7,8-dihydro-8-oxo-guanines (8-oxog). v45 and q182 of ecmuty are considered to be the key determinants of adenine specificity. both residues are spatially close to each other in the active site and are conserved in muty family proteins but not in methanobacterium thermoautotrophicum mig.mthi t/g mismatch dna glycosylase (a50 and l187 at the corresponding respective positions). | 2009 | 19523222 |
| a link between hinge-bending domain motions and the temperature dependence of catalysis in 3-isopropylmalate dehydrogenase. | enzyme function depends on specific conformational motions. we show that the temperature dependence of enzyme kinetic parameters can provide insight into these functionally relevant motions. while investigating the catalytic properties of ipmdh from escherichia coli, we found that its catalytic efficiency (k(cat)/k(m,ipm)) for the substrate ipm has an unusual temperature dependence, showing a local minimum at approximately 35 degrees c. in search of an explanation, we measured the individual con ... | 2009 | 19527660 |
| classification and energetics of the base-phosphate interactions in rna. | structured rna molecules form complex 3d architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. a significant percentage of the bases in structured rna molecules in the protein data bank (pdb) hydrogen-bond with phosphates of other nucleotides. by extracting and superimposing base-phosphate (bph) interactions from a reduced-redundancy subset of 3d structures from the pdb, we identified recurrent phosphate-binding sites on the rna bases. qua ... | 2009 | 19528080 |
| towards the immunoproteome of neisseria meningitidis. | despite the introduction of conjugated polysaccharide vaccines for many of the neisseria meningitidis serogroups, neisserial infections continue to cause septicaemia and meningitis across the world. this is in part due to the difficulties in developing a, cross-protective vaccine that is effective against all serogroups, including serogroup b meningococci. although convalescent n. meningitidis patients develop a natural long-lasting cross-protective immunity, the antigens that mediate this respo ... | 2009 | 19529772 |
| site-directed mutagenesis as a probe of the acid-base catalytic mechanism of homoisocitrate dehydrogenase from saccharomyces cerevisiae. | homoisocitrate dehydrogenase (hicdh) catalyzes the mg2+- and k+-dependent oxidative decarboxylation of homoisocitrate to alpha-ketoadipate using nad as the oxidant. a recent consideration of the structures of enzymes in the same family as hicdh, including isopropylmalate and isocitrate dehydrogenases, suggests all of the family members utilize a lys-tyr pair to catalyze the acid-base chemistry of the reaction [aktas, d. f., and cook, p. f. (2009) biochemistry 48, 3565-3577]. multiple-sequence al ... | 2009 | 19530703 |
| identification of candidate structured rnas in the marine organism 'candidatus pelagibacter ubique'. | metagenomic sequence data are proving to be a vast resource for the discovery of biological components. yet analysis of this data to identify functional rnas lags behind efforts to characterize protein diversity. the genome of 'candidatus pelagibacter ubique' htcc 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. it is also small, contains little non-coding dna, and has strikingly low gc content. | 2009 | 19531245 |
| mechanism for the hydrolysis of a sulfur-sulfur bond based on the crystal structure of the thiosulfohydrolase soxb. | soxb is an essential component of the bacterial sox sulfur oxidation pathway. soxb contains a di-manganese(ii) site and is proposed to catalyze the release of sulfate from a protein-bound cysteine s-thiosulfonate. a direct assay for soxb activity is described. the structure of recombinant thermus thermophilus soxb was determined by x-ray crystallography to a resolution of 1.5 a. structures were also determined for soxb in complex with the substrate analogue thiosulfate and in complex with the pr ... | 2009 | 19535341 |
| conformational changes in switch i of ef-g drive its directional cycling on and off the ribosome. | we have trapped elongation factor g (ef-g) from escherichia coli in six, functionally defined states, representing intermediates in its unidirectional catalytic cycle, which couples gtp hydrolysis to trna-mrna translocation in the ribosome. by probing ef-g with trypsin in each state, we identified a substantial conformational change involving its conserved switch i (sw1) element, which contacts the gtp substrate. by attaching febabe (a hydroxyl radical generating probe) to sw1, we could monitor ... | 2009 | 19536129 |
| a newly discovered protein export machine in malaria parasites. | several hundred malaria parasite proteins are exported beyond an encasing vacuole and into the cytosol of the host erythrocyte, a process that is central to the virulence and viability of the causative plasmodium species. the trafficking machinery responsible for this export is unknown. here we identify in plasmodium falciparum a translocon of exported proteins (ptex), which is located in the vacuole membrane. the ptex complex is atp-powered, and comprises heat shock protein 101 (hsp101; a clpa/ ... | 2009 | 19536257 |
| gain-of-function mutations identify amino acids within transmembrane domains of the yeast vacuolar transporter zrc1 that determine metal specificity. | cation diffusion facilitator transporters are found in all three kingdoms of life and are involved in transporting transition metals out of the cytosol. the metals they transport include zn2+, co2+, fe2+, cd2+, ni2+ and mn2+; however, no single transporter transports all metals. previously we showed that a single amino acid mutation in the yeast vacuolar zinc transporter zrc1 changed its substrate specificity from zn2+ to fe2+ and mn2+ [lin, kumanovics, nelson, warner, ward and kaplan (2008) j. ... | 2009 | 19538181 |
| smpb contributes to reading frame selection in the translation of transfer-messenger rna. | transfer-messenger rna (tmrna) acts first as a trna and then as an mrna template to rescue stalled ribosomes in eubacteria. together with its protein partner, smpb (small protein b), tmrna enters stalled ribosomes and transfers an ala residue to the growing polypeptide chain. a remarkable step then occurs: the ribosome leaves the stalled mrna and resumes translation using tmrna as a template, adding a short peptide tag that destines the aborted protein for destruction. exactly how the ribosome s ... | 2009 | 19540849 |
| anaerobic respiration of elemental sulfur and thiosulfate by shewanella oneidensis mr-1 requires psra, a homolog of the phsa gene of salmonella enterica serovar typhimurium lt2. | shewanella oneidensis mr-1, a facultatively anaerobic gammaproteobacterium, respires a variety of anaerobic terminal electron acceptors, including the inorganic sulfur compounds sulfite (so3(2-)), thiosulfate (s2o3(2-)), tetrathionate (s4o6(2-)), and elemental sulfur (s(0)). the molecular mechanism of anaerobic respiration of inorganic sulfur compounds by s. oneidensis, however, is poorly understood. in the present study, we identified a three-gene cluster in the s. oneidensis genome whose trans ... | 2009 | 19542325 |
| avoiding dangerous missense: thermophiles display especially low mutation rates. | rates of spontaneous mutation have been estimated under optimal growth conditions for a variety of dna-based microbes, including viruses, bacteria, and eukaryotes. when expressed as genomic mutation rates, most of the values were in the vicinity of 0.003-0.004 with a range of less than two-fold. because the genome sizes varied by roughly 10(4)-fold, the mutation rates per average base pair varied inversely by a similar factor. even though the commonality of the observed genomic rates remains une ... | 2009 | 19543367 |
| carboxylic ester hydrolases from hyperthermophiles. | carboxylic ester hydrolyzing enzymes constitute a large group of enzymes that are able to catalyze the hydrolysis, synthesis or transesterification of an ester bond. they can be found in all three domains of life, including the group of hyperthermophilic bacteria and archaea. esterases from the latter group often exhibit a high intrinsic stability, which makes them of interest them for various biotechnological applications. in this review, we aim to give an overview of all characterized carboxyl ... | 2009 | 19544040 |
| the 2.1 a crystal structure of an acyl-coa synthetase from methanosarcina acetivorans reveals an alternate acyl-binding pocket for small branched acyl substrates. | the acyl-amp forming family of adenylating enzymes catalyze two-step reactions to activate a carboxylate with the chemical energy derived from atp hydrolysis. x-ray crystal structures have been determined for multiple members of this family and, together with biochemical studies, provide insights into the active site and catalytic mechanisms used by these enzymes. these studies have shown that the enzymes use a domain rotation of 140 degrees to reconfigure a single active site to catalyze the tw ... | 2009 | 19544569 |
| amino acid changes in elongation factor tu of mycoplasma pneumoniae and mycoplasma genitalium influence fibronectin binding. | mycoplasma pneumoniae and mycoplasma genitalium are closely related organisms that cause distinct clinical manifestations and possess different tissue predilections despite their high degree of genome homology. we reported earlier that surface-localized m. pneumoniae elongation factor tu (ef-tu(mp)) mediates binding to the extracellular matrix component fibronectin (fn) through the carboxyl region of ef-tu. in this study, we demonstrate that surface-associated m. genitalium ef-tu (ef-tu(mg)), in ... | 2009 | 19546194 |
| comparative analysis of activator-esigma54 complexes formed with nucleotide-metal fluoride analogues. | bacterial rna polymerase (rnap) containing the major variant sigma(54) factor forms open promoter complexes in a reaction in which specialized activator proteins hydrolyse atp. here we probe binding interactions between sigma(54)-rnap (esigma(54)) and the atpases associated with various cellular activities (aaa+) domain of the escherichia coli activator protein, pspf, using nucleotide-metal fluoride (bef and alf) analogues representing ground and transition states of atp, which allow complexes ( ... | 2009 | 19553192 |
| fluorescently labeled ribosomes as a tool for analyzing antibiotic binding. | measuring the binding of antibiotics and other small-molecular-weight ligands to the 2.5 mda ribosome often presents formidable challenges. here, we describe a general method for studying binding of ligands to ribosomes that carry a site-specific fluorescent label covalently attached to one of the ribosomal proteins. as a proof of principle, an environment-sensitive fluorescent group was placed at several specific sites within the ribosomal protein s12. small ribosomal subunits were reconstitute ... | 2009 | 19553343 |
| the obge/cgta gtpase influences the stringent response to amino acid starvation in escherichia coli. | the stringent response is important for bacterial survival under stressful conditions, such as amino acid starvation, and is characterized by the accumulation of ppgpp and pppgpp. obge (cgta, yhbz) is an essential conserved gtpase in escherichia coli and several observations have implicated the protein in the control of the stringent response. however, consequences of the protein on specific responses to amino acid starvation have not been noted. we show that obge binds to ppgpp with biologicall ... | 2009 | 19555460 |
| primary structure revision and active site mapping of e. coli isoleucyl-trna synthetase by means of maldi mass spectrometry. | the correct amino acid sequence of e. coli isoleucyl-trna synthetase (ilers) was established by means of peptide mapping by maldi mass spectrometry, using a set of four endoproteases (trypsin, lysc, aspn and gluc). thereafter, the active site of ilers was mapped by affinity labeling with reactive analogs of the substrates. for the atp binding site, the affinity labeling reagent was pyridoxal 5'-diphospho-5'-adenosine (adp-pl), whereas periodate-oxidized trna(ile), the 2',3'-dialdehyde derivative ... | 2009 | 19557155 |
| genome analysis and genome-wide proteomics of thermococcus gammatolerans, the most radioresistant organism known amongst the archaea. | thermococcus gammatolerans was isolated from samples collected from hydrothermal chimneys. it is one of the most radioresistant organisms known amongst the archaea. we report the determination and annotation of its complete genome sequence, its comparison with other thermococcales genomes, and a proteomic analysis. | 2009 | 19558674 |
| groel-assisted protein folding: does it occur within the chaperonin inner cavity? | the folding of protein molecules in the groel inner cavity under the co-chaperonin groes lid is widely accepted as a crucial event of groel-assisted protein folding. this review is focused on the data showing that groel-assisted protein folding may proceed out of the complex with the chaperonin. the models of groel-assisted protein folding assuming ligand-controlled dissociation of nonnative proteins from the groel surface and their folding in the bulk solution are also discussed. | 2009 | 19564940 |
| millisecond dynamics in the allosteric enzyme imidazole glycerol phosphate synthase (igps) from thermotoga maritima. | igps is a 51 kda heterodimeric enzyme comprised of two proteins, hish and hisf, that catalyze the hydrolysis of glutamine to produce nh(3) in the hish active site and the cyclization of ammonia with n'-[(5'-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide (prfar) in hisf to produce imidazole glycerol phosphate (igp) and 5-aminoimidazole-4-carboxamide ribotide (aicar). binding of prfar and igp stimulates glutaminase activity in the hish enzyme over 5,000 and 100-fold, res ... | 2009 | 19565337 |
| properties of arg481 mutants of the aa3-type cytochrome c oxidase from rhodobacter sphaeroides suggest that neither r481 nor the nearby d-propionate of heme a3 is likely to be the proton loading site of the proton pump. | cytochrome c oxidase utilizes the energy from electron transfer and reduction of oxygen to water and pumps protons across the membrane, generating a proton motive force. a large body of biochemical work has shown that all the pumped protons enter the enzyme through the d-channel, which is apparent in x-ray structures as a chain of water molecules connecting d132 at the cytoplasmic surface of the enzyme to e286, near the enzyme active site. the exit pathway utilized by pumped protons beyond this ... | 2009 | 19575527 |
| the biogenesis and function of piwi proteins and pirnas: progress and prospect. | the evolutionarily conserved argonaute/piwi (ago/piwi, also known as paz-piwi domain or ppd) family of proteins is crucial for the biogenesis and function of small noncoding rnas (ncrnas). this family can be divided into ago and piwi subfamilies. the ago proteins are ubiquitously present in diverse tissues. they bind to small interfering rnas (sirnas) and micrornas (mirnas). in contrast, the piwi proteins are predominantly present in the germline and associate with a novel class of small rnas kn ... | 2009 | 19575643 |
| conservation of structure and activity in plasmodium purine nucleoside phosphorylases. | purine nucleoside phosphorylase (pnp) is central to purine salvage mechanisms in plasmodium parasites, the causative agents of malaria. most human malaria results from infection either by plasmodium falciparum (pf), the deadliest form of the parasite, or by the widespread plasmodium vivax (pv). whereas the pnp enzyme from pf has previously been studied in detail, despite the prevalence of pv little is known about many of the key metabolic enzymes from this parasite, including pvpnp. | 2009 | 19575810 |
| domain features of the peripheral stalk subunit h of the methanogenic a1ao atp synthase and the nmr solution structure of h(1-47). | a series of truncated forms of subunit h were generated to establish the domain features of that protein. circular dichroism analysis demonstrated that h is divided at least into a c-terminal coiled-coil domain within residues 54-104, and an n-terminal domain formed by adjacent alpha-helices. with a cysteine at the c-terminus of each of the truncated proteins (h(1-47), h(1-54), h(1-59), h(1-61), h(1-67), h(1-69), h(1-71), h(1-78), h(1-80), h(1-91), and h(47-105)), the residues involved in format ... | 2009 | 19580766 |
| inactivation and unfolding of the hyperthermophilic inorganic pyrophosphatase from thermus thermophilus by sodium dodecyl sulfate. | inorganic pyrophosphatase (ppase, ec 3.6.1.1) is an essential constitutive enzyme for energy metabolism and clearance of excess pyrophosphate. in this research, we investigated the sodium dodecyl sulfate (sds)-induced inactivation and unfolding of ppase from thermus thermophilus (t-ppase), a hyperthermophilic enzyme. the results indicated that like many other mesophilic enzymes, t-ppase could be fully inactivated at a low sds concentration of 2 mm. using an enzyme activity assay, sds was shown t ... | 2009 | 19582233 |
| the closest relatives of icosahedral viruses of thermophilic bacteria are among viruses and plasmids of the halophilic archaea. | we have sequenced the genome and identified the structural proteins and lipids of the novel membrane-containing, icosahedral virus p23-77 of thermus thermophilus. p23-77 has an approximately 17-kb circular double-stranded dna genome, which was annotated to contain 37 putative genes. virions were subjected to dissociation analysis, and five protein species were shown to associate with the internal viral membrane, while three were constituents of the protein capsid. analysis of the bacteriophage g ... | 2009 | 19587059 |
| sequence-based analysis of protein energy landscapes reveals nonuniform thermal adaptation within the proteome. | thermal adaptation of individual proteins is often achieved through modulating protein stability, with proteins that are adapted to extreme cold environments having increased conformational flexibility when brought to mesophilic conditions. conversely, proteins adapted to higher temperatures appear less dynamic and are found to be much more stable against thermal denaturation than their mesophilic counterparts. according to the current paradigm, the adaptation of an organism for survival at high ... | 2009 | 19592668 |
| a structural view on the mechanism of the ribosome-catalyzed peptide bond formation. | the ribosome is a large ribonucleoprotein particle that translates genetic information encoded in mrna into specific proteins. its highly conserved active site, the peptidyl-transferase center (ptc), is located on the large (50s) ribosomal subunit and is comprised solely of rrna, which makes the ribosome the only natural ribozyme with polymerase activity. the last decade witnessed a rapid accumulation of atomic-resolution structural data on both ribosomal subunits as well as on the entire riboso ... | 2009 | 19595805 |
| card is an essential regulator of rrna transcription required for mycobacterium tuberculosis persistence. | mycobacterium tuberculosis is arguably the world's most successful infectious agent because of its ability to control its own cell growth within the host. bacterial growth rate is closely coupled to rrna transcription, which in e. coli is regulated through dksa and (p)ppgpp. the mechanisms of rrna transcriptional control in mycobacteria, which lack dksa, are undefined. here we identify card as an essential mycobacterial protein that controls rrna transcription. loss of card is lethal for mycobac ... | 2009 | 19596241 |
| conformational changes in redox pairs of protein structures. | disulfides are conventionally viewed as structurally stabilizing elements in proteins but emerging evidence suggests two disulfide subproteomes exist. one group mediates the well known role of structural stabilization. a second redox-active group are best known for their catalytic functions but are increasingly being recognized for their roles in regulation of protein function. redox-active disulfides are, by their very nature, more susceptible to reduction than structural disulfides; and conver ... | 2009 | 19598234 |
| probing the relationship between gram-negative and gram-positive s1 proteins by sequence analysis. | escherichia coli ribosomal protein s1 is required for the translation initiation of messenger rnas, in particular when their shine-dalgarno sequence is degenerated. closely related forms of the protein, composed of the same number of domains (six), are found in all gram-negative bacteria. more distant proteins, generally formed of fewer domains, have been identified, by sequence similarities, in gram-positive bacteria and are also termed 's1 proteins'. however in the absence of functional inform ... | 2009 | 19605565 |
| functional role for the conformationally mobile phenylalanine 223 in the reaction of methylenetetrahydrofolate reductase from escherichia coli. | the flavoprotein methylenetetrahydrofolate reductase from escherichia coli catalyzes the reduction of 5,10-methylenetetrahydrofolate (ch(2)-h(4)folate) by nadh via a ping-pong reaction mechanism. structures of the reduced enzyme in complex with nadh and of the oxidized glu28gln enzyme in complex with ch(3)-h(4)folate [pejchal, r., sargeant, r., and ludwig, m. l. (2005) biochemistry 44, 11447-11457] have revealed phe223 as a conformationally mobile active site residue. in the nadh complex, the na ... | 2009 | 19610625 |
| purification and biochemical characterization of a specific beta-glucosidase from the digestive fluid of larvae of the palm weevil, rhynchophorus palmarum. | a beta-glucosidase was purified from the digestive fluid of the palm weevil rhynchophorus palmarum l. (coleoptera: curculionidae) by chromatography on anion-exchange, gel filtration, and hydrophobic interaction columns. the preparation was shown to be homogeneous on polyacrylamide gels, beta-glucosidase is a monomeric protein with a molecular weight of 58 kda based on its mobility in sds-page and 60 kda based on gel filtration. maximal beta-glucosidase activity occurred at 55 degrees c and ph 5. ... | 2009 | 19611239 |
| global stabilization of rrna structure by ribosomal proteins s4, s17, and s20. | ribosomal proteins stabilize the folded structure of the ribosomal rna and enable the recruitment of further proteins to the complex. quantitative hydroxyl radical footprinting was used to measure the extent to which three different primary assembly proteins, s4, s17, and s20, stabilize the three-dimensional structure of the escherichia coli 16s 5' domain. the stability of the complexes was perturbed by varying the concentration of mgcl(2). each protein influences the stability of the ribosomal ... | 2009 | 19616559 |
| an examination of the relationship between active site loop size and thermodynamic activation parameters for orotidine 5'-monophosphate decarboxylase from mesophilic and thermophilic organisms. | closure of the active site phosphate gripper loop of orotidine 5'-monophosphate decarboxylase from saccharomyces cerevisiae (scompdc) over the bound substrate orotidine 5'-monophosphate (omp) activates the bound substrate for decarboxylation by at least 10(4)-fold [amyes, t. l., richard, j. p., and tait, j. j. (2005) j. am. chem. soc. 127, 15708-15709]. the 19-residue phosphate gripper loop of the mesophilic scompdc is much larger than the nine-residue loop at the ortholog from the thermophile m ... | 2009 | 19618917 |
| structural and functional studies of the thermus thermophilus 16s rrna methyltransferase rsmg. | the rsmg methyltransferase is responsible for n(7) methylation of g527 of 16s rrna in bacteria. here, we report the identification of the thermus thermophilus rsmg gene, the isolation of rsmg mutants, and the solution of rsmg x-ray crystal structures at up to 1.5 a resolution. like their counterparts in other species, t. thermophilus rsmg mutants are weakly resistant to the aminoglycoside antibiotic streptomycin. growth competition experiments indicate a physiological cost to loss of rsmg activi ... | 2009 | 19622680 |
| binding and cleavage specificities of human argonaute2. | the endonuclease argonaute2 (ago2) mediates the degradation of the target mrna within the rna-induced silencing complex. we determined the binding and cleavage properties of recombinant human ago2. human ago2 was unable to cleave preformed rna duplexes and exhibited weaker binding affinity for rna duplexes compared with the single strand rna. the enzyme exhibited greater rnase h activity in the presence of mn2+ compared with mg2+. human ago2 exhibited weaker binding affinities and reduced cleava ... | 2009 | 19625255 |
| structural characterization of a viral neil1 ortholog unliganded and bound to abasic site-containing dna. | endonuclease viii (nei) is a dna glycosylase of the base excision repair pathway that recognizes and excises oxidized pyrimidines. we determined the crystal structures of a neil1 ortholog from the giant mimivirus (mvnei1) unliganded and bound to dna containing tetrahydrofuran (thf), which is the first structure of any nei with an abasic site analog. the mvnei1 structures exhibit the same overall architecture as other enzymes of the fpg/nei family, which consists of two globular domains joined by ... | 2009 | 19625256 |
| increasing protein stability by improving beta-turns. | our goal was to gain a better understanding of how protein stability can be increased by improving beta-turns. we studied 22 beta-turns in nine proteins with 66-370 residues by replacing other residues with proline and glycine and measuring the stability. these two residues are statistically preferred in some beta-turn positions. we studied: cold shock protein b (cspb), histidine-containing phosphocarrier protein, ubiquitin, ribonucleases sa2, sa3, t1, and hi, tryptophan synthetase alpha-subunit ... | 2009 | 19626709 |
| structural basis for the mechanism of respiratory complex i. | complex i plays a central role in cellular energy production, coupling electron transfer between nadh and quinone to proton translocation. the mechanism of this highly efficient enzyme is currently unknown. mitochondrial complex i is a major source of reactive oxygen species, which may be one of the causes of aging. dysfunction of complex i is implicated in many human neurodegenerative diseases. we have determined several x-ray structures of the oxidized and reduced hydrophilic domain of complex ... | 2009 | 19635800 |
| acyl-coa dehydrogenases: dynamic history of protein family evolution. | the acyl-coa dehydrogenases (acads) are enzymes that catalyze the alpha,beta-dehydrogenation of acyl-coa esters in fatty acid and amino acid catabolism. eleven acads are now recognized in the sequenced human genome, and several homologs have been reported from bacteria, fungi, plants, and nematodes. we performed a systematic comparative genomic study, integrating homology searches with methods of phylogenetic reconstruction, to investigate the evolutionary history of this family. sequence analys ... | 2009 | 19639238 |
| horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein s4. | the universal ribosomal protein s4 is essential for the initiation of small subunit ribosomal assembly and translational accuracy. being part of the information processing machinery of the cell, the gene for s4 is generally thought of as being inherited vertically and has been used in concatenated gene phylogenies. here we report the evolution of ribosomal protein s4 in relation to a broad sharing of zinc/non-zinc forms of the gene and study the scope of horizontal gene transfer (hgt) of s4 duri ... | 2009 | 19640295 |
| crystal structure of a homolog of mammalian serine racemase from schizosaccharomyces pombe. | d-serine is an endogenous coagonist for the n-methyl-d-aspartate receptor and is involved in excitatory neurotransmission in the brain. mammalian pyridoxal 5'-phosphate-dependent serine racemase, which is localized in the mammalian brain, catalyzes the racemization of l-serine to yield d-serine and vice versa. the enzyme also catalyzes the dehydration of d- and l-serine. both reactions are enhanced by mg.atp in vivo. we have determined the structures of the following three forms of the mammalian ... | 2009 | 19640845 |
| hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16s rrna in the 30s ribosome. | conformational flexibility in structured rna frequently is critical to function. the 30s ribosomal subunit exists in different conformations in different functional states due to changes in the central part of the 16s rrna. we are interested in evaluating the factors that might be responsible for restricting flexibility to specific parts of the 16s rrna using biochemical data obtained from the 30s subunit in solution. this problem was approached taking advantage of the observation that there mus ... | 2009 | 19643000 |
| selection of peptides that target the aminoacyl-trna site of bacterial 16s ribosomal rna. | for almost five decades, antibiotics have been used successfully to control infectious diseases caused by bacterial pathogens. more recently, however, two-thirds of bacterial pathogens exhibit resistance and are continually evolving new resistance mechanisms against almost every clinically used antibiotic. novel efforts are required for the development of new drugs or drug leads to combat these infectious diseases. a number of antibiotics target the bacterial aminoacyl-trna site (a site) of 16s ... | 2009 | 19645415 |
| studying the salt dependence of the binding of sigma70 and sigma32 to core rna polymerase using luminescence resonance energy transfer. | the study of protein-protein interactions is becoming increasingly important for understanding the regulation of many cellular processes. the ability to quantify the strength with which two binding partners interact is desirable but the accurate determination of equilibrium binding constants is a difficult process. the use of luminescence resonance energy transfer (lret) provides a homogeneous binding assay that can be used for the detection of protein-protein interactions. previously, we develo ... | 2009 | 19649256 |
| large facilities and the evolving ribosome, the cellular machine for genetic-code translation. | well-focused x-ray beams, generated by advanced synchrotron radiation facilities, yielded high-resolution diffraction data from crystals of ribosomes, the cellular nano-machines that translate the genetic code into proteins. these structures revealed the decoding mechanism, localized the mrna path and the positions of the trna molecules in the ribosome and illuminated the interactions of the ribosome with initiation, release and recycling factors. they also showed that the ribosome is a ribozyme ... | 2009 | 19656820 |
| molecular design of beta-hairpin peptides for material construction. | self-assembled materials composed of beta-sheet forming peptides hold promise as therapeutics and novel biomaterials. this article focuses on the design and engineering of amphiphilic peptide sequences, especially beta-hairpins. peptides can be designed to intramolecularly fold and then self-assemble on cue, affording hydrogels rich in beta-sheet structure. hydrogels having distinct material properties can be designed at the molecular level by modulating either the peptide's sequence or the envi ... | 2008 | 19662109 |
| evolved beta-galactosidases from geobacillus stearothermophilus with improved transgalactosylation yield for galacto-oligosaccharide production. | a mutagenesis approach was applied to the beta-galactosidase bgab from geobacillus stearothermophilus kve39 in order to improve its enzymatic transglycosylation of lactose into oligosaccharides. a simple screening strategy, which was based on the reduction of the hydrolysis of a potential transglycosylation product (lactosucrose), provided mutant enzymes possessing improved synthetic properties for the autocondensation product from nitrophenyl-galactoside and galacto-oligosaccharides (gos) from ... | 2009 | 19666723 |
| subcomplex ilambda specifically controls integrated mitochondrial functions in caenorhabditis elegans. | complex i dysfunction is a common, heterogeneous cause of human mitochondrial disease having poorly understood pathogenesis. the extensive conservation of complex i composition between humans and caenorhabditis elegans permits analysis of individual subunit contribution to mitochondrial functions at both the whole animal and mitochondrial levels. we provide the first experimentally-verified compilation of complex i composition in c. elegans, demonstrating 84% conservation with human complex i. i ... | 2009 | 19672299 |
| the uracil dna glycosylase udgb of mycobacterium smegmatis protects the organism from the mutagenic effects of cytosine and adenine deamination. | spontaneous hydrolytic deamination of dna bases represents a considerable mutagenic threat to all organisms, particularly those living in extreme habitats. cytosine is readily deaminated to uracil, which base pairs with adenine during replication, and most organisms encode at least one uracil dna glycosylase (udg) that removes this aberrant base from dna with high efficiency. adenine deaminates to hypoxanthine approximately 10-fold less efficiently, and its removal from dna in vivo has to date b ... | 2009 | 19684133 |
| crystal structure of human selenocysteine trna. | selenocysteine (sec) is the 21st amino acid in translation. sec trna (trna(sec)) has an anticodon complementary to the uga codon. we solved the crystal structure of human trna(sec). trna(sec) has a 9-bp acceptor stem and a 4-bp t stem, in contrast with the 7-bp acceptor stem and the 5-bp t stem in the canonical trnas. the acceptor stem is kinked between the u6:u67 and g7:c66 base pairs, leading to a bent acceptor-t stem helix. trna(sec) has a 6-bp d stem and a 4-nt d loop. the long d stem includ ... | 2009 | 19692584 |
| computational design of candida boidinii xylose reductase for altered cofactor specificity. | in this study we introduce a computationally-driven enzyme redesign workflow for altering cofactor specificity from nadph to nadh. by compiling and comparing data from previous studies involving cofactor switching mutations, we show that their effect cannot be explained as straightforward changes in volume, hydrophobicity, charge, or blosum62 scores of the residues populating the cofactor binding site. instead, we find that the use of a detailed cofactor binding energy approximation is needed to ... | 2009 | 19693930 |
| small molecule dnak modulators targeting the beta-domain. | the molecular chaperone dnak is essential for the survival of bacterial pathogens in the hostile environment of the host. hence, it is in principle a promising target for drug design but for which no current inhibitors are available apart from certain antimicrobial peptides. to this end, we have screened libraries of small molecules for their ability to interact with the substrate-binding domain of dnak. the most promising hit from the screen was synthesized and along with its analogs subjected ... | 2009 | 19694756 |
| immunoproteomic analysis of outer membrane proteins and extracellular proteins of actinobacillus pleuropneumoniae jl03 serotype 3. | actinobacillus pleuropneumoniae is the causative agent of porcine contagious pleuropneumonia, a highly contagious respiratory infection in pigs, and all the 15 serotypes are able to cause disease. current vaccines including subunit vaccines could not provide satisfactory protection against a. pleuropneumoniae. in this study, the immunoproteomic approach was applied to the analysis of extracellular and outer membrane proteins of a. pleuropneumoniae jl03 serotype 3 for the identification of novel ... | 2009 | 19695095 |
| formation of the first peptide bond: the structure of ef-p bound to the 70s ribosome. | elongation factor p (ef-p) is an essential protein that stimulates the formation of the first peptide bond in protein synthesis. here we report the crystal structure of ef-p bound to the thermus thermophilus 70s ribosome along with the initiator transfer rna n-formyl-methionyl-trna(i) (fmet-trna(i)(fmet)) and a short piece of messenger rna (mrna) at a resolution of 3.5 angstroms. ef-p binds to a site located between the binding site for the peptidyl trna (p site) and the exiting trna (e site). i ... | 2009 | 19696344 |
| metal uptake by manganese superoxide dismutase. | manganese superoxide dismutase is an important antioxidant defense metalloenzyme that protects cells from damage by the toxic oxygen metabolite, superoxide free radical, formed as an unavoidable by-product of aerobic metabolism. many years of research have gone into understanding how the metal cofactor interacts with small molecules in its catalytic role. in contrast, very little is presently known about how the protein acquires its metal cofactor, an important step in the maturation of the prot ... | 2009 | 19699328 |
| metal uptake by manganese superoxide dismutase. | manganese superoxide dismutase is an important antioxidant defense metalloenzyme that protects cells from damage by the toxic oxygen metabolite, superoxide free radical, formed as an unavoidable by-product of aerobic metabolism. many years of research have gone into understanding how the metal cofactor interacts with small molecules in its catalytic role. in contrast, very little is presently known about how the protein acquires its metal cofactor, an important step in the maturation of the prot ... | 2009 | 19699328 |
| genetic incorporation of a small, environmentally sensitive, fluorescent probe into proteins in saccharomyces cerevisiae. | here, we report that the fluorescent amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (anap), can be genetically incorporated into proteins in yeast with excellent selectivity and efficiency by means of an orthogonal trna/aminoacyl-trna synthetase pair. this small, environmentally sensitive fluorophore was site-specifically incorporated into escherichia coli glutamine binding protein and used to directly probe local structural changes caused by ligand binding. the small size of ... | 2009 | 19702307 |
| a paradigm shift for the amino acid editing mechanism of human cytoplasmic leucyl-trna synthetase. | leucyl-trna synthetase (leurs) has been identified as a target for a novel class of boron-containing small molecules that bind to its editing active site. when the 3' end of trna(leu) binds to the editing active site, the boron cross-links to the cis-diols of its terminal ribose. the cross-linked rna-protein complex blocks the overall aminoacylation activity of the enzyme. similar to those of other leurss, the human cytoplasmic enzyme (hscleurs) editing active site resides in a discrete domain c ... | 2009 | 19702327 |
| phosphorylated proteins of the mammalian mitochondrial ribosome: implications in protein synthesis. | mitochondria, the powerhouse of eukaryotic cells, have their own translation machinery that is solely responsible for synthesis of 13 mitochondrially encoded protein subunits of oxidative phosphorylation complexes. phosphorylation is a well-known post-translational modification in regulation of many processes in mammalian mitochondria including oxidative phosphorylation. however, there is still very limited knowledge on phosphorylation of mitochondrial ribosomal proteins and their role(s) in rib ... | 2009 | 19702336 |
| a rubisco mutant that confers growth under a normally "inhibitory" oxygen concentration. | ribulose-1,5-bisphosphate (rubp) carboxylase/oxygenase (rubisco) is a globally significant biocatalyst that facilitates the removal and sequestration of co2 from the biosphere. rubisco-catalyzed co2 reduction thus provides virtually all of the organic carbon utilized by living organisms. despite catalyzing the rate-limiting step of photosynthetic and chemoautotrophic co2 assimilation, rubisco is markedly inefficient as the competition between o2 and co2 for the same substrate limits the ability ... | 2009 | 19705820 |
| prokaryotic homologs of argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. | in eukaryotes, rna interference (rnai) is a major mechanism of defense against viruses and transposable elements as well of regulating translation of endogenous mrnas. the rnai systems recognize the target rna molecules via small guide rnas that are completely or partially complementary to a region of the target. key components of the rnai systems are proteins of the argonaute-piwi family some of which function as slicers, the nucleases that cleave the target rna that is base-paired to a guide r ... | 2009 | 19706170 |
| structural analysis of polarizing indels: an emerging consensus on the root of the tree of life. | the root of the tree of life has been a holy grail ever since darwin first used the tree as a metaphor for evolution. new methods seek to narrow down the location of the root by excluding it from branches of the tree of life. this is done by finding traits that must be derived, and excluding the root from the taxa those traits cover. however the two most comprehensive attempts at this strategy, performed by cavalier-smith and lake et al., have excluded each other's rootings. | 2009 | 19706177 |
| structure of era in complex with the 3' end of 16s rrna: implications for ribosome biogenesis. | era, composed of an n-terminal gtpase domain followed by an rna-binding kh domain, is essential for bacterial cell viability. it binds to 16s rrna and the 30s ribosomal subunit. however, its rna-binding site, the functional relationship between the two domains, and its role in ribosome biogenesis remain unclear. we have determined two crystal structures of era, a binary complex with gdp and a ternary complex with a gtp-analog and the 1531aucaccuccuua1542 sequence at the 3' end of 16s rrna. in th ... | 2009 | 19706445 |
| mechanism of adp-ribosylation removal revealed by the structure and ligand complexes of the dimanganese mono-adp-ribosylhydrolase drag. | adp-ribosylation is a ubiquitous regulatory posttranslational modification involved in numerous key processes such as dna repair, transcription, cell differentiation, apoptosis, and the pathogenic mechanism of certain bacterial toxins. despite the importance of this reversible process, very little is known about the structure and mechanism of the hydrolases that catalyze removal of the adp-ribose moiety. in the phototrophic bacterium rhodospirillum rubrum, dinitrogenase reductase-activating glyc ... | 2009 | 19706507 |
| nob1 binds the single-stranded cleavage site d at the 3'-end of 18s rrna with its pin domain. | ribosome assembly is a hierarchical process that involves pre-rrna folding, modification, and cleavage and assembly of ribosomal proteins. in eukaryotes, this process requires a macromolecular complex comprising over 200 proteins and rnas. whereas the rrna modification machinery is well-characterized, rrna cleavage to release mature rrnas is poorly understood, and in yeast, only 2 of 8 endonucleases have been identified. the essential and conserved ribosome assembly factor nob1 has been suggeste ... | 2009 | 19706509 |
| crystal structures and biochemical analyses suggest a unique mechanism and role for human glycyl-trna synthetase in ap4a homeostasis. | aminoacyl-trna synthetases catalyze the attachment of amino acids to their cognate trnas for protein synthesis. however, the aminoacylation reaction can be diverted to produce diadenosine tetraphosphate (ap4a), a universal pleiotropic signaling molecule needed for cell regulation pathways. the only known mechanism for ap4a production by a trna synthetase is through the aminoacylation reaction intermediate aminoacyl-amp, thus making ap4a synthesis amino acid-dependent. here, we demonstrate a new ... | 2009 | 19710017 |
| structure of escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site. | three new structures of escherichia coli succinate-quinone oxidoreductase (sqr) have been solved. one with the specific quinone-binding site (q-site) inhibitor carboxin present has been solved at 2.4 a resolution and reveals how carboxin inhibits the q-site. the other new structures are with the q-site inhibitor pentachlorophenol and with an empty q-site. these structures reveal important details unresolved in earlier structures. comparison of the new sqr structures shows how subtle rearrangemen ... | 2009 | 19710024 |
| the thermus thermophilus dead box helicase hera contains a modified rna recognition motif domain loosely connected to the helicase core. | dead box family helicases consist of a helicase core that is formed by two flexibly linked reca-like domains. the helicase activity can be regulated by n- or c-terminal extensions flanking the core. thermus thermophilus heat resistant rna-dependent atpase (hera) is the first dead box helicase that forms a dimer using a unique dimerization domain. in addition to the dimerization domain, hera contains a c-terminal rna binding domain (rbd) that shares sequence homology only to uncharacterized prote ... | 2009 | 19710183 |
| the yeast iron regulatory proteins grx3/4 and fra2 form heterodimeric complexes containing a [2fe-2s] cluster with cysteinyl and histidyl ligation. | the transcription of iron uptake and storage genes in saccharomyces cerevisiae is primarily regulated by the transcription factor aft1. nucleocytoplasmic shuttling of aft1 is dependent upon mitochondrial fe-s cluster biosynthesis via a signaling pathway that includes the cytosolic monothiol glutaredoxins (grx3 and grx4) and the bola homologue fra2. however, the interactions between these proteins and the iron-dependent mechanism by which they control aft1 localization are unclear. to reconstitut ... | 2009 | 19715344 |
| identification of x-ding-cd4, a new member of human ding protein family that is secreted by hiv-1 resistant cd4(+) t cells and has anti-viral activity. | we reported previously the anti-viral activity named hrf (hiv-1 resistance factor) secreted by hiv-1 resistant cells. this work describes the identification of hrf from cell culture supernatant of hrf-producing cells (hrf(+) cells). employing the proteomics and cell based activity assay we recovered ten peptides sharing 80-93% sequence homology with other eukaryotic ding proteins; discrete amino acid characteristics found in our material suggested that hrf is a new member of ding proteins family ... | 2009 | 19720052 |
| interaction of the thermoplasma acidophilum a1a0-atp synthase peripheral stalk with the catalytic domain. | the peripheral stalk of the archaeal atp synthase (a1a0)-atp synthase is formed by the heterodimeric eh complex and is part of the stator domain, which counteracts the torque of rotational catalysis. here we used nuclear magnetic resonance spectroscopy to probe the interaction of the c-terminal domain of the eh heterodimer (e(ct1)h(ct)) with the n-terminal 23 residues of the b subunit (b(nt)). the data show a specific interaction of b(nt) peptide with 26 residues of the e(ct1)h(ct) domain, there ... | 2009 | 19720061 |
| characterization of two seryl-trna synthetases in albomycin-producing streptomyces sp. strain atcc 700974. | the trojan horse antibiotic albomycin, produced by streptomyces sp. strain atcc 700974, contains a thioribosyl nucleoside moiety linked to a hydroxamate siderophore through a serine residue. the seryl nucleoside structure (sb-217452) is a potent inhibitor of seryl-trna synthetase (serrs) in the pathogenic bacterium staphylococcus aureus, with a 50% inhibitory concentration (ic(50)) of approximately 8 nm. in the albomycin-producing streptomyces sp., a bacterial serrs homolog (alb10) was found to ... | 2009 | 19721072 |
| a non-canonical dna structure enables homologous recombination in various genetic systems. | homologous recombination, which is critical to genetic diversity, depends on homologous pairing (hp). hp is the switch from parental to recombinant base pairs, which requires expansion of inter-base pair spaces. this expansion unavoidably causes untwisting of the parental double-stranded dna. reca/rad51-catalyzed atp-dependent hp is extensively stimulated in vitro by negative supercoils, which compensates for untwisting. however, in vivo, double-stranded dna is relaxed by bound proteins and thus ... | 2009 | 19729448 |
| the structure of eukaryotic and prokaryotic complex i. | the structures of the nadh dehydrogenases from bos taurus and aquifex aeolicus have been determined by 3d electron microscopy, and have been analyzed in comparison with the previously determined structure of complex i from yarrowia lipolytica. the results show a clearly preserved domain structure in the peripheral arm of complex i, which is similar in the bacterial and eukaryotic complex. the membrane arms of both eukaryotic complexes show a similar shape but also significant differences in dist ... | 2010 | 19732833 |
| the structure of eukaryotic and prokaryotic complex i. | the structures of the nadh dehydrogenases from bos taurus and aquifex aeolicus have been determined by 3d electron microscopy, and have been analyzed in comparison with the previously determined structure of complex i from yarrowia lipolytica. the results show a clearly preserved domain structure in the peripheral arm of complex i, which is similar in the bacterial and eukaryotic complex. the membrane arms of both eukaryotic complexes show a similar shape but also significant differences in dist ... | 2010 | 19732833 |
| identification of amino acids in the n-terminal domain of atypical methanogenic-type seryl-trna synthetase critical for trna recognition. | seryl-trna synthetase (serrs) from methanogenic archaeon methanosarcina barkeri, contains an idiosyncratic n-terminal domain, composed of an antiparallel beta-sheet capped by a helical bundle, connected to the catalytic core by a short linker peptide. it is very different from the coiled-coil trna binding domain in bacterial-type serrs. because the crystal structure of the methanogenic-type serrsxtrna complex has not been obtained, a docking model was produced, which indicated that highly conser ... | 2009 | 19734148 |
| biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from pyrococcus furiosus. | apurinic/apyrimidinic (ap) sites are the most frequently found mutagenic lesions in dna, and they arise mainly from spontaneous base loss or modified base removal by damage-specific dna glycosylases. ap sites are cleaved by ap endonucleases, and the resultant gaps in the dna are repaired by dna polymerase/dna ligase reactions. we identified the gene product that is responsible for the ap endonuclease activity in the hyperthermophilic euryarchaeon, pyrococcus furiosus. furthermore, we detected th ... | 2009 | 19734344 |
| srmb, a dead-box helicase involved in escherichia coli ribosome assembly, is specifically targeted to 23s rrna in vivo. | dead-box proteins play specific roles in remodeling rna or ribonucleoprotein complexes. yet, in vitro, they generally behave as nonspecific rna-dependent atpases, raising the question of what determines their specificity in vivo. srmb, one of the five escherichia coli dead-box proteins, participates in the assembly of the large ribosomal subunit. moreover, when overexpressed, it compensates for a mutation in l24, the ribosomal protein (r-protein) thought to initiate assembly. here, using the tan ... | 2009 | 19734346 |
| the interaction of bacillus subtilis sigmaa with rna polymerase. | rna polymerase (rnap) is an essential and highly conserved enzyme in all organisms. the process of transcription initiation is fundamentally different between prokaryotes and eukaryotes. in prokaryotes, initiation is regulated by sigma factors, making the essential interaction between sigma factors and rnap an attractive target for antimicrobial agents. our objective was to achieve the first step in the process of developing novel antimicrobial agents, namely to prove experimentally that the int ... | 2009 | 19735077 |
| continuous-wave and pulsed epr characterization of the [2fe-2s](cys)3(his)1 cluster in rat mitoneet. | cw epr spectra of reduced [2fe-2s](cys)(3)(his)(1) clusters of mammalian mitoneet soluble domain appear to produce features resulting from the interaction of the electron spins of the two adjacent clusters, which can be explained by employing the local spin model. this model favors the reduction of the outermost iron with his87 and cys83 ligands, which is supported by orientation-selected hyperfine sublevel correlation (hyscore) characterization of the uniformly (15)n-labeled mitoneet showing on ... | 2009 | 19736979 |
| characterization of rimo, a new member of the methylthiotransferase subclass of the radical sam superfamily. | rimo, encoded by the ylig gene in escherichia coli, has been recently identified in vivo as the enzyme responsible for the attachment of a methylthio group on the beta-carbon of asp88 of the small ribosomal protein s12 [anton, b. p., saleh, l., benner, j. s., raleigh, e. a., kasif, s., and roberts, r. j. (2008) proc. natl. acad. sci. u.s.a. 105, 1826-1831]. to date, it is the only enzyme known to catalyze methylthiolation of a protein substrate; the four other naturally occurring methylthio modi ... | 2009 | 19736993 |
| promiscuous substrate recognition in folding and assembly activities of the trigger factor chaperone. | trigger factor (tf) is a molecular chaperone that binds to bacterial ribosomes where it contacts emerging nascent chains, but tf is also abundant free in the cytosol where its activity is less well characterized. in vitro studies show that tf promotes protein refolding. we find here that ribosome-free tf stably associates with and rescues from misfolding a large repertoire of full-length proteins. we identify over 170 members of this cytosolic escherichia coli tf substrate proteome, including ri ... | 2009 | 19737520 |
| p38sj, a novel dingg protein protects neuronal cells from alcohol induced injury and death. | ethanol induces neuronal cell injury and death by dysregulating several signaling events that are controlled, in part, by activation of mapk/erk1/2 and/or inactivation of its corresponding phosphatase, pp1. recently, we have purified a novel protein of 38 kda in size, p38sj, from a callus culture of hypericum perforatum, which belongs to an emerging dingg family of proteins with phosphate binding activity. here, we show that treatment of neuronal cells with p38sj protects cells against injury in ... | 2009 | 19739100 |
| structural insights into the mechanism of the allosteric transitions of mycobacterium tuberculosis camp receptor protein. | the camp receptor protein (crp) from mycobacterium tuberculosis is a camp-responsive global transcriptional regulator, responsible for the regulation of a multitude of diverse proteins. we have determined the crystal structures of the crp.camp and crp.n(6)-camp derivative-bound forms of the enzyme to 2.2- and 2.3 a-resolution, respectively, to investigate camp-mediated conformational and structural changes. the allosteric switch from the open, inactive conformation to the closed, active conforma ... | 2009 | 19740754 |
| dual role of dna in regulating atp hydrolysis by the sopa partition protein. | in bacteria, mitotic stability of plasmids and many chromosomes depends on replicon-specific systems, which comprise a centromere, a centromere-binding protein and an atpase. dynamic self-assembly of the atpase appears to enable active partition of replicon copies into cell-halves, but for walker-box partition atpases the molecular mechanism is unknown. atpase activity appears to be essential for this process. dna and centromere-binding proteins are known to stimulate the atpase activity but mol ... | 2009 | 19740757 |
| the dimeric proto-ribosome: structural details and possible implications on the origin of life. | a symmetric pocket-like entity, composed of two l-shaped rna units, encircles the peptide synthesis site within the contemporary ribosome. this entity was suggested to be the vestige of a dimeric proto-ribosome, which could have formed spontaneously in the prebiotic world, catalyzing non-coded peptide bond formation and elongation. this structural element, beyond offering the initial step in the evolution of translation, is hypothesized here to be linked to the origin of life. by catalyzing the ... | 2009 | 19742176 |
| in vitro metal uptake by recombinant human manganese superoxide dismutase. | metal uptake by the antioxidant defense metalloenzyme manganese superoxide dismutase (mnsod) is an essential step in the functional maturation of the protein that is just beginning to be investigated in detail. we have extended earlier in vitro studies on metal binding by the dimeric escherichia coli apo-mnsod to investigate the mechanism of metal uptake by tetrameric human and thermus thermophilus apo-mnsods. like the e. coli apo-mnsod, these proteins also bind metal ions in vitro in a thermall ... | 2009 | 19755112 |