Publications

cardiac mitochondrial matrix and respiratory complex protein phosphorylation.	it has become appreciated over the last several years that protein phosphorylation within the cardiac mitochondrial matrix and respiratory complexes is extensive. given the importance of oxidative phosphorylation and the balance of energy metabolism in the heart, the potential regulatory effect of these classical signaling events on mitochondrial function is of interest. however, the functional impact of protein phosphorylation and the kinase/phosphatase system responsible for it are relatively ...	2012	22886415
structure of the rna claw of the dna packaging motor of bacteriophage φ29.	bacteriophage dna packaging motors translocate their genomic dna into viral heads, compacting it to near-crystalline density. the bacillus subtilis phage 29 has a unique ring of rna (prna) that is an essential component of its motor, serving as a scaffold for the packaging atpase. previously, deletion of a three-base bulge (18-cca-20) in the prna a-helix was shown to abolish packaging activity. here, we solved the structure of this crucial bulge by nuclear magnetic resonance (nmr) using a 27mer ...	2012	22879380
characterization of crispr rna processing in clostridium thermocellum and methanococcus maripaludis.	the crispr arrays found in many bacteria and most archaea are transcribed into a long precursor rna that is processed into small clustered regularly interspaced short palindromic repeats (crispr) rnas (crrnas). these rna molecules can contain fragments of viral genomes and mediate, together with a set of crispr-associated (cas) proteins, the prokaryotic immunity against viral attacks. crispr/cas systems are diverse and the cas6 enzymes that process crrnas vary between different subtypes. we anal ...	2012	22879377
functional expression of a penicillin acylase from the extreme thermophile thermus thermophilus hb27 in escherichia coli.	penicillin acylases (pacs) are enzymes of industrial relevance in the manufacture of β-lactam antibiotics. development of a pac with a longer half-life under the reaction conditions used is essential for the improvement of the operational stability of the process. a gene encoding a homologue to escherichia coli pac was found in the genome of the thermophilic bacterium thermus thermophilus (tth) hb27. because of the nature of this pac and its complex maturation that is crucial to reach its functi ...	2012	22876915
crystallization and preliminary x-ray diffraction analysis of a fatty-acid metabolism regulatory protein, fadr, from bacillus halodurans.	fadr is an acyl-coa-dependent transcription factor which regulates genes encoding proteins involved in fatty-acid degradation and synthesis in order to maintain lipid homeostasis. fadr from the alkaliphilic bacterium bacillus halodurans was cloned and overexpressed in escherichia coli. the fadr (bh3102) protein from b. halodurans is composed of 195 amino-acid residues with a molecular mass of 22 378 da. crystals were obtained by the sitting-drop vapour-diffusion method and diffracted to 2.05 å r ...	2012	22869136
crystallization and preliminary x-ray analysis of pac17 from the pacidamycin-biosynthetic cluster of streptomyces coeruleorubidus.	pac17 is an uncharacterized protein from the pacidamycin gene cluster of the soil bacterium streptomyces coeruleorubidus. it is implicated in the biosynthesis of the core diaminobutyric acid residue of the antibiotic, although its precise role is uncertain at present. given that pacidamycins inhibit translocase i of pseudomonas aeruginosa, a clinically unexploited antibiotic target, they offer new hope in the search for antibacterial agents directed against this important pathogen. crystals of p ...	2012	22869135
crystallization and preliminary crystallographic analysis of the c-terminal domain of mamm, a magnetosome-associated protein from magnetospirillum gryphiswaldense msr-1.	mamm is a unique magnetosome-associated protein that shares substantial homology with cation diffusion facilitator (cdf) proteins, a group of heavy-metal-ion efflux transporters that participate in metal-ion homeostasis in all domains of life. magnetotactic bacteria utilize cdf proteins in iron-oxide biomineralization and in magnetosome formation. here, the crystallization and preliminary x-ray analysis of recombinant magnetospirillum gryphiswaldense mamm is reported. the c-terminal domain of ma ...	2012	22869124
characterization of a novel subgroup of extracellular medium-chain-length polyhydroxyalkanoate depolymerases from actinobacteria.	nineteen medium-chain-length (mcl) poly(3-hydroxyalkanoate) (pha)-degrading microorganisms were isolated from natural sources. from them, seven gram-positive and three gram-negative bacteria were identified. the ability of these microorganisms to hydrolyze other biodegradable plastics, such as short-chain-length (scl) pha, poly(ε-caprolactone) (pcl), poly(ethylene succinate) (pes), and poly(l-lactide) (pla), has been studied. on the basis of the great ability to degrade different polyesters, str ...	2012	22865072
altered large-ring cyclodextrin product profile due to a mutation at tyr-172 in the amylomaltase of corynebacterium glutamicum.	corynebacterium glutamicum amylomaltase (cgam) catalyzes the formation of large-ring cyclodextrins (lr-cds) with a degree of polymerization of 19 and higher. the cloned cgam gene was ligated into the pet-17b vector and used to transform escherichia coli bl21(de3). site-directed mutagenesis of tyr-172 in cgam to alanine (y172a) was performed to determine its role in the control of lr-cd production. both the recombinant wild-type (wt) and y172a enzymes were purified to apparent homogeneity and cha ...	2012	22865069
a three-dimensional topology of complex i inferred from evolutionary correlations.	the quaternary structure of eukaryotic nadh:ubiquinone oxidoreductase (complex i), the largest complex of the oxidative phosphorylation, is still mostly unresolved. furthermore, it is unknown where transiently bound assembly factors interact with complex i. we therefore asked whether the evolution of complex i contains information about its 3d topology and the binding positions of its assembly factors. we approached these questions by correlating the evolutionary rates of eukaryotic complex i su ...	2012	22857522
the deactive form of respiratory complex i from mammalian mitochondria is a na+/h+ antiporter.	in mitochondria, complex i (nadh:ubiquinone oxidoreductase) uses the redox potential energy from nadh oxidation by ubiquinone to transport protons across the inner membrane, contributing to the proton-motive force. however, in some prokaryotes, complex i may transport sodium ions instead, and three subunits in the membrane domain of complex i are closely related to subunits from the mrp family of na(+)/h(+) antiporters. here, we define the relationship between complex i from bos taurus heart mit ...	2012	22854968
mechanisms of secm-mediated stalling in the ribosome.	nascent-peptide modulation of translation is a common regulatory mechanism of gene expression. in this mechanism, while the nascent peptide is still in the exit tunnel of the ribosome, it induces translational pausing, thereby controlling the expression of downstream genes. one example is secm, which inhibits peptide-bond formation in the ribosome's peptidyl transferase center (ptc) during its own translation, upregulating the expression of the protein translocase seca. although biochemical expe ...	2012	22853911
phylogenetic position of aquificales based on the whole genome sequences of six aquificales species.	species belonging to the order aquificales are believed to be an early branching lineage within the bacteria. however, the branching order of this group in single-gene phylogenetic trees is highly variable; for example, it has also been proposed that the aquificales should be grouped with ε-proteobacteria. to investigate the phylogenetic position of aquificales at the whole-genome level, here we reconstructed the phylogenetic trees of 18 bacteria including six aquificales species based on the co ...	2012	22844640
dna stabilization at the bacillus subtilis polx core--a binding model to coordinate polymerase, ap-endonuclease and 3'-5' exonuclease activities.	family x dna polymerases (polxs) are involved in dna repair. their binding to gapped dnas relies on two conserved helix-hairpin-helix motifs, one located at the 8-kda domain and the other at the fingers subdomain. bacterial/archaeal polxs have a specifically conserved third helix-hairpin-helix motif (gfgxk) at the fingers subdomain whose putative role in dna binding had not been established. here, mutagenesis at the corresponding residues of bacillus subtilis polx (polxbs), gly130, gly132 and ly ...	2012	22844091
functional characterization of the role of the chromosome i partitioning system in genome segregation in deinococcus radiodurans.	deinococcus radiodurans, a radiation-resistant bacterium, harbors a multipartite genome. chromosome i contains three putative centromeres (segs1, segs2, and segs3), and para (para1) and parb (parb1) homologues. the parb1 interaction with segs was sequence specific, and para1 was shown to be a dna binding atpase. the atpase activity of para1 was stimulated when segs elements were coincubated with parb1, but the greatest increase was observed with segs3. para1 incubated with the segs-parb1 complex ...	2012	22843847
novel rapidly diversifiable antimicrobial rna polymerase switch region inhibitors with confirmed mode of action in haemophilus influenzae.	a series of inhibitors with a squaramide core was synthesized following its discovery in a high-throughput screen for novel inhibitors of a transcription-coupled translation assay using escherichia coli s30 extracts. the inhibitors were inactive when the plasmid substrate was replaced with mrna, suggesting they interfered with transcription. this was confirmed by their inhibition of purified e. coli rna polymerase. the series had antimicrobial activity against efflux-negative strains of e. coli ...	2012	22843845
nuclear rnase p of trypanosoma brucei: a single protein in place of the multicomponent rna-protein complex.	rnase p is the endonuclease that removes 5' extensions from trna precursors. in its best-known form, the enzyme is composed of a catalytic rna and a protein moiety variable in number and mass. this ribonucleoprotein enzyme is widely considered ubiquitous and apparently reached its highest complexity in the eukaryal nucleus, where it is typically composed of at least ten subunits. here, we show that in the protist trypanosoma brucei, two proteins are the sole forms of rnase p. they localize to th ...	2012	22840392
structural analysis of hypothetical proteins from helicobacter pylori: an approach to estimate functions of unknown or hypothetical proteins.	helicobacter pylori (h. pylori) have a unique ability to survive in extreme acidic environments and to colonize the gastric mucosa. it can cause diverse gastric diseases such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue (malt) lymphoma, gastric cancer, etc. based on genomic research of h. pylori, over 1600 genes have been functionally identified so far. however, h. pylori possess some genes that are uncharacterized since: (i) the gene sequences are quite new; (ii) the f ...	2012	22837682
multiple binding of repressed mrnas by the p-body protein rck/p54.	translational repression is achieved by protein complexes that typically bind 3' utr mrna motifs and interfere with the formation of the cap-dependent initiation complex, resulting in mrnps with a closed-loop conformation. we demonstrate here that the human dead-box protein rck/p54, which is a component of such complexes and central to p-body assembly, is in considerable molecular excess with respect to cellular mrnas and enriched to a concentration of 0.5 mm in p-bodies, where it is organized i ...	2012	22836354
go hybrid: em, crystallography, and beyond.	a mechanistic understanding of the molecular transactions that govern cellular function requires knowledge of the dynamic organization of the macromolecular machines involved in these processes. structural biologists employ a variety of biophysical methods to study large macromolecular complexes, but no single technique is likely to provide a complete description of the structure-function relationship of all the constituent components. since structural studies generally only provide snapshots of ...	2012	22835744
role of elongation and secondary pathways in s6 amyloid fibril growth.	the concerted action of a large number of individual molecular level events in the formation and growth of fibrillar protein structures creates a significant challenge for differentiating between the relative contributions of different self-assembly steps to the overall kinetics of this process. the characterization of the individual steps is, however, an important requirement for achieving a quantitative understanding of this general phenomenon which underlies many crucial functional and pathol ...	2012	22824281
from static structure to living protein: computational analysis of cytochrome c oxidase main-chain flexibility.	crystallographic structure and deuterium accessibility comparisons of cco in different redox states have suggested conformational changes of mechanistic significance. to predict the intrinsic flexibility and low energy motions in cco, this work has analyzed available high-resolution crystallographic structures with proflex and elnémo computational methods. the results identify flexible regions and potential conformational changes in cco that correlate well with published structural and biochemic ...	2012	22824280
protein l5 is crucial for in vivo assembly of the bacterial 50s ribosomal subunit central protuberance.	in the present work, ribosomes assembled in bacterial cells in the absence of essential ribosomal protein l5 were obtained. after arresting l5 synthesis, escherichia coli cells divide a limited number of times. during this time, accumulation of defective large ribosomal subunits occurs. these 45s particles lack most of the central protuberance (cp) components (5s rrna and proteins l5, l16, l18, l25, l27, l31, l33 and l35) and are not able to associate with the small ribosomal subunit. at the sam ...	2012	22821559
molecular characterization of nad+-dependent dna ligase from wolbachia endosymbiont of lymphatic filarial parasite brugia malayi.	the lymphatic filarial parasite, brugia malayi contains wolbachia endobacteria that are essential for development, viability and fertility of the parasite. therefore, wolbachial proteins have been currently seen as the potential antifilarial drug targets. nad(+)-dependent dna ligase is characterized as a promising drug target in several organisms due to its crucial, indispensable role in dna replication, recombination and dna repair. we report here the cloning, expression and purification of nad ...	2012	22815933
structural characterization of neutral and acidic glycolipids from thermus thermophilus hb8.	the structural characterization of glycolipids from thermus thermophilus hb8 was performed in this study. two neutral and one acidic glycolipids were extracted and purified by the modified tlc-blotting method, after which their chemical structures were determined by chemical composition analysis, mass spectrometry (ms) and nuclear magnetic resonance (nmr) spectroscopy. the structure of one of the neutral glycolipids, ngl-a, was galp(α1-6)glcpnacyl(β1-2)glcp(α1-)acyl(2)gro, and the other, ngl-c, ...	2012	22815675
molecular dynamics of a thermostable multicopper oxidase from thermus thermophilus hb27: structural differences between the apo and holo forms.	molecular dynamic (md) simulations have been performed on tth-mco, a hyperthermophilic multicopper oxidase from thermus thermophilus hb27, in the apo as well as the holo form, with the aim of exploring the structural dynamic properties common to the two conformational states. according to structural comparison between this enzyme and other mcos, the substrate in process to electron transfer in an outer-sphere event seems to transiently occupy a shallow and overall hydrophobic cavity near the cu ...	2012	22808237
structural basis for intersubunit signaling in a protein disaggregating machine.	clpb is a ring-forming, atp-dependent protein disaggregase that cooperates with the cognate hsp70 system to recover functional protein from aggregates. how clpb harnesses the energy of atp binding and hydrolysis to facilitate the mechanical unfolding of previously aggregated, stress-damaged proteins remains unclear. here, we present crystal structures of the clpb d2 domain in the nucleotide-bound and -free states, and the fitted cryoem structure of the d2 hexamer ring, which provide a structural ...	2012	22802670
re-visiting protein-centric two-tier classification of existing dna-protein complexes.	precise dna-protein interactions play most important and vital role in maintaining the normal physiological functioning of the cell, as it controls many high fidelity cellular processes. detailed study of the nature of these interactions has paved the way for understanding the mechanisms behind the biological processes in which they are involved. earlier in 2000, a systematic classification of dna-protein complexes based on the structural analysis of the proteins was proposed at two tiers, namel ...	2012	22800292
piecing together how a prokaryotic vov1-atpase works}: reconstitution of vacuolar-type rotary h+-atpase/synthase from thermus thermophilus.		2012	22798549
single-molecule analysis of translational dynamics.	decades of extensive biochemical and biophysical research have outlined the mechanism of translation. rich structural studies have provided detailed snapshots of the translational machinery at all phases of the translation cycle. however, the relationship between structural dynamics, composition, and function remains unknown. the multistep nature of each stage of the translation cycle results in rapid desynchronization of individual ribosomes, thus hindering elucidation of the underlying mechani ...	2012	22798542
the chbg gene of the chitobiose (chb) operon of escherichia coli encodes a chitooligosaccharide deacetylase.	the chb operon of escherichia coli is involved in the utilization of the β-glucosides chitobiose and cellobiose. the function of chbg (ydjc), the sixth open reading frame of the operon that codes for an evolutionarily conserved protein is unknown. we show that chbg encodes a monodeacetylase that is essential for growth on the acetylated chitooligosaccharides chitobiose and chitotriose but is dispensable for growth on cellobiose and chitosan dimer, the deacetylated form of chitobiose. the predict ...	2012	22797760
a lon-like protease with no atp-powered unfolding activity.	lon proteases are a family of atp-dependent proteases involved in protein quality control, with a unique proteolytic domain and an aaa(+) (atpases associated with various cellular activities) module accommodated within a single polypeptide chain. they were classified into two types as either the ubiquitous soluble lona or membrane-inserted archaeal lonb. in addition to the energy-dependent forms, a number of medically and ecologically important groups of bacteria encode a third type of lon-like ...	2012	22792246
the porphyrias: advances in diagnosis and treatment.	the inborn errors of heme biosynthesis, the porphyrias, are 8 genetically distinct metabolic disorders that can be classified as "acute hepatic," "hepatic cutaneous," and "erythropoietic cutaneous" diseases. recent advances in understanding their pathogenesis and molecular genetic heterogeneity have led to improved diagnosis and treatment. these advances include dna-based diagnoses for all the porphyrias, new understanding of the pathogenesis of the acute hepatic porphyrias, identification of th ...	2012	22791288
structural basis of biological nitrile reduction.	the enzyme quef catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preq(0)) to 7-aminomethyl-7-deazaguanine (preq(1)), the only nitrile reduction reaction known in biology. we describe here two crystal structures of bacillus subtilis quef, one of the wild-type enzyme in complex with the substrate preq(0), trapped as a covalent thioimide, a putative intermediate in the reaction, and the second of the c55a mutant in complex with the substrate preq(0) bound noncovalently. the q ...	2012	22787148
membrane protein structure determination using crystallography and lipidic mesophases: recent advances and successes.	the crystal structure of the β(2)-adrenergic receptor in complex with an agonist and its cognate g protein has just recently been determined. it is now possible to explore in molecular detail the means by which this paradigmatic transmembrane receptor binds agonist, communicates the impulse or signaling event across the membrane, and sets in motion a series of g protein-directed intracellular responses. the structure was determined using crystals of the ternary complex grown in a rationally desi ...	2012	22783824
capreomycin susceptibility is increased by tlya-directed 2'-o-methylation on both ribosomal subunits.	the binding site of the cyclic peptide antibiotics capreomycin and viomycin is located on the ribosomal subunit interface close to nucleotides c1409 in 16s rrna and c1920 in 23s rrna. in mycobacterium tuberculosis, the 2'-hydroxyls of both nucleotides are methylated by the enzyme tlya. loss of these methylations through inactivation of tlya confers resistance to capreomycin and viomycin. we report here that tlya orthologues occur in diverse bacteria and fall into two distinct groups. one group, ...	2012	22779429
site-directed mutagenesis of a family 42 β-galactosidase from an antarctic bacterium.	site directed mutagenesis was used to modify the active site of a cold active beta-galactosidase taken from an antarctic psychrotolerant planococcus bacterial isolate. the goal was to modify the active site such that there would be an increase in activity on certain substrates which showed little to no activity with the wild type enzyme. a total of 5 mutant enzymes were constructed with amino acid changes based on an analysis done via homology modeling. all 5 modified enzymes were assayed using ...	2012	22773960
mercury resistance and mercuric reductase activities and expression among chemotrophic thermophilic aquificae.	mercury (hg) resistance (mer) by the reduction of mercuric to elemental hg is broadly distributed among the bacteria and archaea and plays an important role in hg detoxification and biogeochemical cycling. mera is the protein subunit of the homodimeric mercuric reductase (mr) enzyme, the central function of the mer system. mera sequences in the phylum aquificae form the deepest-branching lineage in bayesian phylogenetic reconstructions of all known mera homologs. we therefore hypothesized that t ...	2012	22773655
structural basis for translation termination by archaeal rf1 and gtp-bound ef1α complex.	when a stop codon appears at the ribosomal a site, the class i and ii release factors (rfs) terminate translation. in eukaryotes and archaea, the class i and ii rfs form a heterodimeric complex, and complete the overall translation termination process in a gtp-dependent manner. however, the structural mechanism of the translation termination by the class i and ii rf complex remains unresolved. in archaea, archaeal elongation factor 1 alpha (aef1α), a carrier gtpase for trna, acts as a class ii r ...	2012	22772989
the scoi homologue senc is a copper binding protein that interacts directly with the cbb₃-type cytochrome oxidase in rhodobacter capsulatus.	sco proteins are widespread assembly factors for the cu(a) centre of aa₃-type cytochrome oxidases in eukaryotic and prokaryotic organisms. however, sco homologues are also found in bacteria like rhodobacter capsulatus which lack aa₃-type cytochrome oxidases and instead use a cbb₃-type cytochrome oxidase (cbb₃ cox) without a cu(a) centre as a terminal oxidase. in the current study, we have analyzed the role of sco (senc) during cbb₃ cox assembly in r. capsulatus. in agreement with earlier works, ...	2012	22771512
mechanism of elongation factor-g-mediated fusidic acid resistance and fitness compensation in staphylococcus aureus.	antibiotic resistance in bacteria is often associated with fitness loss, which is compensated by secondary mutations. fusidic acid (fa), an antibiotic used against pathogenic bacteria staphylococcus aureus, locks elongation factor-g (ef-g) to the ribosome after gtp hydrolysis. to clarify the mechanism of fitness loss and compensation in relation to fa resistance, we have characterized three s. aureus ef-g mutants with fast kinetics and crystal structures. our results show that a significantly sl ...	2012	22767604
oxidants and not alkylating agents induce rapid mtdna loss and mitochondrial dysfunction.	mitochondrial dna (mtdna) is essential for proper mitochondrial function and encodes 22 trnas, 2 rrnas and 13 polypeptides that make up subunits of complex i, iii, iv, in the electron transport chain and complex v, the atp synthase. although mitochondrial dysfunction has been implicated in processes such as premature aging, neurodegeneration, and cancer, it has not been shown whether persistent mtdna damage causes a loss of oxidative phosphorylation. we addressed this question by treating mouse ...	2012	22766155
structural insights into electron transfer in caa3-type cytochrome oxidase.	cytochrome c oxidase is a member of the haem copper oxidase superfamily (hco). hcos function as the terminal enzymes in the respiratory chain of mitochondria and aerobic prokaryotes, coupling molecular oxygen reduction to transmembrane proton pumping. integral to the enzyme's function is the transfer of electrons from cytochrome c to the oxidase via a transient association of the two proteins. electron entry and exit are proposed to occur from the same site on cytochrome c. here we report the cr ...	2012	22763450
the fragmented mitochondrial ribosomal rnas of plasmodium falciparum.	the mitochondrial genome in the human malaria parasite plasmodium falciparum is most unusual. over half the genome is composed of the genes for three classic mitochondrial proteins: cytochrome oxidase subunits i and iii and apocytochrome b. the remainder encodes numerous small rnas, ranging in size from 23 to 190 nt. previous analysis revealed that some of these transcripts have significant sequence identity with highly conserved regions of large and small subunit rrnas, and can form the expecte ...	2012	22761677
stoichiometry of proton pumping by the cbb3-type oxygen reductase in whole cells of rhodobacter capsulatus at ph 7 is about 0.5 h+ per electron.		2012	22761318
structural insights into the function of 23s rrna methyltransferase rlmg (m²g1835) from escherichia coli.	rlmg is a specific adomet-dependent methyltransferase (mtase) responsible for n²-methylation of g1835 in 23s rrna of escherichia coli. methylation of m²g1835 specifically enhances association of ribosomal subunits and provides a significant advantage for bacteria in osmotic and oxidative stress. here, the crystal structure of rlmg in complex with adomet and its structure in solution were determined. the structure of rlmg is similar to that of the mtase rsmc, consisting of two homologous domains: ...	2012	22753782
arrangement of subunits in intact mammalian mitochondrial atp synthase determined by cryo-em.	mitochondrial atp synthase is responsible for the synthesis of atp, a universal energy currency in cells. whereas x-ray crystallography has revealed the structure of the soluble region of the complex and the membrane-intrinsic c-subunits, little is known about the structure of the six other proteins (a, b, f, a6l, e, and g) that comprise the membrane-bound region of the complex in animal mitochondria. here, we present the structure of intact bovine mitochondrial atp synthase at ∼18 å resolution ...	2012	22753497
transcriptional repression mediated by a tetr family protein, pfmr, from thermus thermophilus hb8.	pfmr is one of four tetr family transcriptional regulators found in the extremely thermophilic bacterium, thermus thermophilus hb8. we identified three promoters with strong negative regulation by pfmr, both in vivo and in vitro. pfmr binds pseudopalindromic sequences, with the consensus sequence of 5'-taccgaccgntnggtn-3' surrounding the promoters. according to the amino acid sequence and three-dimensional structure analyses of the pfmr-regulated gene products, they are predicted to be involved ...	2012	22753056
fidaxomicin is an inhibitor of the initiation of bacterial rna synthesis.	fidaxomicin was recently approved for the treatment of clostridium difficile infection. it inhibits transcription by bacterial rna polymerase. because transcription is a multistep process, experiments were conducted in which fidaxomicin was added at different stages of transcriptional initiation to identify the blocked step. dna footprinting experiments were also conducted to further elucidate the stage inhibited. fidaxomicin blocks initiation only if added before the formation of the "open prom ...	2012	22752861
protection of bacillus pumilus spores by catalases.	bacillus pumilus safr-032, isolated at spacecraft assembly facilities of the national aeronautics and space administration jet propulsion laboratory, is difficult to kill by the sterilization method of choice, which uses liquid or vapor hydrogen peroxide. we identified two manganese catalases, yjqc and bpum_1305, in spore protein extracts of several b. pumilus strains by using page and mass spectrometric analyses. while the bpum_1305 catalase was present in six of the b. pumilus strains tested, ...	2012	22752169
the elongation, termination, and recycling phases of translation in eukaryotes.	this work summarizes our current understanding of the elongation and termination/recycling phases of eukaryotic protein synthesis. we focus here on recent advances in the field. in addition to an overview of translation elongation, we discuss unique aspects of eukaryotic translation elongation including eef1 recycling, eef2 modification, and eef3 and eif5a function. likewise, we highlight the function of the eukaryotic release factors erf1 and erf3 in translation termination, and the functions o ...	2012	22751155
structure of the signal transduction protein trap (target of rnaiii-activating protein).	the crystal structure of the signal transduction protein trap is reported at 1.85 å resolution. the structure of trap consists of a central eight-stranded β-barrel flanked asymmetrically by helices and is monomeric both in solution and in the crystal structure. a formate ion was found bound to trap identically in all four molecules in the asymmetric unit.	2012	22750855
mass spectrometry--from peripheral proteins to membrane motors.	that membrane protein complexes could survive in the gas phase had always seemed impossible. the lack of chargeable residues, high hydrophobicity, and poor solubility and the vast excess of detergent contributed to the view that it would not be possible to obtain mass spectra of intact membrane complexes. with the recent success in recording mass spectra of these complexes, first from recombinant sources and later from the cellular environment, many surprising properties of these gas phase membr ...	2012	22750574
the fpg/nei family of dna glycosylases: substrates, structures, and search for damage.	during the initial stages of the base excision dna repair pathway, dna glycosylases are responsible for locating and removing the majority of endogenous oxidative base lesions. the bifunctional formamidopyrimidine dna glycosylase (fpg) and endonuclease viii (nei) are members of the fpg/nei family, one of the two families of glycosylases that recognize oxidized dna bases, the other being the hhh/gpd (or nth) superfamily. structural and biochemical developments over the past decades have led to no ...	2012	22749143
dnak chaperone-dependent disaggregation by caseinolytic peptidase b (clpb) mutants reveals functional overlap in the n-terminal domain and nucleotide-binding domain-1 pore tyrosine.	protein disaggregation in escherichia coli is carried out by clpb, an aaa(+) (atpases associated with various cellular activities) molecular chaperone, together with the dnak chaperone system. conformational changes in clpb driven by atp binding and hydrolysis promote substrate binding, unfolding, and translocation. conserved pore tyrosines in both nucleotide-binding domain-1 (nbd-1) and -2 (nbd-2), which reside in flexible loops extending into the central pore of the clpb hexamer, bind substrat ...	2012	22745126
structural determinants of the β-selectivity of a bacterial aminotransferase.	chiral β-amino acids occur as constituents of various natural and synthetic compounds with potentially useful bioactivities. the pyridoxal 5'-phosphate (plp)-dependent s-selective transaminase from mesorhizobium sp. strain luk (mesat) is a fold type i aminotransferase that can be used for the preparation of enantiopure β-phe and derivatives thereof. using x-ray crystallography, we solved structures of mesat in complex with (s)-β-phe, (r)-3-amino-5-methylhexanoic acid, 2-oxoglutarate, and the inh ...	2012	22745123
molecular evolution of dihydrouridine synthases.	dihydrouridine (d) is a modified base found in conserved positions in the d-loop of trna in bacteria, eukaryota, and some archaea. despite the abundant occurrence of d, little is known about its biochemical roles in mediating trna function. it is assumed that d may destabilize the structure of trna and thus enhance its conformational flexibility. d is generated post-transcriptionally by the reduction of the 5,6-double bond of a uridine residue in rna transcripts. the reaction is carried out by d ...	2012	22741570
simulation of the opening and closing of hsp70 chaperones by coarse-grained molecular dynamics.	heat-shock proteins 70 (hsp70s) are key molecular chaperones which assist in the folding and refolding/disaggregation of proteins. hsp70s, which consist of a nucleotide-binding domain (nbd, consisting of nbd-i and nbd-ii subdomains) and a substrate-binding domain [sbd, further split into the β-sheet (sbd-β) and α-helical (sbd-α) subdomains], occur in two major conformations having (a) a closed sbd, in which the sbd and nbd domains do not interact, (b) an open sbd, in which sbd-α interacts with n ...	2012	22737044
structural study on the architecture of the bacterial atp synthase fo motor.	we purified the f(o) complex from the ilyobacter tartaricus na(+)-translocating f(1)f(o)-atp synthase and performed a biochemical and structural study. laser-induced liquid bead ion desorption ms analysis demonstrates that all three subunits of the isolated f(o) complex were present and in native stoichiometry (ab(2)c(11)). cryoelectron microscopy of 2d crystals yielded a projection map at a resolution of 7.0 å showing electron densities from the c(11) rotor ring and up to seven adjacent helices ...	2012	22736796
single-molecule analysis of inhibitory pausing states of v1-atpase.	v(1)-atpase, the hydrophilic v-atpase domain, is a rotary motor fueled by atp hydrolysis. here, we found that thermus thermophilus v(1)-atpase shows two types of inhibitory pauses interrupting continuous rotation: a short pause (sp, 4.2 s) that occurred frequently during rotation, and a long inhibitory pause (lp, >30 min) that terminated all active rotations. both pauses occurred at the same angle for atp binding and hydrolysis. kinetic analysis revealed that the time constants of inactivation i ...	2012	22736762
control of electron transport routes through redox-regulated redistribution of respiratory complexes.	in cyanobacteria, respiratory electron transport takes place in close proximity to photosynthetic electron transport, because the complexes required for both processes are located within the thylakoid membranes. the balance of electron transport routes is crucial for cell physiology, yet the factors that control the predominance of particular pathways are poorly understood. here we use a combination of tagging with green fluorescent protein and confocal fluorescence microscopy in live cells of t ...	2012	22733774
crystal structure of xenotropic murine leukaemia virus-related virus (xmrv) ribonuclease h.	rnase h (retroviral ribonuclease h) cleaves the phosphate backbone of the rna template within an rna/dna hybrid to complete the synthesis of double-stranded viral dna. in the present study we have determined the complete structure of the rnase h domain from xmrv (xenotropic murine leukaemia virus-related virus) rt (reverse transcriptase). the basic protrusion motif of the xmrv rnase h domain is folded as a short helix and an adjacent highly bent loop. structural superposition and subsequent muta ...	2012	22724525
structural constraints identified with covariation analysis in ribosomal rna.	covariation analysis is used to identify those positions with similar patterns of sequence variation in an alignment of rna sequences. these constraints on the evolution of two positions are usually associated with a base pair in a helix. while mutual information (mi) has been used to accurately predict an rna secondary structure and a few of its tertiary interactions, early studies revealed that phylogenetic event counting methods are more sensitive and provide extra confidence in the predictio ...	2012	22724009
reconstitution of translation from thermus thermophilus reveals a minimal set of components sufficient for protein synthesis at high temperatures and functional conservation of modern and ancient translation components.	thermus thermophilus is a thermophilic model organism distantly related to the mesophilic model organism e. coli. we reconstituted protein translation of thermus thermophilus in vitro from purified ribosomes, transfer ribonucleic acids (trnas) and 33 recombinant proteins. this reconstituted system was fully functional, capable of translating natural messenger rna (mrna) into active full-length proteins at temperatures up to 65°c and with yields up to 60 μg/ml. surprisingly, the synthesis of acti ...	2012	22723376
structure of yeast argonaute with guide rna.	the rna-induced silencing complex, comprising argonaute and guide rna, mediates rna interference. here we report the 3.2 å crystal structure of kluyveromyces polysporus argonaute (kpago) fortuitously complexed with guide rna originating from small-rna duplexes autonomously loaded by recombinant kpago. despite their diverse sequences, guide-rna nucleotides 1-8 are positioned similarly, with sequence-independent contacts to bases, phosphates and 2'-hydroxyl groups pre-organizing the backbone of nu ...	2012	22722195
thermodynamic characterization of rna 2 × 3 nucleotide internal loops.	to better elucidate rna structure-function relationships and to improve the design of pharmaceutical agents that target specific rna motifs, an understanding of rna primary, secondary, and tertiary structure is necessary. the prediction of rna secondary structure from sequence is an intermediate step in predicting rna three-dimensional structure. rna secondary structure is typically predicted using a nearest neighbor model based on free energy parameters. the current free energy parameters for 2 ...	2012	22720720
glutamine versus ammonia utilization in the nad synthetase family.	nad is a ubiquitous and essential metabolic redox cofactor which also functions as a substrate in certain regulatory pathways. the last step of nad synthesis is the atp-dependent amidation of deamido-nad by nad synthetase (nads). members of the nads family are present in nearly all species across the three kingdoms of life. in eukaryotic nads, the core synthetase domain is fused with a nitrilase-like glutaminase domain supplying ammonia for the reaction. this two-domain nads arrangement enabling ...	2012	22720044
polymorphisms in the mitochondrial ribosome recycling factor ef-g2mt/mef2 compromise cell respiratory function and increase atorvastatin toxicity.	mitochondrial translation, essential for synthesis of the electron transport chain complexes in the mitochondria, is governed by nuclear encoded genes. polymorphisms within these genes are increasingly being implicated in disease and may also trigger adverse drug reactions. statins, a class of hmg-coa reductase inhibitors used to treat hypercholesterolemia, are among the most widely prescribed drugs in the world. however, a significant proportion of users suffer side effects of varying severity ...	2012	22719265
reverse structural genomics: an unusual flavin-binding site in a putative protease from bacteroides thetaiotaomicron.	the structure of a putative protease from bacteroides thetaiotaomicron features an unprecedented binding site for flavin mononucleotide. the flavin isoalloxazine ring is sandwiched between two tryptophan residues in the interface of the dimeric protein. we characterized the recombinant protein with regard to its affinity for naturally occurring flavin derivatives and several chemically modified flavin analogs. dissociation constants were determined by isothermal titration calorimetry. the protei ...	2012	22718753
identification and characterization of the thermus thermophilus 5-methylcytidine (m5c) methyltransferase modifying 23 s ribosomal rna (rrna) base c1942.	methylation of cytidines at carbon-5 is a common posttranscriptional rna modification encountered across all domains of life. here, we characterize the modifications of c1942 and c1962 in thermus thermophilus 23 s rrna as 5-methylcytidines (m(5)c) and identify the two associated methyltransferases. the methyltransferase modifying c1942, named rlmo, has not been characterized previously. rlmo modifies naked 23 s rrna, but not the assembled 50 s subunit or 70 s ribosomes. the x-ray crystal structu ...	2012	22711535
dissociation of antibacterial activity and aminoglycoside ototoxicity in the 4-monosubstituted 2-deoxystreptamine apramycin.	aminoglycosides are potent antibacterials, but therapy is compromised by substantial toxicity causing, in particular, irreversible hearing loss. aminoglycoside ototoxicity occurs both in a sporadic dose-dependent and in a genetically predisposed fashion. we recently have developed a mechanistic concept that postulates a key role for the mitochondrial ribosome (mitoribosome) in aminoglycoside ototoxicity. we now report on the surprising finding that apramycin, a structurally unique aminoglycoside ...	2012	22699498
thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics.	thermodynamic stability, configurational motions and internal forces of haemoglobin (hb) of three endotherms (platypus, ornithorhynchus anatinus; domestic chicken, gallus gallus domesticus and human, homo sapiens) and an ectotherm (salt water crocodile, crocodylus porosus) were investigated using circular dichroism, incoherent elastic neutron scattering and coarse-grained brownian dynamics simulations. the experimental results from hb solutions revealed a direct correlation between protein resil ...	2012	22696485
comparison of segger and other methods for segmentation and rigid-body docking of molecular components in cryo-em density maps.	segmentation and docking are useful methods for the discovery of molecular components in electron cryo-microscopy (cryo-em) density maps of macromolecular complexes. in this article, we describe the segmentation and docking methods implemented in segger. for 11 targets posted in the 2010 cryo-em challenge, we segmented the regions corresponding to individual molecular components using segger. we then used the segmented regions to guide rigid-body docking of individual components. docking results ...	2012	22696409
ancient origin of the divergent forms of leucyl-trna synthetases in the halobacteriales.	horizontal gene transfer (hgt) has greatly impacted the genealogical history of many lineages, particularly for prokaryotes, with genes frequently moving in and out of a line of descent. many genes that were acquired by a lineage in the past likely originated from ancestral relatives that have since gone extinct. during the course of evolution, hgt has played an essential role in the origin and dissemination of genetic and metabolic novelty.	2012	22694720
a comparison of the crystal structures of eukaryotic and bacterial ssu ribosomal rnas reveals common structural features in the hypervariable regions.	while the majority of the ribosomal rna structure is conserved in the three major domains of life--archaea, bacteria, and eukaryotes, specific regions of the rrna structure are unique to at least one of these three primary forms of life. in particular, the comparative secondary structure for the eukaryotic ssu rrna contains several regions that are different from the analogous regions in the bacteria. our detailed analysis of two recently determined eukaryotic 40s ribosomal crystal structures, t ...	2012	22693601
crystallization and preliminary crystallographic analysis of the major capsid proteins vp16 and vp17 of bacteriophage p23-77.	members of the diverse double-β-barrel lineage of viruses are identified by the conserved structure of their major coat protein. new members of this lineage have been discovered based on structural analysis and we are interested in identifying relatives that utilize unusual versions of the double-β-barrel fold. one candidate for such studies is p23-77, an icosahedral dsdna bacteriophage that infects the extremophile thermus thermophilus. p23-77 has two major coat proteins, namely vp16 and vp17, ...	2012	22691792
preliminary crystallographic analysis of two hypothetical ribose-5-phosphate isomerases from streptococcus mutans.	study of the enzymes from sugar metabolic pathways may provide a better understanding of the pathogenesis of the human oral pathogen streptococcus mutans. bioinformatics, biochemical and crystallization methods were used to characterize and understand the function of two putative ribose-5-phosphate isomerases: smu1234 and smu2142. the proteins were cloned and constructed with n-terminal his tags. protein purification was performed by ni(2+)-chelating and size-exclusion chromatography. the crysta ...	2012	22691789
draft genome sequence of thermus sp. strain rl, isolated from a hot water spring located atop the himalayan ranges at manikaran, india.	thermus sp. strain rl was isolated from a hot water spring (90°c to 98°c) at manikaran, himachal pradesh, india. here we report the draft genome sequence (20,36,600 bp) of this strain. the draft genome sequence consists of 17 contigs and 1,986 protein-coding sequences and has an average g+c content of 68.77%.	2012	22689228
evolution and diversification of the organellar release factor family.	translation termination is accomplished by proteins of the class i release factor family (rf) that recognize stop codons and catalyze the ribosomal release of the newly synthesized peptide. bacteria have two canonical rfs: rf1 recognizes uaa and uag, rf2 recognizes uaa and uga. despite that these two release factor proteins are sufficient for de facto translation termination, the eukaryotic organellar rf protein family, which has evolved from bacterial release factors, has expanded considerably, ...	2012	22688947
diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system.	the yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. sensitivity and selectivity have improved because of various technical tricks and experimental designs. here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment comp ...	2012	22688816
phenylacetic acid catabolism and its transcriptional regulation in corynebacterium glutamicum.	the industrially important organism corynebacterium glutamicum has been characterized in recent years for its robust ability to assimilate aromatic compounds. in this study, c. glutamicum strain as 1.542 was investigated for its ability to catabolize phenylacetic acid (paa). the paa genes were identified; they are organized as a continuous paa gene cluster. the type strain of c. glutamicum, atcc 13032, is not able to catabolize paa, but the recombinant strain atcc 13032/pec-k18mob2::paa gained t ...	2012	22685150
crystallization and preliminary x-ray analysis of the reductase component of p-hydroxyphenylacetate 3-hydroxylase from acinetobacter baumannii.	p-hydroxyphenylacetate 3-hydroxylase (hpah) from acinetobacter baumannii catalyzes the hydroxylation of p-hydroxyphenylacetate (hpa) at the ortho position to yield 3,4-dihydroxyphenylacetate (dhpa). hpah from a. baumannii is a two-component flavoprotein consisting of a smaller reductase (c(1)) component and a larger oxygenase (c(2)) component. the c(1) component supplies a reduced flavin in its free form to the c(2) counterpart for hydroxylation. in addition, hpa can bind to c(1) and enhance the ...	2012	22684080
structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-trna synthetase.	leucyl-trna synthetase (leurs) produces error-free leucyl-trna(leu) by coordinating translocation of the 3' end of (mis-)charged trnas from its synthetic site to a separate proofreading site for editing. here we report cocrystal structures of the escherichia coli leurs-trna(leu) complex in the aminoacylation or editing conformations, showing that translocation involves correlated rotations of four flexibly linked leurs domains. this pivots the trna to guide its charged 3' end from the closed ami ...	2012	22683997
the structure of human argonaute-2 in complex with mir-20a.	argonaute proteins lie at the heart of the rna-induced silencing complex (risc), wherein they use small rna guides to recognize targets. initial insight into the architecture of argonautes came from studies of prokaryotic proteins, revealing a crescent-shaped base made up of the amino-terminal, paz, middle, and piwi domains. the recently reported crystal structure of human argonaute-2 (hago2), the "slicer" in rna interference, in complex with a mixed population of rnas derived from insect cells ...	2012	22682761
molecular dynamics and mutational analysis of the catalytic and translocation cycle of rna polymerase.		2012	22676913
comparative analysis of two phenotypically-similar but genomically-distinct burkholderia cenocepacia-specific bacteriophages.	genomic analysis of bacteriophages infecting the burkholderia cepacia complex (bcc) is an important preliminary step in the development of a phage therapy protocol for these opportunistic pathogens. the objective of this study was to characterize kl1 (vb_bces_kl1) and ah2 (vb_bces_ah2), two novel burkholderia cenocepacia-specific siphoviruses isolated from environmental samples.	2012	22676492
complete genome sequence of the aerobic, heterotroph marinithermus hydrothermalis type strain (t1(t)) from a deep-sea hydrothermal vent chimney.	marinithermus hydrothermalis sako et al. 2003 is the type species of the monotypic genus marinithermus. m. hydrothermalis t1(t) was the first isolate within the phylum "thermus-deinococcus" to exhibit optimal growth under a salinity equivalent to that of sea water and to have an absolute requirement for nacl for growth. m. hydrothermalis t1(t) is of interest because it may provide a new insight into the ecological significance of the aerobic, thermophilic decomposers in the circulation of organi ...	2012	22675595
thermostable dna polymerase from a viral metagenome is a potent rt-pcr enzyme.	viral metagenomic libraries are a promising but previously untapped source of new reagent enzymes. deep sequencing and functional screening of viral metagenomic dna from a near-boiling thermal pool identified clones expressing thermostable dna polymerase (pol) activity. among these, 3173 pol demonstrated both high thermostability and innate reverse transcriptase (rt) activity. we describe the biochemistry of 3173 pol and report its use in single-enzyme reverse transcription pcr (rt-pcr). wild-ty ...	2012	22675552
characterization of a conserved interaction between dna glycosylase and para in mycobacterium smegmatis and m. tuberculosis.	the chromosome partitioning proteins, parab, ensure accurate segregation of genetic materials into daughter cells and most bacterial species contain their homologs. however, little is known about the regulation of parab proteins. in this study, we found that 3-methyladenine dna glycosylase i mstag(ms5082) regulates bacterial growth and cell morphology by directly interacting with mspara (ms6939) and inhibiting its atpase activity in mycobacterium smegmatis. using bacterial two-hybrid and pull-do ...	2012	22675536
structural mechanism of atp-induced polymerization of the partition factor parf: implications for dna segregation.	segregation of the bacterial multidrug resistance plasmid tp228 requires the centromere-binding protein parg, the parh centromere, and the walker box atpase parf. the cycling of parf between adp- and atp-bound states drives tp228 partition; atp binding stimulates parf polymerization, which is essential for segregation, whereas adp binding antagonizes polymerization and inhibits dna partition. the molecular mechanism involved in this adenine nucleotide switch is unclear. moreover, it is unknown h ...	2012	22674577
suppression of premature termination codons as a therapeutic approach.	in this review, we describe our current understanding of translation termination and pharmacological agents that influence the accuracy of this process. a number of drugs have been identified that induce suppression of translation termination at in-frame premature termination codons (ptcs; also known as nonsense mutations) in mammalian cells. we discuss efforts to utilize these drugs to suppress disease-causing ptcs that result in the loss of protein expression and function. in-frame ptcs repres ...	2012	22672057
phage-induced expression of crispr-associated proteins is revealed by shotgun proteomics in streptococcus thermophilus.	the crispr/cas system, comprised of clustered regularly interspaced short palindromic repeats along with their associated (cas) proteins, protects bacteria and archaea from viral predation and invading nucleic acids. while the mechanism of action for this acquired immunity is currently under investigation, the response of cas protein expression to phage infection has yet to be elucidated. in this study, we employed shotgun proteomics to measure the global proteome expression in a model system fo ...	2012	22666452
the c-terminal domain of 4-hydroxyphenylacetate 3-hydroxylase from acinetobacter baumannii is an autoinhibitory domain.	p-hydroxyphenylacetate (hpa) 3-hydroxylase from acinetobacter baumannii consists of a reductase component (c(1)) and an oxygenase component (c(2)). c(1) catalyzes the reduction of fmn by nadh to provide fmnh(-) as a substrate for c(2). the rate of reduction of flavin is enhanced ∼20-fold by binding hpa. the n-terminal domain of c(1) is homologous to other flavin reductases, whereas the c-terminal domain (residues 192-315) is similar to marr, a repressor protein involved in bacterial antibiotic r ...	2012	22661720
stable isotope peptide mass spectrometry to decipher amino acid metabolism in dehalococcoides strain cbdb1.	dehalococcoides species are key players in the anaerobic transformation of halogenated solvents at contaminated sites. here, we analyze isotopologue distributions in amino acid pools from peptides of dehalococcoides strain cbdb1 after incubation with (13)c-labeled acetate or bicarbonate as a carbon source. the resulting data were interpreted with regard to genome annotations to identify amino acid biosynthesis pathways. in addition to using gas chromatography-mass spectrometry (gc-ms) for analyz ...	2012	22661690
rational design and directed evolution of a bacterial-type glutaminyl-trna synthetase precursor.	protein biosynthesis requires aminoacyl-transfer rna (trna) synthetases to provide aminoacyl-trna substrates for the ribosome. most bacteria and all archaea lack a glutaminyl-trna synthetase (glnrs); instead, gln-trna(gln) is produced via an indirect pathway: a glutamyl-trna synthetase (glurs) first attaches glutamate (glu) to trna(gln), and an amidotransferase converts glu-trna(gln) to gln-trna(gln). the human pathogen helicobacter pylori encodes two glurs enzymes, with glurs2 specifically amin ...	2012	22661575
a computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly.	assembly of the ribosome from its protein and rna constituents has been studied extensively over the past 50 years, and experimental evidence suggests that prokaryotic ribosomal proteins undergo conformational changes during assembly. however, to date, no studies have attempted to elucidate these conformational changes. the present work utilizes computational methods to analyze protein dynamics and to investigate the linkage between dynamics and binding of these proteins during the assembly of t ...	2012	22654657
glycines: role in α-helical membrane protein structures and a potential indicator of native conformation.	among the growing number of membrane protein structures in the protein data bank, there are many transmembrane domains that appear to be native-like; at the same time, there are others that appear to have less than complete native-like character. hence, there is an increasing need for validation tools that distinguish native-like from non-native-like structures. membrane mimetics used in protein structural characterizations differ in numerous physicochemical properties from native membranes and ...	2012	22650985
a predictive model of intein insertion site for use in the engineering of molecular switches.	inteins are intervening protein domains with self-splicing ability that can be used as molecular switches to control activity of their host protein. successfully engineering an intein into a host protein requires identifying an insertion site that permits intein insertion and splicing while allowing for proper folding of the mature protein post-splicing. by analyzing sequence and structure based properties of native intein insertion sites we have identified four features that showed significant ...	2012	22649521
a thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels.	generation of biofuels from sugars in lignocellulosic biomass is a promising alternative to liquid fossil fuels, but efficient and inexpensive bioprocessing configurations must be developed to make this technology commercially viable. one of the major barriers to commercialization is the recalcitrance of plant cell wall polysaccharides to enzymatic hydrolysis. biomass pretreatment with ionic liquids (ils) enables efficient saccharification of biomass, but residual ils inhibit both saccharificati ...	2012	22649505
steric restrictions of risc in rna interference identified with size-expanded rna nucleobases.	understanding the interactions between small interfering rnas (sirnas) and the rna-induced silencing complex (risc), the key protein complex of rna interference (rnai), is of great importance to the development of sirnas with improved biological and potentially therapeutic function. although various chemically modified sirnas have been reported, relatively few studies with modified nucleobases exist. here we describe the synthesis and hybridization properties of sirnas bearing size-expanded rna ...	2012	22646660