Publications

crystallization and preliminary x-ray crystallographic analysis of yeast nad+-specific isocitrate dehydrogenase.	nad+-specific isocitrate dehydrogenase (idh; ec 1.1.1.41) is a complex allosterically regulated enzyme in the tricarboxylic acid cycle. yeast idh is believed to be an octamer containing four catalytic idh2 and four regulatory idh1 subunits. crystals of yeast idh have been obtained and optimized using sodium citrate, a competitive inhibitor of the enzyme, as the precipitating agent. the crystals belong to space group r3, with unit-cell parameters a = 302.0, c = 112.1 a. diffraction data were coll ...	2005	16511075
extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry.	a protocol has been developed that allows protein identifications using available dna-based or protein sequences from a reference strain of a bacterial species to be extended to bacterial strains for which no prior dna-based or protein sequence information exists. the protocol is predicated on careful isolation of a specific sub-cellular group of proteins. in this study, ribosomal proteins were chosen due to their high relative abundance and similarity in copy number per cell. after isolation of ...	2005	16287167
crystal structure and rna binding of the rpb4/rpb7 subunits of human rna polymerase ii.	the rpb4 and rpb7 subunits of eukaryotic rna polymerase ii (rnap(ii)) form a heterodimer that protrudes from the 10-subunit core of the enzyme. we have obtained crystals of the human rpb4/rpb7 heterodimer and determined the structure to 2.7 a resolution. the presence of putative rna-binding domains on the rpb7 subunit and the position of the heterodimer close to the rna exit groove in the 12 subunit yeast polymerase complex strongly suggests a role for the heterodimer in binding and stabilizing ...	2005	16282592
the proficiency of a thermophilic chorismate mutase enzyme is solely through an entropic advantage in the enzyme reaction.	a study of the thermus thermophilus chorismate mutase (ttcm) is described by using quantum mechanics (self-consistent-charge density-functional tight binding)/molecular mechanics, umbrella sampling, and the weighted histogram analysis method. the computed free energies of activation for the reactions in water and ttcm are comparable to the experimental values. the free energies for formation of near attack conformer have been determined to be 8.06 and 0.05 kcal/mol in water and ttcm, respectivel ...	2005	16344484
accessibility of 18s rrna in human 40s subunits and 80s ribosomes at physiological magnesium ion concentrations--implications for the study of ribosome dynamics.	protein biosynthesis requires numerous conformational rearrangements within the ribosome. the structural core of the ribosome is composed of rna and is therefore dependent on counterions such as magnesium ions for function. many steps of translation can be compromised or inhibited if the concentration of mg(2+) is too low or too high. conditions previously used to probe the conformation of the mammalian ribosome in vitro used high mg(2+) concentrations that we find completely inhibit translation ...	2005	16314459
comparative genomic analyses of the bacterial phosphotransferase system.	we report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (pts). these included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. homologues of pts proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding pts proteins has not occurred between the three domains of life. of the 174 bacterial genomes (136 bacterial species) analyzed, ...	2005	16339738
protein subunit interfaces: heterodimers versus homodimers.	protein dimers are either homodimers (complexation of identical monomers) or heterodimers (complexation of non-identical monomers). these dimers are common in catalysis and regulation. however, the molecular principles of protein dimer interactions are difficult to understand mainly due to the geometrical and chemical characteristics of proteins. nonetheless, the principles of protein dimer interactions are often studied using a dataset of 3d structural complexes determined by x-ray crystallogra ...	2005	17597849
predicted highly expressed genes in archaeal genomes.	based primarily on 16s rrna sequence comparisons, life has been broadly divided into the three domains of bacteria, archaea, and eukarya. archaea is further classified into crenarchaea and euryarchaea. archaea generally thrive in extreme environments as assessed by temperature, ph, and salinity. for many prokaryotic organisms, ribosomal proteins (rp), transcription/translation factors, and chaperone genes tend to be highly expressed. a gene is predicted highly expressed (phx) if its codon usage ...	2005	15883368
transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in is element gene expression.	transcription slippage occurs on certain patterns of repeat mononucleotides, resulting in synthesis of a heterogeneous population of mrnas. individual mrna molecules within this population differ in the number of nucleotides they contain that are not specified by the template. when transcriptional slippage occurs in a coding sequence, translation of the resulting mrnas yields more than one protein product. except where the products of the resulting mrnas have distinct functions, transcription sl ...	2005	15774026
clustering the annotation space of proteins.	current protein clustering methods rely on either sequence or functional similarities between proteins, thereby limiting inferences to one of these areas.	2005	15703069
a unique trna recognition mechanism of caenorhabditis elegans mitochondrial ef-tu2.	nematode mitochondria expresses two types of extremely truncated trnas that are specifically recognized by two distinct elongation factor tu (ef-tu) species named ef-tu1 and ef-tu2. this is unlike the canonical ef-tu molecule that participates in the standard protein biosynthesis systems, which basically recognizes all elongator trnas. ef-tu2 specifically recognizes ser-trna(ser) that lacks a d arm but has a short t arm. our previous study led us to speculate the lack of the d arm may be essenti ...	2005	16113240
molecular mimicry: quantitative methods to study structural similarity between protein and rna.	with rapidly increasing availability of three-dimensional structures, one major challenge for the post-genome era is to infer the functions of biological molecules based on their structural similarity. while quantitative studies of structural similarity between the same type of biological molecules (e.g., protein vs. protein) have been carried out intensively, the comparable study of structural similarity between different types of biological molecules (e.g., protein vs. rna) remains unexplored. ...	2005	16043503
correcting errors in synthetic dna through consensus shuffling.	although efficient methods exist to assemble synthetic oligonucleotides into genes and genomes, these suffer from the presence of 1-3 random errors/kb of dna. here, we introduce a new method termed consensus shuffling and demonstrate its use to significantly reduce random errors in synthetic dna. in this method, errors are revealed as mismatches by re-hybridization of the population. the dna is fragmented, and mismatched fragments are removed upon binding to an immobilized mismatch binding prote ...	2005	15800206
chemical engineering of the peptidyl transferase center reveals an important role of the 2'-hydroxyl group of a2451.	the main enzymatic reaction of the large ribosomal subunit is peptide bond formation. ribosome crystallography showed that a2451 of 23s rrna makes the closest approach to the attacking amino group of aminoacyl-trna. mutations of a2451 had relatively small effects on transpeptidation and failed to unequivocally identify the crucial functional group(s). here, we employed an in vitro reconstitution system for chemical engineering the peptidyl transferase center by introducing non-natural nucleoside ...	2005	15767286
a low-cost open-source snp genotyping platform for association mapping applications.	association mapping aimed at identifying dna polymorphisms that contribute to variation in complex traits entails genotyping a large number of single-nucleotide polymorphisms (snps) in a very large panel of individuals. few technologies, however, provide inexpensive high-throughput genotyping. here, we present an efficient approach developed specifically for genotyping large fixed panels of diploid individuals. the cost-effective, open-source nature of our methodology may make it particularly at ...	2005	16356268
estimation of phylogeny using a general markov model.	the non-homogeneous model of nucleotide substitution proposed by barry and hartigan (stat sci, 2: 191-210) is the most general model of dna evolution assuming an independent and identical process at each site. we present a computational solution for this model, and use it to analyse two data sets, each violating one or more of the assumptions of stationarity, homogeneity, and reversibility. the log likelihood values returned by programs based on the f84 model (j mol evol, 29: 170-179), the gener ...	2005	19325854
estimation of phylogeny using a general markov model.	the non-homogeneous model of nucleotide substitution proposed by barry and hartigan (stat sci, 2: 191-210) is the most general model of dna evolution assuming an independent and identical process at each site. we present a computational solution for this model, and use it to analyse two data sets, each violating one or more of the assumptions of stationarity, homogeneity, and reversibility. the log likelihood values returned by programs based on the f84 model (j mol evol, 29: 170-179), the gener ...	2005	19325854
size matters: a view of selenocysteine incorporation from the ribosome.	this review focuses on the known factors required for selenocysteine (sec) incorporation in eukaryotes and highlights recent findings that have compelled us to propose a new model for the mechanism of sec incorporation. in light of this data we also review the controversial aspects of the previous model specifically regarding the proposed interaction between sbp2 and eefsec. in addition, the relevance of two recently discovered factors in the recoding of sec are reviewed. the role of the ribosom ...	2005	16416259
size matters: a view of selenocysteine incorporation from the ribosome.	this review focuses on the known factors required for selenocysteine (sec) incorporation in eukaryotes and highlights recent findings that have compelled us to propose a new model for the mechanism of sec incorporation. in light of this data we also review the controversial aspects of the previous model specifically regarding the proposed interaction between sbp2 and eefsec. in addition, the relevance of two recently discovered factors in the recoding of sec are reviewed. the role of the ribosom ...	2005	16416259
the structural biology center 19id undulator beamline: facility specifications and protein crystallographic results.	the 19id undulator beamline of the structure biology center has been designed and built to take full advantage of the high flux, brilliance and quality of x-ray beams delivered by the advanced photon source. the beamline optics are capable of delivering monochromatic x-rays with photon energies from 3.5 to 20 kev (3.5-0.6 a wavelength) with fluxes up to 8-18 x 10(12) photons s(-1) (depending on photon energy) onto cryogenically cooled crystal samples. the size of the beam (full width at half-max ...	2005	16371706
the structural biology center 19id undulator beamline: facility specifications and protein crystallographic results.	the 19id undulator beamline of the structure biology center has been designed and built to take full advantage of the high flux, brilliance and quality of x-ray beams delivered by the advanced photon source. the beamline optics are capable of delivering monochromatic x-rays with photon energies from 3.5 to 20 kev (3.5-0.6 a wavelength) with fluxes up to 8-18 x 10(12) photons s(-1) (depending on photon energy) onto cryogenically cooled crystal samples. the size of the beam (full width at half-max ...	2005	16371706
the fidelity of translation initiation: reciprocal activities of eif1, if3 and ycih.	eukaryotic initiation factor eif1 and the functional c-terminal domain of prokaryotic initiation factor if3 maintain the fidelity of initiation codon selection in eukaryotes and prokaryotes, respectively, and bind to the same regions of small ribosomal subunits, between the platform and initiator trna. here we report that these nonhomologous factors can bind to the same regions of heterologous subunits and perform their functions in heterologous systems in a reciprocal manner, discriminating aga ...	2005	16362046
the fidelity of translation initiation: reciprocal activities of eif1, if3 and ycih.	eukaryotic initiation factor eif1 and the functional c-terminal domain of prokaryotic initiation factor if3 maintain the fidelity of initiation codon selection in eukaryotes and prokaryotes, respectively, and bind to the same regions of small ribosomal subunits, between the platform and initiator trna. here we report that these nonhomologous factors can bind to the same regions of heterologous subunits and perform their functions in heterologous systems in a reciprocal manner, discriminating aga ...	2005	16362046
the membrane protein data bank.	the membrane protein data bank (mpdb) is an online, searchable, relational database of structural and functional information on integral, anchored and peripheral membrane proteins and peptides. data originates from the protein data bank and other databases, and from the literature. structures are based on x-ray and electron diffraction, nuclear magnetic resonance and cryoelectron microscopy. the mpdb is searchable online by protein characteristic, structure determination method, crystallization ...	2005	16314922
the membrane protein data bank.	the membrane protein data bank (mpdb) is an online, searchable, relational database of structural and functional information on integral, anchored and peripheral membrane proteins and peptides. data originates from the protein data bank and other databases, and from the literature. structures are based on x-ray and electron diffraction, nuclear magnetic resonance and cryoelectron microscopy. the mpdb is searchable online by protein characteristic, structure determination method, crystallization ...	2005	16314922
multiplexed tandem pcr: gene profiling from small amounts of rna using sybr green detection.	multiplexed tandem pcr (mt-pcr) is a process for highly multiplexed gene expression profiling. in the first step, multiple primer pairs are added to the rna to be analysed together with reverse transcriptase and taq dna polymerase. following reverse transcription, the multiplexed amplicons are simultaneously amplified for a small number of cycles so as to avoid competition between amplicons. the reaction product is then diluted and analysed in multiple individual pcrs using primers nested inside ...	2005	16314310
miniseed3 (mini3), a wrky family gene, and haiku2 (iku2), a leucine-rich repeat (lrr) kinase gene, are regulators of seed size in arabidopsis.	we have identified mutant alleles of two sporophytically acting genes, haiku2 (iku2) and miniseed3 (mini3). homozygotes of these alleles produce a small seed phenotype associated with reduced growth and early cellularization of the endosperm. this phenotype is similar to that described for another seed size gene, iku1. mini3 encodes wrky10, a wrky class transcription factor. mini3 promoter::gus fusions show the gene is expressed in pollen and in the developing endosperm from the two nuclei stage ...	2005	16293693
a mutation in the anticodon of a single trnaala is sufficient to confer auxin resistance in arabidopsis.	auxin-resistant mutants have been useful for dissecting the mechanisms that underlie auxin-mediated biological processes. here we report the isolation and molecular characterization of a novel auxin-resistant mutant in arabidopsis (arabidopsis thaliana). like known mutated aux/iaa transcription factors, the mutant described here displayed dominant resistance to exogenously supplied auxins (sirtinol, 2,4-dichlorophenoxyacetic acid, indole-3-acetic acid) and a host of pleiotropic phenotypes, inclu ...	2005	16244142
a colorimetric method for point mutation detection using high-fidelity dna ligase.	the present study reported proof-of-principle for a genotyping assay approach that can detect single nucleotide polymorphisms (snps) through the gold nanoparticle assembly and the ligase reaction. by incorporating the high-fidelity dna ligase (tth dna ligase) into the allele-specific ligation-based gold nanoparticle assembly, this assay provided a convenient yet powerful colorimetric detection that enabled a straightforward single-base discrimination without the need of precise temperature contr ...	2005	16257979
single-molecule forster resonance energy transfer study of protein dynamics under denaturing conditions.	proteins are highly complex systems, exhibiting a substantial degree of structural variability in their folded state. in the presence of denaturants, the heterogeneity is greatly enhanced, and fluctuations among vast numbers of folded and unfolded conformations occur via many different pathways. here, we have studied the structure and dynamics of the small enzyme ribonuclease hi (rnase h) in the presence of the chemical denaturant guanidinium chloride (gdmcl) using single-molecule fluorescence m ...	2005	16221762
amyloid formation of a protein in the absence of initial unfolding and destabilization of the native state.	in 5% (v/v) trifluoroethanol, ph 5.5, 25 degrees c one of the acylphosphatases from drosophila melanogaster (acpdro2) forms fibrillar aggregates that bind thioflavin t and congo red and have an extensive beta-sheet structure, as revealed by circular dichroism. atomic force microscopy indicates that the fibrils and their constituent protofilaments have diameters compatible with those of natural amyloid fibrils. spectroscopic and biochemical investigation, carried out using near- and far-uv circul ...	2005	16169977
deacylated trna is released from the e site upon a site occupation but before gtp is hydrolyzed by ef-tu.	the presence or absence of deacylated trna at the e site sharply influences the activation energy required for binding of a ternary complex to the ribosomal a site indicating the different conformations that the e-trna imparts on the ribosome. here we address two questions: (i) whether or not peptidyltransferase--the essential catalytic activity of the large ribosomal subunit--also depends on the occupancy state of the e site and (ii) at what stage the e-trna is released during an elongation cyc ...	2005	16166657
protein content of minimal and ancestral ribosome.	minimal genome approaches seek to define the smallest gene complement compatible with modern-type cellular life on earth. a consensus of computational and experimental approaches indicates that a minimal genome is close to 300 protein-coding genes, if a rich medium is provided for cell growth. i relate ribosomal gene content in completely sequenced genomes to ribosomal subunit structure and approximate the protein components of the putative minimal ribosome and the ribosome of the last universal ...	2005	16043494
the genomics of disulfide bonding and protein stabilization in thermophiles.	thermophilic organisms flourish in varied high-temperature environmental niches that are deadly to other organisms. recently, genomic evidence has implicated a critical role for disulfide bonds in the structural stabilization of intracellular proteins from certain of these organisms, contrary to the conventional view that structural disulfide bonds are exclusively extracellular. here both computational and structural data are presented to explore the occurrence of disulfide bonds as a protein-st ...	2005	16111437
recurrent structural rna motifs, isostericity matrices and sequence alignments.	the occurrences of two recurrent motifs in ribosomal rna sequences, the kink-turn and the c-loop, are examined in crystal structures and systematically compared with sequence alignments of rrnas from the three kingdoms of life in order to identify the range of the structural and sequence variations. isostericity matrices are used to analyze structurally the sequence variations of the characteristic non-watson-crick base pairs for each motif. we show that isostericity matrices for non-watson-cric ...	2005	15860776
independent binding sites of small protein b onto transfer-messenger rna during trans-translation.	stalled bacterial ribosomes are freed by transfer-messenger rna (tmrna). with the help of small protein b (smpb), protein synthesis restarts and tmrna adds a tag to the stalled protein for destruction. the conformation of a 347 nt long tmrna from a thermophile and its interactions with smpb were monitored using structural probes. the rna is highly folded, including the reading frame, with <30% of unpaired residues. footprints between smpb and tmrna are in the elbow of the trna domain, in some ps ...	2005	15860775
atp-sensitive k+ channel channel/enzyme multimer: metabolic gating in the heart.	cardiac atp-sensitive k(+) (k(atp)) channels, gated by cellular metabolism, are formed by association of the inwardly rectifying potassium channel kir6.2, the potassium conducting subunit, and sur2a, the atp-binding cassette protein that serves as the regulatory subunit. kir6.2 is the principal site of atp-induced channel inhibition, while sur2a regulates k(+) flux through adenine nucleotide binding and catalysis. the atpase-driven conformations within the regulatory sur2a subunit of the k(atp) ...	2005	15910874
the application of cluster analysis in the intercomparison of loop structures in rna.	we have developed a computational approach for the comparison and classification of rna loop structures. hairpin or interior loops identified in atomic resolution rna structures were intercompared by conformational matching. the root-mean-square deviation (rmsd) values between all pairs of rna fragments of interest, even if from different molecules, are calculated. subsequently, cluster analysis is performed on the resulting matrix of rmsd distances using the unweighted pair group method with ar ...	2005	15769871
towards understanding the molecular basis of bacterial dna segregation.	bacteria ensure the fidelity of genetic inheritance by the coordinated control of chromosome segregation and cell division. here, we review the molecules and mechanisms that govern the correct subcellular positioning and rapid separation of newly replicated chromosomes and plasmids towards the cell poles and, significantly, the emergence of mitotic-like machineries capable of segregating plasmid dna. we further describe surprising similarities between proteins involved in dna partitioning (para/ ...	2005	15897178
graphical representation of ribosomal rna probe accessibility data using arb software package.	taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. a frequently applied technology, fluorescence in situ hybridization (fish), besides single cell identification, allows the localization and functional studies of the microbial community composition. careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridiza ...	2005	15777482
another biological effect of tosylphenylalanylchloromethane (tpck): it prevents p47phox phosphorylation and translocation upon neutrophil stimulation.	tpck (tosylphenylalanylchloromethane), first discovered as a serine protease inhibitor, has been described to affect in diverse systems a number of physiological events probably unrelated to its antiprotease effect, such as proliferation, apoptosis and tumour formation. in the present study, we focus on its inhibition of the neutrophil respiratory burst, an important element of non-specific immunological defence. the superoxide anion-producing enzyme, nadph oxidase, is quiescent in resting cells ...	2005	15498025
hsp70 chaperones: cellular functions and molecular mechanism.	hsp70 proteins are central components of the cellular network of molecular chaperones and folding catalysts. they assist a large variety of protein folding processes in the cell by transient association of their substrate binding domain with short hydrophobic peptide segments within their substrate proteins. the substrate binding and release cycle is driven by the switching of hsp70 between the low-affinity atp bound state and the high-affinity adp bound state. thus, atp binding and hydrolysis a ...	2005	15770419
protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins.	recent years have seen the publication of both empirical and theoretical relationships predicting the rates with which proteins fold. our ability to test and refine these relationships has been limited, however, by a variety of difficulties associated with the comparison of folding and unfolding rates, thermodynamics, and structure across diverse sets of proteins. these difficulties include the wide, potentially confounding range of experimental conditions and methods employed to date and the di ...	2005	15689503
initiation of protein synthesis in bacteria.	valuable information on translation initiation is available from biochemical data and recently solved structures. we present a detailed description of current knowledge about the structure, function, and interactions of the individual components involved in bacterial translation initiation. the first section describes the ribosomal features relevant to the initiation process. subsequent sections describe the structure, function, and interactions of the mrna, the initiator trna, and the initiatio ...	2005	15755955
evolutionary profiles from the qr factorization of multiple sequence alignments.	we present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. the method, based on the multidimensional qr factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of ...	2005	15741270
homology-extended sequence alignment.	we present a profile-profile multiple alignment strategy that uses database searching to collect homologues for each sequence in a given set, in order to enrich their available evolutionary information for the alignment. for each of the alignment sequences, the putative homologous sequences that score above a pre-defined threshold are incorporated into a position-specific pre-alignment profile. the enriched position-specific profile is used for standard progressive alignment, thereby more accura ...	2005	15699183
nadp-malate dehydrogenase from unicellular green alga chlamydomonas reinhardtii. a first step toward redox regulation?	the determinants of the thioredoxin (trx)-dependent redox regulation of the chloroplastic nadp-malate dehydrogenase (nadp-mdh) from the eukaryotic green alga chlamydomonas reinhardtii have been investigated using site-directed mutagenesis. the results indicate that a single c-terminal disulfide is responsible for this regulation. the redox midpoint potential of this disulfide is less negative than that of the higher plant enzyme. the regulation is of an all-or-nothing type, lacking the fine-tuni ...	2005	15579663
ribosomal protein l1 recognizes the same specific structural motif in its target sites on the autoregulatory mrna and 23s rrna.	the rna-binding ability of ribosomal protein l1 is of profound interest since the protein has a dual function as a ribosomal protein binding rrna and as a translational repressor binding its mrna. here, we report the crystal structure of ribosomal protein l1 in complex with a specific fragment of its mrna and compare it with the structure of l1 in complex with a specific fragment of 23s rrna determined earlier. in both complexes, a strongly conserved rna structural motif is involved in l1 bindin ...	2005	15659579
a vibrational spectral maker for probing the hydrogen-bonding status of protonated asp and glu residues.	hydrogen bonding is a fundamental element in protein structure and function. breaking a single hydrogen bond may impair the stability of a protein. we report an infrared vibrational spectral marker for probing the hydrogen-bond number for buried, protonated asp or glu residues in proteins. ab initio computational studies were performed on hydrogen-bonding interactions of a cooh group with a variety of side-chain model compounds of polar and charged amino acids in vacuum using density function th ...	2005	15653739
site-specific labeling of the ribosome for single-molecule spectroscopy.	single-molecule fluorescence spectroscopy can reveal mechanistic and kinetic details that may not be observed in static structural and bulk biochemical studies of protein synthesis. one approach requires site-specific and stable attachment of fluorophores to the components of translation machinery. fluorescent tagging of the ribosome is a prerequisite for the observation of dynamic changes in ribosomal conformation during translation using fluorescence methods. modifications of the ribosomal par ...	2005	15647501
identification of novel restriction endonuclease-like fold families among hypothetical proteins.	restriction endonucleases and other nucleic acid cleaving enzymes form a large and extremely diverse superfamily that display little sequence similarity despite retaining a common core fold responsible for cleavage. the lack of significant sequence similarity between protein families makes homology inference a challenging task and hinders new family identification with traditional sequence-based approaches. using the consensus fold recognition method meta-basic that combines sequence profiles wi ...	2005	15972856
the cryptochromes.	cryptochromes are photoreceptors that regulate entrainment by light of the circadian clock in plants and animals. they also act as integral parts of the central circadian oscillator in animal brains and as receptors controlling photomorphogenesis in response to blue or ultraviolet (uv-a) light in plants. cryptochromes are probably the evolutionary descendents of dna photolyases, which are light-activated dna-repair enzymes, and are classified into three groups -- plant cryptochromes, animal cryp ...	2005	15892880
mapping the interaction of smpb with ribosomes by footprinting of ribosomal rna.	in trans-translation transfer messenger rna (tmrna) and small protein b (smpb) rescue ribosomes stalled on truncated or in other ways problematic mrnas. smpb promotes the binding of tmrna to the ribosome but there is uncertainty about the number of participating smpb molecules as well as their ribosomal location. here, the interaction of smpb with ribosomal subunits and ribosomes was studied by isolation of smpb containing complexes followed by chemical modification of ribosomal rna with dimethy ...	2005	15972795
5s rrna: structure and function from head to toe.	5s rrna is uniquely positioned so as to link together all of the functional centers of the ribosome. previous studies have supported the hypothesis that 5s rrna acts as a physical transducer of information, facilitating communication between the different functional centers and coordinating of the multiple events catalyzed by the ribosome. here, we present a synthesis of both structural and genetic information to construct a more detailed picture of how 5s rrna may act to transmit and coordinate ...	2005	18074004
the acetate switch.	to succeed, many cells must alternate between life-styles that permit rapid growth in the presence of abundant nutrients and ones that enhance survival in the absence of those nutrients. one such change in life-style, the "acetate switch," occurs as cells deplete their environment of acetate-producing carbon sources and begin to rely on their ability to scavenge for acetate. this review explains why, when, and how cells excrete or dissimilate acetate. the central components of the "switch" (phos ...	2005	15755952
rna secondary structure prediction by centroids in a boltzmann weighted ensemble.	prediction of rna secondary structure by free energy minimization has been the standard for over two decades. here we describe a novel method that forsakes this paradigm for predictions based on boltzmann-weighted structure ensemble. we introduce the notion of a centroid structure as a representative for a set of structures and describe a procedure for its identification. in comparison with the minimum free energy (mfe) structure using diverse types of structural rnas, the centroid of the ensemb ...	2005	16043502
the archaeal origins of the eukaryotic translational system.	among the 78 eukaryotic ribosomal proteins, eleven are specific to eukarya, 33 are common only to archaea and eukarya and 34 are homologous (at least in part) to those of both bacteria and archaea. several other translational proteins are common only to eukarya and archaea (e.g., if2a, srp19, etc.), whereas others are shared by the three phyla (e.g., eftu/ef1a and srp54). although this and other analyses strongly support an archaeal origin for a substantial fraction of the eukaryotic translation ...	2005	16877317
the archaeal origins of the eukaryotic translational system.	among the 78 eukaryotic ribosomal proteins, eleven are specific to eukarya, 33 are common only to archaea and eukarya and 34 are homologous (at least in part) to those of both bacteria and archaea. several other translational proteins are common only to eukarya and archaea (e.g., if2a, srp19, etc.), whereas others are shared by the three phyla (e.g., eftu/ef1a and srp54). although this and other analyses strongly support an archaeal origin for a substantial fraction of the eukaryotic translation ...	2005	16877317
inhibition of bacterial rna polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.	we define the target, mechanism, and structural basis of inhibition of bacterial rna polymerase (rnap) by the tetramic acid antibiotic streptolydigin (stl). stl binds to a site adjacent to but not overlapping the rnap active center and stabilizes an rnap-active-center conformational state with a straight-bridge helix. the results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix rnap-active-center conformations exist and that cycling between st ...	2005	16122422
the tyra family of aromatic-pathway dehydrogenases in phylogenetic context.	the tyra protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to l-tyrosine and a third reaction that is not part of tyrosine biosynthesis. family members share a catalytic core region of about 30 kda, where inhibitors operate competitively by acting as substrate mimics. this protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size.	2005	15888209
enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of epsilonproteobacteria.	the carbon and energy metabolisms of a variety of cultured chemolithoautotrophic epsilonproteobacteria from deep-sea hydrothermal environments were characterized by both enzymatic and genetic analyses. all the epsilonproteobacteria tested had all three key reductive tricarboxylic acid (rtca) cycle enzymatic activities--atp-dependent citrate lyase, pyruvate:ferredoxin oxidoreductase, and 2-oxoglutarate:ferredoxin oxidoreductase--while they had no ribulose 1,5-bisphosphate carboxylase (rubisco) ac ...	2005	16269773
profunc: a server for predicting protein function from 3d structure.	profunc (http://www.ebi.ac.uk/thornton-srv/databases/profunc) is a web server for predicting the likely function of proteins whose 3d structure is known but whose function is not. users submit the coordinates of their structure to the server in pdb format. profunc makes use of both existing and novel methods to analyse the protein's sequence and structure identifying functional motifs or close relationships to functionally characterized proteins. a summary of the analyses provides an at-a-glance ...	2005	15980588
popscomp: an automated interaction analysis of biomolecular complexes.	large-scale analysis of biomolecular complexes reveals the functional network within the cell. computational methods are required to extract the essential information from the available data. the popscomp server is designed to calculate the interaction surface between all components of a given complex structure consisting of proteins, dna or rna molecules. the server returns matrices and graphs of surface area burial that can be used to automatically annotate components and residues that are inv ...	2005	15980485
diagnostic application of padlock probes--multiplex detection of plant pathogens using universal microarrays.	padlock probes (plps) are long oligonucleotides, whose ends are complementary to adjacent target sequences. upon hybridization to the target, the two ends are brought into contact, allowing plp circularization by ligation. plps provide extremely specific target recognition, which is followed by universal amplification and microarray detection. since target recognition is separated from downstream processing, plps enable the development of flexible and extendable diagnostic systems, targeting div ...	2005	15860767
functional conformations of the l11-ribosomal rna complex revealed by correlative analysis of cryo-em and molecular dynamics simulations.	the interaction between the gtpase-associated center (gac) and the aminoacyl-trna.ef-tu.gtp ternary complex is of crucial importance in the dynamic process of decoding and trna accommodation. the gac includes protein l11 and helices 43-44 of 23s rrna (referred to as l11-rrna complex). in this study, a method of fitting based on a systematic comparison between cryo-electron microscopy (cryo-em) density maps and structures obtained by molecular dynamics simulations has been developed. this method ...	2006	16682558
the building blocks and motifs of rna architecture.	rna motifs can be defined broadly as recurrent structural elements containing multiple intramolecular rna-rna interactions, as observed in atomic-resolution rna structures. they constitute the modular building blocks of rna architecture, which is organized hierarchically. recent work has focused on analyzing rna backbone conformations to identify, define and search for new instances of recurrent motifs in x-ray structures. one current view asserts that recurrent rna strand segments with characte ...	2006	16713707
activation of superoxide dismutases: putting the metal to the pedal.	superoxide dismutases (sod) are important anti-oxidant enzymes that guard against superoxide toxicity. various sod enzymes have been characterized that employ either a copper, manganese, iron or nickel co-factor to carry out the disproportionation of superoxide. this review focuses on the copper and manganese forms, with particular emphasis on how the metal is inserted in vivo into the active site of sod. copper and manganese sods diverge greatly in sequence and also in the metal insertion proce ...	2006	16828895
evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal rna using arb software package.	availability of high-resolution rna crystal structures for the 30s and 50s ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal rna (rrna) for evaluating sequence alignments of rrna genes. furthermore, the secondary and tertiary structural features of rrna are highly useful and successfully employed in designing rrna targeted oligonucleotide probes intended for in situ hybridization ...	2006	16672074
protrepeatsdb: a database of amino acid repeats in genomes.	genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. innate protein repeats constitute vital functional and structural regions in proteins. repeats are of great consequence in evolution of proteins, as evident from analysis of repeats in different organisms. in the post genomic era, availability of protein sequences encoded in different genomes provides a unique ...	2006	16827924
the prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.	ubiquitin (ub)-mediated signaling is one of the hallmarks of all eukaryotes. prokaryotic homologs of ub (this and moad) and e1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. however, there is no evidence for entire protein modification systems with ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. hence, the evolutionary assembly of the eukaryotic ub-signaling apparatus remains unclea ...	2006	16859499
the tmrdb and srpdb resources.	maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the royal veterinary and agricultural university, denmark (http://tmrdb.kvl.dk/). the signal recognition particle database (srpdb) at http://psyche.uthct.edu/dbs/srpdb/srpdb.html is mirrored at http://srpdb.kvl.dk/ an ...	2006	16381838
the tmrdb and srpdb resources.	maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the royal veterinary and agricultural university, denmark (http://tmrdb.kvl.dk/). the signal recognition particle database (srpdb) at http://psyche.uthct.edu/dbs/srpdb/srpdb.html is mirrored at http://srpdb.kvl.dk/ an ...	2006	16381838
how phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria.	the phosphoenolpyruvate(pep):carbohydrate phosphotransferase system (pts) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. to carry out its catalytic function in sugar transport and phosphorylation, the pts uses pep as an energy source and phosphoryl donor. the phosphoryl group of pep is usually transferred via four distinct proteins (domains) to the transported sugar bo ...	2006	17158705
secretion by numbers: protein traffic in prokaryotes.	almost all aspects of protein traffic in bacteria were covered at the asm-fems meeting on the topic in iraklio, crete in may 2006. the studies presented ranged from mechanistic analysis of specific events leading proteins to their final destinations to the physiological roles of the targeted proteins. among the highlights from the meeting that are reviewed here are the molecular dynamics of seca protein, membrane protein insertion, type iii secretion needles and chaperones, type iv secretion, th ...	2006	17020575
the bacterial cytoskeleton.	in recent years it has been shown that bacteria contain a number of cytoskeletal structures. the bacterial cytoplasmic elements include homologs of the three major types of eukaryotic cytoskeletal proteins (actin, tubulin, and intermediate filament proteins) and a fourth group, the mind-para group, that appears to be unique to bacteria. the cytoskeletal structures play important roles in cell division, cell polarity, cell shape regulation, plasmid partition, and other functions. the proteins sel ...	2006	16959967
comparative analysis of eubacterial dna polymerase iii alpha subunits.	dna polymerase iii is one of the five eubacterial dna polymerases that is responsible for the replication of dna duplex. among the ten subunits of the dna polymerase iii core enzyme, the alpha subunit catalyzes the reaction for polymerizing both dna strands. in this study, we extracted genomic sequences of the alpha subunit from 159 sequenced eubacterial genomes, and carried out sequence-based phylogenetic and structural analyses. we found that all eubacterial genomes have one or more alpha subu ...	2006	17531796
comparative analysis of eubacterial dna polymerase iii alpha subunits.	dna polymerase iii is one of the five eubacterial dna polymerases that is responsible for the replication of dna duplex. among the ten subunits of the dna polymerase iii core enzyme, the alpha subunit catalyzes the reaction for polymerizing both dna strands. in this study, we extracted genomic sequences of the alpha subunit from 159 sequenced eubacterial genomes, and carried out sequence-based phylogenetic and structural analyses. we found that all eubacterial genomes have one or more alpha subu ...	2006	17531796
mechanism of trna-dependent editing in translational quality control.	protein synthesis requires the pairing of amino acids with trnas catalyzed by the aminoacyl-trna synthetases. the synthetases are highly specific, but errors in amino acid selection are occasionally made, opening the door to inaccurate translation of the genetic code. the fidelity of protein synthesis is maintained by the editing activities of synthetases, which remove noncognate amino acids from trnas before they are delivered to the ribosome. although editing has been described in numerous syn ...	2006	17185419
mechanism of trna-dependent editing in translational quality control.	protein synthesis requires the pairing of amino acids with trnas catalyzed by the aminoacyl-trna synthetases. the synthetases are highly specific, but errors in amino acid selection are occasionally made, opening the door to inaccurate translation of the genetic code. the fidelity of protein synthesis is maintained by the editing activities of synthetases, which remove noncognate amino acids from trnas before they are delivered to the ribosome. although editing has been described in numerous syn ...	2006	17185419
a structural model reveals energy transduction in dynein.	intracellular active transport is driven by atp-hydrolyzing motor proteins that move along cytoskeletal filaments. in particular, the microtubule-associated dynein motor is involved in the transport of organelles and vesicles, the maintenance of the golgi, and mitosis. however, unlike kinesin and myosin, the mechanism by which dynein converts chemical energy into mechanical force remains largely a mystery, due primarily to the lack of a high-resolution molecular structure. using homology modelin ...	2006	17121997
structural basis for topoisomerase vi inhibition by the anti-hsp90 drug radicicol.	members of the ghl atpase superfamily, including type ii topoisomerases, hsp90-class chaperones, and mutl, all share a common ghkl-type atp-binding fold and act as nucleotide-controlled 'molecular clamps'. these enzymes' atp-binding sites have proven to be rich drug targets, and certain inhibitors of type ii topoisomerases and hsp90 bind to this region and competitively inhibit these enzymes. recently, it was found that radicicol, a drug known to block hsp90 function, also inhibits the archaeal ...	2006	16920739
a new paradigm: manganese superoxide dismutase influences the production of h2o2 in cells and thereby their biological state.	the principal source of hydrogen peroxide in mitochondria is thought to be from the dismutation of superoxide via the enzyme manganese superoxide dismutase (mnsod). however, the nature of the effect of sod on the cellular production of h(2)o(2) is not widely appreciated. the current paradigm is that the presence of sod results in a lower level of h(2)o(2) because it would prevent the non-enzymatic reactions of superoxide that form h(2)o(2). the goal of this work was to: a) demonstrate that sod c ...	2006	17015180
evidence for existence of "mesotogas," members of the order thermotogales adapted to low-temperature environments.	all cultivated isolates of the bacterial order thermotogales are either thermophiles or hyperthermophiles, but thermotogales 16s rrna gene sequences have been detected in many mesophilic anaerobic and microaerophilic environments, particularly within communities involved in the remediation of pollutants. here we provide metagenomic evidence for the existence of thermotogales lineages, which we informally call "mesotoga," that are adapted to growth at lower temperatures. two fosmid clones contain ...	2006	16820506
dynamic protein domains: identification, interdependence, and stability.	existing methods of domain identification in proteins usually provide no information about the degree of domain independence and stability. however, this information is vital for many areas of protein research. the recently developed hierarchical clustering of correlation patterns (hccp) technique provides machine-based domain identification in a computationally simple and physically consistent way. here we present the modification of this technique, which not only allows determination of the mo ...	2006	16632509
characteristics of the nuclear (18s, 5.8s, 28s and 5s) and mitochondrial (12s and 16s) rrna genes of apis mellifera (insecta: hymenoptera): structure, organization, and retrotransposable elements.	as an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18s, 5.8s, 28s and 5s) and mitochondrial (12s and 16s) ribosomal rna (rrna)-encoding gene sequences (rdna) and related internally and externally transcribed spacer regions of apis mellifera (insecta: hymenoptera: apocrita). additionally, we predict secondary structures for the mature rrna molecules based on comparative sequence analyses with other arthropod taxa and reference to re ...	2006	17069639
diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-i release factor that potentially recognizes atypical mrna signals other than normal stop codons.	while all codons that specify amino acids are universally recognized by trna molecules, codons signaling termination of translation are recognized by proteins known as class-i release factors (rf). in most eukaryotes and archaea a single rf accomplishes termination at all three stop codons. in most bacteria, there are two rfs with overlapping specificity, rf1 recognizes ua(a/g) and rf2 recognizes u(a/g)a.	2006	16970810
the structure and function of frataxin.	frataxin, a highly conserved protein found in prokaryotes and eukaryotes, is required for efficient regulation of cellular iron homeostasis. humans with a frataxin deficiency have the cardio- and neurodegenerative disorder friedreich's ataxia, commonly resulting from a gaa trinucleotide repeat expansion in the frataxin gene. while frataxin's specific function remains a point of controversy, the general consensus is that the protein assists in controlling cellular iron homeostasis by directly bin ...	2006	16911956
nuclear photosynthetic gene expression is synergistically modulated by rates of protein synthesis in chloroplasts and mitochondria.	arabidopsis thaliana mutants prors1-1 and -2 were identified on the basis of a decrease in effective photosystem ii quantum yield. mutations were localized to the 5'-untranslated region of the nuclear gene prolyl-trna synthetase1 (prors1), which acts in both plastids and mitochondria. in prors1-1 and -2, prors1 expression is reduced, along with protein synthesis in both organelles. prors1 null alleles (prors1-3 and -4) result in embryo sac and embryo development arrest. in mutants with the leaky ...	2006	16517761
ribose 2'-hydroxyl groups in the 5' strand of the acceptor arm of p-site trna are not essential for ef-g catalyzed translocation.	the coupled movement of trna-mrna complex through the ribosome is a fundamental step during the protein elongation process. we demonstrate that the ribosome will translocate a p-site-bound trna(met) with a break in the phosphodiester backbone between positions 17 and 18 in the d-loop. crystallographic data showed that the acceptor arms of p- and e-site trna interact extensively with the ribosomal large subunit. therefore, we used this fragmented p-site-bound trna(met) to investigate the contribu ...	2006	16489185
exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds.	as tertiary structure is currently available only for a fraction of known protein families, it is important to assess what parts of sequence space have been structurally characterized. we consider protein domains whose structure can be predicted by sequence similarity to proteins with solved structure and address the following questions. do these domains represent an unbiased random sample of all sequence families? do targets solved by structural genomic initiatives (sgi) provide such a sample? ...	2006	16549009
a putative rna-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic rnai, and hypothetical mechanisms of action.	all archaeal and many bacterial genomes contain clustered regularly interspaced short palindrome repeats (crispr) and variable arrays of the crispr-associated (cas) genes that have been previously implicated in a novel form of dna repair on the basis of comparative analysis of their protein product sequences. however, the proximity of crispr and cas genes strongly suggests that they have related functions which is hard to reconcile with the repair hypothesis.	2006	16545108
nucleotide exchange via local protein unfolding--structure of rab8 in complex with mss4.	rab gtpases function as essential regulators of vesicle transport in eukaryotic cells. mss4 was shown to stimulate nucleotide exchange on rab proteins associated with the exocytic pathway and to have nucleotide-free-rab chaperone activity. a detailed kinetic analysis of mss4 interaction with rab8 showed that mss4 is a relatively slow exchange factor that forms a long-lived nucleotide-free complex with rabgtpase. in contrast to other characterized exchange factor-gtpase complexes, mss4:rab8 compl ...	2006	16541104
methionine oxidation of monomeric lambda repressor: the denatured state ensemble under nondenaturing conditions.	although poorly understood, the properties of the denatured state ensemble are critical to the thermodynamics and the kinetics of protein folding. the most relevant conformations to cellular protein folding are the ones populated under physiological conditions. to avoid the problem of low expression that is seen with unstable variants, we used methionine oxidation to destabilize monomeric lambda repressor and predominantly populate the denatured state under nondenaturing buffer conditions. the d ...	2006	16452618
defining the primary route for lutein synthesis in plants: the role of arabidopsis carotenoid beta-ring hydroxylase cyp97a3.	lutein, a dihydroxy derivative of alpha-carotene (beta,epsilon-carotene), is the most abundant carotenoid in photosynthetic plant tissues where it plays important roles in light-harvesting complex-ii structure and function. the synthesis of lutein from lycopene requires at least four distinct enzymatic reactions: beta- and epsilon-ring cyclizations and hydroxylation of each ring at the c-3 position. three carotenoid hydroxylases have already been identified in arabidopsis, two nonheme diiron bet ...	2006	16492736
nucleic acid visualization with ucsf chimera.	with the increase in the number of large, 3d, high-resolution nucleic acid structures, particularly of the 30s and 50s ribosomal subunits and the intact bacterial ribosome, advancements in the visualization of nucleic acid structural features are essential. large molecular structures are complicated and detailed, and one goal of visualization software is to allow the user to simplify the display of some features and accent others. we describe an extension to the ucsf chimera molecular visualizat ...	2006	16478715
the post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5a (eif5a).	the eukaryotic translation initiation factor 5a (eif5a) is the only cellular protein that contains the unique polyamine-derived amino acid, hypusine [nepsilon-(4-amino-2-hydroxybutyl)lysine]. hypusine is formed in eif5a by a novel post-translational modification reaction that involves two enzymatic steps. in the first step, deoxyhypusine synthase catalyzes the cleavage of the polyamine spermidine and transfer of its 4-aminobutyl moiety to the epsilon-amino group of one specific lysine residue of ...	2006	16452303
structural biology of rna silencing and its functional implications.	we outline structure-function contributions from our laboratories on protein-rna recognition events that monitor sirna length, 5 -phosphate and 2-nucleotide 3 overhangs, as well as the architecture of argonaute, its externally bound sirna complex, and argonaute-based models involving guide-strand-mediated mrna binding, cleavage, and release.	2006	17381284
conserved quantitative stability/flexibility relationships (qsfr) in an orthologous rnase h pair.	many reports qualitatively describe conserved stability and flexibility profiles across protein families, but biophysical modeling schemes have not been available to robustly quantify both. here we investigate an orthologous rnase h pair by using a minimal distance constraint model (dcm). the dcm is an all atom microscopic model [jacobs and dallakyan, biophys j 2005;88(2):903-915] that accurately reproduces heat capacity measurements [livesay et al., febs lett 2004;576(3):468-476], and is unique ...	2006	16287093
participation of the trna a76 hydroxyl groups throughout translation.	the free 2'-3' cis-diol at the 3'-terminus of trna provides a unique juxtaposition of functional groups that play critical roles during protein synthesis. the translation process involves universally conserved chemistry at almost every stage of this multistep procedure, and the 2'- and 3'-ohs are in the immediate vicinity of chemistry at each step. the cis-diol contribution affects steps ranging from trna aminoacylation to peptide bond formation. the contributions have been studied in assays rel ...	2006	16681365
structural perspective on mutations affecting the function of multisubunit rna polymerases.	high-resolution crystallographic structures of multisubunit rna polymerases (rnaps) have increased our understanding of transcriptional mechanisms. based on a thorough review of the literature, we have compiled the mutations affecting the function of multisubunit rna polymerases, many of which having been generated and studied prior to the publication of the first high-resolution structure, and highlighted the positions of the altered amino acids in the structures of both the prokaryotic and euk ...	2006	16524917