| directed evolution of dna polymerases for next-generation sequencing. | | 2010 | 20629059 |
| molecular and biotechnological aspects of microbial proteases. | proteases represent the class of enzymes which occupy a pivotal position with respect to their physiological roles as well as their commercial applications. they perform both degradative and synthetic functions. since they are physiologically necessary for living organisms, proteases occur ubiquitously in a wide diversity of sources such as plants, animals, and microorganisms. microbes are an attractive source of proteases owing to the limited space required for their cultivation and their ready ... | 1998 | 9729602 |
| design and evaluation of useful bacterium-specific pcr primers that amplify genes coding for bacterial 16s rrna. | we report the design and evaluation of pcr primers 63f and 1387r for amplification of 16s rrna genes from bacteria. their specificity and efficacy were tested systematically with a bacterial species and environmental samples. they were found to be more useful for 16s rrna gene amplification in ecological and systematic studies than pcr amplimers that are currently more generally used. | 1998 | 9464425 |
| 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 |
| search and discovery strategies for biotechnology: the paradigm shift. | profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. the advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. in this ... | 2000 | 10974127 |
| 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 |
| accommodation of profound sequence differences at the interfaces of eubacterial rna polymerase multi-protein assembly. | evolutionarily divergent proteins have been shown to change their interacting partners. rna polymerase assembly is one of the rare cases which retain its component proteins in the course of evolution. this ubiquitous molecular assembly, involved in transcription, consists of four core subunits (alpha, beta, betaprime, and omega), which assemble to form the core enzyme. remarkably, the orientation of the four subunits in the complex is conserved from prokaryotes to eukaryotes although their seque ... | 2012 | 22359428 |
| structure of a bacterial rna polymerase holoenzyme open promoter complex. | initiation of transcription is a primary means for controlling gene expression. in bacteria, the rna polymerase (rnap) holoenzyme binds and unwinds promoter dna, forming the transcription bubble of the open promoter complex (rpo). we have determined crystal structures, refined to 4.14 å-resolution, of rpo containing thermus aquaticus rnap holoenzyme and promoter dna that includes the full transcription bubble. the structures, combined with biochemical analyses, reveal key features supporting the ... | 2015 | 26349032 |
| card uses a minor groove wedge mechanism to stabilize the rna polymerase open promoter complex. | a key point to regulate gene expression is at transcription initiation, and activators play a major role. card, an essential activator in mycobacterium tuberculosis, is found in many bacteria, including thermus species, but absent in escherichia coli. to delineate the molecular mechanism of card, we determined crystal structures of thermus transcription initiation complexes containing card. the structures show card interacts with the unique dna topology presented by the upstream double-stranded/ ... | 2015 | 26349034 |
| characterization of the genome, proteome, and structure of yersiniophage ϕr1-37. | the bacteriophage vb_yecm-ϕr1-37 (ϕr1-37) is a lytic yersiniophage that can propagate naturally in different yersinia species carrying the correct lipopolysaccharide receptor. this large-tailed phage has deoxyuridine (du) instead of thymidine in its dna. in this study, we determined the genomic sequence of phage ϕr1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. t ... | 2012 | 22973030 |
| insertion sequences. | insertion sequences (iss) constitute an important component of most bacterial genomes. over 500 individual iss have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. the last 10 years have also seen some striking advances in our understanding of the transposition process itself. not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic e ... | 1998 | 9729608 |
| extremophiles and their application to veterinary medicine. | : extremophiles are organisms that can grow and thrive in harsh conditions, e.g., extremes of temperature, ph, salinity, radiation, pressure and oxygen tension. thermophilic, halophilic and radiation-resistant organisms are all microbes, some of which are able to withstand multiple extremes. psychrophiles, or cold-loving organisms, include not only microbes, but fish that live in polar waters and animals that can withstand freezing. extremophiles are structurally adapted at a molecular level to ... | 2004 | 21851659 |
| the arabidopsis huellenlos gene, which is essential for normal ovule development, encodes a mitochondrial ribosomal protein. | the huellenlos (hll) gene participates in patterning and growth of the arabidopsis ovule. we have isolated the hll gene and shown that it encodes a protein homologous to the l14 proteins of eubacterial ribosomes. the arabidopsis genome also includes a highly similar gene, huellenlos paralog (hlp), and genes for both cytosolic (l23) and chloroplast ribosome l14 proteins. phylogenetic analysis shows that hll and hlp differ significantly from these other two classes of such proteins. hll and hlp fu ... | 2001 | 11752383 |
| dnak dependence of the mycobacterial stress-responsive regulator hspr is mediated through its hydrophobic c-terminal tail. | hspr is a repressor known to control expression of heat shock operons in a number of eubacteria. in mycobacteria and in several other actinobacteria, this protein is synthesized from the dnakje-hspr operon. previous investigations revealed that hspr binds to the operon promoter, thereby controlling its expression in an autoregulatory manner. dnak, which is a product of the same operon, further aids this autoregulatory process by stimulating the operator binding activity of hspr. the molecular me ... | 2012 | 22753065 |
| bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control. | under a shortage of oxygen, bacterial growth can be faced mainly by two atp-generating mechanisms: (i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to use traces of oxygen or (ii) by utilizing other substrates as final electron acceptors such as nitrate, which can be reduced to dinitrogen gas through denitrification or to ammonium. this bacterial respiratory shift from oxic to microoxic and anoxic conditions requires a regulatory strategy which ensures that cells ... | 2012 | 22098259 |
| structural basis of transcription inhibition by cbr hydroxamidines and cbr pyrazoles. | cbr hydroxamidines are small-molecule inhibitors of bacterial rna polymerase (rnap) discovered through high-throughput screening of synthetic-compound libraries. cbr pyrazoles are structurally related rnap inhibitors discovered through scaffold hopping from cbr hydroxamidines. cbr hydroxamidines and pyrazoles selectively inhibit gram-negative bacterial rnap and exhibit selective antibacterial activity against gram-negative bacteria. here, we report crystal structures of the prototype cbr hydroxa ... | 2015 | 26190576 |
| structural biology of bacterial rna polymerase. | since its discovery and characterization in the early 1960s (hurwitz, j. the discovery of rna polymerase. j. biol. chem. 2005, 280, 42477-42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial rna polymerase (rnap). in the late 1990s, structural information pertaining to bacterial rnap has emerged that provided unprecedented insights into the function and mechanism of rna transcription. in this review, i list all structures related to bacterial rn ... | 2015 | 25970587 |
| principles and applications of methods for dna-based typing of microbial organisms. | | 1999 | 10325304 |
| a phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. | it has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms, but up to now, no satisfying approach has been proposed to use efficiently these data. for instance, if the coding of presence or absence of genes in complete genomes gives interesting results, it does not take into account the phylogenetic information contained in sequences and ignores hidden paralogies by using a blast reciprocal best hit definition of orthology. in addition, concaten ... | 2002 | 12097345 |
| structural, functional, and genetic analysis of sorangicin inhibition of bacterial rna polymerase. | a combined structural, functional, and genetic approach was used to investigate inhibition of bacterial rna polymerase (rnap) by sorangicin (sor), a macrolide polyether antibiotic. sor lacks chemical and structural similarity to the ansamycin rifampicin (rif), an rnap inhibitor widely used to treat tuberculosis. nevertheless, structural analysis revealed sor binds in the same rnap beta subunit pocket as rif, with almost complete overlap of rnap binding determinants, and functional analysis revea ... | 2005 | 15692574 |
| frequency, spectrum, and nonzero fitness costs of resistance to myxopyronin in staphylococcus aureus. | the antibiotic myxopyronin (myx) functions by inhibiting bacterial rna polymerase (rnap). the binding site on rnap for myx-the rnap "switch region sw1/sw2 subregion"-is different from the binding site on rnap for the rnap inhibitor currently used in broad-spectrum antibacterial therapy, rifampin (rif). here, we report the frequency, spectrum, and fitness costs of myx resistance in staphylococcus aureus. the resistance rate for myx is 4 × 10(-8) to 7 × 10(-8) per generation, which is equal within ... | 2012 | 23006749 |
| bacterial transcription as a target for antibacterial drug development. | transcription, the first step of gene expression, is carried out by the enzyme rna polymerase (rnap) and is regulated through interaction with a series of protein transcription factors. rnap and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. the determination ... | 2016 | 26764017 |
| directed evolution of polymerase function by compartmentalized self-replication. | we describe compartmentalized self-replication (csr), a strategy for the directed evolution of enzymes, especially polymerases. csr is based on a simple feedback loop consisting of a polymerase that replicates only its own encoding gene. compartmentalization serves to isolate individual self-replication reactions from each other. in such a system, adaptive gains directly (and proportionally) translate into genetic amplification of the encoding gene. csr has applications in the evolution of polym ... | 2001 | 11274352 |
| interaction of card with rna polymerase mediates mycobacterium tuberculosis viability, rifampin resistance, and pathogenesis. | mycobacterium tuberculosis infection continues to cause substantial human suffering. new chemotherapeutic strategies, which require insight into the pathways essential for m. tuberculosis pathogenesis, are imperative. we previously reported that depletion of the card protein in mycobacteria compromises viability, resistance to oxidative stress and fluoroquinolones, and pathogenesis. card associates with the rna polymerase (rnap), but it has been unknown which of the diverse functions of card are ... | 2012 | 22904282 |
| identification and characterization of the cognate anti-sigma factor and specific promoter elements of a t. tengcongensis ecf sigma factor. | extracytoplasmic function (ecf) σ factors, the largest group of alternative σ factors, play important roles in response to environmental stresses. tt-rpoe1 is annotated as an ecf σ factor in thermoanaerobacter tengcongensis. in this study, we revealed that the tt-tolb gene located downstream of the tt-rpoe1 gene encoded the cognate anti-σ factor, which could inhibit the transcription activity of tt-rpoe1 by direct interaction with tt-rpoe1 via its n-terminal domain. by in vitro transcription ass ... | 2012 | 22815853 |
| mycobacterial rna polymerase forms unstable open promoter complexes that are stabilized by card. | escherichia coli has served as the archetypal organism on which the overwhelming majority of biochemical characterizations of bacterial rna polymerase (rnap) have been focused; the properties of e. coli rnap have been accepted as generally representative for all bacterial rnaps. here, we directly compare the initiation properties of a mycobacterial transcription system with e. coli rnap on two different promoters. the detailed characterizations include abortive transcription assays, rnap/promote ... | 2014 | 25510492 |
| mycobacterial rna polymerase forms unstable open promoter complexes that are stabilized by card. | escherichia coli has served as the archetypal organism on which the overwhelming majority of biochemical characterizations of bacterial rna polymerase (rnap) have been focused; the properties of e. coli rnap have been accepted as generally representative for all bacterial rnaps. here, we directly compare the initiation properties of a mycobacterial transcription system with e. coli rnap on two different promoters. the detailed characterizations include abortive transcription assays, rnap/promote ... | 2014 | 25510492 |
| structures of rna polymerase-antibiotic complexes. | inhibition of bacterial rna polymerase (rnap) is an established strategy for antituberculosis therapy and broad-spectrum antibacterial therapy. crystal structures of rnap-inhibitor complexes are available for four classes of antibiotics: rifamycins, sorangicin, streptolydigin, and myxopyronin. the structures define three different targets, and three different mechanisms, for inhibition of bacterial rnap: (1) rifamycins and sorangicin bind near the rnap active center and block extension of rna pr ... | 2009 | 19926275 |
| insights from bacterial subtilases into the mechanisms of intramolecular chaperone-mediated activation of furin. | prokaryotic subtilisins and eukaryotic proprotein convertases (pcs) are two homologous protease subfamilies that belong to the larger ubiquitous super-family called subtilases. members of the subtilase super-family are produced as zymogens wherein their propeptide domains function as dedicated intramolecular chaperones (imcs) that facilitate correct folding and regulate precise activation of their cognate catalytic domains. the molecular and cellular determinants that modulate imc-dependent fold ... | 2011 | 21805238 |
| protein targeting to the bacterial cytoplasmic membrane. | proteins that perform their activity within the cytoplasmic membrane or outside this cell boundary must be targeted to the translocation site prior to their insertion and/or translocation. in bacteria, several targeting routes are known; the secb- and the signal recognition particle-dependent pathways are the best characterized. recently, evidence for the existence of a third major route, the twin-arg pathway, was gathered. proteins that use either one of these three different pathways possess s ... | 1999 | 10066835 |
| predicting transmembrane beta-barrels in proteomes. | very few methods address the problem of predicting beta-barrel membrane proteins directly from sequence. one reason is that only very few high-resolution structures for transmembrane beta-barrel (tmb) proteins have been determined thus far. here we introduced the design, statistics and results of a novel profile-based hidden markov model for the prediction and discrimination of tmbs. the method carefully attempts to avoid over-fitting the sparse experimental data. while our model training and sc ... | 2004 | 15141026 |
| the complete genome sequence of hyperthermophile dictyoglomus turgidum dsm 6724™ reveals a specialized carbohydrate fermentor. | here we report the complete genome sequence of the chemoorganotrophic, extremely thermophilic bacterium, dictyoglomus turgidum, which is a gram negative, strictly anaerobic bacterium. d. turgidum and d. thermophilum together form the dictyoglomi phylum. the two dictyoglomus genomes are highly syntenic, and both are distantly related to caldicellulosiruptor spp. d. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genomic commitment to glycosyl hydrolases, ... | 2016 | 28066333 |
| dna polymerases engineered by directed evolution to incorporate non-standard nucleotides. | dna polymerases have evolved for billions of years to accept natural nucleoside triphosphate substrates with high fidelity and to exclude closely related structures, such as the analogous ribonucleoside triphosphates. however, polymerases that can accept unnatural nucleoside triphosphates are desired for many applications in biotechnology. the focus of this review is on non-standard nucleotides that expand the genetic "alphabet." this review focuses on experiments that, by directed evolution, ha ... | 2014 | 25400626 |
| molecular evolution of multisubunit rna polymerases: sequence analysis. | transcription in all cellular organisms is performed by multisubunit, dna-dependent rna polymerases that synthesize rna from dna templates. previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit rna polymerases. in addition, rna polymerases contain multiple lineage-specific domain insertions involved in protein-protein and protein-nucleic acid interactions. we have created comprehensive multiple sequence alignments using all available ... | 2009 | 19895820 |
| molecular evolution of multisubunit rna polymerases: sequence analysis. | transcription in all cellular organisms is performed by multisubunit, dna-dependent rna polymerases that synthesize rna from dna templates. previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit rna polymerases. in addition, rna polymerases contain multiple lineage-specific domain insertions involved in protein-protein and protein-nucleic acid interactions. we have created comprehensive multiple sequence alignments using all available ... | 2009 | 19895820 |
| extremophiles 2002. | | 2003 | 12813059 |
| potential applications of immobilized β-galactosidase in food processing industries. | the enzyme β-galactosidase can be obtained from a wide variety of sources such as microorganisms, plants, and animals. the use of β-galactosidase for the hydrolysis of lactose in milk and whey is one of the promising enzymatic applications in food and dairy processing industries. the enzyme can be used in either soluble or immobilized forms but the soluble enzyme can be used only for batch processes and the immobilized form has the advantage of being used in batch wise as well as in continuous o ... | 2010 | 21234407 |
| fermentation technologies for the optimization of marine microbial exopolysaccharide production. | in the last decades, research has focused on the capabilities of microbes to secrete exopolysaccharides (eps), because these polymers differ from the commercial ones derived essentially from plants or algae in their numerous valuable qualities. these biopolymers have emerged as new polymeric materials with novel and unique physical characteristics that have found extensive applications. in marine microorganisms the produced eps provide an instrument to survive in adverse conditions: they are fou ... | 2014 | 24857960 |
| cold and hot extremozymes: industrial relevance and current trends. | the development of enzymes for industrial applications relies heavily on the use of microorganisms. the intrinsic properties of microbial enzymes, e.g., consistency, reproducibility, and high yields along with many others, have pushed their introduction into a wide range of products and industrial processes. extremophilic microorganisms represent an underutilized and innovative source of novel enzymes. these microorganisms have developed unique mechanisms and molecular means to cope with extreme ... | 2015 | 26539430 |
| marine extremophiles: a source of hydrolases for biotechnological applications. | the marine environment covers almost three quarters of the planet and is where evolution took its first steps. extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. the ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. hydrolases including amylases, cellulases, peptidases and lipases from hyper ... | 2015 | 25854643 |
| the fggy carbohydrate kinase family: insights into the evolution of functional specificities. | function diversification in large protein families is a major mechanism driving expansion of cellular networks, providing organisms with new metabolic capabilities and thus adding to their evolutionary success. however, our understanding of the evolutionary mechanisms of functional diversity in such families is very limited, which, among many other reasons, is due to the lack of functionally well-characterized sets of proteins. here, using the fggy carbohydrate kinase family as an example, we bu ... | 2011 | 22215998 |
| structure, function and mechanism of exocyclic dna methyltransferases. | dna mtases (methyltransferases) catalyse the transfer of methyl groups to dna from adomet (s-adenosyl-l-methionine) producing adohcy (s-adenosyl-l-homocysteine) and methylated dna. the c5 and n4 positions of cytosine and n6 position of adenine are the target sites for methylation. all three methylation patterns are found in prokaryotes, whereas cytosine at the c5 position is the only methylation reaction that is known to occur in eukaryotes. in general, mtases are two-domain proteins comprising ... | 2006 | 16987108 |
| n-acetyltransferase 2 (nat2) gene polymorphism as a predisposing factor for phenytoin intoxication in tuberculous meningitis or tuberculoma patients having seizures - a pilot study. | simultaneous administration of phenytoin and isoniazid (inh) in tuberculous meningitis (tbm) or tuberculoma patients with seizures results in higher plasma phenytoin level and thus phenytoin intoxication. n-acetyltransferase 2 (nat2) enzyme catalyses two acetylation reactions in inh metabolism and nat2 gene polymorphism leads to slow and rapid acetylators. the present study was aimed to evaluate the effect of allelic variants of n-acetyltransferase 2 (nat2) gene as a predisposing factor for phen ... | 2016 | 27488001 |
| phylogenetic analysis and evolutionary origins of dna polymerase x-family members. | mammalian dna polymerase (pol) β is the founding member of a large group of dna polymerases now termed the x-family. dna polymerase β has been kinetically, structurally, and biologically well characterized and can serve as a phylogenetic reference. accordingly, we have performed a phylogenetic analysis to understand the relationship between pol β and other members of the x-family of dna polymerases. the bacterial x-family dna polymerases, saccharomyces cerevisiae pol iv, and four mammalian x-fam ... | 2014 | 25112931 |
| role of law enforcement response and microbial forensics in investigation of bioterrorism. | the risk and threat of bioterrorism and biocrime have become a large concern and challenge for governments and society to enhance biosecurity. law enforcement plays an important role in assessing and investigating activities involved in an event of bioterrorism or biocrime. key to a successful biosecurity program is increased awareness and early detection of threats facilitated by an integrated network of responsibilities and capabilities from government, academic, private, and public assets. to ... | 2007 | 17696298 |
| ribonucleotide reduction - horizontal transfer of a required function spans all three domains. | ribonucleotide reduction is the only de novo pathway for synthesis of deoxyribonucleotides, the building blocks of dna. the reaction is catalysed by ribonucleotide reductases (rnrs), an ancient enzyme family comprised of three classes. each class has distinct operational constraints, and are broadly distributed across organisms from all three domains, though few class i rnrs have been identified in archaeal genomes, and classes ii and iii likewise appear rare across eukaryotes. in this study, we ... | 2010 | 21143941 |
| architecture and conservation of the bacterial dna replication machinery, an underexploited drug target. | new antibiotics with novel modes of action are required to combat the growing threat posed by multi-drug resistant bacteria. over the last decade, genome sequencing and other high-throughput techniques have provided tremendous insight into the molecular processes underlying cellular functions in a wide range of bacterial species. we can now use these data to assess the degree of conservation of certain aspects of bacterial physiology, to help choose the best cellular targets for development of n ... | 2012 | 22206257 |
| efficiency of dna replication in the polymerase chain reaction. | a detailed quantitative kinetic model for the polymerase chain reaction (pcr) is developed, which allows us to predict the probability of replication of a dna molecule in terms of the physical parameters involved in the system. the important issue of the determination of the number of pcr cycles during which this probability can be considered to be a constant is solved within the framework of the model. new phenomena of multimodality and scaling behavior in the distribution of the number of mole ... | 1996 | 8917524 |
| purification and characterization of a trehalose synthase from the basidiomycete grifola frondosa | a trehalose synthase (tsase) that catalyzes the synthesis of trehalose from d-glucose and alpha-d-glucose 1-phosphate (alpha-d-glucose 1-p) was detected in a basidiomycete, grifola frondosa. tsase was purified 106-fold to homogeneity with 36% recovery by ammonium sulfate precipitation and several steps of column chromatography. the native enzyme appears to be a dimer since it has apparent molecular masses of 120 kda, as determined by gel filtration column chromatography, and 60 kda, as determine ... | 1998 | 9797287 |
| polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases. | a universal base that is capable of substituting for any of the four natural bases in dna would be of great utility in both mutagenesis and recombinant dna experiments. this paper describes the properties of oligonucleotides incorporating two degenerate bases, the pyrimidine base 6h,8h-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one and the purine base n6-methoxy-2,6-diaminopurine, designated p and k, respectively. an equimolar mixture of the analogues p and k (called m) acts, in primers, as a unive ... | 1998 | 9539724 |
| the complete chloroplast dna sequence of the green alga nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes. | green plants seem to form two sister lineages: chlorophyta, comprising the green algal classes prasinophyceae, ulvophyceae, trebouxiophyceae, and chlorophyceae, and streptophyta, comprising the charophyceae and land plants. we have determined the complete chloroplast dna (cpdna) sequence (200,799 bp) of nephroselmis olivacea, a member of the class (prasinophyceae) thought to include descendants of the earliest-diverging green algae. the 127 genes identified in this genome represent the largest g ... | 1999 | 10468594 |
| structure-based design of taq dna polymerases with improved properties of dideoxynucleotide incorporation. | the taq dna polymerase is the most commonly used enzyme in dna sequencing. however, all versions of taq polymerase are deficient in two respects: (i) these enzymes incorporate each of the four dideoxynucleoside 5' triphosphates (ddntps) at widely different rates during sequencing (ddgtp, for example, is incorporated 10 times faster than the other three ddntps), and (ii) these enzymes show uneven band-intensity or peak-height patterns in radio-labeled or dye-labeled dna sequence profiles, respect ... | 1999 | 10449720 |
| relation of a tnf gene polymorphism to severe sepsis in trauma patients. | to investigate the relation of the biallelic nco1 restriction fragment length polymorphism in the first intron of the tumor necrosis factor (tnf) beta gene with the development of severe sepsis in multiply injured patients. | 1999 | 10450735 |
| improved dna sequencing accuracy and detection of heterozygous alleles using manganese citrate and different fluorescent dye terminators. | the use of dideoxynucleotide triphosphates labeled with different fluorescent dyes (dye terminators) is the most versatile method for automated dna sequencing. however, variation in peak heights reduces base-calling accuracy and limits heterozygous allele detection, favoring use of dye-labeled primers for this purpose. we have discovered that the addition of a manganese salt to the pe applied biosystems dye-terminator sequencing kits overcomes these limitations for the older rhodamine dyes as we ... | 1999 | 10400927 |
| estimation of bacterial cell numbers in humic acid-rich salt marsh sediments with probes directed to 16s ribosomal dna | the feasibility of using probes directed towards ribosomal dnas (rdnas) as a quantitative approach to estimating cell numbers was examined and applied to study the structure of a bacterial community in humic acid-rich salt marsh sediments. hybridizations were performed with membrane-bound nucleic acids by using seven group-specific dna oligonucleotide probes complementary to 16s rrna coding regions. these included a general eubacterial probe and probes encompassing most members of the gram-negat ... | 1999 | 10103245 |
| mutagenesis of conserved lysine residues in bacteriophage t5 5'-3' exonuclease suggests separate mechanisms of endo-and exonucleolytic cleavage. | efficient cellular dna replication requires the activity of a 5'-3' exonuclease. these enzymes are able to hydrolyze dna.dna and rna.dna substrates exonucleolytically, and they are structure-specific endonucleases. the 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. crystal structures of three representative enzymes identify two divalent-metal-binding sites typically separated by 8-10 a. site-directed mutagenesis was used to investigate the roles of three l ... | 1999 | 9874768 |
| rapid identification of up to three candida species in a single reaction tube by a 5' exonuclease assay using fluorescent dna probes. | we used fungus-specific pcr primers and species-specific dna probes to detect up to three candida species in a single reaction tube by exploiting the 5' to 3' exonuclease activity of taq dna polymerase. probes to the internal transcribed spacer region of the rrna gene were labeled at the 5' end with one of three fluorescent reporter dyes, 6-carboxy-fluorescein (fam), tetrachloro-6-carboxy-fluorescein (tet), or hexachloro-6-carboxy-fluorescein (hex), and at the 3' end with a quencher dye, 6-carbo ... | 1999 | 9854084 |
| mechanism of promoter melting by the xeroderma pigmentosum complementation group b helicase of transcription factor iih revealed by protein-dna photo-cross-linking. | the p89/xeroderma pigmentosum complementation group b (xpb) atpase-helicase of transcription factor iih (tfiih) is essential for promoter melting prior to transcription initiation by rna polymerase ii (rnapii). by studying the topological organization of the initiation complex using site-specific protein-dna photo-cross-linking, we have shown that p89/xpb makes promoter contacts both upstream and downstream of the initiation site. the upstream contact, which is in the region where promoter melti ... | 2000 | 11027286 |
| decreased c-src expression enhances osteoblast differentiation and bone formation. | c-src deletion in mice leads to osteopetrosis as a result of reduced bone resorption due to an alteration of the osteoclast. we report that deletion/reduction of src expression enhances osteoblast differentiation and bone formation, contributing to the increase in bone mass. bone histomorphometry showed that bone formation was increased in src null compared with wild-type mice. in vitro, alkaline phosphatase (alp) activity and nodule mineralization were increased in primary calvarial cells and i ... | 2000 | 11038178 |
| endoplasmic reticulum quality control of oligomeric membrane proteins: topogenic determinants involved in the degradation of the unassembled na,k-atpase alpha subunit and in its stabilization by beta subunit assembly. | the molecular nature of determinants that mediate degradation of unassembled, polytopic subunits of oligomeric membrane proteins and their stabilization after partner subunit assembly is largely unknown. expressing truncated na,k-atpase alpha subunits alone or together with beta subunits, we find that in unassembled alpha subunits neither the four n-terminal transmembrane segments acting as efficient alternating signal anchor-stop transfer sequences nor the large, central cytoplasmic loop expose ... | 2000 | 10793142 |
| signal amplification through nucleotide extension and excision on a dendritic dna platform. | techniques that provide strong signal amplification are useful in diagnostic applications, especially in detecting low concentrations of non-amplifiable target molecules. a versatile and strong signal amplification method based on activities of a dna polymerase to generate high concentrations of pyrophosphate (ppi) is described. the generation of ppi is catalyzed by nucleotide extension and excision activities of a dna polymerase on an oligonucleotide cassette. the signal is generated upon enzym ... | 2000 | 10710438 |
| macromolecular mimicry. | some proteins have been shown to mimic the overall shape and structure of nucleic acids. for some of the proteins involved in translating the genetic information into proteins on the ribosome particle, there are indications that such observations of macromolecular mimicry even extend to similarity in interaction with and function on the ribosome. a small number of structural results obtained outside the protein biosynthesis machinery could indicate that the concept of macromolecular mimicry betw ... | 2000 | 10675317 |
| lipopolysaccharide pretreatment protects from renal ischemia/reperfusion injury : possible connection to an interleukin-6-dependent pathway. | in vivo administration of low doses of lipopolysaccharide (lps) to rodents can protect these animals from subsequently administrated, usually lethal doses of endotoxin or lps. in this study we tested the effects of lps pretreatment on ischemia/reperfusion injury in the kidney. male c57/b1 mice were pretreated with different doses of lps or phosphate-buffered saline on days -4 and -3. the right kidney was removed, and the vessels of the left kidney were clamped for 30 or 45 minutes on day 0. crea ... | 2000 | 10623677 |
| dna sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient dna. | we show that dna molecules amplified by pcr from dna extracted from animal bones and teeth that vary in age between 25 000 and over 50 000 years carry c-->t and g-->a substitutions. these substitutions can reach high proportions among the molecules amplified and are due to the occurrence of modified deoxycytidine residues in the template dna. if the template dna is treated with uracil n-glycosylase, these substitutions are dramatically reduced. they are thus likely to result from deamination of ... | 2001 | 11726688 |
| dna probes using fluorescence resonance energy transfer (fret): designs and applications. | fluorescence resonance energy transfer (fret) is widely used in biomedical research as a reporter method. oligonucleotides with a dna backbone and one or several chromophore tags have found multiple applications as fret probes. they are especially advantageous for the real-time monitoring of biochemical reactions and in vivo studies. this paper reviews the design and applications of various dna-based probes that use fret the approaches used in the design of new dna fret probes are discussed. | 2001 | 11730017 |
| transient dissociation of polyribosomes and concurrent recruitment of calreticulin and calmodulin transcripts in gravistimulated maize pulvini. | the dynamics of polyribosome abundance were studied in gravistimulated maize (zea mays) stem pulvini. during the initial 15 min of gravistimulation, the amount of large polyribosomes transiently decreased. the transient decrease in polyribosome levels was accompanied by a transient decrease in polyribosome-associated mrna. after 30 min of gravistimulation, the levels of polyribosomes and the amount of polyribosome-associated mrna gradually increased over 24 h up to 3- to 4-fold of the initial va ... | 2001 | 11706198 |
| adomet-dependent methylation, dna methyltransferases and base flipping. | twenty adomet-dependent methyltransferases (mtases) have been characterized structurally by x-ray crystallography and nmr. these include seven dna mtases, five rna mtases, four protein mtases and four small molecule mtases acting on the carbon, oxygen or nitrogen atoms of their substrates. the mtases share a common core structure of a mixed seven-stranded beta-sheet (6 downward arrow 7 upward arrow 5 downward arrow 4 downward arrow 1 downward arrow 2 downward arrow 3 downward arrow) referred to ... | 2001 | 11557810 |
| antiapoptotic signaling generated by caspase-induced cleavage of rasgap. | activation of caspases 3 and 9 is thought to commit a cell irreversibly to apoptosis. there are, however, several documented situations (e.g., during erythroblast differentiation) in which caspases are activated and caspase substrates are cleaved with no associated apoptotic response. why the cleavage of caspase substrates leads to cell death in certain cases but not in others is unclear. one possibility is that some caspase substrates generate antiapoptotic signals when cleaved. here we show th ... | 2001 | 11463818 |
| tuning dna "strings": modulating the rate of dna replication with mechanical tension. | recent experiments have measured the rate of replication of dna catalyzed by a single enzyme moving along a stretched template strand. the dependence on tension was interpreted as evidence that t7 and related dna polymerases convert two (n = 2) or more single-stranded template bases to double helix geometry in the polymerization site during each catalytic cycle. however, we find structural data on the t7 enzyme--template complex indicate n = 1. we also present a model for the "tuning" of replica ... | 2001 | 11447284 |
| molecular markers of serine protease evolution. | the evolutionary history of serine proteases can be accounted for by highly conserved amino acids that form crucial structural and chemical elements of the catalytic apparatus. these residues display non- random dichotomies in either amino acid choice or serine codon usage and serve as discrete markers for tracking changes in the active site environment and supporting structures. these markers categorize serine proteases of the chymotrypsin-like, subtilisin-like and alpha/beta-hydrolase fold cla ... | 2001 | 11406580 |
| homogeneous assays for single-nucleotide polymorphism typing using alphascreen. | alphascreen technology allows the development of high-throughput homogeneous proximity assays. in these assays, signal is generated when 680 nm laser light irradiates a donor bead in close proximity to an acceptor bead. for the detection of nucleic acids, donor and acceptor beads are brought into proximity by two bridging probes that hybridize simultaneously to a common target and to the generic oligonucleotides attached covalently to the beads. this method allows the detection of as little as 1 ... | 2001 | 11282975 |
| evaluation of pcr-generated chimeras, mutations, and heteroduplexes with 16s rrna gene-based cloning. | to evaluate pcr-generated artifacts (i.e., chimeras, mutations, and heteroduplexes) with the 16s ribosomal dna (rdna)-based cloning approach, a model community of four species was constructed from alpha, beta, and gamma subdivisions of the division proteobacteria as well as gram-positive bacterium, all of which could be distinguished by hhai restriction digestion patterns. the overall pcr artifacts were significantly different among the three taq dna polymerases examined: 20% for z-taq, with the ... | 2001 | 11157258 |
| function-structure analysis of proteins using covarion-based evolutionary approaches: elongation factors. | the divergent evolution of protein sequences from genomic databases can be analyzed by the use of different mathematical models. the most common treat all sites in a protein sequence as equally variable. more sophisticated models acknowledge the fact that purifying selection generally tolerates variable amounts of amino acid replacement at different positions in a protein sequence. in their "stationary" versions, such models assume that the replacement rate at individual positions remains consta ... | 2001 | 11209054 |
| replicative dna polymerases. | replicative dna polymerases are essential for the replication of the genomes of all living organisms. on the basis of sequence similarities they can be classified into three types. type a polymerases are homologous to bacterial polymerases i, type b comprises archaebacterial dna polymerases and eukaryotic dna polymerase alpha, and the bacterial polymerase iii class make up type c. structures have been solved for several type a and b polymerases, which share a similar architecture. the structure ... | 2001 | 11178285 |
| demystified... molecular pathology in oncology. | in the past 10 years, molecular biology has found major applications in pathology, particularly in oncology. this has been a field of enormous expansion, where pure science has found a place in clinical practice and is now of everyday use in any academic unit. this demystified review will discuss the techniques used in molecular pathology and then provide examples of how these can be used in oncology. | 2002 | 12456768 |
| tumor necrosis factor gene polymorphisms, leukocyte function, and sepsis susceptibility in blunt trauma patients. | the tumor necrosis factor alpha (tnf-alpha) -308 g/a and tnf-beta nco1 polymorphisms have been described to be associated with an increased risk for sepsis in critically ill patients. functional consequences associated with these polymorphisms remain unclear. we compared the genotype distribution of these tnf polymorphisms with susceptibility to severe sepsis and leukocyte function in blunt trauma patients (n = 70; mean injury severity score, 24 points [range, 4 to 57). severe sepsis was defined ... | 2002 | 12414751 |
| estimating the number of integrations in transformed plants by quantitative real-time pcr. | when generating transformed plants, a first step in their characterization is to obtain, for each new line, an estimate of how many copies of the transgene have been integrated in the plant genome because this can deeply influence the level of transgene expression and the ease of stabilizing expression in following generations. this task is normally achieved by southern analysis, a procedure that requires relatively large amounts of plant material and is both costly and labour-intensive. moreove ... | 2002 | 12398792 |
| helix-hairpin-helix motifs confer salt resistance and processivity on chimeric dna polymerases. | helix-hairpin-helix (hhh) is a widespread motif involved in sequence-nonspecific dna binding. the majority of hhh motifs function as dna-binding modules with typical occurrence of one hhh motif or one or two (hhh)(2) domains in proteins. we recently identified 24 hhh motifs in dna topoisomerase v (topo v). although these motifs are dispensable for the topoisomerase activity of topo v, their removal narrows the salt concentration range for topoisomerase activity tenfold. here, we demonstrate the ... | 2002 | 12368475 |
| ifret: an improved fluorescence system for dna-melting analysis. | fluorescence resonance energy transfer (fret) is a powerful tool for detecting spatial relationships between macromolecules, one use of which is the tracking of dna hybridization status. the process involves measuring changes in fluorescence as fret donor and acceptor moieties are brought closer together or moved farther apart as a result of dna hybridization/denaturation. in the present study, we introduce a new version of fret, which we term induced fret (ifret), that is ideally suited for mel ... | 2002 | 12213777 |
| microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. | microbial communities in cores obtained from methane hydrate-bearing deep marine sediments (down to more than 300 m below the seafloor) in the forearc basin of the nankai trough near japan were characterized with cultivation-dependent and -independent techniques. acridine orange direct count data indicated that cell numbers generally decreased with sediment depth. lipid biomarker analyses indicated the presence of viable biomass at concentrations greater than previously reported for terrestrial ... | 2002 | 12147470 |
| interactions of mutant and wild-type flap endonucleases with oligonucleotide substrates suggest an alternative model of dna binding. | previous structural studies on native t5 5' nuclease, a member of the flap endonuclease family of structure-specific nucleases, demonstrated that this enzyme possesses an unusual helical arch mounted on the enzyme's active site. based on this structure, the protein's surface charge distribution, and biochemical analyses, a model of dna binding was proposed in which single-stranded dna threads through the archway. we investigated the kinetic and substrate-binding characteristics of wild-type and ... | 2002 | 12084915 |
| p53 mutation in breast cancer. correlation with cell kinetics and cell of origin. | several studies have investigated the expression of the cytokeratins (cks), vimentin, the epithelial growth factor receptor (egfr), the oestrogen receptor (er), and the progesterone receptor (pgr), in breast cancer, but no study has directly compared p53 mutations with these phenotypic and differentiation markers in the same case. the present study was designed to provide some of this information. | 2002 | 12037031 |
| perspectives on biotechnological applications of archaea. | many archaea colonize extreme environments. they include hyperthermophiles, sulfur-metabolizing thermophiles, extreme halophiles and methanogens. because extremophilic microorganisms have unusual properties, they are a potentially valuable resource in the development of novel biotechnological processes. despite extensive research, however, there are few existing industrial applications of either archaeal biomass or archaeal enzymes. this review summarizes current knowledge about the biotechnolog ... | 2002 | 15803645 |
| phi29 dna polymerase residues tyr59, his61 and phe69 of the highly conserved exoii motif are essential for interaction with the terminal protein. | phage phi29 encodes a dna-dependent dna polymerase belonging to the eukaryotic-type (family b) subgroup of dna polymerases that use a protein as the primer for initiation of dna synthesis. in one of the most important motifs present in the 3'-->5' exonucleolytic domain of proofreading dna polymerases, the exoii motif, phi29 dna polymerase contains three amino acid residues, y59, h61 and f69, which are highly conserved among most proofreading dna polymerases. these residues have recently been sho ... | 2002 | 11884636 |
| real-time pcr in virology. | the use of the polymerase chain reaction (pcr) in molecular diagnostics has increased to the point where it is now accepted as the gold standard for detecting nucleic acids from a number of origins and it has become an essential tool in the research laboratory. real-time pcr has engendered wider acceptance of the pcr due to its improved rapidity, sensitivity, reproducibility and the reduced risk of carry-over contamination. there are currently five main chemistries used for the detection of pcr ... | 2002 | 11884626 |
| auto-protective redox buffering systems in stimulated macrophages. | macrophages, upon encounter with micro-organisms or stimulated by cytokines, produce various effector molecules aimed at destroying the foreign agents and protecting the organism. reactive oxygen species (ros) and reactive nitrogen species (rns) are front line molecules exerting strong cytotoxic activities against micro-organisms and many cells, including macrophages themselves. using cells of the murine macrophage cell line (raw 264.7) stimulated in vitro with lipopolysaccharide (lps) and/or in ... | 2002 | 11914132 |
| marking the start site of rna polymerase iii transcription: the role of constraint, compaction and continuity of the transcribed dna strand. | the effects of breaks in the individual strands of an rna polymerase iii promoter on initiation of transcription have been examined. single breaks have been introduced at 2 bp intervals in a 24 bp segment that spans the transcriptional start site of the u6 snrna gene promoter. their effects on transcription are asymmetrically distributed: transcribed (template) strand breaks downstream of bp-14 (relative to the normal start as +1) systematically shift the start site, evidently by disrupting the ... | 2002 | 11847118 |
| thermal acclimation and stress in the american lobster, homarus americanus: equivalent temperature shifts elicit unique gene expression patterns for molecular chaperones and polyubiquitin. | using homologous molecular probes, we examined the influence of equivalent temperature shifts on the in vivo expression of genes coding for a constitutive heat shock protein (hsc70), heat shock proteins (hsps) (hsp70 and hsp90), and polyubiquitin, after acclimation in the american lobster, homarus americanus. we acclimated sibling, intermolt, juvenile male lobsters to thermal regimes experienced during overwintering conditions (0.4 +/- 0.3 degrees c), and to ambient pacific ocean temperatures (1 ... | 2002 | 11892992 |
| cleavage of dna without loss of genetic information by incorporation of a disaccharide nucleoside. | a ribose residue inserted between the 3'-oh of one nucleotide and the 5'-phosphate group of the next nucleotide, functions as a site-specific cleavage site within dna. this extra ribose does not interrupt helix formation and it protects duplex dna against cleavage by restriction enzymes. cleavage can be obtained with periodate and all ribose fragments can be removed with sodium hydroxide. as a result of this, an intact natural oligodeoxynucleotide is obtained after ligation reaction, which means ... | 2003 | 14627809 |
| dissimilar mispair-recognition spectra of arabidopsis dna-mismatch-repair proteins msh2*msh6 (mutsalpha) and msh2*msh7 (mutsgamma). | besides orthologs of other eukaryotic mismatch-repair (mmr) proteins, plants encode msh7, a paralog of msh6. the arabidopsis thaliana recognition heterodimers atmsh2*msh6 (atmutsalpha) and atmsh2*msh3 (atmutsbeta) were previously found to bind the same subsets of mismatches as their counterparts in other eukaryotes--respectively, base-base mismatches and single extra nucleotides, loopouts of extra nucleotides (one or more) only--but atmsh2*msh7 (atmutsgamma) bound well only to a g/t mismatch. to ... | 2003 | 14530450 |
| methods for the in vitro determination of an individual disposition towards th1- or th2-reactivity by the application of appropriate stimulatory antigens. | in this study we performed several methods for the determination of cytokines (rt-pcr for the demonstration of cytokine mrna and flow cytometry for the analysis of intracellular cytokines) and compared them with a recently established test system stimulating peripheral blood mononuclear cells (pbmc) with th1- and th2-relevant recall antigens and analysing type 1 and type 2 cytokines by elisa. aim of the study was therefore to evaluate the reliability of th1/th2 cytokine profiles in two individua ... | 2003 | 12974758 |
| expression of cyclins a, e and topoisomerase ii alpha correlates with centrosome amplification and genomic instability and influences the reliability of cytometric s-phase determination. | the progression of normal cells through the cell cycle is meticulously regulated by checkpoints guaranteeing the exact replication of the genome during s-phase and its equal division at mitosis. a prerequisite for this achievement is synchronized dna-replication and centrosome duplication. in this context the expression of cyclins a and e has been shown to play a principal role. | 2003 | 12875657 |
| structure, function and evolution of the signal recognition particle. | the signal recognition particle (srp) is a ribonucleoprotein particle essential for the targeting of signal peptide-bearing proteins to the prokaryotic plasma membrane or the eukaryotic endoplasmic reticulum membrane for secretion or membrane insertion. srp binds to the signal peptide emerging from the exit site of the ribosome and forms a ribosome nascent chain (rnc)-srp complex. the rnc-srp complex then docks in a gtp-dependent manner with a membrane-anchored srp receptor and the protein is tr ... | 2003 | 12853463 |
| many paths to methyltransfer: a chronicle of convergence. | s-adenosyl-l-methionine (adomet) dependent methyltransferases (mtases) are involved in biosynthesis, signal transduction, protein repair, chromatin regulation and gene silencing. five different structural folds (i-v) have been described that bind adomet and catalyze methyltransfer to diverse substrates, although the great majority of known mtases have the class i fold. even within a particular mtase class the amino-acid sequence similarity can be as low as 10%. thus, the structural and catalytic ... | 2003 | 12826405 |
| nucleic acid recognition by ob-fold proteins. | the ob-fold domain is a compact structural motif frequently used for nucleic acid recognition. structural comparison of all ob-fold/nucleic acid complexes solved to date confirms the low degree of sequence similarity among members of this family while highlighting several structural sequence determinants common to most of these ob-folds. loops connecting the secondary structural elements in the ob-fold core are extremely variable in length and in functional detail. however, certain features of l ... | 2003 | 12598368 |
| organ-specific expression of brassinosteroid-biosynthetic genes and distribution of endogenous brassinosteroids in arabidopsis. | brassinosteroids (brs) are steroidal plant hormones that are essential for growth and development. there is only limited information on where brs are synthesized and used. we studied the organ specificity of br biosynthesis in arabidopsis, using two different approaches: we analyzed the expression of br-related genes using real-time quantitative reverse transcriptase-polymerase chain reaction, and analyzed endogenous brs using gas chromatography-mass spectrometry. before starting this study, we ... | 2003 | 12529536 |
| crystallization and preliminary x-ray crystallographic study of disproportionating enzyme from potato. | disproportionating enzyme (d-enzyme; ec 2.4.1.25) is a 59 kda protein that belongs to the alpha-amylase family. d-enzyme catalyses intramolecular and intermolecular transglycosylation reactions of alpha-1,4 glucan. a crystal of the d-enzyme from potato was obtained by the hanging-drop vapour-diffusion method. preliminary x-ray data showed that the crystal diffracts to 2.0 a resolution and belongs to space group c222(1), with unit-cell parameters a = 69.7, b = 120.3, c = 174.2 a. | 2004 | 16508106 |
| crystallization and preliminary x-ray crystallographic study of disproportionating enzyme from potato. | disproportionating enzyme (d-enzyme; ec 2.4.1.25) is a 59 kda protein that belongs to the alpha-amylase family. d-enzyme catalyses intramolecular and intermolecular transglycosylation reactions of alpha-1,4 glucan. a crystal of the d-enzyme from potato was obtained by the hanging-drop vapour-diffusion method. preliminary x-ray data showed that the crystal diffracts to 2.0 a resolution and belongs to space group c222(1), with unit-cell parameters a = 69.7, b = 120.3, c = 174.2 a. | 2004 | 16508106 |
| distance-restrained docking of rifampicin and rifamycin sv to rna polymerase using systematic fret measurements: developing benchmarks of model quality and reliability. | we are developing distance-restrained docking strategies for modeling macromolecular complexes that combine available high-resolution structures of the components and intercomponent distance restraints derived from systematic fluorescence resonance energy transfer (fret) measurements. in this article, we consider the problem of docking small-molecule ligands within macromolecular complexes. using simulated fret data, we have generated a series of benchmarks that permit estimation of model accura ... | 2004 | 15542547 |
| distance-restrained docking of rifampicin and rifamycin sv to rna polymerase using systematic fret measurements: developing benchmarks of model quality and reliability. | we are developing distance-restrained docking strategies for modeling macromolecular complexes that combine available high-resolution structures of the components and intercomponent distance restraints derived from systematic fluorescence resonance energy transfer (fret) measurements. in this article, we consider the problem of docking small-molecule ligands within macromolecular complexes. using simulated fret data, we have generated a series of benchmarks that permit estimation of model accura ... | 2004 | 15542547 |