Publications

helix insertion into bilayers and the evolution of membrane proteins.	polytopic alpha-helical membrane proteins cannot spontaneously insert into lipid bilayers without assistance from polytopic alpha-helical membrane proteins that already reside in the membrane. this raises the question of how these proteins evolved. our current knowledge of the insertion of alpha-helices into natural and model membranes is reviewed with the goal of gaining insight into the evolution of membrane proteins. topics include: translocon-dependent membrane protein insertion, antibiotic ...	2009	20039094
helix insertion into bilayers and the evolution of membrane proteins.	polytopic alpha-helical membrane proteins cannot spontaneously insert into lipid bilayers without assistance from polytopic alpha-helical membrane proteins that already reside in the membrane. this raises the question of how these proteins evolved. our current knowledge of the insertion of alpha-helices into natural and model membranes is reviewed with the goal of gaining insight into the evolution of membrane proteins. topics include: translocon-dependent membrane protein insertion, antibiotic ...	2009	20039094
identification and biochemical characterization of molybdenum cofactor-binding proteins from arabidopsis thaliana.	the molybdenum cofactor (moco) forms part of the catalytic center in all eukaryotic molybdenum enzymes and is synthesized in a highly conserved pathway. among eukaryotes, very little is known about the processes taking place subsequent to moco biosynthesis, i.e. moco transfer, allocation, and insertion into molybdenum enzymes. in the model plant arabidopsis thaliana, we identified a novel protein family consisting of nine members that after recombinant expression are able to bind moco with k(d) ...	2009	20040598
identification and biochemical characterization of molybdenum cofactor-binding proteins from arabidopsis thaliana.	the molybdenum cofactor (moco) forms part of the catalytic center in all eukaryotic molybdenum enzymes and is synthesized in a highly conserved pathway. among eukaryotes, very little is known about the processes taking place subsequent to moco biosynthesis, i.e. moco transfer, allocation, and insertion into molybdenum enzymes. in the model plant arabidopsis thaliana, we identified a novel protein family consisting of nine members that after recombinant expression are able to bind moco with k(d) ...	2009	20040598
amyloidogenic sequences in native protein structures.	numerous short peptides have been shown to form beta-sheet amyloid aggregates in vitro. proteins that contain such sequences are likely to be problematic for a cell, due to their potential to aggregate into toxic structures. we investigated the structures of 30 proteins containing 45 sequences known to form amyloid, to see how the proteins cope with the presence of these potentially toxic sequences, studying secondary structure, hydrogen-bonding, solvent accessible surface area and hydrophobicit ...	2009	20027621
amyloidogenic sequences in native protein structures.	numerous short peptides have been shown to form beta-sheet amyloid aggregates in vitro. proteins that contain such sequences are likely to be problematic for a cell, due to their potential to aggregate into toxic structures. we investigated the structures of 30 proteins containing 45 sequences known to form amyloid, to see how the proteins cope with the presence of these potentially toxic sequences, studying secondary structure, hydrogen-bonding, solvent accessible surface area and hydrophobicit ...	2009	20027621
estimating dna coverage and abundance in metagenomes using a gamma approximation.	shotgun sequencing generates large numbers of short dna reads from either an isolated organism or, in the case of metagenomics projects, from the aggregate genome of a microbial community. these reads are then assembled based on overlapping sequences into larger, contiguous sequences (contigs). the feasibility of assembly and the coverage achieved (reads per nucleotide or distinct sequence of nucleotides) depend on several factors: the number of reads sequenced, the read length and the relative ...	2009	20008478
estimating dna coverage and abundance in metagenomes using a gamma approximation.	shotgun sequencing generates large numbers of short dna reads from either an isolated organism or, in the case of metagenomics projects, from the aggregate genome of a microbial community. these reads are then assembled based on overlapping sequences into larger, contiguous sequences (contigs). the feasibility of assembly and the coverage achieved (reads per nucleotide or distinct sequence of nucleotides) depend on several factors: the number of reads sequenced, the read length and the relative ...	2009	20008478
5-methylcytosine in rna: detection, enzymatic formation and biological functions.	the nucleobase modification 5-methylcytosine (m(5)c) is widespread both in dna and different cellular rnas. the functions and enzymatic mechanisms of dna m(5)c-methylation were extensively studied during the last decades. however, the location, the mechanism of formation and the cellular function(s) of the same modified nucleobase in rna still remain to be elucidated. the recent development of a bisulfite sequencing approach for efficient m(5)c localization in various rna molecules puts ribo-m(5 ...	2009	20007150
5-methylcytosine in rna: detection, enzymatic formation and biological functions.	the nucleobase modification 5-methylcytosine (m(5)c) is widespread both in dna and different cellular rnas. the functions and enzymatic mechanisms of dna m(5)c-methylation were extensively studied during the last decades. however, the location, the mechanism of formation and the cellular function(s) of the same modified nucleobase in rna still remain to be elucidated. the recent development of a bisulfite sequencing approach for efficient m(5)c localization in various rna molecules puts ribo-m(5 ...	2009	20007150
kinetics of stop codon recognition by release factor 1.	recognition of stop codons by class i release factors is a fundamental step in the termination phase of protein synthesis. since premature termination is costly to the cell, release factors have to efficiently discriminate between stop and sense codons. to understand the mechanism of discrimination between stop and sense codons, we developed a new, pre-steady state kinetic assay to monitor the interaction of rf1 with the ribosome. our results show that rf1 associates with similar association rat ...	2009	19874047
aminoglycoside activity observed on single pre-translocation ribosome complexes.	aminoglycoside-class antibiotics bind directly to ribosomal rna, imparting pleiotropic effects on ribosome function. despite in-depth structural investigations of aminoglycoside-rna oligonucleotide and aminoglycoside-ribosome interactions, mechanisms explaining the unique ribosome inhibition profiles of chemically similar aminoglycosides remain elusive. here, using single-molecule fluorescence resonance energy transfer (smfret) methods, we show that high-affinity aminoglycoside binding to the co ...	2009	19946275
aminoglycoside activity observed on single pre-translocation ribosome complexes.	aminoglycoside-class antibiotics bind directly to ribosomal rna, imparting pleiotropic effects on ribosome function. despite in-depth structural investigations of aminoglycoside-rna oligonucleotide and aminoglycoside-ribosome interactions, mechanisms explaining the unique ribosome inhibition profiles of chemically similar aminoglycosides remain elusive. here, using single-molecule fluorescence resonance energy transfer (smfret) methods, we show that high-affinity aminoglycoside binding to the co ...	2009	19946275
the electronic state of flavoproteins: investigations with proton electron-nuclear double resonance.	electron-nuclear double resonance (endor) spectroscopy provides useful information on hyperfine interactions between nuclear magnetic moments and the magnetic moment of an unpaired electron spin. because the hyperfine coupling constant reacts quite sensitively to polarity changes in the direct vicinity of the nucleus under consideration, endor spectroscopy can be favorably used for the detection of subtle protein-cofactor interactions. a number of pulsed endor studies on flavoproteins have been ...	2009	26089595
the electronic state of flavoproteins: investigations with proton electron-nuclear double resonance.	electron-nuclear double resonance (endor) spectroscopy provides useful information on hyperfine interactions between nuclear magnetic moments and the magnetic moment of an unpaired electron spin. because the hyperfine coupling constant reacts quite sensitively to polarity changes in the direct vicinity of the nucleus under consideration, endor spectroscopy can be favorably used for the detection of subtle protein-cofactor interactions. a number of pulsed endor studies on flavoproteins have been ...	2009	26089595
development of a shutterless continuous rotation method using an x-ray cmos detector for protein crystallography.	a new shutterless continuous rotation method using an x-ray complementary metal-oxide semiconductor (cmos) detector has been developed for high-speed, precise data collection in protein crystallography. the principle of operation and the basic performance of the x-ray cmos detector (hamamatsu photonics kk c10158dk) have been shown to be appropriate to the shutterless continuous rotation method. the data quality of the continuous rotation method is comparable to that of the conventional oscillati ...	2009	22477775
the ligand-free state of the tpp riboswitch: a partially folded rna structure.	riboswitches are elements of mrna that regulate gene expression by undergoing structural changes upon binding of small ligands. although the structures of several riboswitches have been solved with their ligands bound, the ligand-free states of only a few riboswitches have been characterized. the ligand-free state is as important for the functionality of the riboswitch as the ligand-bound form, but the ligand-free state is often a partially folded structure of the rna, with conformational hetero ...	2009	19925806
the ligand-free state of the tpp riboswitch: a partially folded rna structure.	riboswitches are elements of mrna that regulate gene expression by undergoing structural changes upon binding of small ligands. although the structures of several riboswitches have been solved with their ligands bound, the ligand-free states of only a few riboswitches have been characterized. the ligand-free state is as important for the functionality of the riboswitch as the ligand-bound form, but the ligand-free state is often a partially folded structure of the rna, with conformational hetero ...	2009	19925806
increasing protein stability by improving beta-turns.	our goal was to gain a better understanding of how protein stability can be increased by improving beta-turns. we studied 22 beta-turns in nine proteins with 66-370 residues by replacing other residues with proline and glycine and measuring the stability. these two residues are statistically preferred in some beta-turn positions. we studied: cold shock protein b (cspb), histidine-containing phosphocarrier protein, ubiquitin, ribonucleases sa2, sa3, t1, and hi, tryptophan synthetase alpha-subunit ...	2009	19626709
shaping the mitochondrion: mitochondrial biogenesis, dynamics and dysfunction. conference on mitochondrial assembly and dynamics in health and disease.		2009	19949411
cryptochromes--a potential magnetoreceptor: what do we know and what do we want to know?	cryptochromes have been suggested to be the primary magnetoreceptor molecules underlying light-dependent magnetic compass detection in migratory birds. here we review and evaluate (i) what is known about these candidate magnetoreceptor molecules, (ii) what characteristics cryptochrome molecules must fulfil to possibly underlie light-dependent, radical pair based magnetoreception, (iii) what evidence supports the involvement of cryptochromes in magnetoreception, and (iv) what needs to be addresse ...	2009	19906675
cryptochromes--a potential magnetoreceptor: what do we know and what do we want to know?	cryptochromes have been suggested to be the primary magnetoreceptor molecules underlying light-dependent magnetic compass detection in migratory birds. here we review and evaluate (i) what is known about these candidate magnetoreceptor molecules, (ii) what characteristics cryptochrome molecules must fulfil to possibly underlie light-dependent, radical pair based magnetoreception, (iii) what evidence supports the involvement of cryptochromes in magnetoreception, and (iv) what needs to be addresse ...	2009	19906675
'rna walk' a novel approach to study rna-rna interactions between a small rna and its target.	in this study we describe a novel method to investigate the rna-rna interactions between a small rna and its target that we termed 'rna walk'. the method is based on uv-induced amt cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by rt-pcr or real-time pcr. domains carrying the cross-linked adducts fail to efficiently amplify by pcr compared with non-cross-linked domains. this method was calibrated and used to study the interacti ...	2009	19854950
'rna walk' a novel approach to study rna-rna interactions between a small rna and its target.	in this study we describe a novel method to investigate the rna-rna interactions between a small rna and its target that we termed 'rna walk'. the method is based on uv-induced amt cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by rt-pcr or real-time pcr. domains carrying the cross-linked adducts fail to efficiently amplify by pcr compared with non-cross-linked domains. this method was calibrated and used to study the interacti ...	2009	19854950
polyamines: ubiquitous polycations with unique roles in growth and stress responses.	polyamines are small polycationic molecules found ubiquitously in all organisms and function in a wide variety of biological processes. in the past decade, molecular and genetic studies using mutants and transgenic plants with an altered activity of enzymes involved in polyamine biosynthesis have contributed much to a better understanding of the biological functions of polyamines in plants.	2009	19828463
polyamines: ubiquitous polycations with unique roles in growth and stress responses.	polyamines are small polycationic molecules found ubiquitously in all organisms and function in a wide variety of biological processes. in the past decade, molecular and genetic studies using mutants and transgenic plants with an altered activity of enzymes involved in polyamine biosynthesis have contributed much to a better understanding of the biological functions of polyamines in plants.	2009	19828463
acyl-coa synthesis, lipid metabolism and lipotoxicity.	although the underlying causes of insulin resistance have not been completely delineated, in most analyses, a recurring theme is dysfunctional metabolism of fatty acids. because the conversion of fatty acids to activated acyl-coas is the first and essential step in the metabolism of long-chain fatty acid metabolism, interest has grown in the synthesis of acyl-coas, their contribution to the formation of signaling molecules like ceramide and diacylglycerol, and their direct effects on cell functi ...	2009	19818872
acyl-coa synthesis, lipid metabolism and lipotoxicity.	although the underlying causes of insulin resistance have not been completely delineated, in most analyses, a recurring theme is dysfunctional metabolism of fatty acids. because the conversion of fatty acids to activated acyl-coas is the first and essential step in the metabolism of long-chain fatty acid metabolism, interest has grown in the synthesis of acyl-coas, their contribution to the formation of signaling molecules like ceramide and diacylglycerol, and their direct effects on cell functi ...	2009	19818872
knowledge-based instantiation of full atomic detail into coarse-grain rna 3d structural models.	the recent development of methods for modeling rna 3d structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications.	2009	19812110
advances in nuclear magnetic resonance for drug discovery.	background: drug discovery is a complex and unpredictable endeavor with a high failure rate. current trends in the pharmaceutical industry have exasperated these challenges and are contributing to the dramatic decline in productivity observed over the last decade. the industrialization of science by forcing the drug discovery process to adhere to assembly-line protocols is imposing unnecessary restrictions, such as short project time-lines. recent advances in nuclear magnetic resonance are respo ...	2009	20333269
tuning the properties of the bacterial membrane with aminoacylated phosphatidylglycerol.	the bacterial envelope is a semi-permeable barrier that protects the cell from the hostilities of the environment. to survive the ever-changing conditions of their surroundings, bacteria need to rapidly adjust the biochemical properties of their cellular envelope. amino acid (aa) addition to phosphatidylglycerol (pg) of the membrane is one of the mechanisms used by bacteria to lower the net negative charge of their cellular envelope, thereby decreasing its affinity for several antibacterial agen ...	2009	19787708
recode-2: new design, new search tools, and many more genes.	'recoding' is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of 'recoded' genes lags far behind annotation of 'standard' genes. in order to address this issue, provide a service to researchers in the field, and offer training data ...	2009	19783826
recode-2: new design, new search tools, and many more genes.	'recoding' is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of 'recoded' genes lags far behind annotation of 'standard' genes. in order to address this issue, provide a service to researchers in the field, and offer training data ...	2009	19783826
crystal structure and functional analysis of homocitrate synthase, an essential enzyme in lysine biosynthesis.	homocitrate synthase (hcs) catalyzes the first and committed step in lysine biosynthesis in many fungi and certain archaea and is a potential target for antifungal drugs. here we report the crystal structure of the hcs apoenzyme from schizosaccharomyces pombe and two distinct structures of the enzyme in complex with the substrate 2-oxoglutarate (2-og). the structures reveal that hcs forms an intertwined homodimer stabilized by domain-swapping between the n- and c-terminal domains of each monomer ...	2009	19776021
exploring conformational modes of macromolecular assemblies by multiparticle cryo-em.	single particle cryo-electron microscopy (cryo-em) is a technique aimed at structure determination of large macromolecular complexes in their unconstrained, physiological conditions. the power of the method has been demonstrated in selected studies where for highly symmetric molecules the resolution attained permitted backbone tracing. however, most molecular complexes appear to exhibit intrinsic conformational variability necessary to perform their functions. therefore, it is now increasingly r ...	2009	19767196
probing protein structure by amino acid-specific covalent labeling and mass spectrometry.	for many years, amino acid-specific covalent labeling has been a valuable tool to study protein structure and protein interactions, especially for systems that are difficult to study by other means. these covalent labeling methods typically map protein structure and interactions by measuring the differential reactivity of amino acid side chains. the reactivity of amino acids in proteins generally depends on the accessibility of the side chain to the reagent, the inherent reactivity of the label ...	2009	19016300
marine-derived metabolites of s-adenosylmethionine as templates for new anti-infectives.	s-adenosylmethionine (adomet) is a key biochemical co-factor whose proximate metabolites include methylated macromolecules (e.g., nucleic acids, proteins, phospholipids), methylated small molecules (e.g., sterols, biogenic amines), polyamines (e.g., spermidine, spermine), ethylene, and n-acyl-homoserine lactones. marine organisms produce numerous adomet metabolites whose novel structures can be regarded as lead compounds for anti-infective drug design.	2009	19841722
structural analysis of polarizing indels: an emerging consensus on the root of the tree of life.	the root of the tree of life has been a holy grail ever since darwin first used the tree as a metaphor for evolution. new methods seek to narrow down the location of the root by excluding it from branches of the tree of life. this is done by finding traits that must be derived, and excluding the root from the taxa those traits cover. however the two most comprehensive attempts at this strategy, performed by cavalier-smith and lake et al., have excluded each other's rootings.	2009	19706177
metal uptake by manganese superoxide dismutase.	manganese superoxide dismutase is an important antioxidant defense metalloenzyme that protects cells from damage by the toxic oxygen metabolite, superoxide free radical, formed as an unavoidable by-product of aerobic metabolism. many years of research have gone into understanding how the metal cofactor interacts with small molecules in its catalytic role. in contrast, very little is presently known about how the protein acquires its metal cofactor, an important step in the maturation of the prot ...	2009	19699328
metal uptake by manganese superoxide dismutase.	manganese superoxide dismutase is an important antioxidant defense metalloenzyme that protects cells from damage by the toxic oxygen metabolite, superoxide free radical, formed as an unavoidable by-product of aerobic metabolism. many years of research have gone into understanding how the metal cofactor interacts with small molecules in its catalytic role. in contrast, very little is presently known about how the protein acquires its metal cofactor, an important step in the maturation of the prot ...	2009	19699328
computational design of candida boidinii xylose reductase for altered cofactor specificity.	in this study we introduce a computationally-driven enzyme redesign workflow for altering cofactor specificity from nadph to nadh. by compiling and comparing data from previous studies involving cofactor switching mutations, we show that their effect cannot be explained as straightforward changes in volume, hydrophobicity, charge, or blosum62 scores of the residues populating the cofactor binding site. instead, we find that the use of a detailed cofactor binding energy approximation is needed to ...	2009	19693930
structure of era in complex with the 3' end of 16s rrna: implications for ribosome biogenesis.	era, composed of an n-terminal gtpase domain followed by an rna-binding kh domain, is essential for bacterial cell viability. it binds to 16s rrna and the 30s ribosomal subunit. however, its rna-binding site, the functional relationship between the two domains, and its role in ribosome biogenesis remain unclear. we have determined two crystal structures of era, a binary complex with gdp and a ternary complex with a gtp-analog and the 1531aucaccuccuua1542 sequence at the 3' end of 16s rrna. in th ...	2009	19706445
large facilities and the evolving ribosome, the cellular machine for genetic-code translation.	well-focused x-ray beams, generated by advanced synchrotron radiation facilities, yielded high-resolution diffraction data from crystals of ribosomes, the cellular nano-machines that translate the genetic code into proteins. these structures revealed the decoding mechanism, localized the mrna path and the positions of the trna molecules in the ribosome and illuminated the interactions of the ribosome with initiation, release and recycling factors. they also showed that the ribosome is a ribozyme ...	2009	19656820
studying the salt dependence of the binding of sigma70 and sigma32 to core rna polymerase using luminescence resonance energy transfer.	the study of protein-protein interactions is becoming increasingly important for understanding the regulation of many cellular processes. the ability to quantify the strength with which two binding partners interact is desirable but the accurate determination of equilibrium binding constants is a difficult process. the use of luminescence resonance energy transfer (lret) provides a homogeneous binding assay that can be used for the detection of protein-protein interactions. previously, we develo ...	2009	19649256
biogenesis and homeostasis of nicotinamide adenine dinucleotide cofactor.	universal and ubiquitous redox cofactors, nicotinamide adenine dinucleotide (nad) and its phosphorylated analog (nadp), collectively contribute to approximately 12% of all biochemical reactions included in the metabolic model of escherichia coli k-12. a homeostasis of the nad pool faithfully maintained by the cells results from a dynamic balance in a network of nad biosynthesis, utilization, decomposition, and recycling pathways that is subject to tight regulation at various levels. a brief over ...	2009	26443758
bis{μ-4,4'-dimeth-oxy-2,2'-[propane-1,2-diylbis(nitrilo-methyl-idyne)]diphenolato}bis-({4,4'-dimeth-oxy-2,2'-[propane-1,2-diylbis(nitrilo-methyl-idyne)]diphenol}manganese(iii)) bis-(hexa-fluorido-phosphate).	in the title complex, [mn(2)(c(19)h(20)n(2)o(4))(2)(c(19)h(22)n(2)o(4))(2)](pf(6))(2), the mn(iii) ion is coordinated by two o [mn-o = 1.855 (2) and 1.887 (2) å] and two n [mn-n = 1.982 (3) and 1.977 (3) å] atoms from the tetra-dentate schiff base ligand and a coordinated axial ligand [mn-o = 2.129 (2) å]. the centrosymmetric dimer contains two jahn-teller-distorted mn(iii) ions, each in a nearly octa-hedral geometry, connected through two phenolate bridges from two ligands. there are two stereo ...	2009	21583304
crystal structure of a homolog of mammalian serine racemase from schizosaccharomyces pombe.	d-serine is an endogenous coagonist for the n-methyl-d-aspartate receptor and is involved in excitatory neurotransmission in the brain. mammalian pyridoxal 5'-phosphate-dependent serine racemase, which is localized in the mammalian brain, catalyzes the racemization of l-serine to yield d-serine and vice versa. the enzyme also catalyzes the dehydration of d- and l-serine. both reactions are enhanced by mg.atp in vivo. we have determined the structures of the following three forms of the mammalian ...	2009	19640845
sequence-based analysis of protein energy landscapes reveals nonuniform thermal adaptation within the proteome.	thermal adaptation of individual proteins is often achieved through modulating protein stability, with proteins that are adapted to extreme cold environments having increased conformational flexibility when brought to mesophilic conditions. conversely, proteins adapted to higher temperatures appear less dynamic and are found to be much more stable against thermal denaturation than their mesophilic counterparts. according to the current paradigm, the adaptation of an organism for survival at high ...	2009	19592668
regulation and function of proline oxidase under nutrient stress.	under conditions of nutrient stress, cells switch to a survival mode catabolizing cellular and tissue constituents for energy. proline metabolism is especially important in nutrient stress because proline is readily available from the breakdown of extracellular matrix (ecm), and the degradation of proline through the proline cycle initiated by proline oxidase (pox), a mitochondrial inner membrane enzyme, can generate atp. this degradative pathway generates glutamate and alpha-ketoglutarate, prod ...	2009	19415679
the dimeric proto-ribosome: structural details and possible implications on the origin of life.	a symmetric pocket-like entity, composed of two l-shaped rna units, encircles the peptide synthesis site within the contemporary ribosome. this entity was suggested to be the vestige of a dimeric proto-ribosome, which could have formed spontaneously in the prebiotic world, catalyzing non-coded peptide bond formation and elongation. this structural element, beyond offering the initial step in the evolution of translation, is hypothesized here to be linked to the origin of life. by catalyzing the ...	2009	19742176
carboxylic ester hydrolases from hyperthermophiles.	carboxylic ester hydrolyzing enzymes constitute a large group of enzymes that are able to catalyze the hydrolysis, synthesis or transesterification of an ester bond. they can be found in all three domains of life, including the group of hyperthermophilic bacteria and archaea. esterases from the latter group often exhibit a high intrinsic stability, which makes them of interest them for various biotechnological applications. in this review, we aim to give an overview of all characterized carboxyl ...	2009	19544040
thermodynamic characterization of tandem mismatches found in naturally occurring rna.	although all sequence symmetric tandem mismatches and some sequence asymmetric tandem mismatches have been thermodynamically characterized and a model has been proposed to predict the stability of previously unmeasured sequence asymmetric tandem mismatches [christiansen,m.e. and znosko,b.m. (2008) biochemistry, 47, 4329-4336], experimental thermodynamic data for frequently occurring tandem mismatches is lacking. since experimental data is preferred over a predictive model, the thermodynamic para ...	2009	19509311
limited proteolysis analysis of the ribosome is affected by subunit association.	our understanding of the structural organization of ribosome assembly intermediates, in particular those intermediates that result from misfolding leading to their eventual degradation within the cell, is limited because of the lack of methods available to characterize assembly intermediate structures. because conventional structural approaches, such as nmr, x-ray crystallography, and cryo-em, are not ideally suited to characterize the structural organization of these flexible and sometimes hete ...	2009	19213046
collective dynamics of the ribosomal tunnel revealed by elastic network modeling.	the collective dynamics of the nascent polypeptide exit tunnel are investigated with the computationally efficient elastic network model using normal mode analysis. the calculated normal modes are considered individually and in linear combinations with different coefficients mimicking the phase angles between modes, in order to follow the mechanistic motions of tunnel wall residues. the low frequency fluctuations indicate three distinct regions along the tunnel-the entrance, the neck, and the ex ...	2009	19004020
evidence for phosphatase activity of p27sj and its impact on the cell cycle.	p27sj, a novel protein isolated from st john's wort (hypericum perforatum), belongs to an emerging family of ding proteins that are related to a prokaryotic phosphate-binding protein superfamily. here we demonstrate that p27sj exhibits phosphatase activity and that its expression in cells decreases the level of phosphorylated erk1/2, a key protein of several signaling pathways. treatment of p27sj-expressing cells with phosphatase inhibitors including okadaic acid, maintained erk1/2 in its phosph ...	2009	19343785
a ca(+) pair adjacent to a sheared ga or aa pair stabilizes size-symmetric rna internal loops.	rna internal loops are often important sites for folding and function. residues in internal loops can have pka values shifted close to neutral ph because of the local structural environment. a series of rna internal loops were studied at different ph by uv absorbance versus temperature melting experiments and imino proton nuclear magnetic resonance (nmr). a stabilizing ca pair forms at ph 7 in the cg/aa and ca/aa nearest neighbors when the ca pair is the first noncanonical pair (loop-terminal pa ...	2009	19485416
nucleic acids: how high resolution structural biology help us to understand darwinian evolution.		2009	19482468
conformational changes in redox pairs of protein structures.	disulfides are conventionally viewed as structurally stabilizing elements in proteins but emerging evidence suggests two disulfide subproteomes exist. one group mediates the well known role of structural stabilization. a second redox-active group are best known for their catalytic functions but are increasingly being recognized for their roles in regulation of protein function. redox-active disulfides are, by their very nature, more susceptible to reduction than structural disulfides; and conver ...	2009	19598234
prediction of the rotational tumbling time for proteins with disordered segments.	for well-structured, rigid proteins, the prediction of rotational tumbling time (tau(c)) using atomic coordinates is reasonably accurate, but is inaccurate for proteins with long unstructured sequences. under physiological conditions, many proteins contain long disordered segments that play important regulatory roles in fundamental biological events including signal transduction and molecular recognition. here we describe an ensemble approach to the boundary element method that accurately predic ...	2009	19391622
carboxylation mechanism and stereochemistry of crotonyl-coa carboxylase/reductase, a carboxylating enoyl-thioester reductase.	chemo- and stereoselective reductions are important reactions in chemistry and biology, and reductases from biological sources are increasingly applied in organic synthesis. in contrast, carboxylases are used only sporadically. we recently described crotonyl-coa carboxylase/reductase, which catalyzes the reduction of (e)-crotonyl-coa to butyryl-coa but also the reductive carboxylation of (e)-crotonyl-coa to ethylmalonyl-coa. in this study, the complete stereochemical course of both reactions was ...	2009	19458256
mm-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming.	structural comparison of multiple-chain protein complexes is essential in many studies of protein-protein interactions. we develop a new algorithm, mm-align, for sequence-independent alignment of protein complex structures. the algorithm is built on a heuristic iteration of a modified needleman-wunsch dynamic programming (dp) algorithm, with the alignment score specified by the inter-complex residue distances. the multiple chains in each complex are first joined, in every possible order, and the ...	2009	19443443
crystal structure of iodotyrosine deiodinase, a novel flavoprotein responsible for iodide salvage in thyroid glands.	the flavoprotein iodotyrosine deiodinase (iyd) salvages iodide from mono- and diiodotyrosine formed during the biosynthesis of the thyroid hormone thyroxine. expression of a soluble domain of this membrane-bound enzyme provided sufficient material for crystallization and characterization by x-ray diffraction. the structures of iyd and two co-crystals containing substrates, mono- and diiodotyrosine, alternatively, were solved at resolutions of 2.0, 2.45, and 2.6 a, respectively. the structure of ...	2009	19436071
groel-assisted protein folding: does it occur within the chaperonin inner cavity?	the folding of protein molecules in the groel inner cavity under the co-chaperonin groes lid is widely accepted as a crucial event of groel-assisted protein folding. this review is focused on the data showing that groel-assisted protein folding may proceed out of the complex with the chaperonin. the models of groel-assisted protein folding assuming ligand-controlled dissociation of nonnative proteins from the groel surface and their folding in the bulk solution are also discussed.	2009	19564940
flexible structural protein alignment by a sequence of local transformations.	throughout evolution, homologous proteins have common regions that stay semi-rigid relative to each other and other parts that vary in a more noticeable way. in order to compare the increasing number of structures in the pdb, flexible geometrical alignments are needed, that are reliable and easy to use.	2009	19417057
the eukaryotic ribosome: current status and challenges.	despite having been identified first, their greater degree of complexity has resulted in our understanding of eukaryotic ribosomes lagging behind that of their bacterial and archaeal counterparts. a much more complicated biogenesis program results in ribosomes that are structurally, biochemically, and functionally more complex. however, recent advances in molecular genetics and structural biology are helping to reveal the intricacies of the eukaryotic ribosome and to address many longstanding qu ...	2009	19117941
distinct functions of elongation factor g in ribosome recycling and translocation.	elongation factor g (ef-g) promotes the translocation step in bacterial protein synthesis and, together with ribosome recycling factor (rrf), the disassembly of the post-termination ribosome. unlike translocation, ribosome disassembly strictly requires gtp hydrolysis by ef-g. here we report that ribosome disassembly is strongly inhibited by vanadate, an analog of inorganic phosphate (pi), indicating that pi release is required for ribosome disassembly. in contrast, the function of ef-g in single ...	2009	19324963
biogenesis of beta-barrel membrane proteins in bacteria and eukaryotes: evolutionary conservation and divergence.	membrane-embedded beta-barrel proteins span the membrane via multiple amphipathic beta-strands arranged in a cylindrical shape. these proteins are found in the outer membranes of gram-negative bacteria, mitochondria and chloroplasts. this situation is thought to reflect the evolutionary origin of mitochondria and chloroplasts from gram-negative bacterial endosymbionts. beta-barrel proteins fulfil a variety of functions; among them are pore-forming proteins that allow the flux of metabolites acro ...	2009	19399587
detection of biochemical pathways by probabilistic matching of phyletic vectors.	a phyletic vector, also known as a phyletic (or phylogenetic) pattern, is a binary representation of the presences and absences of orthologous genes in different genomes. joint occurrence of two or more genes in many genomes results in closely similar binary vectors representing these genes, and this similarity between gene vectors may be used as a measure of functional association between genes. better understanding of quantitative properties of gene co-occurrences is needed for systematic stud ...	2009	19390636
gene composer: database software for protein construct design, codon engineering, and gene synthesis.	to improve efficiency in high throughput protein structure determination, we have developed a database software package, gene composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. with its modular workflow design and numerous graphical user interfaces, gene composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering.	2009	19383142
the evolution of cyclodextrin glucanotransferase product specificity.	cyclodextrin glucanotransferases (cgtases) have attracted major interest from industry due to their unique capacity of forming large quantities of cyclic alpha-(1,4)-linked oligosaccharides (cyclodextrins) from starch. cgtases produce a mixture of cyclodextrins from starch consisting of 6 (alpha), 7 (beta) and 8 (gamma) glucose units. in an effort to identify the structural factors contributing to the evolutionary diversification of product specificity amongst this group of enzymes, we selected ...	2009	19367403
real-time dna microarrays: reality check.	dna microarrays are plagued with inconsistent quantifications and false-positive results. using established mechanisms of surface reactions, we argue that these problems are inherent to the current technology. in particular, the problem of multiplex non-equilibrium reactions cannot be resolved within the framework of the existing paradigm. we discuss the advantages and limitations of changing the paradigm to real-time data acquisition similar to real-time pcr methodology. our analysis suggests t ...	2009	19290884
the rna-induced silencing complex: a versatile gene-silencing machine.	rna interference is a powerful mechanism of gene silencing that underlies many aspects of eukaryotic biology. on the molecular level, rna interference is mediated by a family of ribonucleoprotein complexes called rna-induced silencing complexes (riscs), which can be programmed to target virtually any nucleic acid sequence for silencing. the ability of risc to locate target rnas has been co-opted by evolution many times to generate a broad spectrum of gene-silencing pathways. here, we review the ...	2009	19342379
identification of optimal protocols for sequencing difficult templates: results of the 2008 abrf dna sequencing research group difficult template study 2008.	the 2008 abrf dna sequencing research group (dsrg) difficult template sequencing study was designed to identify a general set of guidelines that would constitute the best approaches for sequencing difficult templates. this was a continuation of previous dsrg difficult template studies performed in 1996, 1997, and 2003. the distinguishing factors in the present study were the number of dna templates used, the number of different types of difficult regions tested, and the inclusion of a follow-up ...	2009	19503623
early events, kinetic intermediates and the mechanism of protein folding in cytochrome c.	kinetic studies of the early events in cytochrome c folding are reviewed with a focus on the evidence for folding intermediates on the submillisecond timescale. evidence from time-resolved absorption, circular dichroism, magnetic circular dichroism, fluorescence energy and electron transfer, small-angle x-ray scattering and amide hydrogen exchange studies on the t < or = 1 ms timescale reveals a picture of cytochrome c folding that starts with the approximately 1-micros conformational diffusion ...	2009	19468320
extension of the tryptophan chi2,1 dihedral angle-w3 band frequency relationship to a full rotation: correlations and caveats.	the correlation of the uvrr nuw3 mode with the tryptophan chi(2,1) dihedral angle [maruyama and takeuchi (1995) j. raman spectrosc. 26, 319; miura et al. (1989) j. raman spectrosc. 20, 667; takeuchi (2003) biopolymers 72, 305] has been extended to a full, 360 degrees rotation. the 3-fold periodicity of the relationship (cos 3chi(2,1)) over 360 degrees results in up to six dihedral angles for a given nuw3. consideration of a newman plot of dihedral angles for proteinaceous tryptophans taken from ...	2009	19267450
length variations amongst protein domain superfamilies and consequences on structure and function.	related protein domains of a superfamily can be specified by proteins of diverse lengths. the structural and functional implications of indels in a domain scaffold have been examined.	2009	19333395
recent developments in parameter estimation and structure identification of biochemical and genomic systems.	the organization, regulation and dynamical responses of biological systems are in many cases too complex to allow intuitive predictions and require the support of mathematical modeling for quantitative assessments and a reliable understanding of system functioning. all steps of constructing mathematical models for biological systems are challenging, but arguably the most difficult task among them is the estimation of model parameters and the identification of the structure and regulation of the ...	2009	19327372
slow unfolding of monomeric proteins from hyperthermophiles with reversible unfolding.	based on the differences in their optimal growth temperatures microorganisms can be classified into psychrophiles, mesophiles, thermophiles, and hyperthermophiles. proteins from hyperthermophiles generally exhibit greater stability than those from other organisms. in this review, we collect data about the stability and folding of monomeric proteins from hyperthermophilies with reversible unfolding, from the equilibrium and kinetic aspects. the results indicate that slow unfolding is a general st ...	2009	19399254
co-evolution of primordial membranes and membrane proteins.	studies of the past several decades have provided major insights into the structural organization of biological membranes and mechanisms of many membrane molecular machines. however, the origin(s) of the membrane(s) and membrane proteins remains enigmatic. we discuss different concepts of the origin and early evolution of membranes with a focus on the evolution of the (im)permeability to charged molecules such as proteins, nucleic acids and small ions. reconstruction of the evolution of f-type a ...	2009	19303305
copper trafficking in biology: an nmr approach.	copper ions are essential for living organisms because they are involved in several fundamental biological processes. biomolecules interacting with copper ions have to be characterized as such, when bound to the metal ion, and when they interact with other biomolecules or substrates. the characterization is both structural and dynamic. in this context, nmr is a preferred tool of investigation because it allows shedding light on what happens in solution. here, the nmr contribution to the copper t ...	2009	19949444
oxidatively modified proteins in alzheimer's disease (ad), mild cognitive impairment and animal models of ad: role of abeta in pathogenesis.	oxidative stress has been implicated in the pathogenesis of a number of diseases including alzheimer's disease (ad). the oxidative stress hypothesis of ad pathogenesis, in part, is based on beta-amyloid peptide (abeta)-induced oxidative stress in both in vitro and in vivo studies. oxidative modification of the protein may induce structural changes in a protein that might lead to its functional impairment. a number of oxidatively modified brain proteins were identified using redox proteomics in a ...	2009	19288120
primary structure revision and active site mapping of e. coli isoleucyl-trna synthetase by means of maldi mass spectrometry.	the correct amino acid sequence of e. coli isoleucyl-trna synthetase (ilers) was established by means of peptide mapping by maldi mass spectrometry, using a set of four endoproteases (trypsin, lysc, aspn and gluc). thereafter, the active site of ilers was mapped by affinity labeling with reactive analogs of the substrates. for the atp binding site, the affinity labeling reagent was pyridoxal 5'-diphospho-5'-adenosine (adp-pl), whereas periodate-oxidized trna(ile), the 2',3'-dialdehyde derivative ...	2009	19557155
identification of rna molecules by specific enzyme digestion and mass spectrometry: software for and implementation of rna mass mapping.	the idea of identifying or characterizing an rna molecule based on a mass spectrum of specifically generated rna fragments has been used in various forms for well over a decade. we have developed software-named rrm for 'rna mass mapping'-which can search whole prokaryotic genomes or rna fasta sequence databases to identify the origin of a given rna based on a mass spectrum of rna fragments. as input, the program uses the masses of specific rnase cleavage of the rna under investigation. rnase t1 ...	2009	19264806
the role of disordered ribosomal protein extensions in the early steps of eubacterial 50 s ribosomal subunit assembly.	although during the past decade research has shown the functional importance of disorder in proteins, many of the structural and dynamics properties of intrinsically unstructured proteins (iups) remain to be elucidated. this review is focused on the role of the extensions of the ribosomal proteins in the early steps of the assembly of the eubacterial 50 s subunit. the recent crystallographic structures of the ribosomal particles have revealed the picture of a complex assembly pathway that conden ...	2009	19399222
properties of the nucleic-acid bases in free and watson-crick hydrogen-bonded states: computational insights into the sequence-dependent features of double-helical dna.	the nucleic-acid bases carry structural and energetic signatures that contribute to the unique features of genetic sequences. here we review the connection between the chemical structure of the constituent nucleotides and the polymeric properties of dna. the sequence-dependent accumulation of charge on the major- and minor-groove edges of the watson-crick base pairs, obtained from ab initio calculations, presents unique motifs for direct sequence recognition. the optimization of base interaction ...	2009	21218180
chemically modified primers for improved multiplex polymerase chain reaction.	multiplex polymerase chain reaction (pcr), the amplification of multiple targets in a single reaction, presents a new set of challenges that further complicate more traditional pcr setups. these complications include a greater probability for nonspecific amplicon formation and for imbalanced amplification of different targets, each of which can compromise quantification and detection of multiple targets. despite these difficulties, multiplex pcr is frequently used in applications such as pathoge ...	2009	19258004
inhibition of bacterial ribosome assembly: a suitable drug target?	the assembly of bacterial ribosomes is viewed with increasing interest as a potential target for new antibiotics. the in vivo synthesis and assembly of ribosomes are briefly reviewed here, highlighting the many ways in which assembly can be perturbed. the process is compared with the model in vitro process from which much of our knowledge is derived. the coordinate synthesis of the ribosomal components is essential for their ordered and efficient assembly; antibiotics interfere with this coordin ...	2009	19258531
crystallization and preliminary x-ray diffraction analysis of a putative two-domain-type laccase from a metagenome.	a putative two-domain-type laccase retrieved from a metagenome was successfully crystallized using the sitting-drop vapour-diffusion method. data were collected to a resolution of 1.7 a at 100 k using synchrotron radiation. the crystal belonged to space group p2(1)2(1)2(1), with unit-cell parameters a = 74.67, b = 100.95, c = 124.11 a. the self-rotation function showed the presence of a noncrystallographic threefold axis in the structure. the presence of one trimer in the asymmetric unit yielded ...	2009	19255479
frequency and isostericity of rna base pairs.	most of the hairpin, internal and junction loops that appear single-stranded in standard rna secondary structures form recurrent 3d motifs, where non-watson-crick base pairs play a central role. non-watson-crick base pairs also play crucial roles in tertiary contacts in structured rna molecules. we previously classified rna base pairs geometrically so as to group together those base pairs that are structurally similar (isosteric) and therefore able to substitute for each other by mutation withou ...	2009	19240142
regulation of translation initiation in eukaryotes: mechanisms and biological targets.	translational control in eukaryotic cells is critical for gene regulation during nutrient deprivation and stress, development and differentiation, nervous system function, aging, and disease. we describe recent advances in our understanding of the molecular structures and biochemical functions of the translation initiation machinery and summarize key strategies that mediate general or gene-specific translational control, particularly in mammalian systems.	2009	19239892
origins and mechanisms of mirnas and sirnas.	over the last decade, approximately 20-30 nucleotide rna molecules have emerged as critical regulators in the expression and function of eukaryotic genomes. two primary categories of these small rnas--short interfering rnas (sirnas) and micrornas (mirnas)--act in both somatic and germline lineages in a broad range of eukaryotic species to regulate endogenous genes and to defend the genome from invasive nucleic acids. recent advances have revealed unexpected diversity in their biogenesis pathways ...	2009	19239886
evolution of mutation rates: phylogenomic analysis of the photolyase/cryptochrome family.	photoreactivation, one of the first dna repair pathways to evolve, is the direct reversal of premutagenic lesions caused by ultraviolet (uv) irradiation, catalyzed by photolyases in a light-dependent, single-enzyme reaction. it has been experimentally shown that photoreactivation prevents uv mutagenesis in a broad range of species. in the absence of photoreactivation, uv-induced photolesions are repaired by the more complex and much less efficient nucleotide excision repair pathway. despite thei ...	2009	19228922
comparison of molecular dynamics and superfamily spaces of protein domain deformation.	it is well known the strong relationship between protein structure and flexibility, on one hand, and biological protein function, on the other hand. technically, protein flexibility exploration is an essential task in many applications, such as protein structure prediction and modeling. in this contribution we have compared two different approaches to explore the flexibility space of protein domains: i) molecular dynamics (md-space), and ii) the study of the structural changes within superfamily ...	2009	19220918
molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils.	the alpha-helical coiled-coil is one of the most common oligomerization motifs found in both native and engineered proteins. to better understand the stability and dynamics of the coiled-coil motifs, including those modified by fluorination, several fluorinated and nonfluorinated parallel dimeric coiled-coil protein structures were designed and modeled. we also attempt to investigate how changing the length and geometry of the important stabilizing salt bridges influences the coiled-coil protein ...	2009	18704948
recurring cluster and operon assembly for phenylacetate degradation genes.	a large number of theories have been advanced to explain why genes involved in the same biochemical processes are often co-located in genomes. most of these theories have been dismissed because empirical data do not match the expectations of the models. in this work we test the hypothesis that cluster formation is most likely due to a selective pressure to gradually co-localise protein products and that operon formation is not an inevitable conclusion of the process.	2009	19208251
predicting peptide structures in native proteins from physical simulations of fragments.	it has long been proposed that much of the information encoding how a protein folds is contained locally in the peptide chain. here we present a large-scale simulation study designed to examine the extent to which conformations of peptide fragments in water predict native conformations in proteins. we perform replica exchange molecular dynamics (remd) simulations of 872 8-mer, 12-mer, and 16-mer peptide fragments from 13 proteins using the amber 96 force field and the obc implicit solvent model. ...	2009	19197352
synthesizing non-natural parts from natural genomic template.	the current knowledge of genes and proteins comes from 'naturally designed' coding and non-coding regions. it would be interesting to move beyond natural boundaries and make user-defined parts. to explore this possibility we made six non-natural proteins in e. coli. we also studied their potential tertiary structure and phenotypic outcomes.	2009	19187561
the ribosome returned.	since the mid-1990s, insights obtained from electron microscopy and x-ray crystallography have transformed our understanding of how the most important ribozyme in the cell, the ribosome, catalyzes protein synthesis. this review provides a brief account of how this structural revolution came to pass, and the impact it has had on our understanding of how the ribosome decodes messenger rnas.	2009	19222865
new information content in rna base pairing deduced from quantitative analysis of high-resolution structures.	non-canonical base pairs play important roles in organizing the complex three-dimensional folding of rna. here, we outline methodology developed both to analyze the spatial patterns of interacting base pairs in known rna structures and to reconstruct models from the collective experimental information. we focus attention on the structural context and deformability of the seven pairing patterns found in greatest abundance in the helical segments in a set of well-resolved crystal structures, inclu ...	2009	19150407
regulation of translation initiation by rna binding proteins.	rna binding proteins are capable of regulating translation initiation by a variety of mechanisms. although the vast majority of these regulatory mechanisms involve translational repression, one example of translational activation has been characterized in detail. the rna recognition targets of these regulatory proteins exhibit a wide range in structural complexity, with some proteins recognizing complex pseudoknot structures and others binding to simple rna hairpins and/or short repeated single- ...	2009	19385727