当前位置： SCI文献检索 > PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA期刊下所有文献 > Evolutionary profiles from the QR factorization of multiple sequence alignments.

Evolutionary profiles from the QR factorization of multiple sequence alignments.

Abstract：

:We present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. We observe a general trend that these smaller, more evolutionarily balanced profiles have comparable and, in many cases, better performance in database searches than conventional profiles containing hundreds of sequences, constructed in an iterative and computationally intensive procedure. For more diverse families or superfamilies, with sequence identity <30%, structural alignments, based purely on the geometry of the protein structures, provide better alignments than pure sequence-based methods. Merging the structure and sequence information allows the construction of accurate profiles for distantly related groups. These structure-based profiles outperformed other sequence-based methods for finding distant homologs and were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that eluded previous annotation studies. Phylogenetic analysis showed the putative class II CysRSs to be a monophyletic group and homology modeling revealed a constellation of active site residues similar to that in the known class I CysRS.

journal_name

Proc Natl Acad Sci U S A

journal_title

Proceedings of the National Academy of Sciences of the United States of America

authors

Sethi A,O'Donoghue P,Luthey-Schulten Z

doi

10.1073/pnas.0409715102

keywords:

subject

Has Abstract

pub_date

2005-03-15 00:00:00

pages

4045-50

issue

11

eissn

0027-8424

issn

1091-6490

pii

0409715102

journal_volume

102

pub_type

杂志文章

相关文献

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA文献大全
  • PARK2 deletions occur frequently in sporadic colorectal cancer and accelerate adenoma development in Apc mutant mice.

    abstract：:In 100 primary colorectal carcinomas, we demonstrate by array comparative genomic hybridization (aCGH) that 33% show DNA copy number (DCN) loss involving PARK2, the gene encoding PARKIN, the E3 ubiquitin ligase whose deficiency is responsible for a form of autosomal recessive juvenile parkinsonism. PARK2 is located on...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1009941107

    authors： Poulogiannis G,McIntyre RE,Dimitriadi M,Apps JR,Wilson CH,Ichimura K,Luo F,Cantley LC,Wyllie AH,Adams DJ,Arends MJ

    更新日期：2010-08-24 00:00:00

  • Exocytosis regulates urinary acidification in turtle bladder by rapid insertion of H+ pumps into the luminal membrane.

    abstract：:Urinary acidification by the turtle bladder is due to a H+-ATPase that is located in the luminal membrane. The rate of H+ transport is stimulated by an increase in the ambient CO2. Using the fluorescent dye acridine orange, we showed that the mitochondria-rich cell of this equilibrium contains vesicles whose internal ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.79.14.4327

    authors： Gluck S,Cannon C,Al-Awqati Q

    更新日期：1982-07-01 00:00:00

  • Crystal structure of the human ATP-dependent splicing and export factor UAP56.

    abstract：:Pre-mRNA splicing requires the function of a number of RNA-dependent ATPases/helicases, yet no three-dimensional structure of any spliceosomal ATPases/helicases is known. The highly conserved DECD-box protein UAP56/Sub2 is an essential splicing factor that is also important for mRNA export. The expected ATPase/helicas...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0408172101

    authors： Shi H,Cordin O,Minder CM,Linder P,Xu RM

    更新日期：2004-12-21 00:00:00

  • The frailty of adaptive hypotheses for the origins of organismal complexity.

    abstract：:The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms. This narrow view of evolution has become untenable in light of recent observations from genomic sequencing and population-genetic theory. Numerous aspects of genomic architecture, gene st...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0702207104

    authors： Lynch M

    更新日期：2007-05-15 00:00:00

  • Multiple evidence for nucleotide metabolism in the chloroplast thylakoid lumen.

    abstract：:The apparatus of photosynthetic energy conversion in chloroplasts is quite well characterized with respect to structure and function. Light-driven electron transport in the thylakoid membrane is coupled to synthesis of ATP, used to drive energy-dependent metabolic processes in the stroma and the outer surface of the t...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0308164100

    authors： Spetea C,Hundal T,Lundin B,Heddad M,Adamska I,Andersson B

    更新日期：2004-02-03 00:00:00

  • Bulk electronic transport impacts on electron transfer at conducting polymer electrode-electrolyte interfaces.

    abstract：:Electrochemistry is an old but still flourishing field of research due to the importance of the efficiency and kinetics of electrochemical reactions in industrial processes and (bio-)electrochemical devices. The heterogeneous electron transfer from an electrode to a reactant in the solution has been well studied for m...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1806087115

    authors： Wijeratne K,Ail U,Brooke R,Vagin M,Liu X,Fahlman M,Crispin X

    更新日期：2018-11-20 00:00:00

  • Dual functions of the Hsm3 protein in chaperoning and scaffolding regulatory particle subunits during the proteasome assembly.

    abstract：:The 26S proteasome, a molecular machine responsible for regulated protein degradation, consists of a proteolytic core particle (20S CP) associated with 19S regulatory particles (19S RPs) subdivided into base and lid subcomplexes. The assembly of 19S RP base subcomplex is mediated by multiple dedicated chaperones. Amon...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1116538109

    authors： Barrault MB,Richet N,Godard C,Murciano B,Le Tallec B,Rousseau E,Legrand P,Charbonnier JB,Le Du MH,Guérois R,Ochsenbein F,Peyroche A

    更新日期：2012-04-24 00:00:00

  • Ataxia telangiectasia-mutated phosphorylates Chk2 in vivo and in vitro.

    abstract：:The protein kinase Chk2, the mammalian homolog of the budding yeast Rad53 and fission yeast Cds1 checkpoint kinases, is phosphorylated and activated in response to DNA damage by ionizing radiation (IR), UV irradiation, and replication blocks by hydroxyurea (HU). Phosphorylation and activation of Chk2 are ataxia telang...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.190030497

    authors： Matsuoka S,Rotman G,Ogawa A,Shiloh Y,Tamai K,Elledge SJ

    更新日期：2000-09-12 00:00:00

  • Extracting multistage screening rules from online dating activity data.

    abstract：:This paper presents a statistical framework for harnessing online activity data to better understand how people make decisions. Building on insights from cognitive science and decision theory, we develop a discrete choice model that allows for exploratory behavior and multiple stages of decision making, with different...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1522494113

    authors： Bruch E,Feinberg F,Lee KY

    更新日期：2016-09-20 00:00:00

  • Partial similarities between yeast and liver alcohol dehydrogenases.

    abstract：:The primary structure of about half of the protein chain of yeast alcohol dehydrogenase has been determined and compared with the amino-acid sequences of other dehydrogenases. The enzyme is found to be distantly related to horse-liver alcohol dehydrogenase, although these two proteins have different quaternary structu...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.70.8.2295

    authors： Jörnvall H

    更新日期：1973-08-01 00:00:00

  • V600E B-Raf requires the Hsp90 chaperone for stability and is degraded in response to Hsp90 inhibitors.

    abstract：:The Raf family includes three members, of which B-Raf is frequently mutated in melanoma and other tumors. We show that Raf-1 and A-Raf require Hsp90 for stability, whereas B-Raf does not. In contrast, mutated, activated B-Raf binds to an Hsp90-cdc37 complex, which is required for its stability and function. Exposure o...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0609973103

    authors： Grbovic OM,Basso AD,Sawai A,Ye Q,Friedlander P,Solit D,Rosen N

    更新日期：2006-01-03 00:00:00

  • Therapeutic antitumor immunity by checkpoint blockade is enhanced by ibrutinib, an inhibitor of both BTK and ITK.

    abstract：:Monoclonal antibodies can block cellular interactions that negatively regulate T-cell immune responses, such as CD80/CTLA-4 and PD-1/PD1-L, amplifying preexisting immunity and thereby evoking antitumor immune responses. Ibrutinib, an approved therapy for B-cell malignancies, is a covalent inhibitor of BTK, a member of...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1500712112

    authors： Sagiv-Barfi I,Kohrt HE,Czerwinski DK,Ng PP,Chang BY,Levy R

    更新日期：2015-03-03 00:00:00

  • Alpha-actinin2 cytoskeletal protein is required for the functional membrane localization of a Ca2+-activated K+ channel (SK2 channel).

    abstract：:The importance of proper ion channel trafficking is underpinned by a number of channel-linked genetic diseases whose defect is associated with failure to reach the cell surface. Conceptually, it is reasonable to suggest that the function of ion channels depends critically on the precise subcellular localization and th...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0908207106

    authors： Lu L,Timofeyev V,Li N,Rafizadeh S,Singapuri A,Harris TR,Chiamvimonvat N

    更新日期：2009-10-27 00:00:00

  • Synaptic mechanisms of persistent reverberatory activity in neuronal networks.

    abstract：:For brain functions such as working memory and motor planning, neuronal circuits are able to sustain persistent activity after transient inputs. Theoretical studies have suggested that persistent activity can exist in recurrently connected networks as active reverberation. However, the actual cellular processes underl...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0500717102

    authors： Lau PM,Bi GQ

    更新日期：2005-07-19 00:00:00

  • Epithelial mouse mammary cell line exhibiting normal morphogenesis in vivo and functional differentiation in vitro.

    abstract：:An epithelial cell line, designated COMMA-1D, was derived from mammary tissue of BALB/c mice in the middle of pregnancy. This line, in continuous cell culture for 12 months, exhibits several characteristics distinctive of normal mammary epithelial cells, including induction of casein synthesis in vitro and normal duct...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.81.12.3756

    authors： Danielson KG,Oborn CJ,Durban EM,Butel JS,Medina D

    更新日期：1984-06-01 00:00:00

  • Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase.

    abstract：:To achieve accurate aminoacylation of tRNAs with their cognate amino acids, errors in aminoacylation are corrected by the "editing" mechanism in several aminoacyl-tRNA synthetases. Phenylalanyl-tRNA synthetase (PheRS) hydrolyzes, or edits, misformed tyrosyl-tRNA with its editing domain in the beta subunit. We report t...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0603182103

    authors： Sasaki HM,Sekine S,Sengoku T,Fukunaga R,Hattori M,Utsunomiya Y,Kuroishi C,Kuramitsu S,Shirouzu M,Yokoyama S

    更新日期：2006-10-03 00:00:00

  • Contribution of canonical nonhomologous end joining to chromosomal rearrangements is enhanced by ATM kinase deficiency.

    abstract：:A likely mechanism of chromosomal rearrangement formation involves joining the ends from two different chromosomal double-strand breaks (DSBs). These events could potentially be mediated by either of two end-joining (EJ) repair pathways [canonical nonhomologous end joining (C-NHEJ) or alternative end joining (ALT-EJ)]...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1612204114

    authors： Bhargava R,Carson CR,Lee G,Stark JM

    更新日期：2017-01-24 00:00:00

  • Replacement of anticodon loop nucleotides to produce functional tRNAs: amber suppressors derived from yeast tRNAPhe.

    abstract：:The method of anticodon loop replacement has been used to make derivatives of yeast tRNAPhe. By constructing tRNAs with a CUA anticodon, complementary to the amber (UAG) terminator, functional amber suppressor tRNAs were produced. The activity of these tRNAs was assayed in a mammalian cell-free protein synthesizing sy...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.79.23.7127

    authors： Bruce AG,Atkins JF,Wills N,Uhlenbeck O,Gesteland RF

    更新日期：1982-12-01 00:00:00

  • Algorithmic design of self-assembling structures.

    abstract：:We study inverse statistical mechanics: how can one design a potential function so as to produce a specified ground state? In this article, we show that unexpectedly simple potential functions suffice for certain symmetrical configurations, and we apply techniques from coding and information theory to provide mathemat...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0901636106

    authors： Cohn H,Kumar A

    更新日期：2009-06-16 00:00:00

  • Linking global climate and temperature variability to widespread amphibian declines putatively caused by disease.

    abstract：:The role of global climate change in the decline of biodiversity and the emergence of infectious diseases remains controversial, and the effect of climatic variability, in particular, has largely been ignored. For instance, it was recently revealed that the proposed link between climate change and widespread amphibian...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0912883107

    authors： Rohr JR,Raffel TR

    更新日期：2010-05-04 00:00:00

  • A heuristic derived from analysis of the ion channel structural proteome permits the rapid identification of hydrophobic gates.

    abstract：:Ion channel proteins control ionic flux across biological membranes through conformational changes in their transmembrane pores. An exponentially increasing number of channel structures captured in different conformational states are now being determined; however, these newly resolved structures are commonly classifie...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1902702116

    authors： Rao S,Klesse G,Stansfeld PJ,Tucker SJ,Sansom MSP

    更新日期：2019-07-09 00:00:00

  • Conformational change of the actomyosin complex drives the multiple stepping movement.

    abstract：:Actin-myosin (actomyosin) generates mechanical force by consuming ATP molecules. We apply the energy landscape perspective to address a controversial issue as to whether the myosin head moves with multiple steps after a single ATP hydrolysis or only a single mechanical event of the lever-arm swinging follows a single ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.132711799

    authors： Terada TP,Sasai M,Yomo T

    更新日期：2002-07-09 00:00:00

  • Conditional steroidogenic cell-targeted deletion of TSPO unveils a crucial role in viability and hormone-dependent steroid formation.

    abstract：:Translocator protein (TSPO) is a key member of the mitochondrial cholesterol transport complex in steroidogenic tissues. To assess the function of TSPO, we generated two lines of Cre-mediated Tspo conditional knockout (cKO) mice. First, gonadal somatic cell-targeting Amhr2-Cre mice were crossed with Tspo-floxed mice t...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1502670112

    authors： Fan J,Campioli E,Midzak A,Culty M,Papadopoulos V

    更新日期：2015-06-09 00:00:00

  • Water conservation in irrigation can increase water use.

    abstract：:Climate change, water supply limits, and continued population growth have intensified the search for measures to conserve water in irrigated agriculture, the world's largest water user. Policy measures that encourage adoption of water-conserving irrigation technologies are widely believed to make more water available ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0805554105

    authors： Ward FA,Pulido-Velazquez M

    更新日期：2008-11-25 00:00:00

  • Evolutionary conservation of the insulinoma gene rig and its possible function.

    abstract：:We have identified a gene, rig (rat insulinoma gene), that is activated in chemically induced rat insulinomas but not in normal pancreatic islets or in regenerating islets. In the present study, we have found that the insulinoma gene was activated in a BK virus-induced hamster insulinoma cell line and in a spontaneous...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.84.19.6659

    authors： Inoue C,Shiga K,Takasawa S,Kitagawa M,Yamamoto H,Okamoto H

    更新日期：1987-10-01 00:00:00

  • The role of seawater endocytosis in the biomineralization process in calcareous foraminifera.

    abstract：:Foraminifera are unicellular organisms that inhabit the oceans in various ecosystems. The majority of the foraminifera precipitate calcitic shells and are among the major CaCO(3) producers in the oceans. They comprise an important component of the global carbon cycle and also provide valuable paleoceanographic informa...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0906636106

    authors： Bentov S,Brownlee C,Erez J

    更新日期：2009-12-22 00:00:00

  • Pseudomonas aeruginosa type III-secreted toxin ExoT inhibits host-cell division by targeting cytokinesis at multiple steps.

    abstract：:Pseudomonas aeruginosa is an opportunistic pathogen that requires preexisiting epithelial injury to cause acute infections. We report that P. aeruginosa inhibits mammalian cytokinesis in a type III secretion system and exotoxin T (ExoT)-dependent manner. ExoT is a bifunctional type III secretion system effector protei...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0605949103

    authors： Shafikhani SH,Engel J

    更新日期：2006-10-17 00:00:00

  • Global transcriptional repression: An initial and essential step for Plasmodium sexual development.

    abstract：:Gametocytes are nonreplicative sexual forms that mediate malaria transmission to a mosquito vector. They are generated from asexual blood-stage parasites that proliferate in the circulation. However, little is known about how this transition is genetically regulated. Here, we report that an Apetala2 (AP2) family trans...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1504389112

    authors： Yuda M,Iwanaga S,Kaneko I,Kato T

    更新日期：2015-10-13 00:00:00

  • Fluorescence correlation analysis of probe diffusion simplifies quantitative pathogen detection by PCR.

    abstract：:A sensitive, labor-saving, and easily automatable nonradioactive procedure named APEX-FCS (amplified probe extension detected by fluorescence correlation spectroscopy) has been established to detect specific in vitro amplification of pathogen genomic sequences. As an example, Mycobacterium tuberculosis genomic DNA was...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.93.23.12805

    authors： Walter NG,Schwille P,Eigen M

    更新日期：1996-11-12 00:00:00

  • Ontogeny and phylogeny of language.

    abstract：:How did language evolve? A popular approach points to the similarities between the ontogeny and phylogeny of language. Young children's language and nonhuman primates' signing both appear formulaic with limited syntactic combinations, thereby suggesting a degree of continuity in their cognitive abilities. To evaluate ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1216803110

    authors： Yang C

    更新日期：2013-04-16 00:00:00