Abstract:
:DynOmics (dynomics.pitt.edu) is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment. At the core of the portal is a newly developed server, ENM 1.0, which permits users to efficiently generate information on the collective dynamics of any structure in PDB format, user-uploaded or database-retrieved. ENM 1.0 integrates two widely used elastic network models (ENMs)-the Gaussian Network Model (GNM) and the Anisotropic Network Model (ANM), extended to take account of molecular environment. It enables users to assess potentially functional sites, signal transduction or allosteric communication mechanisms, and protein-protein and protein-DNA interaction poses, in addition to delivering ensembles of accessible conformers reconstructed at atomic details based on the global modes of motions predicted by the ANM. The 'environment' is defined in a flexible manner, from lipid bilayer and crystal contacts, to substrate or ligands bound to a protein, or surrounding subunits in a multimeric structure or assembly. User-friendly interactive features permit users to easily visualize how the environment alter the intrinsic dynamics of the query systems. ENM 1.0 can be accessed at http://enm.pitt.edu/ or http://dyn.life.nthu.edu.tw/oENM/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Li H,Chang YY,Lee JY,Bahar I,Yang LWdoi
10.1093/nar/gkx385subject
Has Abstractpub_date
2017-07-03 00:00:00pages
W374-W380issue
W1eissn
0305-1048issn
1362-4962pii
3791214journal_volume
45pub_type
杂志文章abstract::The PROSITE pattern Zinc_Finger_C2H2 was extended to permit the detection of all C2H2 zinc fingers and their parent proteins in the recently completed sequence of the yeast genome. Additionally, a new computer program was written that extracts other zinc binding motifs (non C2H2 'fingers'), overlapping with the classi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.12.2464
更新日期:1997-06-15 00:00:00
abstract::Mitochondrial DNA maintenance and segregation are dependent on the actin cytoskeleton in budding yeast. We found two cytoskeletal proteins among six proteins tightly associated with rat liver mitochondrial DNA: non-muscle myosin heavy chain IIA and β-actin. In human cells, transient gene silencing of MYH9 (encoding no...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr052
更新日期:2011-07-01 00:00:00
abstract::The accumulation of somatic mitochondrial DNA (mtDNA) mutations contributes to the pathogenesis of human disease. Currently, mitochondrial mutations are largely considered results of inaccurate processing of its heavily damaged genome. However, mainly from a lack of methods to monitor mtDNA mutations with sufficient s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw716
更新日期:2016-10-14 00:00:00
abstract::The nucleotide sequences of the Streptomyces transposable element IS110 and its insertion site in the DNA of a derivative of the temperate phage luminal diameter C31 were determined. The element is inserted about 460 bp from the right-hand end of luminal diameter C31 DNA, in a region of apparently non-coding DNA. The ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.17.7053
更新日期:1987-09-11 00:00:00
abstract::Human ADAR3 is a catalytically inactive member of the Adenosine Deaminase Acting on RNA (ADAR) protein family, whose active members catalyze A-to-I RNA editing in metazoans. Until now, the reasons for the catalytic incapability of ADAR3 has not been defined and its biological function rarely explored. Yet, its exclusi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz815
更新日期:2019-11-18 00:00:00
abstract::Ribonucleotides are misincorporated into replicating DNA due to the similarity of deoxyribonucleotides and ribonucleotides, the high concentration of ribonucleotides in the nucleus and the imperfect accuracy of replicative DNA polymerases in choosing the base with the correct sugar. Embedded ribonucleotides change cer...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gku773
更新日期:2014-01-01 00:00:00
abstract:UNLABELLED:Partial cleavage of DNA with the restriction endonuclease NotI (5'...GC/GGCCGC...3') is an important technique for genomic mapping. However, partial genomic cleavage with this enzyme is impaired by the agarose matrix in which the DNA must be suspended. To solve this problem we have purified the blocking meth...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.11.3287
更新日期:1990-06-11 00:00:00
abstract::We have adapted a method for making libraries of mutations in any specific gene for use in the fission yeast Schizosaccharomyces pombe . This elegant and simple method consists of PCR amplification of the gene of interest, followed by co-transformation of fission yeast with the PCR fragment and a linearized plasmid ve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.20.4783
更新日期:1998-10-15 00:00:00
abstract::Human stem cells are promising sources for regenerative therapy. To ensure safety of future therapeutic applications, the differentiation potency of stem cells has to be tested and be widely opened to the public. The potency is generally assessed by teratoma formation comprising differentiated cells from all three ger...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1096
更新日期:2016-01-04 00:00:00
abstract::A growing number of whole genome sequencing projects, in combination with development of phylogenetic methods for reconstructing gene evolution, have provided us with a window into genomes that existed millions, and even billions, of years ago. Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1009
更新日期:2019-01-08 00:00:00
abstract::While biallelic mutations in the PALB2 tumor suppressor cause Fanconi anemia subtype FA-N, monoallelic mutations predispose to breast and familial pancreatic cancer. Although hundreds of missense variants in PALB2 have been identified in patients to date, only a few have clear functional and clinical relevance. Herein...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz780
更新日期:2019-11-18 00:00:00
abstract::Prokaryotic genomic DNA is generally negatively supercoiled in vivo. Many regulatory processes, including the initiation of transcription, are known to depend on the superhelical state of the DNA substrate. The stresses induced within DNA by negative superhelicity can destabilize the DNA duplex at specific sites. Vari...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj007
更新日期:2006-01-01 00:00:00
abstract::Sequencing by hybridization (SBH) approaches to DNA sequencing face two conflicting constraints. First, in order to ensure that the target DNA binds reliably, the oligonucleotide probes that are attached to the chip array must be >15 bp in length. Secondly, the total number of possible 15 bp oligonucleotides is too la...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh210
更新日期:2004-02-18 00:00:00
abstract::In Escherichia coli transcription of individual genes generally requires concomitant translation, and thus the decay of mRNAs cannot be studied without the complication of translation. Here we have used T7 RNA polymerase to transcribe in vivo lacZ genes carrying ribosome binding sites of variable efficiency. We show t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.19.5787
更新日期:1990-10-11 00:00:00
abstract::The Dnd (DNA degradation) phenotype, reflecting a novel DNA modification by sulfur in Streptomyces lividans 1326, was strongly aggravated when one (dndB) of the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear change...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm176
更新日期:2007-01-01 00:00:00
abstract::The 3'-untranslated region (UTR) of tobacco mosaic virus (TMV), which terminates in a tRNA-like structure, functionally substitutes for a poly(A) tail in both plant and animal cells. The addition of the TMV 3'-UTR to chimeric mRNA constructs increases their expression up to 100-fold, increasing both translational effi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.18.5031
更新日期:1991-09-25 00:00:00
abstract::Current knowledge of parameters affecting RNA stability is very restricted in plants. Here we investigated factors which might contribute to the stability of a particular plant messenger RNA. To this end, insertion and deletion mutants were made in two different exons and an intron of the transcribed region of a well ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.10.2917
更新日期:1990-05-25 00:00:00
abstract::Reactive oxygen species produced by endogenous metabolic activity and exposure to a multitude of exogenous agents impact cells in a variety of ways. The DNA base damage 8-oxodeoxyguanosine (8-oxodG) is a prominent indicator of oxidative stress and has been well-characterized as a premutagenic lesion in mammalian cells...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.15.3213
更新日期:1999-08-01 00:00:00
abstract::Mutations in mammalian and Drosophila Hel308 and PolQ paralogues cause genome instability but their helicase functions are mysterious. By in vivo and in vitro analysis, we show that Hel308 from archaea (Hel308a) may act at stalled replication forks. Introducing hel308a into Escherichia coli dnaE strains that condition...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki685
更新日期:2005-06-30 00:00:00
abstract::Deregulation of mini-chromosome maintenance (MCM) proteins is associated with genomic instability and cancer. MCM complexes are recruited to replication origins for genome duplication. Paradoxically, MCM proteins are in excess than the number of origins and are associated with chromatin regions away from the origins d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt022
更新日期:2013-03-01 00:00:00
abstract::The promoter of the human BCR gene, regulating the transcription of the chimeric BCR/ABL mRNA in leukemia, has been isolated and characterized. A region of 1.1 kb immediately 5' to the transcription start site was analyzed in detail by sequencing, DNase 1 footprinting, gel retardation and functional studies. These exp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.23.7119
更新日期:1990-12-11 00:00:00
abstract::We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new method for modeling the intron length distribution. This method allows approximation of the true intron length distribution m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh379
更新日期:2004-07-01 00:00:00
abstract::Fragments of SP6 DNA generated by cleavage with Hpa II or Taq I were cloned into the Cla I site of pBR322 and the recombinant plasmids were screened for the presence of SP6 promoter activity by transcription in vitro with purified SP6 RNA polymerase. Three plasmids having promoter activity and small inserts of SP6 DNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.8.3521
更新日期:1986-04-25 00:00:00
abstract::A crucial component of the human mitochondrial DNA replisome is the ring-shaped helicase TWINKLE-a phage T7-gene 4-like protein expressed in the nucleus and localized in the human mitochondria. Our previous studies showed that despite being a helicase, TWINKLE has unique DNA annealing activity. At the time, the implic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw098
更新日期:2016-05-19 00:00:00
abstract::A repeat sequence 682 base pairs (bp) long produced by cleavage of human DNA with Xba I restriction enzyme is composed of four tandemly arranged subunits with lengths of 171, 170, 171, and 170 bp each. The sequence organization of the 682 bp Xba I repeat bears a striking resemblance to other complex satellite DNAs of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.2.521
更新日期:1985-01-25 00:00:00
abstract::The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subuni...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky618
更新日期:2018-09-06 00:00:00
abstract::Stem cell fate decisions are controlled by a molecular network in which transcription factors and miRNAs are of key importance. To systemically investigate their impact on neural stem cell (NSC) maintenance and neuronal commitment, we performed a high-throughput mRNA and miRNA profiling and isolated functional interac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt070
更新日期:2013-04-01 00:00:00
abstract::Type IIS restriction endonuclease BtsCI (GGATG 2/0) is a neoschizomer of FokI (GGATG 9/13) and cleaves closer to the recognition sequence. Although M.BtsCI shows 62% amino acid sequence identity to M.FokI, BtsCI and FokI restriction endonucleases do not share significant amino acid sequence similarity. BtsCI belongs t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1092
更新日期:2010-03-01 00:00:00
abstract::The mouse c-Ki-ras protooncogene promoter contains a homopurine-homopyrimidine domain that exhibits S1 nuclease sensitivity in vitro. We have studied the structure of this DNA region in a supercoiled state using a number of chemical probes for non-B DNA conformations including diethyl pyrocarbonate, osmium tetroxide, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.23.6527
更新日期:1991-12-11 00:00:00
abstract::The assembly of the complex that forms over the simian virus 40 origin to initiate DNA replication is not well understood. This complex is composed of the virus-coded T antigen and three cellular proteins, replication protein A (RPA), DNA polymerase alpha/primase (pol/prim) and topoisomerase I (topo I) in association ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh236
更新日期:2004-02-11 00:00:00