Some of these are believed to affect the shape of nucleic acids (see for example RNA self-splicing), but this is only sometimes ... "An approach to detection of protein structural motifs using an encoding scheme of backbone conformations" (PDF). Proc. of 2nd ... "Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical ... Bailey TL, Williams N, Misleh C, Li WW (2006). "MEME: discovering and analyzing DNA and protein sequence motifs". Nucleic Acids ...
Nucleic Acids Research. 42 (21): 13134-49. doi:10.1093/nar/gku1051. PMC 4245941 . PMID 25378325. Ishida T, Akimitsu N, Kashioka ... Filling of the sites changes origin conformation from its native state. It is hypothesized that DNA stretching by DnaA bound to ...
Kozlowski, LP (26 October 2016). "Proteome-pI: proteome isoelectric point database". Nucleic Acids Research. doi:10.1093/nar/ ... Upon absorption of a photon, retinal changes conformation, causing a conformational change in the bacterioopsin protein which ... Amino acids are the main source of chemical energy for H. salinarum, particularly arginine and aspartate, though they are able ... Vreeland, H; Rosenzweig, W D; Lowenstein, T; Satterfield, C; Ventosa, A (December 2006). "Fatty acid and DNA analyses of ...
Nucleic Acids Res. 44 (D1). doi:10.1093/nar/gkv1187. PMID 26590258. Damas, J; Carneiro, J; Goncalves, J; Stewart, JB; Samwels, ... DC; Amorim, A; Pereira, F (2012). "Mitochondrial DNA deletions are associated with non-B DNA conformations". Nuclei Acids Res. ... Nucleic Acids Research. 39 (21): 9238-49. doi:10.1093/nar/gkr653. PMC 3241658 . PMID 21840902. St. John, J. C.; Facucho- ... Nucleic Acids Research. 40 (Database issue): D1168-72. doi:10.1093/nar/gkr1144. PMC 3245153 . PMID 22123747. Gu, Zuguang; Li, ...
Nucleic Acids Research. Retrieved 24 November 2015. ... in condensing chromatin from the beads-on-a-string conformation ... Histone H2B is a lightweight structural protein made of 126 amino acids. Many of these amino acids have a positive charge at ... All variants of histone H2B contain the same number of amino acids, and the variations in sequence are few in number. Only two ... Adding an acetyl group to lysine residues in one of several positions in the amino acid tail contributes to the activation of ...
The T4's tail is hollow so that it can pass its nucleic acid into the cell it is infecting after attachment. The tail attaches ... The baseplate changes conformation and the tail sheath contracts, causing GP5 at the end of the tail tube to puncture the outer ... HERSHEY AD, CHASE M (1952). "Independent functions of viral protein and nucleic acid in growth of bacteriophage". J. Gen. ... ISBN 0-06-015260-5 (USA and Canada) Bernstein C (1981). "Deoxyribonucleic acid repair in bacteriophage". Microbiol. Rev. 45 (1 ...
"Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification". Nucleic Acids Res. ... Single Strand Conformation Analysis) effectively identify SNPs and small insertions and deletions. MLPA, however, is one of the ...
Nucleic acid - nucleic acid regulatory sequence - nucleic acid repetitive sequence - nucleic acid sequence homology - nucleon ... Conformation - chemical element - Chemical equilibrium - Chemical formula - Chemical nomenclature - Chemical property - ... amino acid - amino acid receptor - amino acid sequence - amino acid sequence homology - aminobutyric acid - ammonia - AMPA ... It deals with the structure and function of cellular components such as proteins, carbohydrates, lipids, nucleic acids and ...
Nucleic Acids Res. 25 (10): 1903-12. doi:10.1093/nar/25.10.1903. PMC 146682 . PMID 9115356. Glass CK, Rosenfeld MG (2000). "The ... Agonist ligands work by inducing a conformation of the receptor which favors coactivator binding (see upper half of the figure ... Some of these receptors such as FXR, LXR, and PPAR bind a number of metabolic intermediates such as fatty acids, bile acids and ... Two putative orphan receptors, HNF4 and USP were found, via structural and mass spectrometry analysis, to bind fatty acids and ...
A pseudoknot is a nucleic acid secondary structure containing at least two stem-loop structures in which half of one stem is ... Pseudoknots fold into knot-shaped three-dimensional conformations but are not true topological knots. The structural ... Pleij CW, Rietveld K, Bosch L (1985). "A new principle of RNA folding based on pseudoknotting". Nucleic Acids Res. 13 (5): 1717 ... Dirks, R.M. Pierce N.A. (2004) An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. "J ...
... instead of in nucleic acids. Several prion-forming proteins have been identified in fungi, primarily in the yeast Saccharomyces ... The amyloid conformation is self-propagating and represents the prion state. It is believed that suppression of nonsense ... The structure is based on the stacking of the prion domains in an in-register and parallel beta sheet conformation. When ... Further investigation found that [PSI+] is the result of a self-propagating misfolded form of Sup35p (a 201 amino acid long ...
1987). ""Homology" in proteins and nucleic acids: a terminology muddle and a way out of it". Nature. 50 (5): 667. doi:10.1016/ ... different probes are generally applied with the goal being to obtain a large number of different protein-probe conformations. ... 2010). "The Pfam protein families database". Nucleic Acids Res. 38 (Database issue): D211-222. doi:10.1093/nar/gkp985. PMC ... Information may come from nucleic acid sequence homology, gene expression profiles, protein domain structures, text mining of ...
Nucleic Acids Research. 39 (8): e52-e52. doi:10.1093/nar/gkr035. PMC 3082908 . PMID 21297115. deltaMasses Detection of ... Wienken CJ, Baaske P, Duhr S, Braun D (2011). "Thermophoretic melting curves quantify the conformation and stability of RNA and ... a general method for the synthesis of pure 2-arylpropionic acids. 2-Phenylpropionic acid". Organic Syntheses. 76: 169. doi: ... Protein methylation typically takes place on arginine or lysine amino acid residues in the protein sequence. Arginine can be ...
The B reader loop is further thought to stabilise NTPs in the active site and, due to its flexibily, allow the nucleic acids to ... The open and closed conformations refer to the state of the DNA and whether the template strand has been separated from the non ... TFIIB is a single 33kDa polypeptide consisting of 316 amino acids. It was originally thought to be essential at all promoters ... Although TFIIB keeps a similar structure in both conformations some of the intramolecular interactions between the core and the ...
... fit a sequence of amino acids in alpha helix conformation into density. Place strand here - fit a sequence of amino acids in ... typically of proteins or nucleic acids, using 3D computer graphics. It is primarily focused on building and validation of ... Pukka puckers - check for unusual DNA/RNA conformations. Coot is built upon a number of libraries. Crystallographic tools ... check for unusual protein side-chain conformations. Density fit analysis - identify parts of the model which don't fit the ...
2006). "The LIFEdb database in 2006". Nucleic Acids Res. 34 (Database issue): D415-8. doi:10.1093/nar/gkj139. PMC 1347501 . ... 2003). "The Apaf-1 internal ribosome entry segment attains the correct structural conformation for function via interactions ... Nucleic Acids Res. 18 (16): 4891-9. PMC 331975 . PMID 2204029. Nagase T, Ishikawa K, Suyama M, Kikuno R, Hirosawa M, Miyajima N ... Nucleic Acids Res. 33 (10): 3095-108. doi:10.1093/nar/gki611. PMC 1142345 . PMID 15928332. Patel GP, Ma S, Bag J (2006). "The ...
Krogh A, Mian IS, Haussler D (1994). "A hidden Markov model that finds genes in E. coli DNA". Nucleic Acids Res. 22 (22): 4768- ... Hamelryck T, Kent JT, Krogh A (2006). "Sampling Realistic Protein Conformations Using Local Structural Bias". PLoS Comput. Biol ... Nucleic Acids Res. 36 (Database issue): D102-6. doi:10.1093/nar/gkm955. PMC 2238834 . PMID 18006571. Lindow M, Jacobsen A, ... Probabilistic Models of Proteins and Nucleic Acids (1st ed.), Cambridge, New York: Cambridge University Press, doi:10.2277/ ...
The nucleic acid is bound in an extended conformation across one side of the domain. The binding occurs in a cleft formed ... An evolutionarily conserved sequence of around 70 amino acids, the KH domain is present in a wide variety of nucleic acid- ... Grishin NV (February 2001). "KH domain: one motif, two folds". Nucleic Acids Res. 29 (3): 638-43. doi:10.1093/nar/29.3.638. PMC ... Valverde and colleagues note that, "Nucleic acid base-to-protein aromatic side chain stacking interactions which are prevalent ...
Nucleic Acids Research. 16 (7): 3109. doi:10.1093/nar/16.7.3109. PMC 336462 . PMID 3368322. MacLeod AR, Houlker C, Reinach FC, ... which adopt a bent coiled coil conformation to wrap around the seven actin molecules in a functional unit of muscle. It is ... β-tropomyosin is roughly 32 kDa in molecular weight (284 amino acids), but multiple splice variants exist. Tropomysin is a ... which is one amino acid away from the C-terminus. β-tropomyosin also has a Serine residue at position 283, thus, it is likely ...
Momand J, Jung D, Wilczynski S, Niland J (August 1998). "The MDM2 gene amplification database". Nucleic Acids Research. 26 (15 ... K29-, K33-, K63- and M1-linked chains have a fairly linear conformation; they are known as open-conformation chains. K6-, K11 ... In contrast, the closed conformation chains have interfaces with interacting residues. Altering the chain conformations exposes ... Journal of Nucleic Acids. 2010: 1-8. doi:10.4061/2010/761217. PMC 2935186 . PMID 20847899. Jackson SP, Durocher D (March 2013 ...
Nucleic Acids Res. 31 (6): 1633-9. doi:10.1093/nar/gkg273. PMC 152875 . PMID 12626704. This article incorporates text from the ... Polosina YY, Cupples CG (2009). "Changes in the conformation of the Vsr endonuclease amino-terminal domain accompany DNA ...
Some RNA sequences have more than one biologically active conformation (i.e., riboswitches) For this reason, the ability to ... Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its ... Macke T, Case D (1998). Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids. Edited by Leontes N, ... Zuker M (2003). "Mfold web server for nucleic acid folding and hybridization prediction". Nucleic Acids Research. 31 (13): 3406 ...
Nucleic Acids Research. 33 (Web Server): W690-W692. doi:10.1093/nar/gki445. PMID 15980564. Chang, T.-H.; Huang, H.-D.; Wu, L.-C ... "Computational identification of riboswitches based on RNA conserved functional sequences and conformations". RNA. 15 (7): 1426- ... Nucleic Acids Res. 35 (14): 4809-19. doi:10.1093/nar/gkm487. PMC 1950547 . PMID 17621584. Weinberg Z, Wang JX, Bogue J, et al ... Nucleic Acids Res. 36 (18): 5955-69. doi:10.1093/nar/gkn601. PMC 2566862 . PMID 18812398. Loh E, Dussurget O, Gripenland J, et ...
Beyond nucleic acid binding, FUS/TLS was also found to associate with both general and more specialized protein factors to ... FUS/TLS interacts with multiple RNA-binding motifs or recognises secondary conformations. FUS/TLS has also been proposed to ... Nucleic Acids Symp Ser (Oxf) (52): 213-4. doi:10.1093/nass/nrn108. PMID 18776329. Law WJ, Cann KL, Hicks GG (March 2006). "TLS ...
You Y, Moreira BG, Behlke MA, Owczarzy R (2006). "Design of LNA probes that improve mismatch discrimination". Nucleic Acids Res ... The locked conformation of LNA results in enhanced hybridization properties and increases sensitivity and selectivity, making ... Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (January 2008). "miRBase: tools for microRNA genomics". Nucleic Acids Res ... Nucleic Acids Symp Ser. 48 (1): 211-2. doi:10.1093/nass/48.1.211. PMID 17150553. Moxon S, Jing R, Szittya G, Schwach F, ...