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  • homology
  • The combination of these factors results in the general observation that many sequences with little or no discernible homology can frequently have the same overall fold, making prediction of 3D structure from sequence highly problematic in such cases. (pnas.org)
  • Homology modeling of the PPIase domain revealed a conserved FKBP(FK506-binding protein)-like binding pocket composed of exposed aromatic residues embedded in a groove with negative surface charge. (pnas.org)
  • TF has a modular structure with an N-terminal domain that mediates ribosome binding, a central peptidyl-prolyl- cis / trans isomerase (PPIase) domain with homology to FK506-binding proteins (FKBPs), and a C-terminal domain with unknown function ( 6 , 9 , 10 ). (pnas.org)
  • ETA was also found to be complementary to sequence homology-based annotations. (biomedcentral.com)
  • When matches are required to both geometrically match the 3D template and to be sequence homologs found by BLAST or PSI-BLAST, the annotation accuracy is greater than either method alone, especially in the region of lower sequence identity where homology-based annotations are least reliable. (biomedcentral.com)
  • genome
  • The Gram-negative bacterium Verrucomicrobium spinosum has attracted interest in recent years following the sequencing and annotation of its genome. (frontiersin.org)
  • Genome sequencing revealed the genetic determinants responsible for a novel version of nisin, designated nisin H, consisting of the nshABTCPRKGEF genes, with transposases encoded between nshP and nshR and between nshK and nshG . (asm.org)
  • genomics
  • Pubmed ID: 12454472 The first results of a medium-scale structural genomics program clearly demonstrate the value of using a medium-throughput crystallization approach based on a two-step procedure: a large screening step employing robotics, followed by manual or automated optimization of the crystallization conditions. (jove.com)
  • The structural genomics program was based on cloning in the Gateway vectors pDEST17, introducing a long 21-residue tail at the N-terminus. (jove.com)
  • These still partial results might indicate present and future directions for those who have to make crucial choices concerning their crystallization platform in structural genomics programs. (jove.com)
  • cytosolic
  • The ribosome-associated chaperone trigger factor (TF) assists the folding of newly synthesized cytosolic proteins in Escherichia coli . (pnas.org)
  • The calcium-sensing receptor (CaSR) is a G protein-coupled receptor (GPCR) that signals through G q/11 and G i/o to stimulate cytosolic calcium (Ca 2+ i ) and mitogen-activated protein kinase (MAPK) signaling to control extracellular calcium homeostasis. (sciencemag.org)
  • amino acids
  • The binding motif of TF was identified as a stretch of eight amino acids, enriched in basic and aromatic residues and with a positive net charge. (pnas.org)
  • According to currently accepted ideas, vegetative storage organs such as bulbs, tubers, corms, rhizomes, and bark act as sinks for soluble nitrogen compounds (mainly amino acids) generated from the leaf proteins when the plant enters a senescing phase. (plantphysiol.org)
  • After transport through the phloem into the storage organs, the amino acids are incorporated into (storage) proteins in the storage parenchyma cells. (plantphysiol.org)
  • Environmental and/or endogenous stimuli induce a regulated degradation of the storage proteins, resulting in a massive release of amino acids that are subsequently transported to the new shoots to satisfy the high nitrogen demand of the rapidly growing tissues. (plantphysiol.org)
  • coli
  • In the Escherichia coli cytosol, three chaperones, trigger factor (TF), DnaK, and GroEL, participate in the folding of newly synthesized proteins ( 1 - 5 ). (pnas.org)
  • In this study, we determined the complete genomic sequence of E. coli H10407, a prototypical strain of enterotoxigenic E. coli , which reproducibly elicits diarrhea in human volunteer studies. (asm.org)
  • We performed genomic and phylogenetic comparisons with other E. coli strains, revealing that the chromosome is closely related to that of the nonpathogenic commensal strain E. coli HS and to those of the laboratory strains E. coli K-12 and C. Furthermore, these analyses demonstrated that there were no chromosomally encoded factors unique to any sequenced ETEC strains. (asm.org)
  • Mutations
  • Thus, conformational switching to an alternative monomeric fold of comparable stability can be effected with just a handful of mutations in a small protein. (pnas.org)
  • Mutations at some positions will have negligible effect on protein stability whereas other residues cannot be altered without resulting in complete unfolding. (pnas.org)
  • The crystal structure of the Pikp-HMA/AVR-PikD complex enabled design of mutations to alter protein interaction in yeast and in vitro, and perturb effector-mediated response both in a rice cultivar containing Pikp and upon expression of AVR-PikD and Pikp in the model plant Nicotiana benthamiana . (elifesciences.org)
  • genes
  • Our findings not only demonstrate the occurrence of a catalytically inactive variant of an S-like RNase, but also provide further evidence that genes encoding storage proteins may have evolved from genes encoding enzymes or other biologically active proteins. (plantphysiol.org)
  • Therefore
  • It is evident, therefore, that vegetative storage proteins (VSPs), even in the absence of a biological activity, are essential for the plant. (plantphysiol.org)
  • results
  • This apparent lack of activity results most probably from the replacement of a conserved His residue, which is essential for the catalytic activity of plant RNases. (plantphysiol.org)
  • identified a CASR mutation that results in an Arg-to-Gly substitution at amino acid residue 680 (R680G) in CaSR in a family with hypocalcemia. (sciencemag.org)
  • Furthermore, the results using a robot dispensing 50-200 nl drops indicate that smaller protein samples can be used for crystallization. (jove.com)
  • Collectively the results obtained with this new structural model of E2c suggest the development of small molecule inhibitors such as 281816 that target E2 and disrupt its interaction with CD81 may provide a new paradigm for HCV treatment. (nih.gov)
  • findings
  • These findings implicate TF as a prime candidate for the first chaperone to interact with newly synthesized proteins ( 1 ). (pnas.org)
  • These findings identify a structural feature of CaSR that is important for controlling signaling bias. (sciencemag.org)
  • important
  • These proteins play a primary role in nitrogen storage and distribution, and make an important contribution to the survival of the plant in its natural environment ( Staswick, 1994 ). (plantphysiol.org)
  • L1 is a myristoylated envelope protein that is a potent target for neutralizing antibodies and an important component of current experimental vaccines. (pnas.org)
  • The locations of amino acid residues that have been reported to be important for E2 binding to CD81 are marked with yellow stars. (nih.gov)
  • recent years
  • Bacteriocins of lactic acid bacteria have received extensive attention in recent years given their structural diversity and activity and their potential as biopreservatives and anti-infectives. (asm.org)
  • function
  • Since, unlike other 3D template approaches, the ETA method bypasses the need for experimental knowledge of the catalytic mechanism, it should prove a useful, large scale, and general adjunct to combine with other methods to decipher protein function in the structural proteome. (biomedcentral.com)
  • large
  • These cells are capable of accumulating large quantities of proteins and store away a corresponding amount of nitrogen in a biologically harmless form. (plantphysiol.org)
  • Development
  • Vaccine development is targeting proteins from each form ( 5 , 6 ), although because of the fragile nature of the EEV outermost membrane, the IMV form of the virus is thought to play the major role in host-to-host transmission ( 7 ). (pnas.org)
  • Thus
  • The nonidentities between these two amino acid sequences would then be responsible for coding one fold topology over the other and, thus, represent a fold-specific folding code. (pnas.org)
  • list
  • In the table for each entity, view a list of similar sequences by selecting the link associated with the percentage cutoff. (rcsb.org)
  • An extended list of storage proteins has been identified, indeed, in various typical vegetative storage tissues of plant species from different taxonomic groups. (plantphysiol.org)
  • essential
  • It is an essential protein because vaccinia viruses with the L1 gene deleted are not capable of maturation ( 8 ). (pnas.org)
  • specific
  • Immunity to nisin is provided by a specific immunity protein, NisI, and a specialized ABC transporter, NisFEG ( 9 ). (asm.org)
  • responsible
  • The gene responsible for FRDA, FXN , located on chromosome 9, is composed by seven exons (exons 1-4, 5a, 5b, and 6) and encodes for a mitochondrial protein, frataxin. (hindawi.com)