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  • Aromatic
  • Aromatic amino acids occur more often in [Formula: see text]-crystallins from vertebrates than on the average in proteins among 17 animal proteomes. (nih.gov)
  • Selected triple mutant was purified and characterized experimentally to successfully hydrolyze aromatic and branched aliphatic D-amino acid derivatives in a full agreement with computational predictions. (msu.ru)
  • substrate
  • Photolabeling studies indicate that TMs 10 and 11 in MSD1 and 16 and 17 in MSD2 contribute to the substrate binding pocket of the protein. (aspetjournals.org)
  • These analyses confirm that several amino acids in TM10 selectively alter the substrate specificity of MRP1, suggesting that they interact directly with certain substrates. (aspetjournals.org)
  • Consequently, in this work we aimed to study structure-function relationship of substrate recognition in DAP and rationally design its specificity toward substrates with bulky side-chain residues - D-phenylalanine and D-leucine derivatives. (msu.ru)
  • A new algorithm Zebra and a corresponding web-server have been developed to systematically study diverse protein superfamilies and identify the subfamily-specific positions (SSPs) - conserved only within functional subfamilies but different between them - that seem to be responsible for different substrate specificity, catalytic activity, stability, etc. . (msu.ru)
  • Molecular modeling was used to evaluate influence of selected residues on binding and catalytic conversion of amide substrate by corresponding in silico library of mutants and to select reactive enzyme-substrate complexes that satisfy knowledge-based criteria of amidase catalytic activity. (msu.ru)
  • Metabolites with a broader protein target range may more likely also fulfill signaling functions in addition to their role as substrate in biochemical reaction. (frontiersin.org)
  • encode
  • We suggest that RNA editing may have conferring evolutionary advantage by acting as a mechanism to reduce susceptibility to DNA damage by allowing the increase in GC content in DNA while maintaining RNA codons essential to encode residues required for protein folding and activity. (biomedcentral.com)
  • The Arabidopsis thaliana disease resistance genes RPS2 and RPM1 belong to a class of plant disease resistance genes that encode proteins that contain an N-terminal tripartite nucleotide binding site (NBS) and a C-terminal tandem array of leucine-rich repeats. (nih.gov)
  • peptide
  • The outcomes of this research show how FUV-TPCD can be used to study peptide and protein structures in a region never evaluated before but packed with important structural information. (rsc.org)
  • The analytical procedure was validated using a model peptide, NH 2 -Gly-Pro-Glu-Ala-Asp-Ser-Gly-OH, and the obtained calibration lines of %D for the 5 target amino acids were linear with correlation coefficients greater than 0.998. (go.jp)
  • While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. (ebi.ac.uk)
  • Proteins can be viewed as copolymers consisting of different amino acids, connected through the so-called peptide bond, and can be studied at various levels of detail, from the quantum mechanical to the statistical mechanical, the choice depending on the type of investigation. (royalsocietypublishing.org)
  • leucine
  • Mutation of a leucine residue in the third coiled-coil heptad impaired CWMV CRP activity for suppression of local silencing, but not for the promotion of cell-to-cell movement of Potato virus X (PVX). (biomedsearch.com)
  • The percentage of identical residues ( percent identity ) or the percentage of residues conserved with similar physicochemical properties ( percent similarity ), e.g. leucine and isoleucine , is usually used to "quantify the homology. (wikipedia.org)
  • Functional
  • We propose that these may be sites of interaction between the E1-E1 and E1-E2 subdomains of the envelope proteins that are required to assemble the functional unit. (springer.com)
  • Although two selective mutants on Leu128, Leu128Ala (L128A) and Leu128Arg (L128R), demonstrated high binding affinity to IL-8, they were not capable of coupling to G proteins and consequently lost the functional response of the receptors. (harvard.edu)
  • Recently developed bioinformatic analysis [1,of penicillin-binding proteins (PBP) family was used to identify subfamily-specific positions (SSPs) that are conserved within functional subfamilies of PBP, but different between subfamilies and therefore expected to be responsible for functional diversity among homologs. (msu.ru)
  • Hence, only the edited form of an mRNA can be translated into a polypeptide with helix-preferring and core-forming residues at the appropriate positions, which is often required for a protein to form a functional three-dimensional (3D) structure. (biomedcentral.com)
  • atoms
  • Using a set of carefully selected globular proteins, we parametrized continuous probability density functions describing preferred central distances of individual protein atoms. (biomedcentral.com)
  • The unexpectedness of extraordinary locations of atoms was evaluated in the information-theoretic manner and used directly for the identification of key amino acids. (biomedcentral.com)
  • If needed, use split or surfcat to make the surface enclose the desired set(s) of atoms, for example, each protein chain individually rather than all of the chains collectively. (ucsf.edu)
  • occur
  • Without RNA editing, protein folding will not occur properly, thus affecting gene expression. (biomedcentral.com)
  • However, it remains unknown which structural changes occur during the membrane insertion process and whether the charged amino acid residues are transported through the lipid bilayer in an ionic state with a hydration shell or whether they are neutralized by protonation or deprotonation. (embopress.org)
  • ligand
  • These results indicate that L128 on TM3.43 is involved in G protein coupling and receptor activation but is unimportant for ligand binding. (harvard.edu)
  • polypeptide
  • This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. (ebi.ac.uk)
  • The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [ PMID: 11297922 , PMID: 11290319 ]. (ebi.ac.uk)
  • nucleic acid
  • 2. The method of claim 1 wherein said nucleic acid is plasmid DNA. (google.com)
  • 6. The vector of claim 5 wherein said nucleic acid is plasmid DNA. (google.com)
  • Several methods have been explored for introducing nucleic acid into a variety of cell types with the hope of developing a successful technique for the transformation of eukaryotic cells of plants and animals. (google.com)
  • eukaryotic
  • Spiess (1995) has suggested that the membrane topology of eukaryotic proteins may be controlled by the translocase or the associated TRAM component of the endoplasmic reticulum which recognizes the charge distribution of the protein regions. (embopress.org)
  • A number of bacterial and plant toxins act by inhibiting protein synthesis in eukaryotic cells. (ebi.ac.uk)
  • peptides
  • D-aminopeptidase from Ochrobactrum anthropi (DAP) is a unique member of penicillin-binding proteins (PBP) family that converts mainly D-alanine containing peptides, amides, and esters with high D-stereospecificity. (msu.ru)
  • ribosome
  • About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. (ebi.ac.uk)
  • The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). (ebi.ac.uk)
  • In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [ PMID: 11290319 , PMID: 11114498 ]. (ebi.ac.uk)
  • Members of the family include shiga and shiga-like toxins, and type I (e.g. trichosanthin and luffin) and type II (e.g. ricin, agglutinin and abrin) ribosome inactivating proteins (RIPs). (ebi.ac.uk)
  • Conserved amino acid residues in ribosome-inactivating proteins from plants. (ebi.ac.uk)
  • vitro
  • In planta and in vitro analysis of wild-type and mutant proteins indicated that the ability of the CRP to self-interact was correlated with its suppression activity. (biomedsearch.com)
  • important
  • Identification of the amino acid residues and domains in the cysteine-rich protein of Chinese wheat mosaic virus that are important for RNA silencing suppression and subcellular localization. (biomedsearch.com)
  • Therefore, to identify functionally important SSPs a novel scoring function is suggested that incorporates structural information as well as physicochemical and residue conservation in protein subfamilies. (msu.ru)
  • Polyglycerol dendrimers as an important class of polymeric materials especially attractive for covalent attachment to therapeutic proteins as a useful alternative to traditional PEGylation procedures. (sfb765.de)
  • BACKGROUND Oxygen-base (O-base) oxidation in protein backbone is important in the protein backbone fragmentation due to the attack from reactive oxygen species (ROS). (semanticscholar.org)
  • However, it is clear that such description provides an oversimplified view of some important details of protein behaviour. (royalsocietypublishing.org)
  • The protein conformation determined by X-ray diffraction (solid state) and NMR (in solution) gives us a detailed description (or a 'snapshot') of the three-dimensional structure of a macromolecule, but other features are also important. (royalsocietypublishing.org)
  • Arabidopsis
  • For instance, the plant Flu regulatory protein is present both in Arabidopsis (multicellular higher plant) and Chlamydomonas (single cell green algae). (wikipedia.org)
  • However it can fully substitute the much simpler Arabidopsis protein, if transferred from algae to plant genome by means of genetic engineering . (wikipedia.org)
  • dependent
  • TGBp3 triggers the unfolded protein response and SKP1-dependent programmed cell death. (biomedsearch.com)
  • Short periplasmic tails or loops, which typically contain few charged residues, are thought to be translocated in a sec ‐independent manner, whereas longer translocated segments can contain several charged residues and their membrane transport is strongly sec dependent. (embopress.org)
  • Proteomic analysis of temperature dependent extracellular proteins from Aspergillus fumigatus grown under solid-state culture condition. (springer.com)
  • mutant
  • The V247N mutant also constitutively activated the \(G\alpha_i\) protein. (harvard.edu)
  • In both systems, the orientation of the protein was completely reversed for the oppositely charged mutant coat protein (RD mutant). (embopress.org)
  • In addition, we show in vivo that the electrochemical membrane potential is necessary for the translocation of both the wild‐type and the mutant Pf3 coat proteins, suggesting that membrane insertion is driven by electrophoretic forces. (embopress.org)
  • novel
  • We have performed a novel analysis of the location of residues affected by RNA editing in proteins in plant organelles. (biomedcentral.com)
  • To determine whether avirulence gene products themselves are the ligands for resistance proteins, we expressed the avrRpt2 and avrB genes directly in plant cell using a novel quantitative transient expression assay, and found that expression of avrRpt2 and avrB elicited a resistance response in plants carrying the corresponding resistance genes. (nih.gov)
  • respectively
  • Only half of the proteins were retained and their abundance declined to 9.7% at 55°C. The activities of the remaining β-glycosidases and proteases were merely 35% and 24%, respectively, when the secretome was treated at 60°C for 2 h. (springer.com)
  • subunit
  • By direct carbonylation modification of the Pro222 residue in the actuator (A) domain of pig Na/K‐ATPase α1 subunit, reactive oxygen species are required for ouabain‐stimulated Na/K‐ATPase/c‐Src signaling and subsequent regulation of active transepithelial 22 Na + transport. (marshall.edu)
  • Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. (ebi.ac.uk)
  • In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. (ebi.ac.uk)
  • Ribosomal protein S16 is one of the proteins from the small ribosomal subunit. (ebi.ac.uk)
  • interfaces
  • Information on residue variability, propensity to be in protein interfaces, and surface exposure on the model was combined to predict surface clusters likely to interact with other viral or cellular proteins. (springer.com)
  • stability
  • A liquid aqueous pharmaceutical formulation is described which has a high protein concentration, a pH of between about 4 and about 8, and enhanced stability. (patents.com)
  • analysis
  • In the present study, a two-dimensional (2D) HPLC-MS/MS system following the hydrolysis with deuterium chloride ( 2 HCl/ 2 H 2 O) and derivatization of amino acids with 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F) has been designed/developed and applied to the analysis of proteins stored under various conditions. (go.jp)
  • To extend this analysis, we mutated six additional polar residues within TM10 and the remaining uncharacterized polar residue in TM16, Asn 1208 . (aspetjournals.org)
  • Earlier analysis [ 15 ] of the location of RNA targets within transcripts did not detect any rules to explain why particular residues within a protein sequence were affected by codon changes while other residues were not altered. (biomedcentral.com)
  • 1994
  • Andersson and von Heijne (1994) have recently shown that, besides the size of a translocated region, positively charged residues influence the Sec dependency of these segments. (embopress.org)
  • surface
  • Relative exposure can be calculated by normalizing the surface area of the residue in the structure by the surface area of the same type of residue in some reference state. (ucsf.edu)
  • Although raw (non-normalized) surface areas could be used to classify residues as buried or exposed, normalization reduces the bias toward classifying smaller residues as more buried and larger as more exposed. (ucsf.edu)
  • This automatically creates the residue attribute areaSES , solvent-excluded surface areas in the structure. (ucsf.edu)
  • This creates the residue attribute areaSESgxg , solvent-excluded surface areas in the Gly-X-Gly context. (ucsf.edu)
  • In this respect, the study of the adsorption mechanism of plasma proteins on the surface of a human health hazardous material is a key step in the possible understanding of its toxicity and mutagenic properties. (royalsocietypublishing.org)
  • coat protein
  • The 44‐aminoacid, single membrane‐spanning (type III) coat protein of the Pseudomonas aeruginosa phage Pf3 has been studied as a model protein for Sec‐independent membrane translocation (Kuhn et al . (embopress.org)
  • A method is provided for introducing a foreign gene into a plant cell by means of an Olpidium zoospore vector having associated with it a reassembled nucleoprotein complex comprising the foreign gene and reassociated coat protein of a zoospore-transmissable virus. (google.com)
  • antigen
  • The present disclosure provides compositions and methods of use involving binding proteins, e.g., antibodies and antigen-binding fragments thereof, that bind to. (patents.com)
  • Processes in which an antigen antibody or binding protein reaction is used to effect separation of a component of a mixture. (patentgenius.com)
  • subfamilies
  • Specific positions that participate in formation of acylgroup binding subsite were selected as hotspots to rationally design specificity of DAP toward selected substrates by introducing amino acid types observed in other subfamilies. (msu.ru)