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  • Superfamily
  • The Major Facilitator Superfamily (MFS), the largest family of secondary transport proteins, catalyzes transport of a wide range of substrates. (pnas.org)
  • This information is exceptionally difficult to obtain with the Major Facilitator Superfamily (MFS) because of the broad sequence diversity of the members. (pnas.org)
  • The exceptionally diverse Major Facilitator Superfamily (MFS) includes over 10,000 sequenced members and is comprised of 74 families with members from Archaea to Homo sapiens ( 1 ⇓ - 3 ). (pnas.org)
  • Probst WC, Snyder LA, Schuster DI, Brosius J, Sealfon SC (1992) Sequence alignment of the G protein-coupled receptor superfamily. (springer.com)
  • However, budding yeast PDAT and its relatives in fission yeast and Arabidopsis form a distinct branch within this protein superfamily, indicating that a separate PDAT enzyme arose at an early point in evolution. (pnas.org)
  • This small (77 amino acid) glycoprotein is a member of the Ly6 superfamily of proteins and is important in protecting host cells from the lytic and proinflammatory activity of the MAC. (nih.gov)
  • CD59 belongs to the Ly6 superfamily of proteins which includes functional CD59 analogues from other species, snake venom neurotoxins, urokinase-type plasminogen activator receptor and murine Ly6 differentiation antigens (17). (nih.gov)
  • substrate
  • One fundamentally important problem for understanding the mechanism of coupling between substrate and H + translocation with secondary active transport proteins is the identification and physical localization of residues involved in substrate and H + binding. (pnas.org)
  • MFS proteins catalyze transport of a wide range of substrates, including amines, acids, amino acids, sugars, peptides, and antibiotics, in many instances by transducing the energy stored in an H + electrochemical gradient (∆ µ ̃ H + , interior negative and/or alkaline) into a concentration gradient of substrate by substrate/H + symport mechanisms ( 4 ). (pnas.org)
  • In this study, we investigated ( i ) which sequences in a polypeptide are recognized by TF, ( ii ) whether substrate binding depends on the presence of prolyl residues, and ( iii ) which domains of TF contribute to substrate specificity and substrate binding. (pnas.org)
  • Predicting
  • The main reasons that predicting protein structure from sequence alone is so difficult, is that the possible ways the amino acids can twist and turn with respect to each other are enormous. (biomedcentral.com)
  • In addition, currently available web servers and software tools for predicting RNA-binding sites, as well as databases that contain valuable information about known protein-RNA complexes, RNA-binding motifs in proteins, and protein-binding recognition sites in RNA are provided. (iastate.edu)
  • extracellular
  • Chemokines exhibit affinity for seven transmembrane-spanning G protein-coupled signaling receptors and extracellular matrix or cell-bound glycosaminoglycans (GAGs). (rupress.org)
  • Despite detailed knowledge about some of the extracellular proteins and several surface-associated components identified in P. aeruginosa , many virulence factors essential for pathogenicity and the mechanisms by which they coordinately function during pathogenesis remain to be elucidated. (pnas.org)
  • Mutations
  • We constructed intra-protein network graphs to discriminate the global conformational changes induced by mutations. (springer.com)
  • Additionally, these mutations lead to compact ICL3 region compared to the wild type, indicating that the receptor would be inaccessible for G protein coupling. (springer.com)
  • If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. (wikipedia.org)
  • clusters
  • Additionally, we find evidence that extensive gene conversion contributes to the maintenance of sequence identity within chromosome-level clusters of MSP genes. (g3journal.org)
  • motifs
  • This protein forms a heterodimeric complex and binds and activates, in a glucose-dependent manner, carbohydrate response element (ChoRE) motifs in the promoters of triglyceride synthesis genes. (genetex.com)
  • substitution
  • Residue burial is confirmed by ensuring that substitution of the residue by Asp leads to protein inactivation. (pnas.org)
  • At such sites, a Ts phenotype can typically be generated either by ( i ) substitution of two predicted, buried residues with the 18 remaining amino acids or ( ii ) introduction of Lys, Ser, Ala, and Trp at three to four predicted buried sites. (pnas.org)
  • genes
  • This unusual evolutionary pattern is likely generated by strong pleiotropic constraints acting on these genes at the sequence level, balanced against expansion at the level of the whole gene family. (g3journal.org)
  • Such Ts mutants of Gal4 can be used for conditional expression of a variety of genes by using the well characterized upstream-activating-sequence-Gal4 system. (pnas.org)
  • yeast
  • The rules were further verified by making several Ts mutants of yeast Gal4 at residues 68, 69, and 70. (pnas.org)
  • conservation
  • Difficulty discerning underlying mechanistic principles is due to low sequence conservation. (pnas.org)
  • Rodriguez-Rivas J, Marsili S, Juan D, Valencia A (2016) Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone. (springer.com)
  • mutants
  • No Ts mutants of either protein have been previously reported. (pnas.org)
  • Ts mutants provide an extremely powerful tool for studying protein function and assembly in vivo and in cell culture ( 1 - 4 ). (pnas.org)
  • The logic was that at least one of this small set of mutants would destabilize the protein to exactly the appropriate extent to generate a Ts phenotype. (pnas.org)
  • It should be noted that the method does not attempt to predict either all buried residues or all possible Ts mutants. (pnas.org)
  • Ts mutants can be produced at noncore residues and at surface positions that may be important for folding, proteolytic sensitivity, or interaction with other proteins. (pnas.org)
  • complexes
  • Recent technical advances have led to several high-throughput experimental methods for identifying partners in protein-RNA complexes, but determining RNA-binding residues in proteins is still expensive and time-consuming. (iastate.edu)
  • Hopf TA, Schärfe CPI, Rodrigues JPGLM et al (2014) Sequence co-evolution gives 3D contacts and structures of protein complexes. (springer.com)
  • segments
  • Secondly, the dihedral angles of residues in coil segments are very flexible and they do not show any simple recurrent pattern like those in helices and sheets. (biomedcentral.com)
  • important
  • Chemokines are a family of small secreted proteins that activate and attract leukocytes during inflammation, but also play an important role in normal leukocyte trafficking, including lymphocyte homing. (rupress.org)
  • typically
  • The hydrophobic moment is a vectorial sum of hydrophobicities calculated over a nine-residue window, with a phase angle optimized for detection of amphiphilic helical structures, which typically would not have a high average hydrophobicity. (pnas.org)
  • Computational
  • This chapter focuses on available computational methods for identifying which amino acids in an RNA-binding protein participate directly in contacting RNA. (iastate.edu)
  • experiments
  • Using iTRAQ and ICAT technology, we can undertake a variety of MS experiments, including the study of differential protein expression levels in normal and disease states. (utsouthwestern.edu)
  • methods
  • The DNA sequence encoding steroid 5α-reductase 2, the major active isozyme of human genital tissue, is disclosed herein, in addition to methods and compositions for its preparation and pharmacological analysis. (google.co.uk)
  • de Juan D, Pazos F, Valencia A (2013) Emerging methods in protein co-evolution. (springer.com)
  • membrane
  • Binding to membrane-coupled peptides occurred through the central peptidyl-prolyl- cis / trans isomerase (PPIase) domain of TF, however, independently of prolyl residues. (pnas.org)
  • We demonstrate that the MvfR protein is membrane-associated and acts as a transcriptional activator until cells reach stationary phase, when a unique negative feedback mechanism is activated to signal the down-regulation of the MvfR protein. (pnas.org)
  • catalyzes
  • The encoded PDAT protein is related to lecithin:cholesterol acyltransferase, which catalyzes the acyl-CoA-independent synthesis of cholesterol esters. (pnas.org)