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Order Nodamuvirales
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
Next, the great Annette Schneemann and her team demonstrated that the display of fragments from the influenza virus hemagglutinin (HA) stem region on the insect-cells produced FHV VLPs resulted in the induction of cross-reactive anti-HA antibodies (Schneemann et al. 2012). The 20-aa residue A-helix of the HA2 chain was selected as an epitope and displayed in 180 copies on the chimeric FHV VLPs. Figure 23.5 illustrates the structural outcome of this delicate structural design. As shown, the structure of helix-turn-helix protein B2 (PDB 2AZ2 and 2AZ0) was spliced first into the structure of the FHV capsid subunit in place of the 206 or 264 loops. The residues near the B2 termini in the best locations to start and end the inserts (i.e., unstructured polypeptide) while maintaining exposure and structure of the B2 helical segments were identified. To display the antigenic helix identified in the structures of the antibody CR6261-HA complexes (PDB 3GBN and 3GBM) (Ekiert et al. 2009), a portion of the long helix in B2 (residues 40–59) was then replaced with the HA2 A-helix (residues 39–58) from the human 1918 H1N1 pandemic virus (A/South Carolina/1/1918, PDB 3GBN). The A-helix was specifically oriented within the B2 helical turns so that residues in contact with the CR6261 antibody had maximum solvent exposure on the surface.
Regulation of Cell Functions
Published in Enrique Pimentel, Handbook of Growth Factors, 2017
Homeobox-containing genes (homeotic genes or Hox genes) have an essential role in the regulation of developmental processes by morphogens and growth factors.114-120 The homeobox is a sequence of 183 bp that was originally discovered in genes associated with homeotic mutations (i.e., changes in segment identity leading to transformation of one body structure into another) in the fruit fly, Drosophila melanogaster. Homeotic genes are activated in a defined spatial and temporal sequence during the process of developmental segmentation of the insect. Homeobox-containing genes are present in vertebrates, including humans.121 No less than 30 homeobox-containing genes have been identified in the human genome.122-124 Human homeotic genes are distributed in four main clusters, termed HOX1 to HOX4, which reside on different human chromosomes: HOX1 includes 8 homeoboxes in 90 kb of DNA on chromosome 7, HOX1 includes 9 homeoboxes in 180 kb of DNA on chromosome 17, HOX3 contains at least 7 homeoboxes in 160 kb of DNA on chromosome 12, and HOX4 includes 6 homeoboxes in 70 kb of DNA on chromosome 2. The homeobox encodes a 61-amino acid helix-turn-helix (HTH) protein structure that binds DNA with sequence specificity. Homeobox proteins may function as transcription factors involved in the regulation of gene expression; however, the identity of target genes regulated by homeobox proteins is almost unknown.
The Cell and Cell Division
Published in Anthony R. Mundy, John M. Fitzpatrick, David E. Neal, Nicholas J. R. George, The Scientific Basis of Urology, 2010
Following histone acetylation, various proteins bind to the promoter regions of genes to act as promoters and repressors. These can be classified into the following types: Helix-turn-helix proteins. These solely comprise amino acids and have a structure that facilitates binding into the major groove of DNA—their binding may block transcription or, conversely, may force bending of the DNA molecule facilitating transcription. The homeo-domain proteins are a type of helix-turn-helix protein involved in sequential embryonic development. Each of these homeo-domain proteins contains an identical section of 60 amino acids.Zinc finger proteins. Some transcription factors are rich in histidine and cysteine residues, which can bind zinc, thereby bending the protein into a finger-like shape. Steroid hormone receptors also contain several zinc fingers and are thought to function as transcription factors.Proteins with a leucine zipper motif. Certain a protein chains can form Y-shaped dimmers, which can attach to DNA; the two chains are held together by interactions between hydrophobic regions that are rich in leucine.Helix-loop-helix proteins. These form structures similar to leucine zippers.
MlrA, a MerR family regulator in Vibrio cholerae, senses the anaerobic signal in the small intestine of the host to promote bacterial intestinal colonization
Published in Gut Microbes, 2022
Jialin Wu, Yutao Liu, Wendi Li, Fan Li, Ruiying Liu, Hao Sun, Jingliang Qin, Xiaohui Feng, Di Huang, Bin Liu
Homologs of MerR family regulators were screened for in the genome of V. cholerae EL2382, the 7th pandemic strain.33 Five genes were annotated as MerR family regulators: vca0056 (mlrA), vca0084 (soxR), vca0264 (merR1), vc0277 (zntR), and vc0974 (cueR). Domain structure analysis of these regulators revealed that all five proteins contain an N-terminal DNA-binding helix-turn-helix (HTH) motif (Figure 1a). C-terminal domain structure analysis showed that VC0277 and VC0974 contain a metal-binding site, VCA0084 contains a [2Fe-2S] cluster-binding site, and VCA0264 contains a methyltransferase domain. No predicted domains were found in VCA0056 (MlrA). This suggests that these five MerR family regulators may have different functions and perform different roles in V. cholerae virulence.
Design of α-helical antimicrobial peptides with a high selectivity index
Published in Expert Opinion on Drug Discovery, 2019
SPLIT [77] or HeliQuest tool [78] with a short sliding window enable quick perusal of top peptides from Table 1 in order to see how hydrophobic moment (HM) changes alongside sequence. This HM-scanning technique illustrated that due to central glycine or glycines each of eight best AMPs has a similar profile for the hydrophobic moment with a central minimum and less than perfect amphipathicity. These peptides can form a helix-turn-helix structure with one or more beta-turns near sequence middle. Partially helical peptides with low or imperfect amphipathicity may have low HM, low MIC and low hemolytic activity at the same time [58,79].