scholarly journals Amphipathic Alpha Helix

2020 ◽  
Author(s):  
Keyword(s):  
Alpha Helix ◽  
Amphipathic Alpha Helix

Sequence of cDNA comprising the human pur gene and sequence-specific single-stranded-DNA-binding properties of the encoded protein

1992 ◽  
Vol 12 (12) ◽  
pp. 5673-5682 ◽  
Author(s):  
A D Bergemann ◽  
Z W Ma ◽  
E M Johnson
Keyword(s):  
Amino Acids ◽  
Alpha Helix ◽  
Element Analysis ◽  
Sequence Element ◽  
Single Stranded Dna ◽  
Reading Frame ◽  
Consensus Motif ◽  
Rich Domain ◽  
Amphipathic Alpha Helix ◽  
Dna Binding Properties

The human Pur factor binds strongly to a sequence element repeated within zones of initiation of DNA replication in several eukaryotic cells. The protein binds preferentially to the purine-rich single strand of this element, PUR. We report here the cloning and sequencing of a cDNA encoding a protein with strong affinity for the PUR element. Analysis with a series of mutated oligonucleotides defines a minimal single-stranded DNA Pur-binding element. The expressed Pur open reading frame encodes a protein of 322 amino acids. This protein, Pur alpha, contains three repeats of a consensus motif of 23 amino acids and two repeats of a second consensus motif of 26 amino acids. Near its carboxy terminus, the protein possesses an amphipathic alpha-helix and a glutamine-rich domain. The repeat region of Pur cDNA is homologous to multiple mRNA species in each of several human cell lines and tissues. The HeLa cDNA library also includes a clone encoding a related gene, Pur beta, containing a version of the 23-amino-acid consensus motif similar, but not identical, to those in Pur alpha. Results indicate a novel type of modular protein with capacity to bind repeated elements in single-stranded DNA.

The Drosophila gene Bearded encodes a novel small protein and shares 3′ UTR sequence motifs with multiple Enhancer of split complex genes

Development ◽  
1997 ◽  
Vol 124 (20) ◽  
pp. 4039-4051 ◽  
Author(s):  
M.W. Leviten ◽  
E.C. Lai ◽  
J.W. Posakony
Keyword(s):  
Sequence Similarity ◽  
Notch Pathway ◽  
Alpha Helix ◽  
Sequence Motifs ◽  
Wild Type ◽  
Gain Of Function ◽  
Small Protein ◽  
Drosophila Gene ◽  
Amphipathic Alpha Helix ◽  
Enhancer Of Split

Gain-of-function alleles of the Drosophila gene Bearded (Brd) cause sensory organ multiplication and loss phenotypes indistinguishable at the cellular level from those caused by loss-of-function mutations in the genes of the Notch pathway (Leviten, M. W. and Posakony, J. W. (1996). Dev. Biol. 176, 264–283). We have carried out a molecular analysis of the structure and expression of both wild-type and mutant Brd transcription units. We find that the Brd transcript is truncated and accumulates to substantially higher levels in the gain-of-function mutants, due to the insertion of a transposable element of the blood family in the Brd 3′ untranslated region (UTR). The wild-type Brd 3′ UTR includes three copies of a 9-nucleotide sequence (CAGCTTTAA) that we refer to as the ‘Brd box’. Moreover, the 3′ UTRs of Brd and of the m4 transcription unit of the Enhancer of split gene complex [E(spl)-C] exhibit an unusually high degree of sequence identity that includes not only Brd box sequences but also a second motif we refer to as the ‘GY box’ (GTCTTCC). We find that both the Brd box and the GY box are also present in the 3′ UTRs of several basic helix-loop-helix repressor-encoding genes of the E(spl)-C, often in multiple copies, suggesting that a novel mode of post-transcriptional regulation applies to Brd and many E(spl)-C genes. The fact that the more abundant Brd mutant mRNA lacks the GY box and two of the Brd boxes present in wild-type Brd mRNA suggests that either or both of these elements may confer instability on transcripts that contain them. Finally, we find that Brd encodes a novel small protein of only 81 amino acids that is predicted to include a basic amphipathic alpha-helix. The deduced Brd protein shows sequence similarity to the E(spl)m4 protein, which is likewise expected to include a basic amphipathic alpha-helix, suggesting that the two proteins have related biochemical functions.

Protein Sequence and Structure of N-terminal Amino Acids of Subunit Delta of Spinach Photosynthetic ATP-Synthase CF1

1987 ◽  
Vol 42 (11-12) ◽  
pp. 1231-1238 ◽  
Author(s):  
Richard J. Berzborn ◽  
Werner Finke ◽  
Joachim Otto ◽  
Helmut E . Meyer
Keyword(s):  
Secondary Structure ◽  
Atp Synthase ◽  
Protein Sequence ◽  
Alpha Helix ◽  
Amino Acid Residues ◽  
E Coli ◽  
Helical Wheel ◽  
Terminal Amino ◽  
Amphipathic Alpha Helix ◽  
Structure Calculations

Chloroplast ATP-synthase (CF1) subunit delta (δ) has been isolated from spinach thylakoids in the presence of SDS. By automated Edman degradation and online analysis of PTH derivatives the 35 N-terminal amino acid residues were sequenced. The mature protein starts with: NH2-Val-Asp-Ser-Thr-Ala-Ser-Arg-Tyr-Ala-. This protein sequence allows alignment of spinach δ with the sequences of Z. mays 25 kDa polypeptide, the δ subunit of Rps. blastica, Rsp. rubrum and E. coli F1, and of bovine OSCP, but not with mitochondrial δ. Secondary structure calculations and helical wheel plots reveal a conserved secondary structure. The analyzed N-terminal sequences probably build a short amphipathic alpha helix with two adjacent turns. The such aligned polar residues around Tyr8 of subunit δ are suitable to channel protons.

scholarly journals Conserved Determinants for Membrane Association of Nonstructural Protein 5A fromHepatitis C Virus and Related Viruses

2006 ◽  
Vol 81 (6) ◽  
pp. 2745-2757 ◽  
Author(s):  
Volker Brass ◽  
Zsuzsanna Pal ◽  
Nicolas Sapay ◽  
Gilbert Deléage ◽  
Hubert E. Blum ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nonstructural Protein ◽  
Alpha Helix ◽  
Laser Scanning Microscopy ◽  
Membrane Association ◽  
Alpha Helices ◽  
Replication Complex ◽  
Diarrhea Virus ◽  
Amphipathic Alpha Helix ◽  
Nonstructural Protein 5A

ABSTRACT Nonstructural protein 5A (NS5A) is a membrane-associated essential component of the hepatitis C virus (HCV) replication complex. An N-terminal amphipathic alpha helix mediates in-plane membrane association of HCV NS5A and at the same time is likely involved in specific protein-protein interactions required for the assembly of a functional replication complex. The aim of this study was to identify the determinants for membrane association of NS5A from the related GB viruses and pestiviruses. Although primary amino acid sequences differed considerably, putative membrane anchor domains with amphipathic features were predicted in the N-terminal domains of NS5A proteins from these viruses. Confocal laser scanning microscopy, as well as membrane flotation analyses, demonstrated that NS5As from GB virus B (GBV-B), GBV-C, and bovine viral diarrhea virus, the prototype pestivirus, display membrane association characteristics very similar to those of HCV NS5A. The N-terminal 27 to 33 amino acid residues of these NS5A proteins were sufficient for membrane association. Circular dichroism analyses confirmed the capacity of these segments to fold into alpha helices upon association with lipid-like molecules. Despite structural conservation, only very limited exchanges with sequences from related viruses were tolerated in the context of functional HCV RNA replication, suggesting virus-specific interactions of these segments. In conclusion, membrane association of NS5A by an N-terminal amphipathic alpha helix is a feature shared by HCV and related members of the family Flaviviridae. This observation points to conserved roles of the N-terminal amphipathic alpha helices of NS5A in replication complex formation.

scholarly journals Fine dissection of a nine amino acid glycoprotein epitope, a major determinant recognized by lymphocytic choriomeningitis virus-specific class I-restricted H-2Db cytotoxic T lymphocytes.

1988 ◽  
Vol 168 (2) ◽  
pp. 559-570 ◽  
Author(s):  
M B Oldstone ◽  
J L Whitton ◽  
H Lewicki ◽  
A Tishon
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Aromatic Amino Acids ◽  
Alpha Helix ◽  
Lymphocytic Choriomeningitis ◽  
Lymphocytic Choriomeningitis Virus ◽  
Specific Class ◽  
Viral Glycoprotein ◽  
Viral Epitope ◽  
Amphipathic Alpha Helix

We define a nine-amino acid (aa) sequence of VAL-GLU-ASN-PRO-GLY-GLY-TYR-CYS-LEU as a major epitope for immunologic recognition of lymphocytic choriomeningitis virus (LCMV) by H-2b-restricted CTL. The epitope was characterized using molecular genetics to bracket broadly and chemistry to precisely identify aa residues 278-286 of the viral glycoprotein. The epitope's composition is characteristic of a reverse (beta turn) but not an amphipathic alpha helix. A series of peptides with a single aa substitution in position 278 of VAL with other nonpolar (hydrophobic) amino acids (LEU, ILE, ALA, or GLY) coat targets that are recognized and lysed by CTL clones recognizing this epitope. In contrast, substitution of VAL with either large aromatic amino acids (that add bulk: PHE, TYR) or polar side chains (SER, THR) segregates CTL clones normally recognizing aa 278-286 into two groups, one that remains lytic (permissive) despite these changes and another that fails to lyse, indicating CTL can discriminate at a single aa. A change in charge at this position (VAL----ASP or GLU), in general, reduces CTL lysis while a change of VAL to LYS or ASN has minimal affect for four of the five CTL clones analyzed. CTL reactivity with the viral epitope is restricted by the Db but not the Kb of the murine MHC haplotype. A 16-aa peptide of Db that spans alpha 1 residues 37-52 blocks CTL lysis, whereas the corresponding Kb peptide that differs from Db in a single aa in position 50 does not.

scholarly journals An Arginine-Faced Amphipathic Alpha Helix Is Required for Adenovirus Type 5 E4orf6 Protein Function

1999 ◽  
Vol 73 (6) ◽  
pp. 4600-4610 ◽  
Author(s):  
Joseph S. Orlando ◽  
David A. Ornelles
Keyword(s):  
Amino Acids ◽  
Nuclear Localization ◽  
Protein Function ◽  
Alpha Helix ◽  
Adenovirus Type ◽  
Wild Type ◽  
Reading Frame ◽  
Α Helix ◽  
Amphipathic Alpha Helix ◽  
Adenovirus Type 5

ABSTRACT A region in the carboxy terminus of the protein encoded by open reading frame 6 in early region 4 (E4orf6) of adenovirus type 5 was determined to be required for directing nuclear localization of the E1B 55-kDa protein and for efficient virus replication. A peptide encompassing this region, corresponding to amino acids 239 through 255 of the E4orf6 protein, was analyzed by circular dichroism spectroscopy. The peptide showed evidence of self-interaction and displayed the characteristic spectra of an amphipathic α helix in the helix-stabilizing solvent trifluoroethanol. Disrupting the integrity of this α helix in the E4orf6 protein by proline substitutions or by removing amino acids 241 through 250 abolished its ability to direct the E1B 55-kDa protein to the nucleus when both proteins were transiently expressed in HeLa cells. Expression of E4orf6 variants that failed to direct nuclear localization of the E1B 55-kDa protein failed to enhance replication of the E4 mutant virus, dl1014, whereas expression of the wild-type E4orf6 protein restored growth of dl1014 to near-wild-type levels. These results suggest that the E4orf6 protein contains an arginine-faced, amphipathic α helix that is critical for a functional interaction with the E1B 55-kDa protein in the cell and for the function of the E4orf6 protein during a lytic infection.

scholarly journals A Putative Amphipathic Alpha Helix in Hepatitis B Virus Small Envelope Protein Plays a Critical Role in the Morphogenesis of Subviral Particles

2021 ◽  
Vol 95 (8) ◽  
Author(s):  
Sisi Yang ◽  
Zhongliang Shen ◽  
Yaoyue Kang ◽  
Liren Sun ◽  
Usha Viswanathan ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Envelope Protein ◽  
Alpha Helix ◽  
Hbv Infection ◽  
20S Proteasome ◽  
S Protein ◽  
B Virus ◽  
Amphipathic Alpha Helix ◽  
Subviral Particles

ABSTRACT Hepatitis B virus (HBV) small (S) envelope protein has the intrinsic ability to direct the formation of small spherical subviral particles (SVPs) in eukaryotic cells. However, the molecular mechanism underlying the morphogenesis of SVPs from the monomeric S protein initially synthesized at the endoplasmic reticulum (ER) membrane remains largely elusive. Structure prediction and extensive mutagenesis analysis suggested that the amino acid residues spanning W156 to R169 of S protein form an amphipathic alpha helix and play essential roles in SVP production and S protein metabolic stability. Further biochemical analyses showed that the putative amphipathic alpha helix was not required for the disulfide-linked S protein oligomerization but was essential for SVP morphogenesis. Pharmacological disruption of vesicle trafficking between the ER and Golgi complex in SVP-producing cells supported the hypothesis that S protein-directed SVP morphogenesis takes place at the ER-Golgi intermediate compartment (ERGIC). Moreover, it was demonstrated that S protein is degraded in hepatocytes via a 20S proteasome-dependent but ubiquitination-independent nonclassic ER-associated degradation pathway. Taken together, the results reported here favor a model in which the amphipathic alpha helix at the antigenic loop of S protein attaches to the lumen leaflet to facilitate SVP budding from the ERGIC, whereas the failure of the budding process may result in S protein degradation by 20S proteasome in a ubiquitination-independent manner. IMPORTANCE SVPs are the predominant viral product produced by HBV-infected hepatocytes. Their levels exceed those of virion particles by 10,000- to 100,000-fold in the blood of HBV-infected individuals. The high levels of SVPs, or HBV surface antigen (HBsAg), in the circulation induce immune tolerance and contribute to the establishment of persistent HBV infection. The loss of HBsAg, often accompanied by the appearance of anti-HBsAg antibodies, is the hallmark of durable immune control of HBV infection. Therapeutic induction of HBsAg loss is thus considered to be essential for the restoration of the host antiviral immune response and functional cure of chronic hepatitis B. Our findings on the mechanism of SVP morphogenesis and S protein metabolism will facilitate the rational discovery and development of antiviral drugs to achieve this therapeutic goal.

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