scholarly journals Functional analysis of the polar amino acid in TatA transmembrane helix

2021 ◽  
Author(s):  
Binhan Hao ◽  
Wenjie Zhou ◽  
Steven M Theg
Keyword(s):  
Amino Acid ◽  
Potential Role ◽  
Transmembrane Helix ◽  
Amino Acid Side Chain ◽  
Polar Amino Acid ◽  
Twin Arginine Translocation ◽  
N Terminus ◽  
Biochemical Approach ◽  
Folded Proteins ◽  
Highly Correlated

The twin-arginine translocation (Tat) pathway utilizes the proton-motive force (PMF) to transport folded proteins across cytoplasmic membranes in bacteria and archaea, as well as across the thylakoid membrane in plants and the inner membrane in mitochondria. In most species, the minimal components required for Tat activity consist of three subunits, TatA, TatB, and TatC. Previous studies have shown that a polar amino acid is present at the N-terminus of the TatA transmembrane helix (TMH) across many different species. In order to systematically assess the functional importance of this polar amino acid in the TatA TMH in Escherichia coli, a complete set of 19-amino-acid substitutions was examined. Unexpectedly, although being preferred overall, our experiments suggest that the polar amino acid is not necessary for a functional TatA. Hydrophobicity and helix stabilizing properties of this polar amino acid were found to be highly correlated with the Tat activity. Specifically, change in charge status of the amino acid side chain due to pH resulted in a shift in hydrophobicity, which was demonstrated to impact the Tat transport activity. Furthermore, a four-residue motif at the N-terminus of the TatA TMH was identified by sequence alignment. Using a biochemical approach, the N-terminal motif was found to be functionally significant, with evidence indicating a potential role in the preference for utilizing different PMF components. Taken together, these findings yield new insights into the functionality of TatA and its potential role in the Tat transport mechanism.

scholarly journals tRNA acceptor stem and anticodon bases form independent codes related to protein folding

2015 ◽  
Vol 112 (24) ◽  
pp. 7489-7494 ◽  
Author(s):  
Charles W. Carter ◽  
Richard Wolfenden
Keyword(s):  
Amino Acid ◽  
Distribution Coefficient ◽  
Surface Area ◽  
Protein Structures ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Trna Synthetases ◽  
Acceptor Stem ◽  
Binding Domains ◽  
Folded Proteins

Aminoacyl-tRNA synthetases recognize tRNA anticodon and 3′ acceptor stem bases. Synthetase Urzymes acylate cognate tRNAs even without anticodon-binding domains, in keeping with the possibility that acceptor stem recognition preceded anticodon recognition. Representing tRNA identity elements with two bits per base, we show that the anticodon encodes the hydrophobicity of each amino acid side-chain as represented by its water-to-cyclohexane distribution coefficient, and this relationship holds true over the entire temperature range of liquid water. The acceptor stem codes preferentially for the surface area or size of each side-chain, as represented by its vapor-to-cyclohexane distribution coefficient. These orthogonal experimental properties are both necessary to account satisfactorily for the exposed surface area of amino acids in folded proteins. Moreover, the acceptor stem codes correctly for β-branched and carboxylic acid side-chains, whereas the anticodon codes for a wider range of such properties, but not for size or β-branching. These and other results suggest that genetic coding of 3D protein structures evolved in distinct stages, based initially on the size of the amino acid and later on its compatibility with globular folding in water.

scholarly journals The human erythrocyte anion-transport protein. Further amino acid sequence from the integral membrane domain homologous with the murine protein

1986 ◽  
Vol 235 (3) ◽  
pp. 899-901 ◽  
Author(s):  
C J Brock ◽  
M J A Tanner
Keyword(s):  
Amino Acid ◽  
Human Erythrocyte ◽  
Proteolytic Enzymes ◽  
Transmembrane Helix ◽  
Anion Transport ◽  
Transport Protein ◽  
Membrane Domain ◽  
C Terminus ◽  
N Terminus ◽  
Almost All

Sequences from the human erythrocyte anion-transport protein homologous with residues 417-449 and 794-813 of the murine erythrocyte anion-transport protein have been determined. The former sequence includes the putative transmembrane helix closest to the N-terminus of the protein. The latter sequence traverses almost all of the lipid bilayer and is located towards the C-terminus of the protein. Sites have been identified by alignment with the murine sequence in the integral membrane domain that are accessible to proteolytic enzymes. Sequences from the integral membrane domain of the erythrocyte anion-transport protein are highly conserved.

Peptide vaccine against canine parvovirus: identification of two neutralization subsites in the N terminus of VP2 and optimization of the amino acid sequence.

1995 ◽  
Vol 69 (11) ◽  
pp. 7274-7277 ◽  
Author(s):  
J I Casal ◽  
J P Langeveld ◽  
E Cortés ◽  
W W Schaaper ◽  
E van Dijk ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Peptide Vaccine ◽  
Canine Parvovirus ◽  
N Terminus

scholarly journals Specificity of the HIV-1 Protease on Substrates Representing the Cleavage Site in the Proximal Zinc-Finger of HIV-1 Nucleocapsid Protein

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1092
Author(s):  
János András Mótyán ◽  
Márió Miczi ◽  
Stephen Oroszlan ◽  
József Tőzsér
Keyword(s):  
Amino Acid ◽  
Zinc Finger ◽  
Cleavage Site ◽  
Potential Role ◽  
Binding Mode ◽  
Interaction Energies ◽  
Vitro Assay ◽  
Hiv 1

To explore the sequence context-dependent nature of the human immunodeficiency virus type 1 (HIV-1) protease’s specificity and to provide a rationale for viral mutagenesis to study the potential role of the nucleocapsid (NC) processing in HIV-1 replication, synthetic oligopeptide substrates representing the wild-type and modified versions of the proximal cleavage site of HIV-1 NC were assayed as substrates of the HIV-1 protease (PR). The S1′ substrate binding site of HIV-1 PR was studied by an in vitro assay using KIVKCF↓NCGK decapeptides having amino acid substitutions of N17 residue of the cleavage site of the first zinc-finger domain, and in silico calculations were also performed to investigate amino acid preferences of S1′ site. Second site substitutions have also been designed to produce “revertant” substrates and convert a non-hydrolysable sequence (having glycine in place of N17) to a substrate. The specificity constants obtained for peptides containing non-charged P1′ substitutions correlated well with the residue volume, while the correlation with the calculated interaction energies showed the importance of hydrophobicity: interaction energies with polar residues were related to substantially lower specificity constants. Cleavable “revertants” showed one residue shift of cleavage position due to an alternative productive binding mode, and surprisingly, a double cleavage of a substrate was also observed. The results revealed the importance of alternative binding possibilities of substrates into the HIV-1 PR. The introduction of the “revertant” mutations into infectious virus clones may provide further insights into the potential role of NC processing in the early phase of the viral life-cycle.

CLEAVAGE PATHWAY,AND SPECIFICITY OF LEUCOCYTE ELASTASE AS COMPARED TO PLASMIN DURING FIBRINOGEN DEGRADATION

1987 ◽  
Author(s):  
L Goretzki ◽  
E Miller ◽  
A Henschen
Keyword(s):  
Amino Acid ◽  
Time Course ◽  
Proteolytic Enzymes ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecylsulfate ◽  
Reversed Phase ◽  
Cleavage Sites ◽  
Human Fibrinogen ◽  
Leucocyte Elastase ◽  
N Terminus

Plasmin and leucocyte elastase are regarded as the two medically most important fibrin(ogen)-degrading proteolytic enzymes. There is, however, a considerable difference in information available about the cleavage specificities and fragmentation pathways of these two enzymes. Degradation by plasmin has been studied already for a long time in great detail so that now the time course of the degradation, the cleavage sites and the functional properties of many fragments are well known. In contrast, relatively little is known about the degradation by leucocyte elastase, except that the overall cleavage pattern resembles that obtained with plasminIn this investigation the leucocyte elastase-mediated degradation of fibrinogen has been examined by means of proteinchemi-cal methods. Human fibrinogen was incubated with human enzyme material for various periods of time and at some different enzyme concentrations. The split products formed at the various stages were isolated in pure form by gel filtration followed by reversed-phase high-performance liquid chromatography. The fragments were identified by N-terminal amino acid sequence and amino acid composition. The course of the degradation was also monitored by sodium dodecylsulfate-polyacrylamide gel electrophoresis. All cleavage patterns were compared with the corresponding patterns from plasmic degradation. It could be confirmed that X-, D- and E-like fragments are formed also with elastase. However, several early elastolytic Aα-chain fragments are characteristically different from plasmic fragments. The previously identified N-terminal cleavage site in the Aα-chain, i.e. after position 21, was found to be the most important site in this region of fibrinogen. The very early degradation of the Aα-chain N-terminus by elastase is in strong contrast to the stability against plasmin. Several cleavage sites in N-terminal region of the Bβ-chain were observed, though the low amino acid specificity of elastase partly hampered the identification. The γ-chain N-terminus was found to be as highly stable towards elastase as towards plasmin. The results are expected to contribute to the understanding of the role of leucocyte elastase in pathophysiologic fibrino(geno)lysis

scholarly journals Rapid resensitization of ASIC2a is conferred by three amino acid residues in the N-terminus

IBRO Reports ◽  
2019 ◽  
Vol 6 ◽  
pp. S427-S428
Author(s):  
Jae Seung Lee ◽  
Hae-Jin Kweon ◽  
Byung-Chang Suh ◽  
Hyosang Lee
Keyword(s):  
Amino Acid ◽  
Amino Acid Residues ◽  
N Terminus

Amino acid side-chain populations in aqueous and saline solution: Bis-penicillamine enkephalin

Biopolymers ◽  
1992 ◽  
Vol 32 (12) ◽  
pp. 1623-1629 ◽  
Author(s):  
Paul E. Smith ◽  
B. Montgomery Pettitt
Keyword(s):  
Amino Acid ◽  
Saline Solution ◽  
Side Chain ◽  
Amino Acid Side Chain
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