Alpha-periodicity analysis of small multidrug resistance (SMR) efflux transporters

1998 ◽  
Vol 76 (5) ◽  
pp. 791-797 ◽  
Author(s):  
Robert A Edwards ◽  
Raymond J Turner
Keyword(s):  
Amino Acids ◽  
Multidrug Resistance ◽  
Transmembrane Helix ◽  
Power Spectra ◽  
Substitution Matrix ◽  
Transmembrane Helices ◽  
Homologous Proteins ◽  
Small Multidrug Resistance ◽  
Amino Acid Properties ◽  
Periodicity Analysis

Proteins in the small multidrug resistance (SMR) family of transport proteins are about 110 amino acids in length and are predicted to have four transmembrane helices. This family is divided into a two groups, one of which we have referred to as small multidrug pumps (Smp) and confer resistance to a wide variety of quaternary ammonium compounds through a proton-drug efflux antiport mechanism. Members of the second group within this family have, as yet, not had their substrate profile characterized and are referred to as Sug proteins. Alpha-periodicity analysis was conducted on a set of six homologous proteins of the SMR family consisting of three established Smp and three Sug proteins. Several amino acid properties were used in the analysis including hydropathy, variability, and a substitution matrix for lipid exposed amino acids. The scanning window was varied between 8 and 14 residues and the alpha-periodicity was calculated from the peaks in the Fourier transform power spectra in the region between 3.0 and 4.3 residues/turn. This analysis adds to the hydropathy analysis to give a more confident prediction of which residues are within the lipid bilayer for each of the four transmembrane helices. Information was also obtained that allowed for the identification of zones within each transmembrane helix that face the interior of the helical bundle on one side and are lipid exposed on the other face.Key words: modeling, SMR, QAC, multidrug resistance, transporter, hydrophopathy, periodicity, amphipathicity.

scholarly journals Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 555
Author(s):  
Emily L. Gordon ◽  
Rebecca T. Kimball ◽  
Edward L. Braun
Keyword(s):  
Amino Acids ◽  
Protein Structure ◽  
Amino Acid ◽  
Bird Species ◽  
Data Type ◽  
Substitution Matrix ◽  
Sequence Evolution ◽  
Transmembrane Helices ◽  
Encoded Proteins ◽  
The Impact

Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acid exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution matrix for transmembrane helices estimated using a variety of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa.

scholarly journals Oligomerization of the antimalarial drug target PfATP4 is essential for parasite survival

2019 ◽  
Author(s):  
Aarti A. Ramanathan ◽  
Joanne M. Morrisey ◽  
Thomas M. Daly ◽  
Lawrence W. Bergman ◽  
Michael W. Mather ◽  
...  
Keyword(s):  
Amino Acids ◽  
Plasmodium Falciparum ◽  
Antimalarial Drug ◽  
Efflux Pump ◽  
Transmembrane Helix ◽  
Aromatic Amino Acids ◽  
Transmembrane Helices ◽  
Parasite Survival ◽  
Oligomeric Complex ◽  
P Type

AbstractPlasmodium falciparum P-type ATPase (PfATP4) is a Na+ efflux pump crucial for maintaining low [Na+]i in malaria parasites during their intraerythrocytic development cycle. In recent years, multiple studies have shown PfATP4 to be the target of a large number of chemical scaffolds, including current candidate antimalarials KAE609 and SJ733. Here we show that PfATP4 exists as a large complex. Immunopurification and proteomic studies revealed the complex to be homooligomeric in nature. The complex appears to be assembled co-translationally. Phylogenetic analysis suggests that ATP4 from apicomplexans and chromerids form a distinct class of P-type ATPases having fewer transmembrane helices compared to their orthologues. We hypothesized that reduction of transmembrane helices in PfATP4 might necessitate oligomerization to maintain its function. We further suspected potential involvement of π-π interactions between aromatic amino acids within the terminal transmembrane helix of each monomer to be critical for oligomerization. To test this hypothesis, we mutated three aromatic amino acids in the last transmembrane helix of PfATP4. Wildtype and the mutated PfATP4 genes were introduced at an ectopic locus in a P. falciparum line, in which endogenous PfATP4 was conditionally expressed. Whereas the wildtype copy of PfATP4 expressed from the ectopic locus was able to form the oligomeric complex, the mutant PfATP4 failed to do so. Strikingly, unlike the wildtype, the mutant PfATP4 failed to functionally complement the knockdown of the endogenous gene, leading to parasite demise. These results strongly suggest that co-translational oligomerization of PfATP4 is essential for its function and for parasite survival.Significance StatementPlasmodium falciparum ATP4 (PfATP4) is a Na+ efflux pump and is the target of at least two antimalarial drug candidates (KAE609, SJ733) currently in clinical trials. With a rapid parasite clearance rate (t99=12h) in initial clinical studies, PfATP4-active drugs present the prospect of taking us a step closer to malaria elimination in a world that is currently threatened by artemisinin resistance. In this study, we have established that PfATP4 exists as a homo-oligomeric complex, which is assembled co-translationally through interactions facilitated by aromatic amino acids in its last transmembrane helix. Crucially, its existence as a complex is essential for its function. This exposes a vulnerability in the target that could be potentially exploited for drug design.

scholarly journals Small Residues Inhibit Homo-Dimerization of the Human Carbonic Anhydrase XII Transmembrane Domain

Membranes ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 512
Author(s):  
Florian Cymer ◽  
Dirk Schneider
Keyword(s):  
Amino Acids ◽  
Transmembrane Domain ◽  
Biological Membrane ◽  
Transmembrane Helix ◽  
Accessible Surface Area ◽  
Side Chains ◽  
Carbonic Anhydrases ◽  
Transmembrane Helices ◽  
Accessible Surface ◽  
Small Side

Amino acids with small side chains and motifs of small residues in a distance of four are rather abundant in human single-span transmembrane helices. While interaction of such helices appears to be common, the role of the small residues in mediating and/or stabilizing transmembrane helix oligomers remains mostly elusive. Yet, the mere existence of (small)xxx(small) motifs in transmembrane helices is frequently used to model dimeric TM helix structures. The single transmembrane helix of the human carbonic anhydrases XII contains a large number of amino acids with small side chains, and critical involvement of these small amino acids in dimerization of the transmembrane domain has been suggested. Using the GALLEX assay, we show here that the transmembrane domain indeed forms a strong transmembrane helix oligomer within a biological membrane. However, single or multiple mutations of small residue(s) to isoleucine almost always increased, rather than decreased, the interaction propensities. Reduction of helix flexibility and of protein–lipid contacts caused by a reduced lipid accessible surface area likely results in stabilization of helix–helix interactions within the membrane.

scholarly journals Few Conserved Amino Acids in the Small Multidrug Resistance Transporter EmrE Influence Drug Polyselectivity

2018 ◽  
Vol 62 (8) ◽  
Author(s):  
Marwah Saleh ◽  
Denice C. Bay ◽  
Raymond J. Turner
Keyword(s):  
Amino Acids ◽  
Multidrug Resistance ◽  
Drug Binding ◽  
Conserved Residues ◽  
Content Type ◽  
Small Multidrug Resistance ◽  
Transporter Family ◽  
Wide Range ◽  
Multidrug Resistance Transporter ◽  
Conserved Amino Acids

ABSTRACT EmrE is the archetypical member of the small multidrug resistance transporter family and confers resistance to a wide range of disinfectants and dyes known as quaternary cation compounds (QCCs). The aim of this study was to examine which conserved amino acids play an important role in substrate selectivity. On the basis of a previous analysis of EmrE homologues, a total of 33 conserved residues were targeted for cysteine or alanine replacement within E. coli EmrE. The antimicrobial resistance of each EmrE variant expressed in Escherichia coli strain JW0451 (lacking dominant pump acrB) to a collection of 16 different QCCs was tested using agar spot dilution plating to determine MIC values. The results determined that only a few conserved residues were drug polyselective, based on ≥4-fold decreases in MIC values: the active-site residue E14 (E14D and E14A) and 4 additional conserved residues (A10C, F44C, L47C, W63A). EmrE variants I11C, V15C, P32C, I62C, L93C, and S105C enhanced resistance to polyaromatic QCCs, while the remaining EmrE variants reduced resistance to one or more QCCs with shared chemical features: acylation, tri- and tetraphenylation, aromaticity, and dicationic charge. Mapping of EmrE variants onto transmembrane helical wheel projections using the highest resolved EmrE structure suggests that polyselective EmrE variants were located closest to the helical faces surrounding the predicted drug binding pocket, while EmrE variants with greater drug specificity mapped onto distal helical faces. This study reveals that few conserved residues are essential for drug polyselectivity and indicates that aromatic QCC selection involves a greater portion of conserved residues than that in other QCCs.

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