PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments

Caffrey, Daniel R.; Dana, Paul H; Mathur, Vidhya; Ocano, Marco; Hong, Eun-Jong; Wang, Yaoyu E.; Somaroo, Shyamal; Caffrey, Brian E.; Potluri, Shobha; Huang, Enoch S.

doi:10.1186/1471-2105-8-381

Cited by 65 publications

(49 citation statements)

References 20 publications

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“…The resulting protein alignment was used for subsequent analysis using Jalview (Waterhouse et al, 2009) and for phylogenetic analyses. A protein identity matrix was calculated from the alignment using the PFAAT program (Caffrey et al, 2007).…”

Section: Methodsmentioning

confidence: 99%

Genomics and Localization of the Arabidopsis DHHC-Cysteine-Rich Domain S-Acyltransferase Protein Family

Batistič

2012

Plant Physiology

128

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Protein lipid modification of cysteine residues, referred to as S-palmitoylation or S-acylation, is an important secondary and reversible modification that regulates membrane association, trafficking, and function of target proteins. This enzymatic reaction is mediated by protein S-acyl transferases (PATs). Here, the phylogeny, genomic organization, protein topology, expression, and localization pattern of the 24 PAT family members from Arabidopsis (Arabidopsis thaliana) is described. Most PATs are expressed at ubiquitous levels and tissues throughout the development, while few genes are expressed especially during flower development preferentially in pollen and stamen. The proteins display large sequence and structural variations but exhibit a common protein topology that is preserved in PATs from various organisms. Arabidopsis PAT proteins display a complex targeting pattern and were detected at the endoplasmic reticulum, Golgi, endosomal compartments, and the vacuolar membrane. However, most proteins were targeted to the plasma membrane. This large concentration of plant PAT activity to the plasma membrane suggests that the plant cellular S-acylation machinery is functionally different compared with that of yeast (Saccharomyces cerevisiae) and mammalians.

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Section: Methodsmentioning

confidence: 99%

Genomics and Localization of the Arabidopsis DHHC-Cysteine-Rich Domain S-Acyltransferase Protein Family

Batistič

2012

Plant Physiology

128

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“…Modeling of Indinavir Binding to GLUT4-GLUT4 models are based on sequence alignments with major facilitator superfamily transporters XylE (Protein Data Bank code 4GBZ) for the outward open conformation and Staphylococcus epidermidis glucose/H ϩ symporter (Protein Data Bank code 4LDS) for the inward open conformation using Clustal⍀ (21) and PFAAT (22). A homology model of the TM helices was done using Molecular Operating Environment (MOE 2013.08) (Chemical Computing Group Inc., Montreal, Canada).…”

Section: Isolation Of Myc-glut-his Proteins and Quantification Of Thementioning

confidence: 99%

Isoform-selective Inhibition of Facilitative Glucose Transporters

Hresko¹,

Kraft²,

Tzekov³

et al. 2014

Journal of Biological Chemistry

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“…A structure with the lowest MODELLER's target energy function was chosen as the final model. A multiple alignment of the L. stagnalis AChBP protein sequence with sequences of H. sapiens GABA C (q1, q2), GABA A (a1, b2, c2), glycine receptor (a1, b), and T. marmorata nAChR (a, b, c, d) was obtained using CLUSTALW, 51 followed by a manual adjustment with PFAAT program 52 (Fig. 2).…”

Section: Determination Of Evolutionary Selection Pressurementioning

confidence: 99%

Structural model of ρ1 GABA_C receptor based on evolutionary analysis: Testing of predicted protein–protein interactions involved in receptor assembly and function

et al. 2009

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The homopentameric q1 GABA C receptor is a ligand-gated ion channel with a binding pocket for c-aminobutyric acid (GABA) at the interfaces of N-terminal extracellular domains. We combined evolutionary analysis, structural modeling, and experimental testing to study determinants of GABA C receptor assembly and channel gating. We estimated the posterior probability of selection pressure at amino acid residue sites measured as x-values and built a comparative structural model, which identified several polar residues under strong selection pressure at the subunit interfaces that may form intersubunit hydrogen bonds or salt bridges. At three selected sites (R111, T151, and E55), mutations disrupting intersubunit interactions had strong effects on receptor folding, assembly, and function. We next examined the role of a predicted intersubunit salt bridge for residue pair R158-D204. The mutant R158D, where the positively charged residue is replaced by a negatively charged aspartate, yielded a partially degraded receptor and lacked membrane surface expression. The membrane surface expression was rescued by the double mutant R158D-D204R, where positive and negative charges are switched, although the mutant receptor was inactive. The single mutants R158A, D204R, and D204A exhibited diminished activities and altered kinetic profiles with fast recovery kinetics, suggesting that R158-D204 salt bridge perhaps stabilizes the open state of the GABA C receptor. Our results emphasize the functional importance of highly conserved polar residues at the proteinprotein interfaces in GABA C q1 receptors and demonstrate how the integration of computational and experimental approaches can aid discovery of functionally important interactions.

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PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments

Cited by 65 publications

References 20 publications

Genomics and Localization of the Arabidopsis DHHC-Cysteine-Rich Domain S-Acyltransferase Protein Family

Genomics and Localization of the Arabidopsis DHHC-Cysteine-Rich Domain S-Acyltransferase Protein Family

Isoform-selective Inhibition of Facilitative Glucose Transporters

Structural model of ρ1 GABA_C receptor based on evolutionary analysis: Testing of predicted protein–protein interactions involved in receptor assembly and function

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PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments

Cited by 65 publications

References 20 publications

Genomics and Localization of the Arabidopsis DHHC-Cysteine-Rich Domain S-Acyltransferase Protein Family

Genomics and Localization of the Arabidopsis DHHC-Cysteine-Rich Domain S-Acyltransferase Protein Family

Isoform-selective Inhibition of Facilitative Glucose Transporters

Structural model of ρ1 GABAC receptor based on evolutionary analysis: Testing of predicted protein–protein interactions involved in receptor assembly and function

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Structural model of ρ1 GABA_C receptor based on evolutionary analysis: Testing of predicted protein–protein interactions involved in receptor assembly and function