Amino acid sequence analysis

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Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.: species‟ sequence - structure relationship

Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.: species‟ sequence - structure relationship

1. Introduction The knowledge of three dimensional structures of proteins gives valuable insights into their functions. Prediction of different features of protein structure like secondary structures (Jones, 1999; Madera et al., 2010; Pollastri et al., 2002), protein disorder (Madera et al., 2010; Xue et al., 2010), transmembrane regions (Illergard et al., 2010; Pylouster et al., 2010), phosphorylation sites (Biswas et al., 2010), protein flexibility (Bornot et al., 2011) or the generation of structural models (de Brevern, 2010; Kelley and Sternberg, 2009), are mainly based on machine learning algorithms (Brylinski and Skolnick, 2008; Rangwala et al., 2009; Xu et al., 2008). Protein structure analyses and prediction methods derive information from non-redundant databanks that represent the state-of-the-art of available data (i.e., solved protein structures). In a way, they reflect a generic („expected‟) distribution of amino acid sequence – protein structure (AAS-PS) relationship. Though the term “protein sequence- structure relationships” have been used extensively in literature, to avoid confusion with a few discussions on genomic data and to add clarity, we use the abbreviation AAS-PS here.
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Species specific amino acid sequence - Protein local structure relationships: An analysis in the light of a structural alphabet

Species specific amino acid sequence - Protein local structure relationships: An analysis in the light of a structural alphabet

shows that Pf is quite far from the other species, and also from the expected view of AAS-PS (NR, see Supplementary material 5). The last remark is promising indeed. The extensive genetic diversity of blood stage antigens is one of the key challenges for vaccine development against malaria. A recent approach proposed for antigen discovery is based on the bioinformatic selection of heptad repeat motifs corresponding to α-helical coiled coil structures (Kulangara et al., 2009). Considering the fact that the AAS-PS seen in Pf is diverged when compared to the expected / observed values (NR), such approaches could be refined or improved. For At, the differences with respect to the expected amino acid distributions are mainly due to new amino acids preferences (52), coupled with the absence of certain amino acid preferences observed in NR (15), some inversions of preferences are also observed (6). Indeed, this can be considered as a specialization unique for the species. This ratio of significant new and missing amino acid preferences is about 3.47 for At, whereas this is not the case for Pf where the ratio is only 0.59.
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Amino acid supplementation decreases plasma and liver triacylglycerols in elderly

Amino acid supplementation decreases plasma and liver triacylglycerols in elderly

Magnetic Resonance Spectroscopy (MRS) Every 8 th week, the intramuscular lipid concentration of m. soleus was measured with a 1 H knee coil on a GE Advantage 1.5 Tesla whole-body imager (General Electric, Milwaukee, WI), as previously described [16]. The widest part of the calf was located during the first study, and measured from the floor and marked. A marker was placed at the location during the scan, and this slice of leg was always used for scans. Four areas were selected from the coronal slice localizer and were traced onto a transparency along with multiple anatomic landmarks. These four areas were then rescanned during each subsequent MRS analysis. A tube of 20% Intralipid (i.v. high-fat total parenteral feeding solution; Baxter Healthcare, Deerfield Park, IL) was placed inside the knee coil to obtain a standard external reference [23]. After a preliminary localization image, three to seven voxels (~7 mm × 7 mm × 10 mm each) were chosen in m. soleus free from fascia, gross fat marbling, and vessels. The exact voxel volumes were recorded. A voxel was also chosen from the Intralipid external reference. An optimized PRESS (Point RESolved Spectroscopy) sequence with a repetition time of 2000 ms and an echo time of 35 ms was run. Peak positions and areas of interest [extramuscular (CH 2 ) n , intramuscular
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The Dawn of the Age of Amino Acid Sensors for the mTORC1 Pathway

The Dawn of the Age of Amino Acid Sensors for the mTORC1 Pathway

hypothesize that dSestrin could act, at least under certain situations, as a methionine sensor in this organism. Conservation of the amino acid sensors across evolution Study of the nutrient sensing pathway revealed that some of its components were conserved in many eukaryotes (Figure S1). Components of mTORC1, such as TOR itself and raptor, are conserved throughout all eukaryotes, including plants (Figure 3). Much of the rest of the core machinery of the pathway, such as the Rag GTPases, or components that control the nucleotide loading state of the Rags (like GATOR1), are conserved through fungi (Figures 3–4). Additionally, GATOR2, a complex of unknown function that acts upstream or parallel to GATOR1, has a relatively similar pattern of conservation as GATOR1 (Figure S1). Two components of Ragulator that lack homologues by sequence were recently found to have structural homologues in yeast (Kogan et al., 2010; Zhang et al., 2012). Similarly, structural homologues that were not uncovered by sequence analysis alone allowed for the
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Conserved amino acid networks modulate discrete functional properties in an enzyme superfamily

Conserved amino acid networks modulate discrete functional properties in an enzyme superfamily

Chitra Narayanan 1 , Donald Gagné 1,5 , Kimberly A. Reynolds 2 & Nicolas Doucet 1,3,4 In this work, we applied the sequence-based statistical coupling analysis approach to characterize conserved amino acid networks important for biochemical function in the pancreatic-type ribonuclease (ptRNase) superfamily. This superfamily-wide analysis indicates a decomposition of the RNase tertiary structure into spatially distributed yet physically connected networks of co-evolving amino acids, termed sectors. Comparison of this statistics-based description with new NMR experiments data shows that discrete amino acid networks, termed sectors, control the tuning of distinct functional properties in different enzyme homologs. Further, experimental characterization of evolutionarily distant sequences reveals that sequence variation at sector positions can distinguish homologs with a conserved dynamic pattern and optimal catalytic activity from those with altered dynamics and diminished catalytic activities. Taken together, these results provide important insights into the mechanistic design of the ptRNase superfamily, and presents a structural basis for evolutionary tuning of function in functionally diverse enzyme homologs.
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Specificity of amino acid regulated gene expression: Analysis of genes subjected to either complete or single amino acid deprivation

Specificity of amino acid regulated gene expression: Analysis of genes subjected to either complete or single amino acid deprivation

AARE within the SNAT2 gene had not yet been identified at the time of that report, so the genomic element(s) mediating those responses were unknown. To further investigate those observations, HepG2 cells transiently transfected with the wild type or mutated AARE sequence were incubated MEM, MEM lacking just histidine, or in two different media that are completely devoid of amino acids, KRB and EBSS (Fig. 2b). All three media that were amino acid deficient caused induced transcription of the reporter gene, although the magnitude of the increase in response to KRB was slightly less than that for either EBSS or MEM lacking histidine (MEM-His). Surprisingly however, the increased transcription induced by incubation in either EBSS or MEM-His was completely blocked by mutation of the SNAT2 AARE, whereas the activation by KRB was not significantly reduced compared to the wild type sequence (Fig. 2b). These results indicate that, in contrast to EBSS or single amino acid limitation, the KRB medium is triggering a transcriptional response from this SNAT2 genomic fragment that does not require the AARE.
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Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments

Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments

When writing down a protein sequence, amino acids are usually pictured either with a one-letter code, or a three-letter code. Both encodings are simply representations of the amino acid name, and therefore do not contain any information per se. Alternately, encoding amino acids as vectors of numerical values has the advantage of increasing the information content of a protein sequence, should those numerical values represent physico-chemical, or other properties of the amino acids. Such representations are expected to allow finer analyses of the functions of the proteins they represent. French and Robson [ 28 ], Swanson [ 29 ], and Kidera et al. [ 30 ] may have been the first to implement this concept in the early 1980s. Swanson observed that the 20 × 20 Dayhoff substitution matrix [ 31 ] is akin to mapping amino acids into a 20-dimensional feature space. By applying dimension reduction techniques, three lower dimensional representations of amino acids were proposed in 1D, 2D, and 3D spaces, with the 2D version expected to be the most reasonable as it was consistent with other amino acid properties [ 29 ]. In parallel, Kidera et al. proposed to encode each amino acid with ten independent factors obtained by principal component analyses (PCA) of more than one hundred and eighty properties of the twenty amino acids [ 30 ]. Such a representation has been used to analyze protein sequences using Fourier analysis [ 32 – 34 ], with applications to fold recognition for homology modeling [ 35 ]. It should be noted also that a numerical encoding of amino acids enables the definition of sophisticated metrics for comparing sequences [ 36 ]. It also leads to the concept of geometric representations of protein sequences, and their applications for sequence classification and protein fold recognition (see [ 37 ] and references therein).
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Control of puberty by excitatory amino acid neurotransmitters and its clinical implications

Control of puberty by excitatory amino acid neurotransmitters and its clinical implications

Precocious Puberty Associated with Hyperglycinemia: Illustration of NMDA Involvement in Puberty in Humans Until recently, there was no evidence of NMDA recep- tor involvement in the regulation of puberty in human. Bour- guignon et al. reported a case of precocious puberty in a 11-mo-old girl suffering from nonketotic hyperglycinemia (NKH) (64), which is a severe genetic disease caused by an inherited defect in the enzymatic system cleaving gly- cine. This results in an increase of glycine concentration in the cerebrospinal fluid. Some nonketotic hyperglycinemia symptoms involve the inhibitory strychnine-sensitive gly- cine receptors (65), whereas the pathogenesis of seizures involves the excitatory strychnine-insensitive glycine recep- tors belonging to the NMDA–receptor complex (66). The occurrence of precocious puberty in this patient was thought to result from excessive stimulation by glycine of the NMDA receptors linked to the GnRH neurons. This hypothesis was supported by in vitro observations. Glycine increased the pulse frequency of GnRH secretion from hypothalamic explants of immature female rats and this effect was pre- vented by 7-chlorokynurenic acid, a glycin antagonist at the NMDA receptor complex. Regression of pubertal devel- opment under anticonvulsive treatment with GABA ago- nists suggested that the stimulatory effect of glycine could be overcome by GABA receptor–mediated inhibition. Those
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Rapid assembly of the polyhydroxylated b-amino acid constituents of microsclerodermins C, D et E.

Rapid assembly of the polyhydroxylated b-amino acid constituents of microsclerodermins C, D et E.

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Amino-acid substitutions in acetylcholinesterase 1 involved in insecticide resistance in mosquitoes

Amino-acid substitutions in acetylcholinesterase 1 involved in insecticide resistance in mosquitoes

Fig. 2. 3D view point of the entrance of the catalytic gorge of AChE1. The backbone of the enzyme structure is rendered as ribbon with secondary structure. (a) The catalytic triad is represented as black sticks. G119, F290, F331 are represented as light grey van der Waals spheres. Amino-acid substitutions are represented in dark grey: (b) the G119S, (c) the F290V and (d) the F331W. niorhynchus from China where the species is controlled by the use of fenitrothion and dichlorvos. G119S resistant allele was found in C. pipiens from France, where chlorpyrifos has been the only insecticide used to control this species until the late 1990s.
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Chemo-enzymatic synthesis of (2S,4R)-2-amino-4-(3-(2,2-diphenylethylamino)-3 oxopropyl)pentanedioic acid: A novel Selective inhibitor of human excitatory amino acid transporter subtype 2

Chemo-enzymatic synthesis of (2S,4R)-2-amino-4-(3-(2,2-diphenylethylamino)-3 oxopropyl)pentanedioic acid: A novel Selective inhibitor of human excitatory amino acid transporter subtype 2

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Amino acids regulate the transcription, internal sorting, and intrinsic activity of the general amino acid permease (GAP1) in S. cerevisiae

Amino acids regulate the transcription, internal sorting, and intrinsic activity of the general amino acid permease (GAP1) in S. cerevisiae

Any Gaplp that is expressed in the presence of elevated internal amino acids is sorted to the vacuole and degraded or stored in internal compartments from which the permease can[r]

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A study of Kv channel dynamics using a fluorescent unnatural amino acid

A study of Kv channel dynamics using a fluorescent unnatural amino acid

115 Figure 6.1 Translation reinitiation, Shaker channel topology, and current phenotypes A) Simplified model for translation initiation in eukaryotes. First, the 40S small ribosomal subunit associates with initiation factors (shown as squares) and Met-tRNA Met on the mRNA 5’ cap structure. The assembled complex then scans the mRNA sequence until it meets the first AUG codon, after which a fraction of initiation factors are released and the 60S large ribosomal subunit is recruited. Elongation of peptide bonds can then begin and the rest of the initiation factors are released. For a more detailed view see Jackson, et al.[15] B) Topology of the Shaker Kv channel (top) and the N-terminal (below) with annotated positions used in this study. C) Ionic currents from WT and ∆6-46 Shaker channels upon depolarization from −100 mV to +60 mV in steps of +10 mV from a holding potential of –90 mV. The corresponding structures of each constructs are shown. Previously, we successfully incorporated a fluorescent UAA into the Shaker voltage-gated potassium (Kv) channel [2]. The nonsense stop codons were located either central or C-terminal, and no leak expression was detected in the absence of the UAA, reflecting a strong orthogonality of the tRNA/RS pair used. Here, we show that when stop codons are introduced in the region near the N-terminus of the same Kv channel, a considerable amount of leak expression results from translation reinitiation which do not reinitiate at downstream methionines, but rather uses non-canonical (non-AUG) start codons.
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Studies on rosin acid analysis

Studies on rosin acid analysis

The effects beyond an esterification time of 60 minutes and an acid catalyst content of 10 per cent were not studied.. From the results it is seen that about 20 per cent of the abietic a[r]

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Long term nutritional outcome of children fed an amino-acid formula

Long term nutritional outcome of children fed an amino-acid formula

From Food Allergy and Anaphylaxis Meeting (FAAM 2013) Nice, France. 7-9 February 2013 Background Some cases of cow’s milk protein allergy (CMPA) require the use of an amino-acids based formula (AAF), with a with a protein level higher than in standard infant formulas. This study assessed the long term con- sequences of an AAF-based elimination diet on the clin- ical and biological outcome of CMPA children.

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Discovery of Novel Functional Centers With Rationally Designed Amino Acid Motifs

Discovery of Novel Functional Centers With Rationally Designed Amino Acid Motifs

generated N40 fmol/μg protein of cAMP in vitro as detected by mass spectrometry [ 90 ]. Importantly, recombinant AtKUP7 was also able to complement the AC-de ficient mutant cyaA in Escherichia coli [ 90 ]. This method of identi fication was possible because the catalytic cen- tres of ACs and GCs differ only in the amino acid that confers substrate speci ficity and native GCs have been previously shown to be able to as- sume the catalytic function of ACs and vice versa when this amino acid residue implicated in substrate recognition was mutated [ 71 , 91 ]. This GC-derived AC motif has further identi fied a functional AC center in a pentatricopeptide repeat-containing protein (AtPPR) [ 92 ] and predicted several candidate ACs in Arabidopsis thaliana [ 15 , 17 ] some of which are currently under experimental evaluation. Recently, a functional AC domain that contains the AC catalytic center motif has been reported in liverwort Marchantia polymorpha and interestingly, this protein also harbors a phosphodiesterase (PDE) domain that is capable of degrading cyclic nucleotide monophosphates [ 93 ] thus representing an example of a complex multi-domain plant protein capable of regulating cellular cyclic nucleotide monophosphates levels. However, this protein has orthologues only in basal land plants and charophytes that use motile sperms as the male gamete [ 93 ] and thus a bona fide PDE-AC in higher plants remains elusive.
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Amino Acid Sequence of the Penicillin-Binding Protein/DD-Peptidase of Streptomyces K15. Predicted Secondary Structures of the Low Mr Penicillin-Binding Proteins of Class A

Amino Acid Sequence of the Penicillin-Binding Protein/DD-Peptidase of Streptomyces K15. Predicted Secondary Structures of the Low Mr Penicillin-Binding Proteins of Class A

low-M, PBPs of known primary structure has led to the conclusion that (1) the Streptomyces K15 PBP, the Escherichia coli PBPs 5 and 6 (Broome-Smith et al., 1988), the Bacillus subtilis P[r]

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Phase behavior and chain dynamics of elastin-like peptides versus amino acid sequences

Phase behavior and chain dynamics of elastin-like peptides versus amino acid sequences

Abstract Elastin fibrillogenesis is conditioned by multiple self-assembly processes. Previous studies have evidenced the crucial influence of amino acid specificities on molecular organization of glycine-rich elastin-like pep- tides, but also the important role of environment on the self-assembly processes. For the first time, we combined a differential scanning calorimetry (DSC) study on aqueous solutions of three elastin-like peptides with thermally stimulated currents (TSC) experiments in the condensed state. We have studied three pentadecapeptides having the XGGZG motif threefold repeated with X and Z residues constituted of valine and leucine, known to form fiber structures. Valine and leucine moieties differ only by the presence of –CH 2 – spacer occupying in the pattern the first
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Phase behavior and chain dynamics of elastin-like peptides versus amino acid sequences

Phase behavior and chain dynamics of elastin-like peptides versus amino acid sequences

Materials and methods Peptide synthesis, disaggregation and purification The peptides were synthesized by SPPS on the Tribute automatic peptide synthesizer (Protein Technologies Inc, Arizona, USA) by using a standard 9-fluorenylmethoxy- carbonyl (Fmoc) protection peptide synthesis protocol. The cleavage of peptide from the resin was achieved by using an aqueous mixture of 95% trifluoroacetic acid (TFA). The peptides were lyophilized. Three milligrams of lyophilized peptides was dissolved in 1 cm -3 of TFA and gently stirred at 373 K for 3 h to completely dissolve the seeds respon- sible for the insolubility of peptide (unseeded peptide). Upon addition of 9 cm -3 of ultrapure water, the solution was fractionated into equal parts and lyophilized. This procedure provided a powder aliquot for HPLC. The pep- tides were purified by semi-preparative reversed-phase high-performance chromatography on a Shimadzu auto- mated HPLC system supplied with a semi-preparative Jupiter C18 column (Phenomenex, 250. 10 mm, 5 lm). A binary gradient was used, and the solvents were H 2 O (0.1%
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Is the information provided by amino acid PET radiopharmaceuticals clinically equivalent in gliomas?

Is the information provided by amino acid PET radiopharmaceuticals clinically equivalent in gliomas?

8. Moulin-Romsée G, D’Hondt E, de Groot T, Goffin J, Sciot R, Mortelmans L, et al. Non- invasive grading of brain tumours using dynamic amino acid PET imaging: does it work for 11C-methionine? Eur. J. Nucl. Med. Mol. Imaging. 2007;34:2082–7. 9. Janvier L, Olivier P, Blonski M, Morel O, Vignaud J-M, Karcher G, et al. Correlation of SUV-Derived Indices With Tumoral Aggressiveness of Gliomas in Static 18F-FDOPA PET: Use in Clinical Practice. Clin. Nucl. Med. 2015;40:e429-435.

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