scholarly journals Proteins of generalist and specialist pathogens differ in their amino acid composition

2018 ◽  
Vol 1 (4) ◽  
pp. e201800017 ◽  
Author(s):  
Luz P Blanco ◽  
Bryan L Payne ◽  
Felix Feyertag ◽  
David Alvarez-Ponce
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Host Range ◽  
Acid Composition ◽  
Secreted Proteins ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Cytoplasmic Proteins ◽  
Disordered Regions

Pathogens differ in their host specificities, with species infecting a unique host (specialist pathogens) and others having a wide host range (generalists). Molecular determinants of pathogen’s host range remain poorly understood. Secreted proteins of generalist pathogens are expected to have a broader range of intermolecular interactions (i.e., higher promiscuity) compared with their specialist counterparts. We hypothesize that this increased promiscuity of generalist secretomes may be based on an elevated content of primitive amino acids and intrinsically disordered regions, as these features are known to increase protein flexibility and interactivity. Here, we measure the proportion of primitive amino acids and percentage of intrinsically disordered residues in secreted, membrane, and cytoplasmic proteins from pathogens with different host specificity. Supporting our prediction, there is a significant general enrichment for primitive amino acids and intrinsically disordered regions in proteins from generalists compared to specialists, particularly among secreted proteins in prokaryotes. Our findings support our hypothesis that secreted proteins' amino acid composition and disordered content influence the pathogens' host range.

scholarly journals Why do eukaryotic proteins contain more intrinsically disordered regions?

2018 ◽  
Author(s):  
Walter Basile ◽  
Marco Salvatore ◽  
Claudio Bassot ◽  
Arne Elofsson
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Intrinsic Disorder ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Significant Difference ◽  
Eukaryotic Proteins ◽  
The Difference ◽  
Almost All ◽  
Disordered Regions

AbstractIntrinsic disorder is much more abundant in eukaryotic than in prokaryotic proteins. However, the reason behind this is unclear. It has been proposed that the disordered regions are functionally important for regulation in eukaryotes, but it has also been proposed that the difference is a result of lower selective pressure in eukaryotes. Almost all studies intrinsic disorder is predicted from the amino acid sequence of a protein. Therefore, there should exist an underlying difference in the amino acid distributions between eukaryotic and prokaryotic proteins causing the predicted difference in intrinsic disorder. To obtain a better understanding of why eukaryotic proteins contain more intrinsically disordered regions we compare proteins from complete eukaryotic and prokaryotic proteomes.Here, we show that the difference in intrinsic disorder origin from differences in the linker regions. Eukaryotic proteins have more extended linker regions and, in particular, the eukaryotic linker regions are more disordered. The average eukaryotic protein is about 500 residues long; it contains 250 residues in linker regions, of which 80 are disordered. In comparison, prokaryotic proteins are about 350 residues long and only have 100-110 residues in linker regions, and less than 10 of these are intrinsically disordered.Further, we show that there is no systematic increase in the frequency of disorder-promoting residues in eukaryotic linker regions. Instead, the difference in frequency of only three amino acids seems to lie behind the difference. The most significant difference is that eukaryotic linkers contain about 9% serine, while prokaryotic linkers have roughly 6.5%. Eukaryotic linkers also contain about 2% more proline and 2-3% fewer isoleucine residues. The reason why primarily these amino acids vary in frequency is not apparent, but it cannot be excluded that the difference is serine is related to the increased need for regulation through phosphorylation and that the proline difference is related to increase of eukaryotic specific repeats.

scholarly journals Sequence determinants of in cell condensate assembly morphology, dynamics, and oligomerization as measured by number and brightness analysis

2021 ◽  
Author(s):  
Ryan J Emenecker ◽  
Alex S Holehouse ◽  
Lucia Strader
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Material Properties ◽  
Oligomeric State ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Brightness Analysis ◽  
Oligomerization Domain

Background: Biomolecular condensates are non-stoichiometric assemblies that are characterized by their capacity to spatially concentrate biomolecules and play a key role in cellular organization. Proteins that drive the formation of biomolecular condensates frequently contain oligomerization domains and intrinsically disordered regions (IDRs), both of which can contribute multivalent interactions that drive higher-order assembly. Our understanding of the relative and temporal contribution of oligomerization domains and IDRs to the material properties of in vivo biomolecular condensates is limited. Similarly, the spatial and temporal dependence of protein oligomeric state inside condensates has been largely unexplored in vivo. Methods: In this study, we combined quantitative microscopy with number and brightness analysis to investigate the aging, material properties, and protein oligomeric state of biomolecular condensates in vivo. Our work is focused on condensates formed by AUXIN RESPONSE FACTOR 19 (ARF19), which is a transcription factor integral to the signaling pathway for the plant hormone auxin. ARF19 contains a large central glutamine-rich IDR and a C-terminal Phox Bem1 (PB1) oligomerization domain and forms cytoplasmic condensates. Results: Our results reveal that the IDR amino acid composition can influence the morphology and material properties of ARF19 condensates. In contrast the distribution of oligomeric species within condensates appears insensitive to the IDR composition. In addition, we identified a relationship between the abundance of higher- and lower-order oligomers within individual condensates and their apparent fluidity. Conclusions: IDR amino acid composition affects condensate morphology and material properties. In ARF condensates, altering the amino acid composition of the IDR did not greatly affect the oligomeric state of proteins within the condensate.

scholarly journals Sequence determinants of in cell condensate morphology, dynamics, and oligomerization as measured by number and brightness analysis

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Ryan J. Emenecker ◽  
Alex S. Holehouse ◽  
Lucia C. Strader
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Material Properties ◽  
Auxin Signaling ◽  
Oligomeric State ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Brightness Analysis

Abstract Background Biomolecular condensates are non-stoichiometric assemblies that are characterized by their capacity to spatially concentrate biomolecules and play a key role in cellular organization. Proteins that drive the formation of biomolecular condensates frequently contain oligomerization domains and intrinsically disordered regions (IDRs), both of which can contribute multivalent interactions that drive higher-order assembly. Our understanding of the relative and temporal contribution of oligomerization domains and IDRs to the material properties of in vivo biomolecular condensates is limited. Similarly, the spatial and temporal dependence of protein oligomeric state inside condensates has been largely unexplored in vivo. Methods In this study, we combined quantitative microscopy with number and brightness analysis to investigate the aging, material properties, and protein oligomeric state of biomolecular condensates in vivo. Our work is focused on condensates formed by AUXIN RESPONSE FACTOR 19 (ARF19), a transcription factor integral to the auxin signaling pathway in plants. ARF19 contains a large central glutamine-rich IDR and a C-terminal Phox Bem1 (PB1) oligomerization domain and forms cytoplasmic condensates. Results Our results reveal that the IDR amino acid composition can influence the morphology and material properties of ARF19 condensates. In contrast the distribution of oligomeric species within condensates appears insensitive to the IDR composition. In addition, we identified a relationship between the abundance of higher- and lower-order oligomers within individual condensates and their apparent fluidity. Conclusions IDR amino acid composition affects condensate morphology and material properties. In ARF condensates, altering the amino acid composition of the IDR did not greatly affect the oligomeric state of proteins within the condensate.

scholarly journals Arabidopsis Heat Stress-Induced Proteins Are Enriched in Electrostatically Charged Amino Acids and Intrinsically Disordered Regions

2018 ◽  
Vol 19 (8) ◽  
pp. 2276 ◽  
Author(s):  
David Alvarez-Ponce ◽  
Mario Ruiz-González ◽  
Francisco Vera-Sirera ◽  
Felix Feyertag ◽  
Miguel Perez-Amador ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
High Temperatures ◽  
Hydrophobic Interactions ◽  
Intrinsic Disorder ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Charged Amino Acids ◽  
Induced Proteins ◽  
Disordered Regions

Comparison of the proteins of thermophilic, mesophilic, and psychrophilic prokaryotes has revealed several features characteristic to proteins adapted to high temperatures, which increase their thermostability. These characteristics include a profusion of disulfide bonds, salt bridges, hydrogen bonds, and hydrophobic interactions, and a depletion in intrinsically disordered regions. It is unclear, however, whether such differences can also be observed in eukaryotic proteins or when comparing proteins that are adapted to temperatures that are more subtly different. When an organism is exposed to high temperatures, a subset of its proteins is overexpressed (heat-induced proteins), whereas others are either repressed (heat-repressed proteins) or remain unaffected. Here, we determine the expression levels of all genes in the eukaryotic model system Arabidopsis thaliana at 22 and 37 °C, and compare both the amino acid compositions and levels of intrinsic disorder of heat-induced and heat-repressed proteins. We show that, compared to heat-repressed proteins, heat-induced proteins are enriched in electrostatically charged amino acids and depleted in polar amino acids, mirroring thermophile proteins. However, in contrast with thermophile proteins, heat-induced proteins are enriched in intrinsically disordered regions, and depleted in hydrophobic amino acids. Our results indicate that temperature adaptation at the level of amino acid composition and intrinsic disorder can be observed not only in proteins of thermophilic organisms, but also in eukaryotic heat-induced proteins; the underlying adaptation pathways, however, are similar but not the same.

iSP-RAAC: Identify Secretory Proteins of Malaria Parasite Using Reduced Amino Acid Composition

2020 ◽  
Vol 23 (6) ◽  
pp. 536-545
Author(s):  
Haoyue Zhang ◽  
Qilemuge Xi ◽  
Shenghui Huang ◽  
Lei Zheng ◽  
Wuritu Yang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Malaria Parasite ◽  
Secreted Proteins ◽  
Secretory Proteins ◽  
Dipeptide Composition ◽  
Malaria Vaccines ◽  
Growth And Reproduction

Background: As the pathogen of malaria, malaria parasite secretes a variety of proteins for its growth and reproduction. Objective: The identification of the secretory proteins of malaria parasite has crucial reference significance for the development of anti-malaria vaccines as well as medicine. Methods: In this study, a computational classification method was developed to identify the secreted proteins of Plasmodium. Amino acid composition, dipeptide composition, and tripeptide composition as well as reduced amino acids alphabets were proposed to illuminate protein sequences. We further used SVM to train and predict respectively and optimized the features. Results: 74 types of reduced amino acids alphabets were employed to predict secretory proteins. The results showed that the accuracy improved to 91.67% with 0.84 Mathew’s correlation coefficient (MCC) by dipeptide composition, and the highest prediction accuracy reached 92.26% after feature selection, which demonstrated that our method is prominent and reliable in the field of malaria parasite secreted proteins prediction. Conclusion: A intuitive web server iSP-RAAC (http://bioinfor.imu.edu.cn/isppseraac) was established for the convenience of most experimental scientists.

scholarly journals The Amino Acid Composition of Keratins

1955 ◽  
Vol 8 (4) ◽  
pp. 537 ◽  
Author(s):  
DH Simmonds
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Merino Wool

The amino acid composition of 16-hr 6N HCI hydrolysates of three qualities of commercially classified wools has now been determined using the technique of Moore and Stein (1951). In this paper the results obtained on samples of Merino 70's and Corriedale 56's wool are compared with those previously reported for Merino wool of 64's quality. The overall pattern of the amino acid composition of the three wools is similar although small variations between the wools are observed with some of the amino acids.

scholarly journals Amino acid production in isolated rat liver mitochondria

1973 ◽  
Vol 134 (2) ◽  
pp. 431-436 ◽  
Author(s):  
W. Ferdinand ◽  
W. Bartley ◽  
V. Broomhead
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Lipid Hydroperoxide ◽  
Liver Mitochondria ◽  
Cysteic Acid ◽  
Rat Liver Mitochondria ◽  
Isolated Mitochondria ◽  
Selective Retention

Amino acid analyses of mitochondrial membranes are compared with the amino acid composition of whole mitochondria (Alberti, 1964) and found to be very similar except in the cystine content. The composition of the endogenous amino acids found in freshly prepared mitochondria has been established and shown to differ considerably from the amino acid composition of membranes or whole mitochondria. The amino acids produced during anaerobic incubation of mitochondria at pH7.4, on the other hand, resemble the membrane in composition, supporting the view that neutral proteinase activity is responsible for their appearance. Aerobic incubation produces a similar pattern of amino acids except that amino acids such as proline, serine, asparagine, glutamic acid and glutamine, which can be metabolically utilized under aerobic conditions, are present to a smaller extent. The presence of large relative concentrations of endogenous taurine, cysteic acid and oxidized glutathione and the accumulation of taurine during incubation is found. The selective retention of taurine and cysteic acid within the mitochondria is established. It is proposed that the first step in the degeneration of isolated mitochondria results from lipid hydroperoxide accumulation caused by the lack of glutathione reductase in isolated mitochondria.

scholarly journals AMINO ACID COMPOSITION AND ELECTROPHORETIC PROPERTIES OF HYPERTENSIN I

1955 ◽  
Vol 102 (4) ◽  
pp. 435-440 ◽  
Author(s):  
Leonard T. Skeggs ◽  
Walton H. Marsh ◽  
Joseph R. Kahn ◽  
Norman P. Shumway
Keyword(s):  
Amino Acids ◽  
Quantitative Analysis ◽  
Amino Acid ◽  
Ion Exchange ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Isoelectric Point ◽  
Column Chromatography ◽  
Isoleucine Leucine ◽  
Ion Exchange Column

A preparation of hypertensin I was purified by countercurrent distribution and was shown to migrate as a single component in starch blocks at pH 9.3 and 4.2. It had an isoelectric point of 7.7. Quantitative analysis by ion exchange column chromatography showed eight amino acids in approximately unimolar proportion: aspartic, proline, valine, isoleucine, leucine, tyrosine, phenylalanine, and arginine. There were in addition two moles of histidine.

scholarly journals WRAP-based nanoparticles for siRNA delivery: a SAR study and a comparison with lipid-based transfection reagents

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Karidia Konate ◽  
Emilie Josse ◽  
Milana Tasic ◽  
Karima Redjatti ◽  
Gudrun Aldrian ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Gene Silencing ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Sirna Delivery ◽  
Cell Penetrating Peptides ◽  
Sirna Transfection ◽  
Arginine Residues ◽  
Sar Study

AbstractRecently, we designed novel amphipathic cell-penetrating peptides, called WRAP, able to transfer efficiently siRNA molecules into cells. In order to gain more information about the relationship between amino acid composition, nanoparticle formation and cellular internalization of these peptides composed of only three amino acids (leucine, arginine and tryptophan), we performed a structure–activity relationship (SAR) study. First, we compared our WRAP1 and WRAP5 peptides with the C6M1 peptide also composed of the same three amino acids and showing similar behaviors in siRNA transfection. Afterwards, to further define the main determinants in the WRAP activity, we synthesized 13 new WRAP analogues harboring different modifications like the number and location of leucine and arginine residues, the relative location of tryptophan residues, as well as the role of the α-helix formation upon proline insertions within the native WRAP sequence. After having compared the ability of these peptides to form peptide-based nanoparticles (PBNs) using different biophysical methods and to induce a targeted gene silencing in cells, we established the main sequential requirements of the amino acid composition of the WRAP peptide. In addition, upon measuring the WRAP-based siRNA transfection ability into cells compared to several non-peptide transfection agents available on the markets, we confirmed that WRAP peptides induced an equivalent level of targeted gene silencing but in most of the cases with lower cell toxicity as clearly shown in clonogenic assays.

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