scholarly journals Compositional Determinants of Prion Formation in Yeast

2009 ◽  
Vol 30 (1) ◽  
pp. 319-332 ◽  
Author(s):  
James A. Toombs ◽  
Blake R. McCarty ◽  
Eric D. Ross
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Amyloid Formation ◽  
Yeast Prion ◽  
Hydrophobic Residues ◽  
Predictive Methods ◽  
Infectious Proteins ◽  
Β Sheet ◽  
Eukaryotic Genomes

ABSTRACT Numerous prions (infectious proteins) have been identified in yeast that result from the conversion of soluble proteins into β-sheet-rich amyloid-like protein aggregates. Yeast prion formation is driven primarily by amino acid composition. However, yeast prion domains are generally lacking in the bulky hydrophobic residues most strongly associated with amyloid formation and are instead enriched in glutamines and asparagines. Glutamine/asparagine-rich domains are thought to be involved in both disease-related and beneficial amyloid formation. These domains are overrepresented in eukaryotic genomes, but predictive methods have not yet been developed to efficiently distinguish between prion and nonprion glutamine/asparagine-rich domains. We have developed a novel in vivo assay to quantitatively assess how composition affects prion formation. Using our results, we have defined the compositional features that promote prion formation, allowing us to accurately distinguish between glutamine/asparagine-rich domains that can form prion-like aggregates and those that cannot. Additionally, our results explain why traditional amyloid prediction algorithms fail to accurately predict amyloid formation by the glutamine/asparagine-rich yeast prion domains.

scholarly journals A Promiscuous Prion: Efficient Induction of [URE3] Prion Formation by Heterologous Prion Domains

Genetics ◽  
2009 ◽  
Vol 183 (3) ◽  
pp. 929-940 ◽  
Author(s):  
Carley D. Ross ◽  
Blake R. McCarty ◽  
Michael Hamilton ◽  
Asa Ben-Hur ◽  
Eric D. Ross
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
De Novo ◽  
Amyloid Formation ◽  
Wild Type ◽  
Amyloid Aggregates ◽  
Efficient Induction

The [URE3] and [PSI+] prions are the infections amyloid forms of the Saccharomyces cerevisiae proteins Ure2p and Sup35p, respectively. Randomizing the order of the amino acids in the Ure2 and Sup35 prion domains while retaining amino acid composition does not block prion formation, indicating that amino acid composition, not primary sequence, is the predominant feature driving [URE3] and [PSI+] formation. Here we show that Ure2p promiscuously interacts with various compositionally similar proteins to influence [URE3] levels. Overexpression of scrambled Ure2p prion domains efficiently increases de novo formation of wild-type [URE3] in vivo. In vitro, amyloid aggregates of the scrambled prion domains efficiently seed wild-type Ure2p amyloid formation, suggesting that the wild-type and scrambled prion domains can directly interact to seed prion formation. To test whether interactions between Ure2p and naturally occurring yeast proteins could similarly affect [URE3] formation, we identified yeast proteins with domains that are compositionally similar to the Ure2p prion domain. Remarkably, all but one of these domains were also able to efficiently increase [URE3] formation. These results suggest that a wide variety of proteins could potentially affect [URE3] formation.

scholarly journals Extensive mutagenesis of a transcriptional activation domain identifies single hydrophobic and acidic amino acids important for activation in vivo.

1997 ◽  
Vol 17 (1) ◽  
pp. 115-122 ◽  
Author(s):  
M B Sainz ◽  
S A Goff ◽  
V L Chandler
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Transcriptional Activation ◽  
Carboxyl Terminus ◽  
Wild Type ◽  
Activation Domain ◽  
Hydrophobic Residues ◽  
Transcriptional Activation Domain ◽  
Acidic Amino Acids

C1 is a transcriptional activator of genes encoding biosynthetic enzymes of the maize anthocyanin pigment pathway. C1 has an amino terminus homologous to Myb DNA-binding domains and an acidic carboxyl terminus that is a transcriptional activation domain in maize and yeast cells. To identify amino acids critical for transcriptional activation, an extensive random mutagenesis of the C1 carboxyl terminus was done. The C1 activation domain is remarkably tolerant of amino acid substitutions, as changes at 34 residues had little or no effect on transcriptional activity. These changes include introduction of helix-incompatible amino acids throughout the C1 activation domain and alteration of most single acidic amino acids, suggesting that a previously postulated amphipathic alpha-helix is not required for activation. Substitutions at two positions revealed amino acids important for transcriptional activation. Replacement of leucine 253 with a proline or glutamine resulted in approximately 10% of wild-type transcriptional activation. Leucine 253 is in a region of C1 in which several hydrophobic residues align with residues important for transcriptional activation by the herpes simplex virus VP16 protein. However, changes at all other hydrophobic residues in C1 indicate that none are critical for C1 transcriptional activation. The other important amino acid in C1 is aspartate 262, as a change to valine resulted in only 24% of wild-type transcriptional activation. Comparison of our C1 results with those from VP16 reveal substantial differences in which amino acids are required for transcriptional activation in vivo by these two acidic activation domains.

scholarly journals Analysis of Heterodimeric “Mutual Synergistic Folding”-Complexes

2019 ◽  
Vol 20 (20) ◽  
pp. 5136 ◽  
Author(s):  
Mentes ◽  
Magyar ◽  
Fichó ◽  
Simon
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Intrinsically Disordered Proteins ◽  
Driving Forces ◽  
Disordered Proteins ◽  
Subunit Interactions ◽  
Amino Acid Compositions ◽  
Intrinsically Disordered ◽  
Β Sheet

Several intrinsically disordered proteins (IDPs) are capable to adopt stable structures without interacting with a folded partner. When the folding of all interacting partners happens at the same time, coupled with the interaction in a synergistic manner, the process is called Mutual Synergistic Folding (MSF). These complexes represent a discrete subset of IDPs. Recently, we collected information on their complexes and created the MFIB (Mutual Folding Induced by Binding) database. In a previous study, we compared homodimeric MSF complexes with homodimeric and monomeric globular proteins with similar amino acid sequence lengths. We concluded that MSF homodimers, compared to globular homodimeric proteins, have a greater solvent accessible main-chain surface area on the contact surface of the subunits, which becomes buried during dimerization. The main driving force of the folding is the mutual shielding of the water-accessible backbones, but the formation of further intermolecular interactions can also be relevant. In this paper, we will report analyses of heterodimeric MSF complexes. Our results indicate that the amino acid composition of the heterodimeric MSF monomer subunits slightly diverges from globular monomer proteins, while after dimerization, the amino acid composition of the overall MSF complexes becomes more similar to overall amino acid compositions of globular complexes. We found that inter-subunit interactions are strengthened, and additionally to the shielding of the solvent accessible backbone, other factors might play an important role in the stabilization of the heterodimeric structures, likewise energy gain resulting from the interaction of the two subunits with different amino acid compositions. We suggest that the shielding of the β-sheet backbones and the formation of a buried structural core along with the general strengthening of inter-subunit interactions together could be the driving forces of MSF protein structural ordering upon dimerization.

Predicting Interactions Between Pathogen and Human Proteins Based on the Relation Between Sequence Length and Amino Acid Composition

2021 ◽  
Vol 16 ◽  
Author(s):  
Saud Alguwaizani ◽  
Shulei Ren ◽  
De-Shuang Huang ◽  
Kyungsook Han
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Yersinia Pestis ◽  
Acid Composition ◽  
Sequence Length ◽  
Support Vector ◽  
Human Ppis ◽  
Svm Model

Aim: Both bacterial infection and viral infection involve a large number of protein-protein interactions (PPIs) between a pathogen and its target host. Background: So far, many computational methods have focused on predicting PPIs within the same species rather than PPIs across different species. Methods: From the extensive analysis of PPIs between Yersinia pestis bacteria and humans, we recently discovered an interesting relation; a linear relation between amino acid composition and sequence length was observed in many proteins involved in PPIs. We have built a support vector machine (SVM) model, which predicts PPIs between human and bacteria using two feature types derived from the relation. The two feature types used in the SVM are the amino acid composition group (AACG) and the difference in amino acid composition between host and pathogen proteins. Result: The SVM model achieved high performance in predicting bacteria-human PPIs. The model showed an accuracy of 96%, sensitivity of 94%, and specificity of 98% in predicting PPIs between humans and Yersinia pestis, in which there is a strong relation between amino acid composition and sequence length. The SVM model was also tested in predicting PPIs between human and viruses, which include Ebola, HCV, and SARSCoV-2, and showed a good performance. Conclusion: The feature types identified in our study are simple yet powerful in predicting pathogen-human PPIs. Although preliminary, our method will be useful for finding unknown target host proteins or pathogen proteins and designing in vitro or in vivo experiments.

Proteolytic Degradation of the Aα Chain of Human Fibrinogen

1979 ◽  
Author(s):  
J.A. Conkie ◽  
Isobel D. Walker ◽  
J.F. Davidson
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Proteolytic Degradation ◽  
Composition Analysis ◽  
Terminal Part ◽  
High Solubility ◽  
Human Fibrinogen

On plasmin degradation of human fibrinogen, a number of polypeptides are released from the COOH-terminal part of the Aα chain. One of these fragments has been previously named by us as Aα-RA(26,000). By comparison of its molecular weight and amino acid composition analysis, this fragment is similar to the fragments A,H and Hi2-Met. Aα-RA(26,00O) appears to be derived from a precursor polypeptide of Mw 44,000, while in vitro and in vivo activation of the plasma fibrinolytic system also gives rise to an Aα-related antigen which is immunologically similar to the 44,000 MW polypeptide. On immunodiffusion with antiserum to the carboxymethylated Aα chain, Aα-RA(26 000) revealed a reaction of identity with the high solubility fibrinogen fraction 1-9 (major NH2-terminal Aα remnant, MW 34,000) and a reaction of non-identity with the ancrod-proauced COOH-terminal Aα polypeptides (MW 27,000-31,000). These immunodiffusion results provide evidence that the sequence of bond cleavages in the Aα chain leading to the formaron of fibrinogen 1-9 is different from that leading to the formation of Aα-Ra (126,000).

scholarly journals Specific Amyloid Binding of Polybasic Peptides In Vivo Is Retained by β-Sheet Conformers but Lost in the Disrupted Coil and All D-Amino Acid Variants

2017 ◽  
Vol 19 (5) ◽  
pp. 714-722 ◽  
Author(s):  
Jonathan S. Wall ◽  
Angela Williams ◽  
Tina Richey ◽  
Alan Stuckey ◽  
Craig Wooliver ◽  
...  
Keyword(s):  
Amino Acid ◽  
Β Sheet ◽  
Amino Acid Variants

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.

The Potential of Serratiopetidase and Lumbrokinase for the Degradation of Prion Peptide 106-126 - an In Vitro and In Silico Perspective

2020 ◽  
Vol 18 (9) ◽  
pp. 723-731
Author(s):  
Sanjay Kisan Metkar ◽  
Suparna Ghosh ◽  
Agnishwar Girigoswami ◽  
Koyeli Girigoswami
Keyword(s):  
Cell Viability ◽  
Serine Proteases ◽  
Prion Diseases ◽  
Dynamics Simulation ◽  
In Vivo Studies ◽  
Drug Candidate ◽  
Amyloid Formation ◽  
Β Sheet

Background: PrPC is a host-encoded prion protein, which gets post translationally modified into a transmissible, β-sheet rich disease associated protein called PrPSc, responsible for the Prion disease including mad cow disease in cattle and CJD in humans. The PrP 106-126 region in PrPSc peptide initiates the conformational change in that protein leading to fibrillation. Any agent that can destabilize or disintegrate such proteins can be served as a potential drug candidate for Prion diseases. Methods: In the present study, an enzyme Lumbrokinase (LK) was isolated from earthworm and its activity was exploited towards PrP 106-126 amyloids in vitro along with another enzyme Serratiopeptidase (SP) taking Nattokinase (NK) as a standard. Results: The results showed that PrP 106-126 amyloid formation was inhibited by both LK and SP, as evidenced from Thioflavin T fluorescence assay. Further, the size of fibrils as estimated by dynamic light scattering, was also found to be lower at different time intervals after incubation of the prion amyloids with LK and SP. Additionally, the molecular dynamics simulation revealed the thermodynamically favorable interaction of PrP 106-126 with LK as well as with SP with high affinity. Conclusion: Finally, the toxicity of the disintegrated amyloids was assessed using PC12 cell lines which showed higher cell viability in case of LK and SP treated amyloids compared to only PrP 106- 126 amyloid treatment. Altogether, the study concluded that the serine proteases like LK and SP have the potential to disintegrate PrP 106-126 amyloids with improved cell viability. The in vivo studies are needed to be executed in future.

scholarly journals Scrambled Prion Domains Form Prions and Amyloid

2004 ◽  
Vol 24 (16) ◽  
pp. 7206-7213 ◽  
Author(s):  
Eric D. Ross ◽  
Ulrich Baxa ◽  
Reed B. Wickner
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Sequence Composition ◽  
Amino Terminal ◽  
Rich Domain ◽  
The Many ◽  
Necessary And Sufficient

ABSTRACT The [URE3] prion of Saccharomyces cerevisiae is a self-propagating amyloid form of Ure2p. The amino-terminal prion domain of Ure2p is necessary and sufficient for prion formation and has a high glutamine (Q) and asparagine (N) content. Such Q/N-rich domains are found in two other yeast prion proteins, Sup35p and Rnq1p, although none of the many other yeast Q/N-rich domain proteins have yet been found to be prions. To examine the role of amino acid sequence composition in prion formation, we used Ure2p as a model system and generated five Ure2p variants in which the order of the amino acids in the prion domain was randomly shuffled while keeping the amino acid composition and C-terminal domain unchanged. Surprisingly, all five formed prions in vivo, with a range of frequencies and stabilities, and the prion domains of all five readily formed amyloid fibers in vitro. Although it is unclear whether other amyloid-forming proteins would be equally resistant to scrambling, this result demonstrates that [URE3] formation is driven primarily by amino acid composition, largely independent of primary sequence.

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