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Journal articles on the topic 'Prone proteins'

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Author: Grafiati

Published: 6 September 2023

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1

De Baets, Greet, Joost Schymkowitz, and Frederic Rousseau. "Predicting aggregation-prone sequences in proteins." Essays in Biochemistry 56 (August 18, 2014): 41–52. http://dx.doi.org/10.1042/bse0560041.

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Owing to its association with a diverse range of human diseases, the determinants of protein aggregation are studied intensively. It is generally accepted that the effective aggregation tendency of a protein depends on many factors such as folding efficiency towards the native state, thermodynamic stability of that conformation, intrinsic aggregation propensity of the polypeptide sequence and its ability to be recognized by the protein quality control system. The intrinsic aggregation propensity of a polypeptide sequence is related to the presence of short APRs (aggregation-prone regions) that self-associate to form intermolecular β-structured assemblies. These are typically short sequence segments (5–15 amino acids) that display high hydrophobicity, low net charge and a high tendency to form β-structures. As the presence of such APRs is a prerequisite for aggregation, a plethora of methods have been developed to identify APRs in amino acid sequences. In the present chapter, the methodological basis of these approaches is discussed, as well as some practical applications.

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2

Lebendiker, Mario, and Tsafi Danieli. "Production of prone-to-aggregate proteins." FEBS Letters 588, no. 2 (November 6, 2013): 236–46. http://dx.doi.org/10.1016/j.febslet.2013.10.044.

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3

Galves, Margarita, Ritu Rathi, Gali Prag, and Avraham Ashkenazi. "Ubiquitin Signaling and Degradation of Aggregate-Prone Proteins." Trends in Biochemical Sciences 44, no. 10 (October 2019): 872–84. http://dx.doi.org/10.1016/j.tibs.2019.04.007.

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4

Tartaglia, Gian Gaetano, Amol P. Pawar, Silvia Campioni, Christopher M. Dobson, Fabrizio Chiti, and Michele Vendruscolo. "Prediction of Aggregation-Prone Regions in Structured Proteins." Journal of Molecular Biology 380, no. 2 (July 2008): 425–36. http://dx.doi.org/10.1016/j.jmb.2008.05.013.

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5

Berger, Zdenek, Brinda Ravikumar, Fiona M. Menzies, Lourdes Garcia Oroz, Benjamin R. Underwood, Menelas N. Pangalos, Ina Schmitt, et al. "Rapamycin alleviates toxicity of different aggregate-prone proteins." Human Molecular Genetics 15, no. 3 (December 20, 2005): 433–42. http://dx.doi.org/10.1093/hmg/ddi458.

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6

Chennamsetty, Naresh, Vladimir Voynov, Veysel Kayser, Bernhard Helk, and Bernhardt L. Trout. "Prediction of Aggregation Prone Regions of Therapeutic Proteins." Journal of Physical Chemistry B 114, no. 19 (May 20, 2010): 6614–24. http://dx.doi.org/10.1021/jp911706q.

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7

Salomons, Florian A., Victoria Menéndez-Benito, Claudia Böttcher, Brett A. McCray, J. Paul Taylor, and Nico P. Dantuma. "Selective Accumulation of Aggregation-Prone Proteasome Substrates in Response to Proteotoxic Stress." Molecular and Cellular Biology 29, no. 7 (January 21, 2009): 1774–85. http://dx.doi.org/10.1128/mcb.01485-08.

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ABSTRACT Conditions causing an increase in misfolded or aberrant proteins can impair the activity of the ubiquitin/proteasome system (UPS). This observation is of particular interest, given the fact that proteotoxic stress is closely associated with a large variety of disorders. Although impairment of the UPS appears to be a general consequence of proteotoxic insults, the underlying mechanisms remain enigmatic. Here, we show that heat shock-induced proteotoxic stress resulted in conjugation of ubiquitin to detergent-insoluble protein aggregates, which coincided with reduced levels of free ubiquitin and impediment of ubiquitin-dependent proteasomal degradation. Interestingly, whereas soluble proteasome substrates returned to normal levels after a transient accumulation, the levels of an aggregation-prone substrate remained high even when the free ubiquitin levels were restored. Consistently, overexpression of ubiquitin prevented accumulation of soluble but not aggregation-prone substrates in thermally stressed cells. Notably, cells were also unable to resume degradation of aggregation-prone substrates after treatment with the translation inhibitor puromycin, indicating that selective accumulation of aggregation-prone proteins is a consistent feature of proteotoxic stress. Our data suggest that the failure of the UPS to clear aggregated proteins in the aftermath of proteotoxic stress episodes may contribute to the selective deposition of aggregation-prone proteins in conformational diseases.

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Ravikumar, Brinda, Abraham Acevedo-Arozena, Sara Imarisio, Zdenek Berger, Coralie Vacher, Cahir J. O'Kane, Steve D. M. Brown, and David C. Rubinsztein. "Dynein mutations impair autophagic clearance of aggregate-prone proteins." Nature Genetics 37, no. 7 (June 26, 2005): 771–76. http://dx.doi.org/10.1038/ng1591.

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9

Knaevelsrud, Helene, and Anne Simonsen. "Fighting disease by selective autophagy of aggregate-prone proteins." FEBS Letters 584, no. 12 (April 20, 2010): 2635–45. http://dx.doi.org/10.1016/j.febslet.2010.04.041.

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10

Källquist, Linda, Markus Hansson, Ann-Maj Persson, Hans Janssen, Jero Calafat, Hans Tapper, and Inge Olsson. "The tetraspanin CD63 is involved in granule targeting of neutrophil elastase." Blood 112, no. 8 (October 15, 2008): 3444–54. http://dx.doi.org/10.1182/blood-2007-10-116285.

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Abstract Targeting mechanisms of neutrophil elastase (NE) and other luminal proteins stored in myeloperoxidase (MPO)–positive secretory lysosomes/primary granules of neutrophils are unknown. These granules contain an integral membrane protein, CD63, with an adaptor protein-3–dependent granule delivery system. Therefore, we hypothesized that CD63 cooperates in granule delivery of the precursor of NE (proNE). Supporting this hypothesis, an association was demonstrated between CD63 and proNE upon coexpression in COS cells. This also involved augmented cellular retention of proNE requiring intact large extracellular loop of CD63. Furthermore, depletion of CD63 in promyelocytic HL-60 cells with RNA interference or a CD63 mutant caused reduction of cellular NE. However, the proNE steady-state level was similar to wild type in CD63-depleted clones, making it feasible to examine possible effects of CD63 on NE trafficking. Thus, depletion of CD63 led to reduced processing of proNE into mature NE and reduced constitutive secretion. Furthermore, CD63-depleted cells showed a lack of morphologically normal granules, but contained MPO-positive cytoplasmic vacuoles with a lack of proNE and NE. Collectively, our data suggest that granule proteins may cooperate in targeting; CD63 can be involved in ER or Golgi export, cellular retention, and granule targeting of proNE before storage as mature NE.

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11

Bitran, Amir, William M. Jacobs, Xiadi Zhai, and Eugene Shakhnovich. "Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps." Proceedings of the National Academy of Sciences 117, no. 3 (January 7, 2020): 1485–95. http://dx.doi.org/10.1073/pnas.1913207117.

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Many large proteins suffer from slow or inefficient folding in vitro. It has long been known that this problem can be alleviated in vivo if proteins start folding cotranslationally. However, the molecular mechanisms underlying this improvement have not been well established. To address this question, we use an all-atom simulation-based algorithm to compute the folding properties of various large protein domains as a function of nascent chain length. We find that for certain proteins, there exists a narrow window of lengths that confers both thermodynamic stability and fast folding kinetics. Beyond these lengths, folding is drastically slowed by nonnative interactions involving C-terminal residues. Thus, cotranslational folding is predicted to be beneficial because it allows proteins to take advantage of this optimal window of lengths and thus avoid kinetic traps. Interestingly, many of these proteins’ sequences contain conserved rare codons that may slow down synthesis at this optimal window, suggesting that synthesis rates may be evolutionarily tuned to optimize folding. Using kinetic modeling, we show that under certain conditions, such a slowdown indeed improves cotranslational folding efficiency by giving these nascent chains more time to fold. In contrast, other proteins are predicted not to benefit from cotranslational folding due to a lack of significant nonnative interactions, and indeed these proteins’ sequences lack conserved C-terminal rare codons. Together, these results shed light on the factors that promote proper protein folding in the cell and how biomolecular self-assembly may be optimized evolutionarily.

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12

Royster, Austin, Sheema Mir, and Mohammad Ayoub Mir. "A novel approach for the purification of aggregation prone proteins." PLOS ONE 16, no. 11 (November 22, 2021): e0260143. http://dx.doi.org/10.1371/journal.pone.0260143.

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The protein aggregation is one of the major challenges of the biotechnological industry, especially in the areas of development and commercialization of successful protein-based drug products. The inherent high aggregation tendency of proteins during various manufacturing processes, storage, and administration has significant impact upon the product quality, safety and efficacy. We have developed an interesting protein purification approach that separates the functionally active protein from inactive aggregates using a detergent concentration gradient. The C-terminally His tagged nucleocapsid protein of Crimean Congo Hemorrhagic fever virus (CCHFV) has high aggregation tendency and rapidly precipitates upon purification by NiNTA chromatography. Using the new purification approach reported here, the freshly purified protein by NiNTA chromatography was further processed using a detergent gradient. In this new purification approach the active protein is retained in the low detergent concentration zone while the inactive aggregates are promptly removed by their rapid migration to the high detergent concentration zone. The method prevented further aggregation and retained the RNA binding activity in the native protein despite numerous freeze thaw cycles. This simple approach prevents protein aggregation by rapidly separating the preformed early aggregates and creating the appropriate microenvironment for correctly folded proteins to retain their biological activity. It will be of potential importance to the biotechnological industry and other fields of protein biochemistry that routinely face the challenges of protein aggregation.

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13

Grosch, Hans-Wilhelm, and Andrej Hasilik. "Protection of Proteolysis-Prone Recombinant Proteins in Baculovirus Expression Systems." BioTechniques 24, no. 6 (June 1998): 930–34. http://dx.doi.org/10.2144/98246bm05.

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14

Menzies, Fiona M., Raphael Hourez, Sara Imarisio, Marcel Raspe, Oana Sadiq, Dhia Chandraratna, Cahir O'Kane, et al. "Puromycin-sensitive aminopeptidase protects against aggregation-prone proteins via autophagy." Human Molecular Genetics 19, no. 23 (September 9, 2010): 4573–86. http://dx.doi.org/10.1093/hmg/ddq385.

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15

Ravikumar, Brinda, and David C. Rubinsztein. "Can autophagy protect against neurodegeneration caused by aggregate-prone proteins?" NeuroReport 15, no. 16 (November 2004): 2443–45. http://dx.doi.org/10.1097/00001756-200411150-00001.

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16

Sanders, Charles R. "The Scarlet Letter: Cellular Recognition of Misfolding-Prone Membrane Proteins." Biophysical Journal 112, no. 3 (February 2017): 329a. http://dx.doi.org/10.1016/j.bpj.2016.11.1780.

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17

Lee, Yaelim, Tong Zhou, Gian Gaetano Tartaglia, Michele Vendruscolo, and Claus O. Wilke. "Translationally optimal codons associate with aggregation-prone sites in proteins." PROTEOMICS 10, no. 23 (November 2, 2010): 4163–71. http://dx.doi.org/10.1002/pmic.201000229.

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18

Sironi, Luigi, Elena Tremoli, Ingrid Miller, Uliano Guerrini, Anna Maria Calvio, Ivano Eberini, Manfred Gemeiner, Maria Asdente, Rodolfo Paoletti, and Elisabetta Gianazza. "Acute-Phase Proteins Before Cerebral Ischemia in Stroke-Prone Rats." Stroke 32, no. 3 (March 2001): 753–60. http://dx.doi.org/10.1161/01.str.32.3.753.

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19

Bernstein, Joel M., Paul M. Bronson, and Mark E. Wilson. "Immunoglobulin G Subclass Response to Major outer Membrane Proteins of Nontypable Haemophilus Influenzae in Children with Acute Otitis Media." Otolaryngology–Head and Neck Surgery 116, no. 3 (March 1997): 363–71. http://dx.doi.org/10.1016/s0194-59989770275-4.

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Children with acute otitis media as the result of nontypable Haemophilus influenzae often develop serum bactericidal and/or opsonic IgG antibodies to this organism during convalescence. Outer membrane proteins appear to be the principal targets for such antibodies. In this study we characterized the IgG subclass responses to major outer membrane proteins of nontypable H. influenzae in otitis-prone children in whom this organism had colonized. Three of the major outer membrane proteins (P2, P5, and P6) were isolated from the homologous nontypable H. influenzae strain recovered from the middle ear at the time of acute infection. Sera were obtained during the acute phase and at 1 and 6 months thereafter. The outer membrane proteins, which were isolated by preparative sodium dodecylsulfate-polyacrylamide gel electrophoresis, were used as test antigens in a quantitative IgG subclass enzyme immunoassay. The results of this analysis indicate that the temporal characteristics and distribution of IgG subclass antibodies were found to differ for each of the outer membrane proteins. Moreover, substantial variation between patients was observed with respect to both temporal characteristics and subclass distribution of the IgG response to the three outer membrane proteins. Significantly, sera from two of three otitis-prone subjects contained detectable levels of IgG antibody to the conserved P6 outer membrane protein at the time of acute infection, with serum from one subject also containing detectable levels of lgG3 antibody to this same protein. Nevertheless, the organism persisted in the middle ears of these patients. The results of this study indicate that otitis-prone children manifest a highly variable IgG subclass response to both conserved (P6) and variable (P2) outer membrane proteins of nontypable H. influenzae. Further study is required to ascertain whether these IgG subclass antibodies are biologically efficacious and whether otitis-prone children possess the immunologic maturity to respond to nontypable H. influenzae outer membrane protein-based vaccines in a predictable manner.

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20

Zhou, Ren-Bin, Xiao-Li Lu, Chen Dong, Fiaz Ahmad, Chen-Yan Zhang, and Da-Chuan Yin. "Application of protein crystallization methodologies to enhance the solubility, stability and monodispersity of proteins." CrystEngComm 20, no. 14 (2018): 1923–27. http://dx.doi.org/10.1039/c7ce02189e.

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21

Poboinev, V. V., V. V. Khrustalev, T. A. Khrustaleva, and A. N. Stojarov. "Structural transitions in mixed classes of proteins." Proceedings of the National Academy of Sciences of Belarus, Biological Series 64, no. 3 (August 17, 2019): 326–37. http://dx.doi.org/10.29235/1029-8940-2019-64-3-326-337.

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It was studied the features of amino acid content of protein regions of “alpha + beta” and “alpha/beta” classes, that are prone to structural transitions. The data have been obtained by the way of the comparison of different threedimensional structures of proteins with absolutely identical amino acid sequence. In this study we ignored fragments of proteins in which positions of atoms cannot be determined with the help of X-ray crystallography. Proteins of “alpha + beta” class are less stable than proteins of “alpha/beta” class, since the percent of structurally instable residues in them is higher. Most frequent type of structural transitions is the decrease of length of N-terminal and C-terminal parts of alpha helices and beta strands. Alpha helices and beta strands that can completely disappear (turn to coil) have also been found. The data of their amino acid content is important for the development of the method able to detect fragments of proteins prone to transitions from alpha helix to beta strand. Those fragments should combine characteristic features of amino acid content of both completely disappearing alpha helices and completely disappearing beta strands. The amino acid composition of alpha-helices capable to complete disappearance is significantly different from that for beta-strands capable to complete disappearance: frequencies of alanine, glutamine and glutamic acid usage are increased, frequencies of isoleucine, threonine and glycine usage are reduced.

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22

Bock, Josephine, Nathalie Kühnle, Julia D. Knopf, Nina Landscheidt, Jin-Gu Lee, Yihong Ye, and Marius K. Lemberg. "Rhomboid protease RHBDL4 promotes retrotranslocation of aggregation-prone proteins for degradation." Cell Reports 40, no. 6 (August 2022): 111175. http://dx.doi.org/10.1016/j.celrep.2022.111175.

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23

Branco dos Santos, J., G. Staniforth, C. Breda, F. Herrera, T. Outeiro, M. Tuite, and F. Giorgini. "B07 Aggregation-prone Proteins Exacerbate Huntingtin Toxicity In Yeast And Drosophila." Journal of Neurology, Neurosurgery & Psychiatry 85, Suppl 1 (September 1, 2014): A11. http://dx.doi.org/10.1136/jnnp-2014-309032.35.

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24

Mittag, Tanja, and Melissa R. Marzahn. "Short Aggregation-Prone Peptide Detectives: Finding Proteins and Truths about Aggregation." Journal of Molecular Biology 427, no. 2 (January 2015): 221–24. http://dx.doi.org/10.1016/j.jmb.2014.10.017.

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25

Lee, Minjung, and Jaekyoon Shin. "Triage of oxidation-prone proteins by Sqstm1/p62 within the mitochondria." Biochemical and Biophysical Research Communications 413, no. 1 (September 2011): 122–27. http://dx.doi.org/10.1016/j.bbrc.2011.08.067.

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26

Fang, Yaping, and Jianwen Fang. "Discrimination of soluble and aggregation-prone proteins based on sequence information." Molecular BioSystems 9, no. 4 (2013): 806. http://dx.doi.org/10.1039/c3mb70033j.

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27

Karabiyik, Cansu, Min Jae Lee, and David C. Rubinsztein. "Autophagy impairment in Parkinson’s disease." Essays in Biochemistry 61, no. 6 (December 12, 2017): 711–20. http://dx.doi.org/10.1042/ebc20170023.

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Parkinson’s disease (PD) is a debilitating movement disorder typically associated with the accumulation of intracytoplasmic aggregate prone protein deposits. Over recent years, increasing evidence has led to the suggestion that the mutations underlying certain forms of PD impair autophagy. Autophagy is a degradative pathway that delivers cytoplasmic content to lysosomes for degradation and represents a major route for degradation of aggregated cellular proteins and dysfunctional organelles. Autophagy up-regulation is a promising therapeutic strategy that is being explored for its potential to protect cells against the toxicity of aggregate-prone proteins in neurodegenerative diseases. Here, we describe how the mutations in different subtypes of PD can affect different stages of autophagy.

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28

Han, K. Y., J. A. Song, K. Y. Ahn, J. S. Park, H. S. Seo, and J. Lee. "Solubilization of aggregation-prone heterologous proteins by covalent fusion of stress-responsive Escherichia coli protein, SlyD." Protein Engineering Design and Selection 20, no. 11 (October 30, 2007): 543–49. http://dx.doi.org/10.1093/protein/gzm055.

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29

Auth, Mariann, Tünde Nyikó, Andor Auber, and Dániel Silhavy. "The role of RST1 and RIPR proteins in plant RNA quality control systems." Plant Molecular Biology 106, no. 3 (April 17, 2021): 271–84. http://dx.doi.org/10.1007/s11103-021-01145-9.

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AbstractTo keep mRNA homeostasis, the RNA degradation, quality control and silencing systems should act in balance in plants. Degradation of normal mRNA starts with deadenylation, then deadenylated transcripts are degraded by the SKI-exosome 3′-5′ and/or XRN4 5′-3′ exonucleases. RNA quality control systems identify and decay different aberrant transcripts. RNA silencing degrades double-stranded transcripts and homologous mRNAs. It also targets aberrant and silencing prone transcripts. The SKI-exosome is essential for mRNA homeostasis, it functions in normal mRNA degradation and different RNA quality control systems, and in its absence silencing targets normal transcripts. It is highly conserved in eukaryotes, thus recent reports that the plant SKI-exosome is associated with RST1 and RIPR proteins and that, they are required for SKI-exosome–mediated decay of silencing prone transcripts were unexpected. To clarify whether RST1 and RIPR are essential for all SKI-exosome functions or only for the elimination of silencing prone transcripts, degradation of different reporter transcripts was studied in RST1 and RIPR inactivated Nicotiana benthamiana plants. As RST1 and RIPR, like the SKI-exosome, were essential for Non-stop and No-go decay quality control systems, and for RNA silencing- and minimum ORF-mediated decay, we propose that RST1 and RIPR are essential components of plant SKI-exosome supercomplex.

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30

Ciryam, Prajwal, Isabella A. Lambert-Smith, Daniel M. Bean, Rosie Freer, Fernando Cid, Gian Gaetano Tartaglia, Darren N. Saunders, et al. "Spinal motor neuron protein supersaturation patterns are associated with inclusion body formation in ALS." Proceedings of the National Academy of Sciences 114, no. 20 (April 10, 2017): E3935—E3943. http://dx.doi.org/10.1073/pnas.1613854114.

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Amyotrophic lateral sclerosis (ALS) is a heterogeneous degenerative motor neuron disease linked to numerous genetic mutations in apparently unrelated proteins. These proteins, including SOD1, TDP-43, and FUS, are highly aggregation-prone and form a variety of intracellular inclusion bodies that are characteristic of different neuropathological subtypes of the disease. Contained within these inclusions are a variety of proteins that do not share obvious characteristics other than coaggregation. However, recent evidence from other neurodegenerative disorders suggests that disease-affected biochemical pathways can be characterized by the presence of proteins that are supersaturated, with cellular concentrations significantly greater than their solubilities. Here, we show that the proteins that form inclusions of mutant SOD1, TDP-43, and FUS are not merely a subset of the native interaction partners of these three proteins, which are themselves supersaturated. To explain the presence of coaggregating proteins in inclusions in the brain and spinal cord, we observe that they have an average supersaturation even greater than the average supersaturation of the native interaction partners in motor neurons, but not when scores are generated from an average of other human tissues. These results suggest that inclusion bodies in various forms of ALS result from a set of proteins that are metastable in motor neurons, and thus prone to aggregation upon a disease-related progressive collapse of protein homeostasis in this specific setting.

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31

Das Roy, Rishi, Manju Bhardwaj, Vasudha Bhatnagar, Kausik Chakraborty, and Debasis Dash. "How do eubacterial organisms manage aggregation-prone proteome?" F1000Research 3 (June 27, 2014): 137. http://dx.doi.org/10.12688/f1000research.4307.1.

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Eubacterial genomes vary considerably in their nucleotide composition. The percentage of genetic material constituted by guanosine and cytosine (GC) nucleotides ranges from 20% to 70%. It has been posited that GC-poor organisms are more dependent on protein folding machinery. Previous studies have ascribed this to the accumulation of mildly deleterious mutations in these organisms due to population bottlenecks. This phenomenon has been supported by protein folding simulations, which showed that proteins encoded by GC-poor organisms are more prone to aggregation than proteins encoded by GC-rich organisms. To test this proposition using a genome-wide approach, we classified different eubacterial proteomes in terms of their aggregation propensity and chaperone-dependence using multiple machine learning models. In contrast to the expected decrease in protein aggregation with an increase in GC richness, we found that the aggregation propensity of proteomes increases with GC content. A similar and even more significant correlation was obtained with the GroEL-dependence of proteomes: GC-poor proteomes have evolved to be less dependent on GroEL than GC-rich proteomes. We thus propose that a decrease in eubacterial GC content may have been selected in organisms facing proteostasis problems.

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32

Nichols, Michael R. "Disentangling aggregation‐prone proteins: a new method for isolating α‐synuclein species." Journal of Neurochemistry 153, no. 1 (February 10, 2020): 7–9. http://dx.doi.org/10.1111/jnc.14973.

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33

Carvalho, Sofia B., Hugo M. Botelho, Sónia S. Leal, Isabel Cardoso, Günter Fritz, and Cláudio M. Gomes. "Intrinsically Disordered and Aggregation Prone Regions Underlie β-Aggregation in S100 Proteins." PLoS ONE 8, no. 10 (October 1, 2013): e76629. http://dx.doi.org/10.1371/journal.pone.0076629.

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34

Uchio, Naohiro, Yoko Oma, Kazuya Toriumi, Noboru Sasagawa, Isei Tanida, Eriko Fujita, Yoriko Kouroku, Reiko Kuroda, Takashi Momoi, and Shoichi Ishiura. "Endoplasmic reticulum stress caused by aggregate-prone proteins containing homopolymeric amino acids." FEBS Journal 274, no. 21 (October 8, 2007): 5619–27. http://dx.doi.org/10.1111/j.1742-4658.2007.06085.x.

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35

Lok, Chun-Nam, Lai-King Sy, Fuli Liu, and Chi-Ming Che. "Activation of Autophagy of Aggregation-prone Ubiquitinated Proteins by Timosaponin A-III." Journal of Biological Chemistry 286, no. 36 (July 8, 2011): 31684–96. http://dx.doi.org/10.1074/jbc.m110.202531.

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36

Kang, S. H., D. M. Kim, H. J. Kim, S. Y. Jun, K. Y. Lee, and H. J. Kim. "Cell-Free Production of Aggregation-Prone Proteins in Soluble and Active Forms." Biotechnology Progress 21, no. 5 (October 7, 2005): 1412–19. http://dx.doi.org/10.1021/bp050087y.

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37

Melnik, Andre, Valentina Cappelletti, Federico Vaggi, Ilaria Piazza, Marco Tognetti, Carmen Schwarz, Gea Cereghetti, et al. "Comparative analysis of the intracellular responses to disease-related aggregation-prone proteins." Journal of Proteomics 225 (August 2020): 103862. http://dx.doi.org/10.1016/j.jprot.2020.103862.

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38

Ravikumar, B. "Aggregate-prone proteins with polyglutamine and polyalanine expansions are degraded by autophagy." Human Molecular Genetics 11, no. 9 (May 1, 2002): 1107–17. http://dx.doi.org/10.1093/hmg/11.9.1107.

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39

Murakumo, Yoshiki, Yukiko Ogura, Hideshi Ishii, Shin-ichiro Numata, Masatoshi Ichihara, Carlo M. Croce, Richard Fishel, and Masahide Takahashi. "Interactions in the Error-prone Postreplication Repair Proteins hREV1, hREV3, and hREV7." Journal of Biological Chemistry 276, no. 38 (August 2, 2001): 35644–51. http://dx.doi.org/10.1074/jbc.m102051200.

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40

Yacoubian, Talene A., and David G. Standaert. "Reaping what you sow: Cross-seeding between aggregation-prone proteins in neurodegeneration." Movement Disorders 29, no. 3 (January 2, 2014): 306. http://dx.doi.org/10.1002/mds.25766.

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41

Higuchi, Kae, Takashi Yabuki, Masahiro Ito, and Takanori Kigawa. "Cold shock proteins improve E. coli cell‐free synthesis in terms of soluble yields of aggregation‐prone proteins." Biotechnology and Bioengineering 117, no. 6 (March 26, 2020): 1628–39. http://dx.doi.org/10.1002/bit.27326.

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42

Kleppe, April Snofrid, and Erich Bornberg-Bauer. "Robustness by intrinsically disordered C-termini and translational readthrough." Nucleic Acids Research 46, no. 19 (September 22, 2018): 10184–94. http://dx.doi.org/10.1093/nar/gky778.

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Abstract During protein synthesis genetic instructions are passed from DNA via mRNA to the ribosome to assemble a protein chain. Occasionally, stop codons in the mRNA are bypassed and translation continues into the untranslated region (3′-UTR). This process, called translational readthrough (TR), yields a protein chain that becomes longer than would be predicted from the DNA sequence alone. Protein sequences vary in propensity for translational errors, which may yield evolutionary constraints by limiting evolutionary paths. Here we investigated TR in Saccharomyces cerevisiae by analysing ribosome profiling data. We clustered proteins as either prone or non-prone to TR, and conducted comparative analyses. We find that a relatively high frequency (5%) of genes undergo TR, including ribosomal subunit proteins. Our main finding is that proteins undergoing TR are highly expressed and have a higher proportion of intrinsically disordered C-termini. We suggest that highly expressed proteins may compensate for the deleterious effects of TR by having intrinsically disordered C-termini, which may provide conformational flexibility but without distorting native function. Moreover, we discuss whether minimizing deleterious effects of TR is also enabling exploration of the phenotypic landscape of protein isoforms.

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Onwezen, Marleen C., Muriel C. D. Verain, and Hans Dagevos. "Social Norms Support the Protein Transition: The Relevance of Social Norms to Explain Increased Acceptance of Alternative Protein Burgers over 5 Years." Foods 11, no. 21 (October 28, 2022): 3413. http://dx.doi.org/10.3390/foods11213413.

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Developing alternative protein products—based on protein sources other than regular meat—is a possible pathway to counter environmental and health burdens. However, alternative proteins are not always accepted by consumers, and more research is needed to support a shift to more alternative proteins. Prior studies have mainly focused on individual drivers and perceptions; although we expect that social norms—the perceptions of the opinions of relevant others—are highly relevant in accepting alternative proteins. Online surveys were conducted among 2461 respondents in 2015 and 2000 respondents in 2019 (cross-sectional datasets); a subsample (n = 500) responded to both surveys (longitudinal dataset). We add to the literature by (1) demonstrating the added explanatory value of social norms beyond a range of individual drivers; (2) showing that this finding holds over time, and (3) comparing the impact of social norms across different dietary consumer groups. Meat lovers and flexitarians are more prone to follow social norms whereas meat abstainers are more prone to follow their individual attitudes and values. This study highlights the relevance of investigations beyond personal variables such as personal norms and attitudes and underscores the relevance of considering the social aspects of accepting alternative proteins.

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Davis, John N., and Anthony N. van den Pol. "Viral Mutagenesis as a Means for Generating Novel Proteins." Journal of Virology 84, no. 3 (November 11, 2009): 1625–30. http://dx.doi.org/10.1128/jvi.01747-09.

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ABSTRACT We demonstrate that a mutation-prone virus engineered to express a foreign gene is an expedient means for generating novel mutant nonviral proteins in mammalian cells. Using vesicular stomatitis virus to express a gene coding for a fluorescent DsRed protein, a number of green mutant variants including a new variant not previously described were rapidly isolated from infected cells, sequenced, and cloned. Similar methods may be useful in the development of physiologically sensitive fluorescent reporter proteins and directed evolution or mutagenesis of proteins in general.

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Sánchez-Pérez, Ana María, Berta Claramonte-Clausell, Juan Vicente Sánchez-Andrés, and María Trinidad Herrero. "Parkinson’s Disease and Autophagy." Parkinson's Disease 2012 (2012): 1–6. http://dx.doi.org/10.1155/2012/429524.

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It is generally accepted that a correlation between neurodegenerative disease and protein aggregation in the brain exists; however, a causal relationship has not been elucidated. In neurons, failure of autophagy may result in the accumulation of aggregate-prone proteins and subsequent neurodegeneration. Thus, pharmacological induction of autophagy to enhance the clearance of intracytoplasmic aggregate-prone proteins has been considered as a therapeutic strategy to ameliorate pathology in cell and animal models of neurodegenerative disorders. However, autophagy has also been found to be a factor in the onset of these diseases, which raises the question of whether autophagy induction is an effective therapeutic strategy, or, on the contrary, can result in cell death. In this paper, we will first describe the autophagic machinery, and we will consider the literature to discuss the neuroprotective effects of autophagy.

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Kaur, Ravinder, Janet R. Casey, and Michael E. Pichichero. "Serum Antibody Response to Five Streptococcus pneumoniae Proteins During Acute Otitis Media in Otitis-prone and Non–otitis-prone Children." Pediatric Infectious Disease Journal 30, no. 8 (August 2011): 645–50. http://dx.doi.org/10.1097/inf.0b013e31821c2d8b.

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Metskas, Lauren Ann, and Elizabeth Rhoades. "Single-Molecule FRET of Intrinsically Disordered Proteins." Annual Review of Physical Chemistry 71, no. 1 (April 20, 2020): 391–414. http://dx.doi.org/10.1146/annurev-physchem-012420-104917.

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Intrinsically disordered proteins (IDPs) are now widely recognized as playing critical roles in a broad range of cellular functions as well as being implicated in diverse diseases. Their lack of stable secondary structure and tertiary interactions, coupled with their sensitivity to measurement conditions, stymies many traditional structural biology approaches. Single-molecule Förster resonance energy transfer (smFRET) is now widely used to characterize the physicochemical properties of these proteins in isolation and is being increasingly applied to more complex assemblies and experimental environments. This review provides an overview of confocal diffusion-based smFRET as an experimental tool, including descriptions of instrumentation, data analysis, and protein labeling. Recent papers are discussed that illustrate the unique capability of smFRET to provide insight into aggregation-prone IDPs, protein–protein interactions involving IDPs, and IDPs in complex experimental milieus.

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Sun, Xiaolin, William T. Jones, and Erik H. A. Rikkerink. "GRAS proteins: the versatile roles of intrinsically disordered proteins in plant signalling." Biochemical Journal 442, no. 1 (January 27, 2012): 1–12. http://dx.doi.org/10.1042/bj20111766.

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IDPs (intrinsically disordered proteins) are highly abundant in eukaryotic proteomes and important for cellular functions, especially in cell signalling and transcriptional regulation. An IDR (intrinsically disordered region) within an IDP often undergoes disorder-to-order transitions upon binding to various partners, allowing an IDP to recognize and bind different partners at various binding interfaces. Plant-specific GRAS proteins play critical and diverse roles in plant development and signalling, and act as integrators of signals from multiple plant growth regulatory and environmental inputs. Possessing an intrinsically disordered N-terminal domain, the GRAS proteins constitute the first functionally required unfoldome from the plant kingdom. Furthermore, the N-terminal domains of GRAS proteins contain MoRFs (molecular recognition features), short interaction-prone segments that are located within IDRs and are able to recognize their interacting partners by undergoing disorder-to-order transitions upon binding to these specific partners. These MoRFs represent potential protein–protein binding sites and may be acting as molecular bait in recognition events during plant development. Intrinsic disorder provides GRAS proteins with a degree of binding plasticity that may be linked to their functional versatility. As an overview of structure–function relationships for GRAS proteins, the present review covers the main biological functions of the GRAS family, the IDRs within these proteins and their implications for understanding mode-of-action.

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Monti, Paola, Vaclav Brazda, Natália Bohálová, Otília Porubiaková, Paola Menichini, Andrea Speciale, Renata Bocciardi, Alberto Inga, and Gilberto Fronza. "Evaluating the Influence of a G-Quadruplex Prone Sequence on the Transactivation Potential by Wild-Type and/or Mutant P53 Family Proteins through a Yeast-Based Functional Assay." Genes 12, no. 2 (February 15, 2021): 277. http://dx.doi.org/10.3390/genes12020277.

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P53, P63, and P73 proteins belong to the P53 family of transcription factors, sharing a common gene organization that, from the P1 and P2 promoters, produces two groups of mRNAs encoding proteins with different N-terminal regions; moreover, alternative splicing events at C-terminus further contribute to the generation of multiple isoforms. P53 family proteins can influence a plethora of cellular pathways mainly through the direct binding to specific DNA sequences known as response elements (REs), and the transactivation of the corresponding target genes. However, the transcriptional activation by P53 family members can be regulated at multiple levels, including the DNA topology at responsive promoters. Here, by using a yeast-based functional assay, we evaluated the influence that a G-quadruplex (G4) prone sequence adjacent to the p53 RE derived from the apoptotic PUMA target gene can exert on the transactivation potential of full-length and N-terminal truncated P53 family α isoforms (wild-type and mutant). Our results show that the presence of a G4 prone sequence upstream or downstream of the P53 RE leads to significant changes in the relative activity of P53 family proteins, emphasizing the potential role of structural DNA features as modifiers of P53 family functions at target promoter sites.

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Dumas, Louis, Francesca Zito, Pascaline Auroy, Xenie Johnson, Gilles Peltier, and Jean Alric. "Structure-Function Analysis of Chloroplast Proteins via Random Mutagenesis Using Error-Prone PCR." Plant Physiology 177, no. 2 (April 27, 2018): 465–75. http://dx.doi.org/10.1104/pp.17.01618.

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