Investigation of the sequence features controlling aggregation or degradation of prion-like proteins

2017 Summer.Includes bibliographical references.Protein aggregates result from the conversion of soluble proteins to an insoluble form. In some cases, protein aggregates are capable of catalyzing the conversion of their soluble protein counterparts to the insoluble form, resulting in a mode of molecular self-replication. Many of these infectious proteins, or "prions", have been identified and characterized in yeast. This has led to the development of prediction algorithms designed to identify protein domains capable of forming prions. Recently, a number human proteins with aggregation-prone prion-like domains (PrLDs) have been identified, and mutations within PrLDs have been linked to muscular and neurodegenerative disorders. However, the number and diversity of PrLD mutations linked to disease are currently limited. Therefore, the extent to which a broad assortment of PrLD mutations affect intrinsic aggregation propensity, and how well this correlates with aggregation in a cellular context, has not been systematically examined. In Chapter 2, I present evidence suggesting that our prion aggregation prediction algorithm (PAPA) is capable of predicting the effects of a diverse range of mutations on the aggregation propensity of PrLDs in vitro and in yeast. PAPA was also able to predict the effects of many but not all PrLD mutations when the protein was expressed in Drosophila, but with slightly. Therefore, while great strides have been made in predicting intrinsic aggregation propensity, a more complete understanding of the cellular factors that influence aggregation in vivo may lead to further improvement of prion prediction methods. Many intracellular protein quality control factors specialize in recognizing and degrading aggregation-prone proteins. Therefore, prions must evade or outcompete these quality control systems in order to form and propagate in a cellular context. However, the sequence features that promote degradation versus aggregation of prion domains and PrLDs have not been systematically defined. In Chapter 3, I present evidence that aggregation propensity and degradation propensity can be uncoupled in multiple ways. First, we find that only a subset of classically aggregation-promoting amino acids elicit a strong degradation response in PrLDs. Second, the amino acids that promoted degradation of the PrLDs did not induce degradation of a glutamine/asparagine (Q/N)-rich prion domain, and instead led to a dose-dependent increase in the frequency of spontaneous prion formation, suggesting that protein features surrounding aggregation-prone amino acids can modulate their ultimate effects. Furthermore, degradation suppression correlated with Q/N content of the surrounding prion domain, potentially indicating an underappreciated role for these residues in yeast prion domains. The protein features that foster susceptibility or resistance to degradation are further explored in Chapter 4. We find that Q/N-rich domains resist degradation in a primary sequence-independent manner, and can even exert a dominant degradation-inhibiting effect when coupled to a degradation-prone PrLD. Furthermore, susceptibility to degradation was a relatively de-centralized feature of the PrLD, requiring a large portion of the domain surrounding degradation-promoting amino acids to permit efficient protein turnover. Collectively, these results provide key insights into the relationship between intrinsically aggregation-prone protein features and the ability to aggregate in the context of intracellular protein quality control factors

KINETIC EFFECT OF A FOUR-STEP AND STEP-CLOSE APPROACH IN A VOLLEYBALL SPIKE JUMP FOR FEMALE ATHLETES

The purpose of the present study was to investigate the kinetic difference between two different volleyball spike jump techniques: a complete four-step approach and step-close approach. Five female collegiate volleyball players (age: 20.40 ± 1.85, height: 1.80 ± 0.02 m, body weight: 71.71 ± 4.18 kg) who play the middle hitter position were recruited. Each participant performed ten jumps for both four-step and step-close approaches and takeoff from two Kistler force platforms. Results indicated that there is no significant difference (P = .18) of vertical propulsive impulse between the two types of jump. The anterior-posterior (AP) net impulse of the four-step approach was significantly greater than a step-close approach (P < .01). Finally, the contact duration of propulsive phase for step-close technique is significantly greater than four-step approach technique (P < .05)

Self-referencing rates in biological disciplines

The use of citation counts (among other bibliometrics) as a facet of academic research evaluation can influence citation behavior in scientific publications. One possible unintended consequence of this bibliometric is excessive self-referencing, where an author favors referencing their own publications over related publications from different research groups. Peer reviewers are often prompted by journals to determine whether references listed in the manuscript under review are unbiased, but there is no consensus on what is considered “excessive” self-referencing. Here, self-referencing rates are examined across multiple journals in the fields of biology, genetics, computational biology, medicine, pathology, and cell biology. Median self-referencing rates are between 8–13% across a range of journals within these disciplines. However, self-referencing rates vary as a function of total number of references, number of authors, author status/rank, author position, and total number of publications for each author. Importantly, these relationships exhibit interdisciplinary and journal-dependent differences that are not captured by examining broader fields in aggregate (e.g., Biology, Chemistry, Physics, etc.). These results provide useful statistical guidelines for authors, editors, reviewers, and journals when considering referencing practices for individual publications, and highlight the effects of additional factors influencing self-referencing rates

Generalizable Compositional Features Influencing the Proteostatic Fates of Polar Low-Complexity Domains

Protein aggregation is associated with a growing list of human diseases. A substantial fraction of proteins in eukaryotic proteomes constitutes a proteostasis network—a collection of proteins that work together to maintain properly folded proteins. One of the overarching functions of the proteostasis network is the prevention or reversal of protein aggregation. How proteins aggregate in spite of the anti-aggregation activity of the proteostasis machinery is incompletely understood. Exposed hydrophobic patches can trigger degradation by the ubiquitin-proteasome system, a key branch of the proteostasis network. However, in a recent study, we found that model glycine (G)-rich or glutamine/asparagine (Q/N)-rich prion-like domains differ in their susceptibility to detection and degradation by this system. Here, we expand upon this work by examining whether the features controlling the degradation of our model prion-like domains generalize broadly to G-rich and Q/N-rich domains. Experimentally, native yeast G-rich domains in isolation are sensitive to the degradation-promoting effects of hydrophobic residues, whereas native Q/N-rich domains completely resist these effects and tend to aggregate instead. Bioinformatic analyses indicate that native G-rich domains from yeast and humans tend to avoid degradation-promoting features, suggesting that the proteostasis network may act as a form of selection at the molecular level that constrains the sequence space accessible to G-rich domains. However, the sensitivity or resistance of G-rich and Q/N-rich domains, respectively, was not always preserved in their native protein contexts, highlighting that proteins can evolve other sequence features to overcome the intrinsic sensitivity of some LCDs to degradation

Table_3_Self-referencing rates in biological disciplines.XLSX

The use of citation counts (among other bibliometrics) as a facet of academic research evaluation can influence citation behavior in scientific publications. One possible unintended consequence of this bibliometric is excessive self-referencing, where an author favors referencing their own publications over related publications from different research groups. Peer reviewers are often prompted by journals to determine whether references listed in the manuscript under review are unbiased, but there is no consensus on what is considered “excessive” self-referencing. Here, self-referencing rates are examined across multiple journals in the fields of biology, genetics, computational biology, medicine, pathology, and cell biology. Median self-referencing rates are between 8–13% across a range of journals within these disciplines. However, self-referencing rates vary as a function of total number of references, number of authors, author status/rank, author position, and total number of publications for each author. Importantly, these relationships exhibit interdisciplinary and journal-dependent differences that are not captured by examining broader fields in aggregate (e.g., Biology, Chemistry, Physics, etc.). These results provide useful statistical guidelines for authors, editors, reviewers, and journals when considering referencing practices for individual publications, and highlight the effects of additional factors influencing self-referencing rates.</p

Table_4_Self-referencing rates in biological disciplines.XLSX

The use of citation counts (among other bibliometrics) as a facet of academic research evaluation can influence citation behavior in scientific publications. One possible unintended consequence of this bibliometric is excessive self-referencing, where an author favors referencing their own publications over related publications from different research groups. Peer reviewers are often prompted by journals to determine whether references listed in the manuscript under review are unbiased, but there is no consensus on what is considered “excessive” self-referencing. Here, self-referencing rates are examined across multiple journals in the fields of biology, genetics, computational biology, medicine, pathology, and cell biology. Median self-referencing rates are between 8–13% across a range of journals within these disciplines. However, self-referencing rates vary as a function of total number of references, number of authors, author status/rank, author position, and total number of publications for each author. Importantly, these relationships exhibit interdisciplinary and journal-dependent differences that are not captured by examining broader fields in aggregate (e.g., Biology, Chemistry, Physics, etc.). These results provide useful statistical guidelines for authors, editors, reviewers, and journals when considering referencing practices for individual publications, and highlight the effects of additional factors influencing self-referencing rates.</p

Image_4_Self-referencing rates in biological disciplines.TIF

The use of citation counts (among other bibliometrics) as a facet of academic research evaluation can influence citation behavior in scientific publications. One possible unintended consequence of this bibliometric is excessive self-referencing, where an author favors referencing their own publications over related publications from different research groups. Peer reviewers are often prompted by journals to determine whether references listed in the manuscript under review are unbiased, but there is no consensus on what is considered “excessive” self-referencing. Here, self-referencing rates are examined across multiple journals in the fields of biology, genetics, computational biology, medicine, pathology, and cell biology. Median self-referencing rates are between 8–13% across a range of journals within these disciplines. However, self-referencing rates vary as a function of total number of references, number of authors, author status/rank, author position, and total number of publications for each author. Importantly, these relationships exhibit interdisciplinary and journal-dependent differences that are not captured by examining broader fields in aggregate (e.g., Biology, Chemistry, Physics, etc.). These results provide useful statistical guidelines for authors, editors, reviewers, and journals when considering referencing practices for individual publications, and highlight the effects of additional factors influencing self-referencing rates.</p

Table_2_Self-referencing rates in biological disciplines.XLSX

The use of citation counts (among other bibliometrics) as a facet of academic research evaluation can influence citation behavior in scientific publications. One possible unintended consequence of this bibliometric is excessive self-referencing, where an author favors referencing their own publications over related publications from different research groups. Peer reviewers are often prompted by journals to determine whether references listed in the manuscript under review are unbiased, but there is no consensus on what is considered “excessive” self-referencing. Here, self-referencing rates are examined across multiple journals in the fields of biology, genetics, computational biology, medicine, pathology, and cell biology. Median self-referencing rates are between 8–13% across a range of journals within these disciplines. However, self-referencing rates vary as a function of total number of references, number of authors, author status/rank, author position, and total number of publications for each author. Importantly, these relationships exhibit interdisciplinary and journal-dependent differences that are not captured by examining broader fields in aggregate (e.g., Biology, Chemistry, Physics, etc.). These results provide useful statistical guidelines for authors, editors, reviewers, and journals when considering referencing practices for individual publications, and highlight the effects of additional factors influencing self-referencing rates.</p

Image_1_Self-referencing rates in biological disciplines.TIF

The use of citation counts (among other bibliometrics) as a facet of academic research evaluation can influence citation behavior in scientific publications. One possible unintended consequence of this bibliometric is excessive self-referencing, where an author favors referencing their own publications over related publications from different research groups. Peer reviewers are often prompted by journals to determine whether references listed in the manuscript under review are unbiased, but there is no consensus on what is considered “excessive” self-referencing. Here, self-referencing rates are examined across multiple journals in the fields of biology, genetics, computational biology, medicine, pathology, and cell biology. Median self-referencing rates are between 8–13% across a range of journals within these disciplines. However, self-referencing rates vary as a function of total number of references, number of authors, author status/rank, author position, and total number of publications for each author. Importantly, these relationships exhibit interdisciplinary and journal-dependent differences that are not captured by examining broader fields in aggregate (e.g., Biology, Chemistry, Physics, etc.). These results provide useful statistical guidelines for authors, editors, reviewers, and journals when considering referencing practices for individual publications, and highlight the effects of additional factors influencing self-referencing rates.</p