CHARACTERIZATION OF POLYUBIQUITIN CHAINS BY MASS SPECTROMETRY

The work outlined in this dissertation will allow biochemists and cellular biologists to characterize polyubiquitin chains involved in their cellular environment by following a facile mass spectrometric based workflow. The characterization of polyubiquitin chains has been of interest since their discovery in 1984. The profound effects of ubiquitination on the movement and processing of cellular proteins depend exclusively on the structures of mono and polyubiquitin modifications anchored or unanchored on the protein within the cellular environment. However, structure-function studies have been hindered by the difficulty in identifying complex chain structures due to limited instrument capabilities of the past. Genetic mutations or reiterative immunoprecipitations have been used previously to characterize the polyubiquitin chains, but their tedium makes it difficult to study a broad ubiquitinome. Top-down and middle-out mass spectral based proteomic studies have been reported for polyubiquitin and have had success in characterizing parts of the chain, but no method to date has been successful at differentiating all theoretical ubiquitin chain isomers (ubiquitin chain lengths from dimer to tetramer alone have 1340 possible isomers). The workflow presented here can identify chain length, topology and linkages present using a chromatographic-time-scale compatible, LC-MS/MS based workflow. To accomplish this feat, the strategy had to exploit the most recent advances in top-down mass spectrometry. This included the most advanced electron transfer dissociation (ETD) activation and sensitivity for large masses from the orbitrap Fusion Lumos. The spectral interpretation had to be done manually with the aid of a graphical interface to assign mass shifts because of a lack of software capable to interpret fragmentation across isopeptide linkages. However, the method outlined can be applied to any mass spectral based system granted it results in extensive fragmentation across the polyubiquitin chain; making this method adaptable to future advances in the field.

Parsing, Generation and Grammar

Humans use their grammatical knowledge in more than one way. On one hand, they use it to understand what others say. On the other hand, they use it to say what they want to convey to others (or to themselves). In either case, they need to assemble the structure of sentences in a systematic fashion, in accordance with the grammar of their language. Despite the fact that the structures that comprehenders and speakers assemble are systematic in an identical fashion (i.e., obey the same grammatical constraints), the two ‘modes’ of assembling sentence structures might or might not be performed by the same cognitive mechanisms. Currently, the field of psycholinguistics implicitly adopts the position that they are supported by different cognitive mechanisms, as evident from the fact that most psycholinguistic models seek to explain either comprehension or production phenomena. The potential existence of two independent cognitive systems underlying linguistic performance doubles the problem of linking the theory of linguistic knowledge and the theory of linguistic performance, making the integration of linguistics and psycholinguistic harder. This thesis thus aims to unify the structure building system in comprehension, i.e., parser, and the structure building system in production, i.e., generator, into one, so that the linking theory between knowledge and performance can also be unified into one. I will discuss and unify both existing and new data pertaining to how structures are assembled in understanding and speaking, and attempt to show that the unification between parsing and generation is at least a plausible research enterprise. In Chapter 1, I will discuss the previous and current views on how parsing and generation are related to each other. I will outline the challenges for the current view that the parser and the generator are the same cognitive mechanism. This single system view is discussed and evaluated in the rest of the chapters. In Chapter 2, I will present new experimental evidence suggesting that the grain size of the pre-compiled structural units (henceforth simply structural units) is rather small, contrary to some models of sentence production. In particular, I will show that the internal structure of the verb phrase in a ditransitive sentence (e.g., The chef is donating the book to the monk) is not specified at the onset of speech, but is specified before the first internal argument (the book) needs to be uttered. I will also show that this timing of structural processes with respect to the verb phrase structure is earlier than the lexical processes of verb internal arguments. These two results in concert show that the size of structure building units in sentence production is rather small, contrary to some models of sentence production, yet structural processes still precede lexical processes. I argue that this view of generation resembles the widely accepted model of parsing that utilizes both top-down and bottom-up structure building procedures. In Chapter 3, I will present new experimental evidence suggesting that the structural representation strongly constrains the subsequent lexical processes. In particular, I will show that conceptually similar lexical items interfere with each other only when they share the same syntactic category in sentence production. The mechanism that I call syntactic gating, will be proposed, and this mechanism characterizes how the structural and lexical processes interact in generation. I will present two Event Related Potential (ERP) experiments that show that the lexical retrieval in (predictive) comprehension is also constrained by syntactic categories. I will argue that the syntactic gating mechanism is operative both in parsing and generation, and that the interaction between structural and lexical processes in both parsing and generation can be characterized in the same fashion. In Chapter 4, I will present a series of experiments examining the timing at which verbs’ lexical representations are planned in sentence production. It will be shown that verbs are planned before the articulation of their internal arguments, regardless of the target language (Japanese or English) and regardless of the sentence type (active object-initial sentence in Japanese, passive sentences in English, and unaccusative sentences in English). I will discuss how this result sheds light on the notion of incrementality in generation. In Chapter 5, I will synthesize the experimental findings presented in this thesis and in previous research to address the challenges to the single system view I outlined in Chapter 1. I will then conclude by presenting a preliminary single system model that can potentially capture both the key sentence comprehension and sentence production data without assuming distinct mechanisms for each.