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Showing 1 to 20 of 145 for “"intrinsically disordered"”.
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Probing Order within Intrinsically Disordered Proteins
… the field of natively unfolded – or so-called intrinsically disordered – proteins, is rapidly developing. Protein disorder content has been positively correlated with organismal complexity, with over thirty percent of eukaryotic proteins predicted to contain disordered regions. However, the …
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Intrinsically Disordered Proteins within the Genome
… structure determination, the `plasticity’ of the disordered proteins challenges the use of such ensemble averaged techniques. In this thesis, Molecular Dynamics simulations are used to characterize the disordered regions of three proteins that form the core of chromatin structure: histones, linker …
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Modeling and simulation of intrinsically disordered biomolecular systems
Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2024-05-01
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Decoding the Sequence-Dependent Properties of Intrinsically Disordered Proteins
… binding partner, thus imparting functionality. Intrinsically disordered proteins (IDPs) lack a well-defined structure yet manage to interact with a variety of partners. At a basic level we can use amino-acid sequences to predict disordered content, but the sequence profile of an IDP can tell us …
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Intrinsically disordered proteins in molecular recognition and structural proteomics
Intrinsically disordered proteins (IDPs) are abundant in nature, being more prevalent in the proteomes of eukaryotes than those of bacteria or archaea. As introduced in Chapter I, these proteins, or portions of these proteins, lack stable equilibrium structures and instead have dynamic …
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Investigating Cold Adaptation of Intrinsically Disordered Proteins in p53 Homologs
No abstract prepared.
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Structural and functional studies of intrinsically disordered fibronectin-binding proteins
… (Fn). FnBPs are predicted to contain a series of intrinsically disordered Fn-binding repeats (FnBRs), which undergo a disorder-to-order transition on binding up to five F1-modules (1−5F1) from the N terminal domain of Fn through a tandem β-zipper interaction. This work investigated these …
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An investigation of intrinsically disordered proteins in Gram-negative bacteria
Sporulation in Gram-positive bacteria results in the production of small acid-soluble proteins (SASPs) to coat the spore DNA and shield it from UV radiation. While orthologs of these SASPs exist in many sporulating and non-sporulating bacteria, they are noticeably absent from the Gram-negative …
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Modeling intrinsically disordered proteins ; a comprehensive study of [alpha]-synuclein
… challenging to study because it is an Intrinsically Disordered Protein (IDP); i.e., it lacks a well-defined structure in aqueous solution. Unlike folded proteins, IDPs typically interconvert between many different conformations during their biological lifetime. In this thesis we apply …
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A Highly Charged Topic: Intrinsically Disordered Proteins and Protein pKa Values
Intrinsically disordered proteins (IDPs) are known not only for their roles in disease but also for their conformational flexibility, which makes them elusive for experimentation. We consider the role played by theory and simulation in resolving important questions pertaining to IDP structure and …
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Sequence-Based Properties that Identify Intrinsically Disordered Phase-Separating Protein Regions
… drive liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs). This phenomenon is critical in many cellular processes (including RNA metabolism, chromatin rearrangement, and signal transduction), and known to be driven primarily, but not exclusively, by IDPs. To fully …
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Intrinsically Disordered Protein Polymer Libraries as Tools to Understand Protein Hydrophobicity
<p>Intrinsically disordered protein polymers (IDPPs) are repetitive biopolymers that, when enriched with prolines, glycines, and aliphatic amino acids, have observable lower critical solution temperature (LCST) phase transition behavior at physiologically relevant temperature and concentration …
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Primary Structure and Solution Conditions Determine Conformational Ensemble Properties of Intrinsically Disordered Proteins
<p>Intrinsically disordered proteins (IDPs) are a class of proteins that do not exhibit well-defined three-dimensional structures. The absence of structure is intrinsic to their amino acid sequences, which are characterized by low hydrophobicity and high net charge per residue compared to folded …
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Regulation of E. coli SOS mutagenesis by dimeric intrinsically disordered umuD gene products
… umuD gene products share characteristics with intrinsically disordered proteins, which lack a defined secondary or tertiary structure when purified and many of which have important roles in regulation. Counterintuitively, UmuD2 and UmuD'2 form stable homodimers in vitro at concentrations where …
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Characterizing Multivalent Interactions Between Folded Protein Domains and Intrinsically Disordered Regions or Peptide Substrates
… on interactions between structured domains and intrinsically disordered regions or peptide substrates.The subject of Chapter two is prolyl isomerase Ess1, which is an essential enzyme found in Saccharomyces cerevisiae. Ess1 regulates the transcription and co-transcriptional RNA processing by …
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Biomolecular condensation of intrinsically disordered regions in P. falciparum and H. sapiens transcription factors
… control. Biomolecular condensation, driven by intrinsically disordered regions (IDRs) in proteins, has emerged as a previously underappreciated mechanism of cellular compartmentalisation and regulation. The study of eukaryotic transcription has been revolutionised by the understanding that …
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Phosphoserine Incorporation into the Intrinsically Disordered N-terminal Domain of the p53 Tumor Suppressor Protein
… usually occurs within protein regions that are intrinsically disordered, quantitative and structural descriptions of phosphorylation effects in intrinsically disordered proteins (IDPs) are needed to understand the molecular basis of key aspects of development, aging, and disease. A few studies …
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Characterization of the Roles of Intrinsically Disordered Regions from RNA-Binding Proteins in Phase Separation
… enrich RNA and RNA-binding proteins containing intrinsically disordered regions (IDRs). I demonstrate that IDRs, coupled with RNA binding domain and RNA, can phase separate in vitro, producing dynamic liquid droplets. Over time, these droplets mature into more stable states, as assessed by …
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Mechanisms of Adsorption and Surface-Mediated Aggregation of Intrinsically Disordered Protein Tau at Model Surfaces
The adsorption and aggregation of an intrinsically disordered soluble protein, tau, into insoluble filaments is a defining hallmark of many neurodegenerative diseases, commonly referred to as tauopathies. In its native state, the protein tau’s function is to promote the assembly, and aid in the …
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Elucidating the Structural and Dynamical Properties of the Intrinsically Disordered Protein Nrf2 Using Molecular Dynamics Simulations
… transcriptional activation. Since Nrf2 is an intrinsically disordered protein (IDP), molecular dynamics simulations were employed to capture its dynamic nature and conformational heterogeneity. The Neh4 and Neh5 domains differed in their structural propensities, where the phosphorylation of …
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