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Showing 1 to 20 of 59 for “"Protein Domain"”.
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Classification of Protein Domain Movements using Dynamic Contact Graphs
Protein domain movements are of critical importance for understanding macromolecular function, but little is understood about how they are controlled, their energetics, and how to characterize them into meaningful descriptions for the purpose of understanding their relation to function. Here we …
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Analysis of variation in protein domain families and interfaces
… availability of over 110,000 three-dimensional protein structures allows the structural context of many SNPs to be examined in atomic detail. Interfaces are essential sites for protein function and adaptation, and key in a majority of biological processes. A computational framework, ProIntVar, …
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Molecular Dynamics Simulation of Force-Induced Protein Domain Unfolding
Force-induced protein domain unfolding has been studied by steered molecular dynamics simulations (SMD). Two pulling protocols were adopted in the simulation. SMD with constant velocity pulling protocol qualitatively reproduced atomic force microscopy (AFM) observation that immunoglobulin and …
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Thioaptamers Targeting Dengue Virus Type-2 Envelope Protein Domain III
… the host cell membrane using surface envelope protein (E). The E protein ectodomain contains three domains, EDI, EDII and EDIII. The highly immunogenic EDIII is the putative receptor binding domain that also binds neutralizing antibodies. Thus, EDIII is an attractive target for development of …
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Discovery of Novel Ubiquitin- and Methylation-Dependent Interactions Using Protein Domain Microarrays
… signal transduction by interacting with "reader" proteins. Protein domain microarray is a high throughput platform to identify novel readers for PTMs. In this dissertation, I applied two protein domain microarrays identifying novel readers for histone H2Aub1 and H2Bub1, and H3TM K4me3. …
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Origin of viruses revealed by the genomic study of protein domain structures
… describing the evolution of proteomes and protein domain structures of viruses and cells that define viruses as a ‘fourth supergroup’ along with cellular superkingdoms Archaea, Bacteria, and Eukarya. Universal trees of life (uToLs) place viruses at their root and trees of domains indicate …
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Structure-function of Dengue 2 virus envelope protein domain III with neutralizing antibodies
… disease caused by the DENVs and the envelope (E) protein is the primary target. Potency of neutralization has been correlated with the particular domain on the E protein recognized by a neutralizing antibody, with domain III of the E protein (ED3) being the target of the most potent neutralizing …
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Tracing history of protein domain organization, functional loops, and dipeptides with chronologies and networks
This Dissertation was approved for publication on 2022-07-14 at 09:55.
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STRUCTURE DETERMINATION, BIOCHEMICAL CHARACTERIZATION, AND PROTEIN ENGINEERING OF THE ACYL CARRIER PROTEIN DOMAIN FROM 6-DEOXYERYTHRONOLIDE B SYNTHASE
… drug erythromycin. DEBS is a large multi-domain enzyme complex containing multiple enzymatic domains, including acyl carrier protein (ACP). ACPs are involved in chain transfer and chain elongation during polyketide biosynthesis. Structural characterization of all seven ACPs could lead to a …
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Exploring the function and evolution of proteins using domain families
Proteins are frequently composed of multiple domains which fold independently. These are often evolutionarily distinct units which can be adapted and reused in other proteins. The classification of protein domains into evolutionary families facilitates the study of their evolution and function. In …
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Simulation and optimization tools to study design principles of biological networks
… of signal transduction networks based on a protein-domain network representation. This method generates models whose number of species, in the worst case, scales quadratically to the number of protein-domain sites and modification states, a tremendous saving over the combinatorial scaling in …
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Protein Shape Description and its Application to Shape Comparison
… structures deposited in the wwPDB (Worldwide Protein Data Bank) database. While all the macromolecular structure files contain information about a particular structure, the collection of these files also allows combining the macromolecular structures to obtain statistical information about …
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The Role of Sulfatide in the Development and Maintenance of the Nodal and Paranodal Domains in the Peripheral Nervous System
… proper initial clustering of paranodal proteins and cluster maintenance of nodal proteins is impaired suggesting that paranodal domains are important for long-term node stability. In contrast to the CNS, a requirement for sulfatide in the initiation of myelination, and in initiation of …
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Functional Sorting of Evolutionary Effects in Protein Domains
… But for the comparatively more conservative protein domain data, the absence of enough variations makes these general methods incompetent. The other problem lies at the difficulty of discerning the difference between positive selection and relaxation of functional constraint; both processes …
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Correlated long-distance dynamics modulate monoclonal antibody binding resistance in flaviviral envelope pretein domain-3: A molecular dynamics simulations study
… mutations have been localized to the envelope protein domain-3 (ED3) of flaviviruses. Previously it was shown that regions constituting antibody binding sites of dengue-2 (DEN2) and West Nile virus (WNV) ED3 were energetically coupled with the interior of the protein. Protein-protein …
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Plant Homeodomain Finger Protein 20 (Phf20) and Its Homolog Phf20 Like 1 (Phf20L1) Define Two Distinct Non-Specific Lethal (Nsl) Complexes
<p>Plant Homeodomain Finger Protein 20 (PHF20) and its homolog PHF20 Like 1 (PHF20L1) are known subunits of the Non-Specific Lethal (NSL) complex, which acetylates lysine residues on histone H4 and regulates gene expression. The current model assumes that PHF20 and PHF20L1 are present together in …
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Micro and Nano patterns for Biosensing: from enzymatic assays to single cells interaction arrays
… Immobilization for the creation of complex protein biochips on modified glass surfaces displaying spots of cell-specific ligands with lateral dimensions minor than one single cell. In a first application the epidermal growth factor (EFG) protein arrays were realized to display specific …
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Identification and Characterization of Novel CRISPR-Cas Immune Effectors
… of three new CRISPR-Cas effector proteins that provide immunity in bacteria in response to phage challenge with highly diverse activities. CRISPR-Cas systems are the only known adaptive immune system found in bacteria. Immunity by these systems is achieved in two main steps: (1) …
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Identification and Functional Role of Myo-Inositol Polyphosphate 5-Phosphatase Protein Complexes
… of which contain a single 5PTase catalytic domain. Four members of the Arabidopsis 5PTase family, however, have a unique protein domain structure, with additional N-terminal WD40 repeats that are implicated in protein-protein interactions. The research presented here focused on the …
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Engineering and characterisation of anti-progesterone OBodies
… More recently, novel non-immunoglobulin binding proteins, have been similarly engineered to produce high affinity binding proteins that can potentially replace the binding function(s) of antibodies or even surpass them. The OB-fold is a high affinity binding protein domain which has previously …
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