Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 37 for “"protein backbone"”.
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Modelling protein backbone loops using the Monte Carlo method
… main aim of my work was to study and include backbone moves<br/>for proteins, such as the Concerted Rotation with Angle (CRA) and the<br/>gaussian bias in the ProtoMS package. The CRA was then applied to several<br/>systems of biological interest to compute relative binding free energies …
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Biophysical mechanisms of intrinsic protein disorder: lessons from a protein backbone model
Intrinsically disordered regions (IDRs) in proteins populate a dynamic, heterogenous ensemble of structures. Proteins involved in the regulation of critical cellular functions rely on IDRs to carry out their functions. IDRs have been implicated in a number of diseases for which there are currently …
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Dynafold: A Dynamic Programming Approach to Protein Structure Calculation From Residual Dipolar Couplings
… involves the interactions of one or more proteins. As a result, methods for determining the three dimensional structure of proteins are of tremendous interest to researchers in a variety of fields. Presently, methods of protein structure determination are dominated by X-ray crystallography …
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Diffusion Probabilistic Modeling of Protein Backbones in 3D for the Motif-Scaffolding problem
… that supports a desired motif, conferring protein function, shows promise for the design of vaccines and enzymes. But a general solution to this motif-scaffolding problem remains open. Current machine-learning techniques for scaffold design are either limited to unrealistically small …
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Designing Novel DNA-Binding Proteins with Generative Deep Learning
Protein-DNA interactions play a critical role in various biological processes, such as gene regulation and genome maintenance. Designing protein backbones specifically tailored for DNA binding remains a challenging task, requiring the exploration of novel computational approaches. This thesis …
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Structural Characterization of Donkey Lactoferrin: Amino Acid Sequence and Glycan Compositions
Lactoferrin, a protein showing an array of biochemical properties, including immuno-modulation, iron-binding ability, as well as antioxidant, antibacterial and antiviral activities, was isolated from donkey milk by ion exchange chromatography.The characterization of its primary structure, by means …
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A Geometric Approach for Deciphering Protein Structure from Cryo-EM Volumes
… creates new computational challenges for protein structure identification. In this dissertation, we present a suite of geometric algorithms to address several aspects of protein modeling using cryo-EM density maps. Specifically, we develop novel methods to capture the shape of density …
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Solid-State 17O NMR as a New Probe to Study Acyl-Enzyme Intermediates
… the acyl moiety and the two NH groups from the protein backbone in the so-called oxyanion hole. This work represents the first use of solid-state 17O NMR spectroscopy to study acyl-enzyme intermediates and demonstrates the great potential of this new technique.
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Molecular structure, dynamics and hydration studies of soybean storage proteins and model systems by nuclear magnetic resonance
… NMR for the characterization of soybean storage proteins was explored. The spectra of a commercial soy protein isolate as well as those of alkali-denatured 7S and 11S soybean globulins were well resolved and tentatively assigned. Relaxation measurements indicated fast motion for several side …
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Multinuclear magnetic resonance studies of proteins
We have used a multinuclear approach to study proteins in the work described in this dissertation. We first studied fluorine labeled avian egg white lysozymes. Mutagenesis and other chemical modification methods were used to assign resonances from (4-F) Phe- and (4;F) Trp- hen egg white lysozyme. …
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Multistate Computational Protein Design: Theories, Methods, and Applications
Traditional computational protein design (CPD) calculations model sequence perturbations and evaluate their stabilities using a single fixed protein backbone template in an approach referred to as single‐state design (SSD). However, certain design objectives require the explicit consideration of …
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The Application of Pulsed Electron Paramagnetic Resonance to the Investigation of Protein Structure
… a method for introducing EPR active species into protein structures, the majority of these species are too flexible for the use of orientation measurements unless their introduced into sites that restrict the motion of the label. Additionally the quality of information gathered by PELDOR is …
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Electron spin-lattice relaxation in proteins, model heme complexes and ferricyanide solutions at helium temperatures
… reported for frozen solutions of the blue-copper proteins azurin and plastocyanin, the low-spin iron heme protein cytochrome-c, two (bis)imidazole ferric heme complexes in three different organic solvents and two ferricyanide solutions. Measurements were performed at X-band frequencies and …
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Equivariant Autoregressive Models for Molecular Generation
… a variety of tasks, including small molecule and protein backbone generation.
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Urinary prothrombin fragment 1 : a potential role-player in the protection of South African blacks from calcium oxalate kidney stone disease
… presents a study of the inhibitory role of the protein, urinary prothrombin fragment 1 (UPTFI ), and its biochemical characterisation in both population groups. In a preliminary study, the urine composition and inhibitory activity of urine and urinary macromolecules from healthy white and black …
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Automated and accurate description of protein structure -- from secondary to tertiary structure
<p>The automated protein structure analysis (APSA) has been developed that describes protein structure via its backbone in a novel way. APSA generates a smooth line for the backbone which is completely described using curvature κ and torsion τ as a function of arc lengths. Diagrams of κ(s) and τ(s) …
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Design, synthesis and development of novel indolocarbazole derivatives as potential anti-cancer agents
… order to probe the chemical space for potential protein backbone H-bonding interactions. Synthesis of a related 3,4-arylindolyl-5-aminopyrazole series was also undertaken, based on identification of potent kinase inhibition within a closely related heterocyclic template. Following synthesis of …
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Kinetics and regulation of the initial stages of cadherin-mediated adhesion
… Cadherins are calcium-dependent adhesion proteins which mediate cell adhesion in soft tissues. Several theories have been offered to explain the mechanism of cadherin adhesion. The first proposed mechanism put forth held that cadherins mediated binding through exchange of a tryptophan …
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Mucin and mucin glycans alter behaviorof mucosal pathogens
… of mucin from the rest of mucus, such as other proteins and salts. I first explore mucin’s impact on Klebsiella pneumoniae, an often multi-drug resistant and sometimes hypervirulent bacterium. I determine that mucin decreases K. pneumoniae surface attachment and biofilm formation, major sources …
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Metal complexes of non-heme ligands: biological applications
<p>Oxidative inactivation of proteins (carbonic anhydrase–I, trypsin, chymotrypsin and 20S proteasome) by non–heme iron complexes, and glutathionylation of non–heme cobalt complexes mimicking the N5 coordination environment like that of biologically important cofactor cobalamin or B<sub>12</sub> …
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