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Full-Text Articles in Biochemistry
Protein Stability In Solution And In The Gas Phase., Yousef Haidar
Protein Stability In Solution And In The Gas Phase., Yousef Haidar
Electronic Thesis and Dissertation Repository
Electrospray Ionization mass spectrometry (ESI-MS) is widely used for probing proteins, yet many aspects of this technique remain elusive. Using MS, ion mobility spectrometry (IMS), and circular dichroism (CD) spectroscopy, this thesis sheds light on the stability differences of proteins in the gas phase and solution. After a general introduction (Chapter 1), Chapter 2 scrutinizes some aspects of native ESI. Our data highlight the significance of cone voltage in maintaining a native-like fold and show the advantage of using NH4Ac in protein experiments. Chapter 3 focuses on hydrogen/deuterium exchange (HDX)-MS. Several studies have reported that D2O …
Investigating The Rotary Mechanism Of Atp Synthase Using Molecular Dynamics Simulations, Angela Marcela Murcia Rios
Investigating The Rotary Mechanism Of Atp Synthase Using Molecular Dynamics Simulations, Angela Marcela Murcia Rios
Electronic Thesis and Dissertation Repository
F1-ATPase is a motor protein that can use ATP hydrolysis to drive rotation of the central subunit. The γ C-terminal helix constitutes of the rotor tip that is seated in an apical bearing formed by the α3β3 head. It remains uncertain to what extent the γ conformation during rotation differs from that seen in rigid crystal structures. Existing models assume that the entire γ subunit participates in every rotation. Here we develop a molecular dynamics (MD) strategy to model the off-axis forces acting on γ in F1-ATPase. MD runs showed stalling of the …
Nbpmf: Novel Network-Based Inference Methods For Peptide Mass Fingerprinting, Zhewei Liang
Nbpmf: Novel Network-Based Inference Methods For Peptide Mass Fingerprinting, Zhewei Liang
Electronic Thesis and Dissertation Repository
Proteins are large, complex molecules that perform a vast array of functions in every living cell. A proteome is a set of proteins produced in an organism, and proteomics is the large-scale study of proteomes. Several high-throughput technologies have been developed in proteomics, where the most commonly applied are mass spectrometry (MS) based approaches. MS is an analytical technique for determining the composition of a sample. Recently it has become a primary tool for protein identification, quantification, and post translational modification (PTM) characterization in proteomics research. There are usually two different ways to identify proteins: top-down and bottom-up. Top-down approaches …
An Investigation Of The Ck2-Dependent Phosphoproteome Using Inhibitor Refractory Ck2-Alpha, Edward Cruise
An Investigation Of The Ck2-Dependent Phosphoproteome Using Inhibitor Refractory Ck2-Alpha, Edward Cruise
Electronic Thesis and Dissertation Repository
Protein kinase CK2 is a constitutively active serine/threonine kinase that is overexpressed in several human cancers, and by virtue of the vast number of putative substrates in the phosphoproteome, is implicated in the regulation of numerous cellular processes. Consequently, CK2 is an emerging therapeutic target with many CK2 inhibitors having been developed. An example of one such inhibitor is the clinical stage compound CX-4945. Although highly selective for CK2, the ATP competitive CX-4945 has demonstrated affinity for other kinases. Unique features of the catalytic pocket of CK2 have allowed for the development of inhibitor refractory mutants, which have since been …