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- PH-dependent effects (2)
- PH-optimum (2)
- Protein stability (2)
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Articles 1 - 7 of 7
Full-Text Articles in Physical Sciences and Mathematics
In Silico Modeling Of Ph-Optimum Of Protein-Protein Binding, Rooplekha C. Mitra, Zhe Zhang, Emil Alexov
In Silico Modeling Of Ph-Optimum Of Protein-Protein Binding, Rooplekha C. Mitra, Zhe Zhang, Emil Alexov
Publications
Protein-protein association is a pH-dependent process and thus the binding affinity depends on the local pH. In vivo the association occurs in a particular cellular compartment, where the individual monomers are supposed to meet and form a complex. Since the monomers and the complex exist in the same micro environment, it is plausible that they coevolved toward its properties, in particular, toward the characteristic subcellular pH. Here we show that the pH at which the monomers are most stable (pH-optimum) or the pH at which stability is almost pH-independent (pH-flat) of monomers are correlated with the pH-optimum of maximal affinity …
Computational Analysis Of Missense Mutations Causing Snyder-Robinson Syndrome, Zhe Zhang, Shaolei Teng, Liangjiang Wang, Charles E. Schwartz, Emil Alexov
Computational Analysis Of Missense Mutations Causing Snyder-Robinson Syndrome, Zhe Zhang, Shaolei Teng, Liangjiang Wang, Charles E. Schwartz, Emil Alexov
Publications
The Snyder-Robinson syndrome is caused by missense mutations in the spermine sythase gene that encodes a protein (SMS) of 529 amino acids. Here we investigate, in silico, the molecular effect of three missense mutations, c.267G>A (p.G56S), c.496T>G (p.V132G), and c.550T>C (p.I150T) in SMS that were clinically identified to cause the disease. Single-point energy calculations, molecular dynamics simulations, and pKa calculations revealed the effects of these mutations on SMS's stability, flexibility, and interactions. It was predicted that the catalytic residue, Asp276, should be protonated prior binding the substrates. The pKa calculations indicated the p.I150T mutation causes pKa changes …
Understanding The Role Of Electrostatics On Protein-Protein Binding, Rooplekha C Mitra
Understanding The Role Of Electrostatics On Protein-Protein Binding, Rooplekha C Mitra
All Theses
Ionized groups carry net charge and thus play a major role in the electrostatic interactions between the ligand and receptor. So understanding the role of electrostatics on protein-protein interactions is crucial for understanding the contribution of ionizable groups to the binding. However, their ionization states depend on many factors including pH of water phase. The complexity comes from the fact that the pKa's of ionizable groups may be quite different from their standard values and even may change due to protein-protein binding. The main difficulty in modeling plausible ionization changes induced by the complex formation arises from the differences in …
On The Ph-Optimum Of Activity And Stability Of Proteins, Kemper Tally, Emil Alexov
On The Ph-Optimum Of Activity And Stability Of Proteins, Kemper Tally, Emil Alexov
Publications
Biological macromolecules evolved to perform their function in specific cellular environment (subcellular compartments or tissues); therefore, they should be adapted to the biophysical characteristics of the corresponding environment, one of them being the characteristic pH. Many macromolecular properties are pH dependent, such as activity and stability. However, only activity is biologically important, while stability may not be crucial for the corresponding reaction. Here, we show that the pH-optimum of activity (the pH of maximal activity) is correlated with the pH-optimum of stability (the pH of maximal stability) on a set of 310 proteins with available experimental data. We speculate that …
Understanding The Biological And Environmental Implications Of Nanomaterials, Sijie Lin
Understanding The Biological And Environmental Implications Of Nanomaterials, Sijie Lin
All Dissertations
The last two decades have witnessed the discovery, development, and large-scale manufacturing of novel nanomaterials. While nanomaterials bring in exciting and extraordinary properties in all areas of materials, electronics, mechanics, and medicine, they also could generate potential adverse effects in biological systems and in the environment. The currently limited application of nanomaterials in biological and ecological systems results from the insufficient and often controversial data on describing the complex behaviors of nanomaterials in living systems. The purpose of this dissertation intends to fill such a knowledge void with methodologies from the disciplines of biophysics, biology, and materials science and engineering. …
Structural Assessment Of The Effects Of Amino Acid Substitutions On Protein Stability And Protein-Protein Interaction, Shaolei Teng, Liangjiang Wang, Anand K. Srivastava, Charles E. Schwartz, Emil Alexov
Structural Assessment Of The Effects Of Amino Acid Substitutions On Protein Stability And Protein-Protein Interaction, Shaolei Teng, Liangjiang Wang, Anand K. Srivastava, Charles E. Schwartz, Emil Alexov
Publications
A structure-based approach is described for predicting the effects of amino acid substitutions on protein function. Structures were predicted using a homology modelling method. Folding and binding energy differences between wild-type and mutant structures were computed to quantitatively assess the effects of amino acid substitutions on protein stability and protein–protein interaction, respectively. We demonstrated that pathogenic mutations at the interaction interface could affect binding energy and destabilise protein complex, whereas mutations at the non-interface might reduce folding energy and destabilise monomer structure. The results suggest that the structure-based analysis can provide useful information for understanding the molecular mechanisms of diseases.
A Solution-Based Approach To The Fabrication Of Novel Chalcogenide Glass Materials And Structures, Nathan Carlie
A Solution-Based Approach To The Fabrication Of Novel Chalcogenide Glass Materials And Structures, Nathan Carlie
All Dissertations
Chalcogenide glasses (ChGs) are well known for their large optical nonlinearities and high infrared transparency, and are candidate materials for next-generation thin film-based planar infrared (IR) optical applications. They are also known, however, to possess low thermal and mechanical stability as compared to oxide glasses. Traditional physical vapor deposition (PVD) methods used for the deposition of these materials as thin films often suffer from low deposition rates, deviation from stoichiometry, and cannot coat over complex surfaces. In order to retain the attractive optical properties of ChGs while enabling new fabrication routes and hybrid and composite material systems, we have developed …