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Full-Text Articles in Life Sciences
Blocking The Dimerization Of Polyglutamine-Expanded Androgen Receptor Protects Cells From Dht-Induced Toxicity By Increasing Ar Turnover, Allison Lisberg, Yuhong Liu, Diane E. Merry
Blocking The Dimerization Of Polyglutamine-Expanded Androgen Receptor Protects Cells From Dht-Induced Toxicity By Increasing Ar Turnover, Allison Lisberg, Yuhong Liu, Diane E. Merry
Department of Biochemistry and Molecular Biology Faculty Papers
Spinal and bulbar muscular atrophy (SBMA) is a neuromuscular degenerative disease caused by a polyglutamine expansion in the androgen receptor (AR). This mutation causes AR to misfold and aggregate, contributing to toxicity in and degeneration of motor neurons and skeletal muscle. There is currently no effective treatment or cure for this disease. The role of an interdomain interaction between the amino- and carboxyl-termini of AR, termed the N/C interaction, has been previously identified as a component of androgen receptor-induced toxicity in cell and mouse models of SBMA. However, the mechanism by which this interaction contributes to disease pathology is unclear. …
Effects Of Mono- And Di- Saccharide Osmolytes On The Stability And Folding Dynamics Of Src Sh3, Mahmoud Abouelkheir, Emily Guinn
Effects Of Mono- And Di- Saccharide Osmolytes On The Stability And Folding Dynamics Of Src Sh3, Mahmoud Abouelkheir, Emily Guinn
Annual Student Research Poster Session
No abstract provided.
Structural Dynamics Of A Mitochondrial Trna Possessing Weak Thermodynamic Stability, Hari Bhaskaran, Takaaki Taniguchi, Takeo Suzuki, Tsutomu Suzuki, John J. Perona
Structural Dynamics Of A Mitochondrial Trna Possessing Weak Thermodynamic Stability, Hari Bhaskaran, Takaaki Taniguchi, Takeo Suzuki, Tsutomu Suzuki, John J. Perona
Chemistry Faculty Publications and Presentations
Folding dynamics are ubiquitously involved in controlling the multivariate functions of RNAs. While the high thermodynamic stabilities of some RNAs favor purely native states at equilibrium, it is unclear whether weakly stable RNAs exist in random, partially folded states or sample well-defined, globally folded conformations. Using a folding assay that precisely tracks the formation of native aminoacylable tRNA, we show that the folding of a weakly stable human mitochondrial (hmt) leucine tRNA is hierarchical with a distinct kinetic folding intermediate. The stabilities of the native and intermediate conformers are separated by only about 1.2 kcal/mol, and the species are readily …
Investigating The In Vitro Oxidative Folding Pathways Of Bovine Pancreatic Trypsin Inhibitor (Bpti), Yingsong Wang
Investigating The In Vitro Oxidative Folding Pathways Of Bovine Pancreatic Trypsin Inhibitor (Bpti), Yingsong Wang
FIU Electronic Theses and Dissertations
The oxidative folding pathway of the disulfide containing protein bovine pancreatic trypsin inhibitor (BPTI) was one of the first to be elucidated and has served as a basis for understanding the folding pathways of other proteins. During the oxidative folding of reduced BPTI, two intermediates (N' and N*) accumulate in significant amounts and act as kinetic traps. Both N' and N* bury their two remaining free thiols in their hydrophobic cores, which inhibits further oxidation. Historically, the rate limiting step was considered to be the intramolecular rearrangements of N' and N* to another intermediate with two free thiols, NSH …
Protein Folding By 'Levels Of Separation': A Hypothesis, Lesley H. Greene, Terri M. Grant
Protein Folding By 'Levels Of Separation': A Hypothesis, Lesley H. Greene, Terri M. Grant
Chemistry & Biochemistry Faculty Publications
The protein folding process has been studied both computationally and experimentally for over 30 years. To date there is no detailed mechanism to explain the formation of long-range interactions between the transition and native states. Long-range interactions are the principle determinants of the tertiary structure. We present a theoretical model which proposes a mechanism for the acquisition of these interactions as they form in a modified version of ‘degrees of separation’, that we term ‘levels of separation’. It is based on the integration of network science and biochemistry. (C) 2012 Federation of European Biochemical Societies.
Protein Structure Networks, Lesley H. Greene
Protein Structure Networks, Lesley H. Greene
Chemistry & Biochemistry Faculty Publications
The application of the field of network science to the scientific disciplines of structural biology and biochemistry, have yielded important new insights into the nature and determinants of protein structures, function, dynamics and the folding process. Advancements in further understanding protein relationships through network science have also reshaped the way we view the connectivity of proteins in the protein universe. The canonical hierarchical classification can now be visualized for example, as a protein fold continuum. This review will survey several key advances in the expanding area of research being conducted to study protein structures and folding using network approaches.
Planning Combinatorial Disulfide Cross-Links For Protein Fold Determination, Fei Xiong, Alan M Friedman, Chris Bailey-Kellogg
Planning Combinatorial Disulfide Cross-Links For Protein Fold Determination, Fei Xiong, Alan M Friedman, Chris Bailey-Kellogg
Dartmouth Scholarship
Fold recognition techniques take advantage of the limited number of overall structural organizations, and have become increasingly effective at identifying the fold of a given target sequence. However, in the absence of sufficient sequence identity, it remains difficult for fold recognition methods to always select the correct model. While a native-like model is often among a pool of highly ranked models, it is not necessarily the highest-ranked one, and the model rankings depend sensitively on the scoring function used. Structure elucidation methods can then be employed to decide among the models based on relatively rapid biochemical/biophysical experiments.
Solving The Low Dimensional Smoluchowski Equation With A Singular Value Basis Set, Gregory E. Scott, Martin Gruebele
Solving The Low Dimensional Smoluchowski Equation With A Singular Value Basis Set, Gregory E. Scott, Martin Gruebele
Chemistry and Biochemistry
Reaction kinetics on free energy surfaces with small activation barriers can be computed directly with the Smoluchowski equation. The procedure is computationally expensive even in a few dimensions. We present a propagation method that considerably reduces computational time for a particular class of problems: when the free energy surface suddenly switches by a small amount, and the probability distribution relaxes to a new equilibrium value. This case describes relaxation experiments. To achieve efficient solution, we expand the density matrix in a basis set obtained by singular value decomposition of equilibrium density matrices. Grid size during propagation is reduced from (100–1000) …
Expression, Purification, And Analysis Of Unknown Translation Factors From Escherichia Coli: A Synthesis Approach, Justin D. Walter, Peter Littlefield, Scott P. Delbecq, Gerry Prody, P. Clint Spiegel
Expression, Purification, And Analysis Of Unknown Translation Factors From Escherichia Coli: A Synthesis Approach, Justin D. Walter, Peter Littlefield, Scott P. Delbecq, Gerry Prody, P. Clint Spiegel
Chemistry Faculty and Staff Publications
New approaches are currently being developed to expose biochemistry and molecular biology undergraduates to a more interactive learning environment. Here, we propose a unique project-based laboratory module, which incorporates exposure to biophysical chemistry approaches to address problems in protein chemistry. Each of the experiments described herein contributes to the stepwise process of isolating, identifying, and analyzing a protein involved in a central biological process, prokaryotic translation. Students are provided with expression plasmids that harbor an unknown translation factor, and it is their charge to complete a series of experiments that will allow them to develop hypotheses for discovering the identity …
Small Heat Shock Protein Activity Is Regulated By Variable Oligomeric Substructure, J. L. Benesch, M. Ayoub, C. V. Robinson, J. A. Aquilina
Small Heat Shock Protein Activity Is Regulated By Variable Oligomeric Substructure, J. L. Benesch, M. Ayoub, C. V. Robinson, J. A. Aquilina
Faculty of Science - Papers (Archive)
The alpha-crystallins are members of the small heat shock protein (sHSP) family of molecular chaperones which have evolved to minimize intracellular protein aggregation, however they are also implicated in a number of protein deposition diseases. In this study we have employed novel mass spectrometry techniques to investigate the changes in quaternary structure associated with this switch from chaperone to adjuvant of aggregation. We have replicated the oligomeric rearrangements observed for in vivo disease-related modifications, without altering the protein sequence, by refolding the alpha-crystallins in vitro. This refolding results in a loss of dimeric substructure concomitant with an augmentation of substrate …