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The intricate involvement of Peroxisome Proliferator-Activated Receptor Gamma (PPARγ) in glucose homeostasis and adipogenesis is well-established. However, its role in cancer, particularly luminal bladder cancer, remains debated. The overexpression and activation of PPARγ are implicated in tumorigenesis. Specific gain-of-function mutations (M280I, I290M, and T475M) within the ligand-binding domain of PPARγ are associated with bladder cancer and receptor activation. The underlying molecular pathways prompted by these mutations remain unclear. We employed a dual-basin structure-based model (db-SBM) to explore the conformational dynamics between the inactive and active states of PPARγ and examined the effects of the M280I, I290M, and T475M mutations. Our findings, consistent with the existing literature, reveal heightened ligand-independent transcriptional activity in the I290M and T475M mutants. Both mutants showed enhanced stabilization of the active state compared to the wild-type receptor, with the I290M mutation promoting a specific transition route, making it a prime candidate for further study. Electrostatic analysis identified residues K303 and E488 as pivotal in the I290M activation cascade. Biophysical assays confirmed that disrupting the K303–E488 interaction reduced the thermal stabilization characteristic of the I290M mutation. Our study demonstrates the predictive capabilities of combining simulation and cheminformatics methods, validated by biochemical experiments, to gain insights into molecular activation mechanisms and identify target residues for protein modulation. [ABSTRACT FROM AUTHOR]

Through the years, many governments around the globe have invested in sending postsecondary students abroad through providing scholarships for university-level study -- at both the undergraduate and graduate levels. Filling their country's immediate and future demands for professional and academic development through offering grants, and then maximizing on the students' educational experiences once they return home, is the major overarching objective of this activity. What motivates a government to invest in a study abroad exchange program on a large scale? Darla K. Deardorff (2014) explored "the why" for global educational mobility. She found that when research partnerships are established between foreign universities, positive impacts on key global societal problems are created and enhanced. Therefore, these investments not only have a positive impact in meeting the needs of a country, but can have a constructive global influence, as well.

In recent years, there has been a growing interest to quantify the energy landscape that governs ribosome dynamics. However, in order to quantitatively integrate theoretical predictions and experimental measurements, it is essential that one has a detailed understanding of the associated diffusive properties. Here, all-atom explicit-solvent simulations (50 μs of aggregate sampling) predict that the diffusion coefficient of a tRNA molecule will depend on its position within the ribosome. Specifically, during aa-tRNA accommodation (i.e., the process by which tRNA enters the ribosome), the apparent diffusion coefficient decreases by approximately an order of magnitude. By comparing these to values obtained with an energetically "smooth" model, we show that the observed nonuniform behavior likely arises from electrostatic and solvation interactions between the tRNA and ribosome. These calculations also reveal the hierarchical character of ribosomal energetics, where steric interactions induce a large-scale free-energy barrier, and short-scale roughness determines the rate of diffusive movement across the landscape. [ABSTRACT FROM AUTHOR]

Ankyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein-protein interactions in a diversity of biological systems. These proteins have an elongated non-globular shape and often display complex folding mechanisms. This work investigates the energy landscape of representative proteins of this class made up of 3, 4 and 6 ANK repeats using the energy-landscape visualisation method (ELViM). By combining biased and unbiased coarse-grained molecular dynamics AWSEM simulations that sample conformations along the folding trajectories with the ELViM structurebased phase space, one finds a three-dimensional representation of the globally funnelled energy surface. In this representation, it is possible to delineate distinct folding pathways. We show that ELViMs can project, in a natural way, the intricacies of the highly dimensional energy landscapes encoded by the highly symmetric ankyrin repeat proteins into useful low-dimensional representations. These projections can discriminate between multiplicities of specific parallel folding mechanisms that otherwise can be hidden in oversimplified depictions. [ABSTRACT FROM AUTHOR]

Dynamics of the environments of complex systems such as biomolecules, polar solvents, and glass plays an important role in controlling electron transfer reactions. The kinetics is determined by the nature of a complex multidimensional landscape. By quantifying the mean and high-order statistics of the first-passage time and the associated ratios, the dynamics in electron transfer reactions controlled by the environments can be revealed. We consider real experimental conditions with finite observation time windows. At high temperatures, exponential kinetics is observed and there are multiple kinetic paths leading to the product state. At and below an intermediate temperature, nonexponential kinetics starts to appear, revealing the nature of the distribution of local traps on the landscape. Discrete kinetic paths emerge. At very low temperatures, nonexponential kinetics continues to be observed. We point out that the size of the observational time window is crucial in revealing the intrinsic nature of the real kinetics. The mean first-passage time is defined as a characteristic time. Only when the observational time window is significantly larger than this characteristic time does one have the opportunity to collect enough statistics to capture rare statistical fluctuations and characterize the kinetics accurately. [ABSTRACT FROM AUTHOR]

A lattice model is used to study mutations and compacting effects on protein folding rates and folding temperature. In the context of protein evolution, we address the question regarding the best scenario for a polypeptide chain to fold: either a fast nonspecific collapse followed by a slow rearrangement to form the native structure or a specific collapse from the unfolded state with the simultaneous formation of the native state. This question is investigated for optimized sequences, whose native state has no frustrated contacts between monomers, and also for mutated sequences, whose native state has some degree of frustration. It is found that the best scenario for folding may depend on the amount of frustration of the native structure. The implication of this result on protein evolution is discussed. [ABSTRACT FROM AUTHOR]

Discusses the role of solvent effects in controlling electron-transfer reactions. Conditions under which the solvent dynamics can be represented by a single collective reaction coordinate; Description of the single shell of solvent molecules around a cavity by two-dimensional system with periodic boundary conditions with nearest neighbor interactions.