Showing papers by "Adrian E. Roitberg published in 2016"

Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations

Abstract: Intrinsically disordered proteins (IDPs) are a set of proteins that lack a definite secondary structure in solution. IDPs can acquire tertiary structure when bound to their partners; therefore, the recognition process must also involve protein folding. The nature of the transition state (TS), structured or unstructured, determines the binding mechanism. The characterization of the TS has become a major challenge for experimental techniques and molecular simulations approaches since diffusion, recognition, and binding is coupled to folding. In this work we present atomistic molecular dynamics (MD) simulations that sample the free energy surface of the coupled folding and binding of the transcription factor c-myb to the cotranscription factor CREB binding protein (CBP). This process has been recently studied and became a model to study IDPs. Despite the plethora of available information, we still do not know how c-myb binds to CBP. We performed a set of atomistic biased MD simulations running a total of 15....

Ultrafast electronic energy relaxation in a conjugated dendrimer leading to inter-branch energy redistribution.

Abstract: Dendrimers are arrays of coupled chromophores, where the energy of each unit depends on its structure and conformation. The light harvesting and energy funneling properties are strongly dependent on their highly branched conjugated architecture. Herein, the photoexcitation and subsequent ultrafast electronic energy relaxation and redistribution of a first generation dendrimer (1) are analyzed combining theoretical and experimental studies. Dendrimer 1 consists of three linear phenylene-ethynylene (PE) units, or branches, attached in the meta position to a central group opening up the possibility of inter-branch energy transfer. Excited state dynamics are explored using both time-resolved spectroscopy and non-adiabatic excited state molecular dynamics simulations. Our results indicate a subpicosecond loss of anisotropy due to an initial excitation into several states with different spatial localizations, followed by exciton self-trapping on different units. This exciton hops between branches. The absence of an energy gradient leads to an ultrafast energy redistribution among isoenergetic chromophore units. At long times we observe similar probabilities for each branch to retain significant contributions of the transition density of the lowest electronic excited-state. The observed unpolarized emission is attributed to the contraction of the electronic wavefunction onto a single branch with frequent interbranch hops, and not to its delocalization over the whole dendrimer.

Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics

Abstract: One of the main goals of chemistry is to understand the underlying principles of chemical reactions, in terms of both its reaction mechanism and the thermodynamics that govern it. Using hybrid quantum mechanics/molecular mechanics (QM/MM)-based methods in combination with a biased sampling scheme, it is possible to simulate chemical reactions occurring inside complex environments such as an enzyme, or aqueous solution, and determining the corresponding free energy profile, which provides direct comparison with experimental determined kinetic and equilibrium parameters. Among the most promising biasing schemes is the multiple steered molecular dynamics method, which in combination with Jarzynski's Relationship (JR) allows obtaining the equilibrium free energy profile, from a finite set of nonequilibrium reactive trajectories by exponentially averaging the individual work profiles. However, obtaining statistically converged and accurate profiles is far from easy and may result in increased computational cost if the selected steering speed and number of trajectories are inappropriately chosen. In this small review, using the extensively studied chorismate to prephenate conversion reaction, we first present a systematic study of how key parameters such as pulling speed, number of trajectories, and reaction progress are related to the resulting work distributions and in turn the accuracy of the free energy obtained with JR. Second, and in the context of QM/MM strategies, we introduce the Hybrid Differential Relaxation Algorithm, and show how it allows obtaining more accurate free energy profiles using faster pulling speeds and smaller number of trajectories and thus smaller computational cost.

Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications.

Abstract: Human indoleamine 2,3-dioxygenase catalyzes the oxidative cleavage of tryptophan to N-formyl kynurenine, the initial and rate-limiting step in the kynurenine pathway. Additionally, this enzyme has been identified as a possible target for cancer therapy. A 20-amino acid protein segment (the JK loop), which connects the J and K helices, was not resolved in the reported hIDO crystal structure. Previous studies have shown that this loop undergoes structural rearrangement upon substrate binding. In this work, we apply a combination of replica exchange molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure and dynamics of this protein region. Our simulations show that the JK loop can be divided into two regions: the first region (JK loopC) displays specific and well-defined conformations and is within hydrogen bonding distance of the substrate, while the second region (JK loopN) is highly disordered and exposed to the solvent. The peculiar flexible nature of JK lo...

Coarse-Grained Simulations of Heme Proteins: Validation and Study of Large Conformational Transitions.

Abstract: Heme proteins are ubiquitous in nature and perform many diverse functions in all kingdoms of life. Many of these functions are related to large-scale conformational transitions and allosteric processes. Sampling of these large conformational changes is computationally very challenging. In this context, coarse-grain simulations emerge as an efficient approach to explore the conformational landscape. In this work, we present a coarse-grained model of the heme group and thoroughly validate this model in different benchmark examples, which include the monomeric heme proteins myoglobin and neuroglobin and the tetrameric human hemoglobin where we evaluated the method’s ability to explore conformational changes (as the formation of hexacoordinated species) and allosteric transitions (as the well-known R → T transition). The obtained results are compared with atomistic molecular dynamics simulations. Overall, the results indicate that this approach conserves the essential dynamical information on different allost...

Interactively Applying the Variational Method to the Dihydrogen Molecule: Exploring Bonding and Antibonding

Abstract: In this work we are going to present how an interactive platform can be used as a powerful tool to allow students to better explore a foundational problem in quantum chemistry: the application of the variational method to the dihydrogen molecule using simple Gaussian trial functions. The theoretical approach for the hydrogen atom is quite straightforward, however, the level of complexity increases considerably for the dihydrogen molecule. Although, as shown in this work, it is possible to obtain an analytical expression for the dihydrogen molecule variational integral by “pen-and-paper”, this expression cannot be completely appreciated without the proper tools. In this work the “dry” analytical equations were implemented into an interactive platform that allows the students to visualize results (like probability densities and meaningful graphs), play with parameters, and thus gain a deeper understanding of the problem itself. Having an interactive environment is also important as a way of minimizing compl...