49 research outputs found
Glycated Bovine Serum Albumin for Curcumin Nanoencapsulation: Bio-Nano Interactions
No full textGlycation of whey proteins results in food-grade composites with modified physicochemical properties. Here, the reaction between glucose and bovine serum albumin (BSA) is promoted under wet-heating conditions. The glycated protein is characterized in depth and compared to the native counterpart and the impact of glycation on properties like net surface charge, particle size and surface hydrophobicity are observed. Conjugation with glucose reduced the surface hydrophobicity of BSA but the interactions between albumin and curcumin became stronger, which contradicts the direct relationship between curcumin binding affinity and protein surface hydrophobicity described in the literature. Nonetheless, curcumin was still capable of quenching the intrinsic fluorescence of the protein after conjugation with glucose and leads to the conclusion that curcumin and BSA interact in a different manner upon glycation. This thesis also depicts mucin as a forthcoming model in the study of nanoparticle interactions with intestinal mucus and glycation posed no effect on such interactions
Coupling Protonation States of Acid-Sensing Ion Channels to Dynamics and Function
No full textAcid-sensing ion channels (ASICs) are trimeric, sodium-selective proton-gated ion channels. Having ligands as small as protons presents a challenge when studying the structure-function relationships of pH-dependent gating. Knowing where protons must bind to evoke a pH-dependent conformational change related to gating would provide one with insights into the molecular mechanisms underlying pH-dependent function in ASICs. We use molecular dynamics (MD) simulations that allow us to model explicit protons and directly examine the effects of changing protonation states on ASIC1 dynamics. We first combine the use of unbiased MD simulations with pKₐ prediction on the three functional states of cASIC1 to identify the effects of protonation state changes on interactions between ionizable residues in the acidic pocket (ACP), a region rich in acidic residues in the protein that plays a role in pH-sensing. We interpret the importance of E98, a buried residue in the ACP with a highly shifted pKₐ value, as well as the positively charged R191, also in the ACP, which has a flexible side chain and can interact with multiple negatively charged side chains, and the role of these residues in the pH-dependent collapse of the ACP. Additionally, we identify a hydrogen-bond network in the palm domain that consists of the Q277 side chain that interacts with the E80 side chain and L414 backbone carbonyl. This network contributes to a stable desensitized state and is stabilized by an E80-/E412H/E417H protonation configuration. Next, targeted MD was combined with pKₐ prediction to simulate the full transition pathways and to link protonation states with the molecular mechanisms involved in conformational changes. Our results suggest four residues, E98, E314, H328, and E374, that may be important in pH-sensing and gating, and that require further functional investigation in the context of activation and desensitization. This research exemplifies how MD is a useful tool in studying how protonation directly affects the structural dynamics of a protein and how it can complement existing functional studies and be used to suggest future experimental investigations
Conformation-Specific Statistical Coupling Analysis of the α7 Acetylcholine Receptor
No full textIt is well known that information contained in a protein sequence is what allows it to fold into its three-dimensional shape, which performs a specific function. It has been possible for some time to search for proteins with similar sequences, using bioinformatics tools such as BLAST. But it is also known that proteins with similar, or even the same sequence can adopt different structures and vice-versa. With this in mind, we look to use a method called Rosetta-HMMER to perform conformationally specific sequence searches in order to exploit this property of proteins. This method involves the use of Rosetta to redesign protein structures to fit a specified α-carbon backbone, and then uses HMMER to generate a sequence profile. This profile can then be used to query for sequences able to adopt the specified backbone structure. These collected sequences can then be aligned for the purpose of performing statistical coupling analysis. We have used this Rosetta-HMMER method in conjunction with available structures of the α7 acetylcholine receptor to show that distinct sequence profiles generated from different conformations of the same protein are capable of retrieving unique sets of natural sequences when used as a query. We have also shown that when these unique sets of natural sequences are used to perform statistical coupling analysis, different residues are identified as statistically coupled, potentially generating insight into residues that have more potential importance for one backbone conformation over another
Molecular Insight into the Dynamics of α7 Acetylcholine Receptor Function
No full textAt the author’s request, the abstract has been removed due to the confidential nature of the thesis. It will be added once the embargo period has passed.
À la demande de l'auteur, le résumé a été retiré en raison de la nature confidentielle de la thèse. Il sera ajouté une fois la période d'embargo terminée
Steered Molecular Dynamics Simulations Predict Conformational Stability of Glutamate Receptors
No full textThe stability of
protein–protein interfaces can be essential
for protein function. For ionotropic glutamate receptors, a family
of ligand-gated ion channels vital for normal function of the central
nervous system, such an interface exists between the extracellular
ligand binding domains (LBDs). In the full-length protein, the LBDs
are arranged as a dimer of dimers. Agonist binding to the LBDs opens
the ion channel, and briefly after activation the receptor desensitizes.
Several residues at the LBD dimer interface are known to modulate
desensitization, and conformational changes around these residues
are believed to be involved in the state transition. The general hypothesis
is that the interface is disrupted upon desensitization, and structural
evidence suggests that the disruption might be substantial. However,
when cross-linking the central part of this interface, functional
data suggest that the receptor can still undergo desensitization,
contradicting the hypothesis of major interface disruption. Here,
we illustrate how opening the dimer interface using steered molecular
dynamics (SMD) simulations, and analyzing the work values required,
provides a quantitative measure for interface stability. For one subtype
of glutamate receptors, which is regulated by ion binding to the dimer
interface, we show that opening the interface without ions bound requires
less work than with ions present, suggesting that ion binding indeed
stabilizes the interface. Likewise, for interface mutants with longer-lived
active states, the interface is more stable, while the work required
to open the interface is reduced for less active mutants. Moreover,
a cross-linked mutant can still undergo initial interface opening
motions similar to the native receptor and at similar energetic cost.
Thus, our results support that interface opening is involved in desensitization.
Furthermore, they provide reconciliation of apparently opposing data
and demonstrate that SMD simulations can give relevant biological
insight into longer time scale processes without the need for expensive
calculations
Computational studies of receptors
No full textCell surface receptors are the principle molecules by which communication is managed between cells. They are essential, for example, in the transmission of neuronal signals in the brain and central nervous system. The propagation of the signal involves conformational changes in the receptor that can sometimes be quite large. Thus, as they are inherently dynamic molecules, computational methods such as normal modes and molecular dynamics are ideally suited to studying receptors in atomistic detail and can provide unique insight that would otherwise be impossible to obtain. In this chapter, we illustrate, with some recent examples, the various approaches that have been taken in recent years and the kind of information that can be gleaned. As computer power continues to increase, so will the scale and sophistication of the problems that these methods can address
Protonation States of Important Acidic Residues in the Central Ca<sup>2+</sup> Ion Binding Sites of the Ca<sup>2+</sup>-ATPase: A Molecular Modeling Study
No full text
Insights into channel dysfunction from modelling and molecular dynamics simulations
No full textDevelopments in structural biology mean that the number of different ion channel structures has increased significantly in recent years. Structures of ion channels enable us to rationalize how mutations may lead to channelopathies. However, determining the structures of ion channels is still not trivial, especially as they necessarily exist in many distinct functional states. Therefore, the use of computational modelling can provide complementary information that can refine working hypotheses of both wild type and mutant ion channels. The simplest but still powerful tool is homology modelling. Many structures are available now that can provide suitable templates for many different types of ion channels, allowing a full three-dimensional interpretation of mutational effects. These structural models, and indeed the structures themselves obtained by X-ray crystallography, and more recently cryo-electron microscopy, can be subjected to molecular dynamics simulations, either as a tool to help explore the conformational dynamics in detail or simply as a means to refine the models further. Here we review how these approaches have been used to improve our understanding of how diseases might be linked to specific mutations in ion channel proteins. This article is part of the Special Issue entitled 'Channelopathies.
