scholarly journals Ligand-Induced Conformational Dynamics of A Tyramine Receptor from Sitophilus oryzae

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mac Kevin E. Braza ◽  
Jerrica Dominique N. Gazmen ◽  
Eizadora T. Yu ◽  
Ricky B. Nellas
Keyword(s):  
Conformational Changes ◽  
Cellular Response ◽  
Conformational Dynamics ◽  
Sitophilus Oryzae ◽  
Md Simulations ◽  
Homology Model ◽  
Activation Process ◽  
Intracellular Loop ◽  
Binding Effect ◽  
Natural Ligand

Abstract Tyramine receptor (TyrR) is a biogenic amine G protein-coupled receptor (GPCR) associated with many important physiological functions in insect locomotion, reproduction, and pheromone response. Binding of specific ligands to the TyrR triggers conformational changes, relays the signal to G proteins, and initiates an appropriate cellular response. Here, we monitor the binding effect of agonist compounds, tyramine and amitraz, to a Sitophilus oryzae tyramine receptor (SoTyrR) homology model and their elicited conformational changes. All-atom molecular dynamics (MD) simulations of SoTyrR-ligand complexes have shown varying dynamic behavior, especially at the intracellular loop 3 (IL3) region. Moreover, in contrast to SoTyrR-tyramine, SoTyrR-amitraz and non-liganded SoTyrR shows greater flexibility at IL3 residues and were found to be coupled to the most dominant motion in the receptor. Our results suggest that the conformational changes induced by amitraz are different from the natural ligand tyramine, albeit being both agonists of SoTyrR. This is the first attempt to understand the biophysical implication of amitraz and tyramine binding to the intracellular domains of TyrR. Our data may provide insights into the early effects of ligand binding to the activation process of SoTyrR.

Using molecular simulation to explore the nanoscale dynamics of the plant kinome

2018 ◽  
Vol 475 (5) ◽  
pp. 905-921 ◽  
Author(s):  
Alexander S. Moffett ◽  
Diwakar Shukla
Keyword(s):  
Molecular Simulation ◽  
Conformational Changes ◽  
Cellular Response ◽  
Md Simulation ◽  
Conformational Dynamics ◽  
Large Family ◽  
Md Simulations ◽  
The Future ◽  
Catalytically Active ◽  
Domains Of Life

Eukaryotic protein kinases (PKs) are a large family of proteins critical for cellular response to external signals, acting as molecular switches. PKs propagate biochemical signals by catalyzing phosphorylation of other proteins, including other PKs, which can undergo conformational changes upon phosphorylation and catalyze further phosphorylations. Although PKs have been studied thoroughly across the domains of life, the structures of these proteins are sparsely understood in numerous groups of organisms, including plants. In addition to efforts towards determining crystal structures of PKs, research on human PKs has incorporated molecular dynamics (MD) simulations to study the conformational dynamics underlying the switching of PK function. This approach of experimental structural biology coupled with computational biophysics has led to improved understanding of how PKs become catalytically active and why mutations cause pathological PK behavior, at spatial and temporal resolutions inaccessible to current experimental methods alone. In this review, we argue for the value of applying MD simulation to plant PKs. We review the basics of MD simulation methodology, the successes achieved through MD simulation in animal PKs, and current work on plant PKs using MD simulation. We conclude with a discussion of the future of MD simulations and plant PKs, arguing for the importance of molecular simulation in the future of plant PK research.

scholarly journals Correlation of membrane protein conformational and functional dynamics

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Raghavendar Reddy Sanganna Gari ◽  
Joel José Montalvo‐Acosta ◽  
George R. Heath ◽  
Yining Jiang ◽  
Xiaolong Gao ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Conformational Changes ◽  
Single Channel ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
High Temporal Resolution ◽  
Dependent Manner ◽  
Functional Dynamics ◽  
Ph Dependent ◽  
Open States

AbstractConformational changes in ion channels lead to gating of an ion-conductive pore. Ion flux has been measured with high temporal resolution by single-channel electrophysiology for decades. However, correlation between functional and conformational dynamics remained difficult, lacking experimental techniques to monitor sub-millisecond conformational changes. Here, we use the outer membrane protein G (OmpG) as a model system where loop-6 opens and closes the β-barrel pore like a lid in a pH-dependent manner. Functionally, single-channel electrophysiology shows that while closed states are favored at acidic pH and open states are favored at physiological pH, both states coexist and rapidly interchange in all conditions. Using HS-AFM height spectroscopy (HS-AFM-HS), we monitor sub-millisecond loop-6 conformational dynamics, and compare them to the functional dynamics from single-channel recordings, while MD simulations provide atomistic details and energy landscapes of the pH-dependent loop-6 fluctuations. HS-AFM-HS offers new opportunities to analyze conformational dynamics at timescales of domain and loop fluctuations.

scholarly journals Biophysical and functional characterization of Norrin signaling through Frizzled4

2018 ◽  
Vol 115 (35) ◽  
pp. 8787-8792 ◽  
Author(s):  
Injin Bang ◽  
Hee Ryung Kim ◽  
Andrew H. Beaven ◽  
Jinuk Kim ◽  
Seung-Bum Ko ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Wnt Signaling ◽  
Conformational Changes ◽  
Cellular Response ◽  
Transmembrane Domain ◽  
Functional Characterization ◽  
Intracellular Loop ◽  
Ligand Interaction ◽  
Rich Domain ◽  
Linker Domain

Wnt signaling is initiated by Wnt ligand binding to the extracellular ligand binding domain, called the cysteine-rich domain (CRD), of a Frizzled (Fzd) receptor. Norrin, an atypical Fzd ligand, specifically interacts with Fzd4 to activate β-catenin–dependent canonical Wnt signaling. Much of the molecular basis that confers Norrin selectivity in binding to Fzd4 was revealed through the structural study of the Fzd4CRD–Norrin complex. However, how the ligand interaction, seemingly localized at the CRD, is transmitted across full-length Fzd4 to the cytoplasm remains largely unknown. Here, we show that a flexible linker domain, which connects the CRD to the transmembrane domain, plays an important role in Norrin signaling. The linker domain directly contributes to the high-affinity interaction between Fzd4 and Norrin as shown by ∼10-fold higher binding affinity of Fzd4CRD to Norrin in the presence of the linker. Swapping the Fzd4 linker with the Fzd5 linker resulted in the loss of Norrin signaling, suggesting the importance of the linker in ligand-specific cellular response. In addition, structural dynamics of Fzd4 associated with Norrin binding investigated by hydrogen/deuterium exchange MS revealed Norrin-induced conformational changes on the linker domain and the intracellular loop 3 (ICL3) region of Fzd4. Cell-based functional assays showed that linker deletion, L430A and L433A mutations at ICL3, and C-terminal tail truncation displayed reduced β-catenin–dependent signaling activity, indicating the functional significance of these sites. Together, our results provide functional and biochemical dissection of Fzd4 in Norrin signaling.

scholarly journals High-Speed AFM directly visualizes conformational dynamics of the HIV-Vif protein complex

2020 ◽  
Author(s):  
Yangang Pan ◽  
Luda S. Shlyakhtenko ◽  
Yuri L. Lyubchenko
Keyword(s):  
Conformational Changes ◽  
Protein Complex ◽  
High Speed ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Time Lapse ◽  
Hiv Treatment ◽  
X Ray Crystallography ◽  
Host Cell Proteins ◽  
Virus Survival

AbstractViral infectivity factor (Vif) is a protein that is essential for the replication of the HIV-1 virus. The key function of Vif is to disrupt the antiviral activity of APOBEC3 proteins, which mutate viral nucleic acids. Inside the cell, Vif binds to the host cell proteins Elongin-C, Elongin-B, and CBF-β, forming a four-protein complex called VCBC. The structure of VCBC in complex with the Cullin5 (Cul5) protein has been solved by X-ray crystallography, and recently, using molecular dynamic (MD) simulations, the dynamics of VCBC and VCBC-Cul5 complexes were characterized. Here, we applied time-lapse high-speed atomic force microscopy (HS-AFM) to visualize the conformational changes of the VCBC complex. We determined the three most favorable conformations of the VCBC complex, which we identified as triangle, dumbbell, and globular structures. In addition, we characterized the dynamics of each of these structures. While our data show a very dynamic behavior for all these structures, we found the triangle and dumbbell structures to be the most dynamic. These findings provide insight into the structure and dynamics of the VCBC complex and support further research into the improvement of HIV treatment, as Vif is essential for virus survival in the cell.

scholarly journals Conformational Transition Pathways in Major Facilitator Superfamily Transporters

2019 ◽  
Author(s):  
Dylan Ogden ◽  
Kalyan Immadisetty ◽  
Mahmoud Moradi
Keyword(s):  
Conformational Changes ◽  
Glucose Transporter ◽  
Conformational Transition ◽  
Conformational Dynamics ◽  
Salt Bridge ◽  
Md Simulations ◽  
Major Facilitator Superfamily ◽  
Glucose Transporter 1 ◽  
Major Facilitator ◽  
Mfs Transporters

AbstractMajor facilitator superfamily (MFS) of transporters consists of three classes of membrane transporters: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformational changes within their distinct transport cycles. While the similarities between conformational changes are noteworthy, the differences are also important since they could potentially explain the distinct functions of symporters, uniporters, and antiporters of MFS superfamily. We have performed a variety of equilibrium, non-equilibrium, biased, and unbiased all-atom molecular dynamics (MD) simulations of bacterial proton-coupled oligopeptide transporter GkPOT, glucose transporter 1 (GluT1), and glycerol-3-phosphate transporter (GlpT) to compare the similarities and differences of the conformational dynamics of three different classes of transporters. Here we have simulated the apo protein in an explicit membrane environment. Our results suggest a very similar conformational transition involving interbundle salt-bridge formation/disruption coupled with the orientation changes of transmembrane (TM) helices, specifically H1/H7 and H5/H11, resulting in an alternation in the accessibility of water at the cyto- and periplasmic gates.

scholarly journals Pyrococcus furiosus Prolyl Oligopeptidase: A Dynamic Supramolecular Host for Peptidase and Dirhodium Catalysis

2018 ◽  
Author(s):  
Ken Ellis-Guardiola ◽  
Huan Rui ◽  
Ryan Beckner ◽  
Poonam Srivastava ◽  
Narayanasami Sukumar ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Pyrococcus Furiosus ◽  
Conformational Dynamics ◽  
Domain Architecture ◽  
Md Simulations ◽  
Peptidase Activity ◽  
Prolyl Oligopeptidase ◽  
Supramolecular Catalysis ◽  
Wide Range ◽  
Synthetic Macromolecules

Supramolecular catalysis involves the design and characterization of synthetic macromolecules that catalyze chemical reactions. While enzymes are often cited as the inspiration for such catalysts, enzymes can also serve as hosts for non-native catalytic components. Protein-based hosts can be readily produced in E. coli and rapidly evolved for particular applications. Moreover, inherent properties of these systems, including their conformational dynamics, can be exploited for non-native transformations that occur within their interior. Studies on the peptidase activity of a prolyl oligopeptidase from Pyrococcus furiosus (Pfu POP) suggest that its unique two-domain architecture regulates substrate access and specificity. We have established that Pfu POP also serves as an efficient host for asymmetric cyclopropanation upon active-site modification with a dirhodium cofactor. To understand how Pfu POP controls both peptidase and dirhodium catalysis, we determined the crystal structures of this enzyme and its S477C mutant and used these structures as starting points for MD simulations of both the apo structures and systems containing a covalently linked peptidase inhibitor or a dirhodium catalyst. Pfu POP was crystalized in an open conformation, and MD simulations reveal spontaneous transitions between open and closed states, in addition to a number of smaller scale conformational changes, suggesting facile inter-domain movement. Importantly, key aspects of previously reported peptidase kinetics and cyclopropanation selectivity can be rationalized in the context of this inter-domain opening and closing. This finding constitutes a remarkable example in which the conformational dynamics of a supramolecular host affect two different catalytic activities and suggests that Pfu POP could serve as a host for a wide range of non-native catalysts.

scholarly journals Molecular dynamics simulations disclose early stages of the photo-activation of cryptochrome 4

2018 ◽  
Author(s):  
D. R. Kattnig ◽  
C. Nielsen ◽  
I. A. Solov’yov
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Large Scale ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Quantum Processes ◽  
Helical Segment ◽  
High Betweenness ◽  
Dynamics Simulations ◽  
Fad Binding

AbstractBirds appear to be equipped with a light-dependent, radical-pair-based magnetic compass that relies on truly quantum processes. While the identity of the sensory protein has remained speculative, cryptochrome 4 has recently been identified as the most auspicious candidate. Here, we report on allatom molecular dynamics (MD) simulations addressing the structural reorganisations that accompany the photoreduction of the flavin cofactor in a model of the European robin cryptochrome 4 (ErCry4). Extensive MD simulations reveal that the photo-activation of ErCry4 induces large-scale conformational changes on short (hundreds of nanoseconds) timescales. Specifically, the photo-reduction is accompanied with the release of the C-terminal tail, structural rearrangements in the vicinity of the FAD-binding site, and the noteworthy formation of an α-helical segment at the N-terminal part. Some of these rearrangements appear to expose potential phosphorylation sites. We describe the conformational dynamics of the protein using a graph-based approach that is informed by the adjacency of residues and the correlation of their local motions. This approach reveals densely coupled reorganisation communities, which facilitate an efficient signal transduction due to a high density of hubs. These communities are interconnected by a small number of highly important residues characterized by high betweenness centrality. The network approach clearly identifies the sites restructuring upon photoactivation, which appear as protrusions or delicate bridges in the reorganisation network. We also find that, unlike in the homologous cryptochrome from D. melanogaster, the release of the C-terminal domain does not appear to be correlated with the transposition of a histidine residue close to the FAD cofactor.

scholarly journals Conformational Characterization of the Co-Activator Binding Site Revealed the Mechanism to Achieve the Bioactive State of FXR

2021 ◽  
Vol 8 ◽  
Author(s):  
Anita Kumari ◽  
Lovika Mittal ◽  
Mitul Srivastava ◽  
Dharam Pal Pathak ◽  
Shailendra Asthana
Keyword(s):  
Conformational Changes ◽  
Rational Design ◽  
Conformational Dynamics ◽  
Activation Mechanism ◽  
Activation Process ◽  
Bioactive Conformation ◽  
Structural Determinants ◽  
Critical Residue ◽  
Molecular Bonding

FXR bioactive states are responsible for the regulation of metabolic pathways, which are modulated by agonists and co-activators. The synergy between agonist binding and ‘co-activator’ recruitment is highly conformationally driven. The characterization of conformational dynamics is essential for mechanistic and therapeutic understanding. To shed light on the conformational ensembles, dynamics, and structural determinants that govern the activation process of FXR, molecular dynamic (MD) simulation is employed. Atomic insights into the ligand binding domain (LBD) of FXR revealed significant differences in inter/intra molecular bonding patterns, leading to structural anomalies in different systems of FXR. The sole presence of an agonist or ‘co-activator’ fails to achieve the essential bioactive conformation of FXR. However, the presence of both establishes the bioactive conformation of FXR as they modulate the internal wiring of key residues that coordinate allosteric structural transitions and their activity. We provide a precise description of critical residue positioning during conformational changes that elucidate the synergy between its binding partners to achieve an FXR activation state. Our study offers insights into the associated modulation occurring in FXR at bound and unbound forms. Thereafter, we also identified hot-spots that are critical to arrest the activation mechanism of FXR that would be helpful for the rational design of its agonists.

scholarly journals Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Ruyu Jia ◽  
Chloe Martens ◽  
Mrinal Shekhar ◽  
Shashank Pant ◽  
Grant A. Pellowe ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Conformational Transition ◽  
Substrate Binding ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Allosteric Coupling ◽  
Exchange Mass Spectrometry ◽  
Hydrogen Deuterium ◽  
Deuterium Exchange Mass Spectrometry ◽  
Hdx Ms

AbstractProton-coupled transporters use transmembrane proton gradients to power active transport of nutrients inside the cell. High-resolution structures often fail to capture the coupling between proton and ligand binding, and conformational changes associated with transport. We combine HDX-MS with mutagenesis and MD simulations to dissect the molecular mechanism of the prototypical transporter XylE. We show that protonation of a conserved aspartate triggers conformational transition from outward-facing to inward-facing state. This transition only occurs in the presence of substrate xylose, while the inhibitor glucose locks the transporter in the outward-facing state. MD simulations corroborate the experiments by showing that only the combination of protonation and xylose binding, and not glucose, sets up the transporter for conformational switch. Overall, we demonstrate the unique ability of HDX-MS to distinguish between the conformational dynamics of inhibitor and substrate binding, and show that a specific allosteric coupling between substrate binding and protonation is a key step to initiate transport.

scholarly journals Pyrococcus furiosus Prolyl Oligopeptidase: A Dynamic Supramolecular Host for Peptidase and Dirhodium Catalysis

2018 ◽  
Author(s):  
Ken Ellis-Guardiola ◽  
Huan Rui ◽  
Ryan Beckner ◽  
Poonam Srivastava ◽  
Narayanasami Sukumar ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Pyrococcus Furiosus ◽  
Conformational Dynamics ◽  
Domain Architecture ◽  
Md Simulations ◽  
Peptidase Activity ◽  
Prolyl Oligopeptidase ◽  
Supramolecular Catalysis ◽  
Wide Range ◽  
Synthetic Macromolecules

Supramolecular catalysis involves the design and characterization of synthetic macromolecules that catalyze chemical reactions. While enzymes are often cited as the inspiration for such catalysts, enzymes can also serve as hosts for non-native catalytic components. Protein-based hosts can be readily produced in E. coli and rapidly evolved for particular applications. Moreover, inherent properties of these systems, including their conformational dynamics, can be exploited for non-native transformations that occur within their interior. Studies on the peptidase activity of a prolyl oligopeptidase from Pyrococcus furiosus (Pfu POP) suggest that its unique two-domain architecture regulates substrate access and specificity. We have established that Pfu POP also serves as an efficient host for asymmetric cyclopropanation upon active-site modification with a dirhodium cofactor. To understand how Pfu POP controls both peptidase and dirhodium catalysis, we determined the crystal structures of this enzyme and its S477C mutant and used these structures as starting points for MD simulations of both the apo structures and systems containing a covalently linked peptidase inhibitor or a dirhodium catalyst. Pfu POP was crystalized in an open conformation, and MD simulations reveal spontaneous transitions between open and closed states, in addition to a number of smaller scale conformational changes, suggesting facile inter-domain movement. Importantly, key aspects of previously reported peptidase kinetics and cyclopropanation selectivity can be rationalized in the context of this inter-domain opening and closing. This finding constitutes a remarkable example in which the conformational dynamics of a supramolecular host affect two different catalytic activities and suggests that Pfu POP could serve as a host for a wide range of non-native catalysts.

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