scholarly journals The structural changes in the signaling mechanism of bacteriophytochromes in solution revealed by a multiscale computational investigation

2021 ◽  
Vol 12 (15) ◽  
pp. 5555-5565
Author(s):  
Veronica Macaluso ◽  
Giacomo Salvadori ◽  
Lorenzo Cupellini ◽  
Benedetta Mennucci
Keyword(s):  
Structural Changes ◽  
Md Simulations ◽  
Binding Pocket ◽  
Computational Investigation ◽  
Signaling Mechanism

A combination of MD simulations and a polarizable QM/MM description of a bacteriophytochrome in solution reveals the changes in the chromophore-binding pocket and in the overall structure of the phytochrome involved in the signaling mechanism.

scholarly journals Study on the influence of G82S RAGE polymorphism on RAGE-Amyloid interaction in AD pathology

2019 ◽  
Author(s):  
Rani Cathrine. C ◽  
Bincy Lukose ◽  
P. Rani
Keyword(s):  
Cell Line ◽  
Binding Affinity ◽  
Structural Changes ◽  
Md Simulations ◽  
Binding Pocket ◽  
Enhanced Expression ◽  
Shsy5y Cell ◽  
High Affinity Receptor ◽  
Aβ42 Peptide

AbstractReceptor for advanced glycation end products (RAGE) has been implicated in the pathophysiology of AD due to its ability to bind amyloid-beta and mediate inflammatory response. G82S RAGE polymorphism is associated with AD but the molecular mechanism for this association is not understood. Our previous in silico study indicated a higher binding affinity for mutated G82S RAGE, which could be caused due to changes in N linked glycosylation at residue N81. To confirm this hypothesis, in the present study molecular dynamics (MD) simulations were used to simulate the wild type (WT) and G82S glycosylated structures of RAGE to identify the global structural changes and to find the binding efficiency with Aβ42 peptide. Binding pocket analysis of the MD trajectory showed that cavity/binding pocket in mutant G82S glycosylated RAGE variants is more exposed and accessible to external ligands compared to WT RAGE, which can enhance the affinity of RAGE for Aβ. To validate the above concept, an in vitro binding study was carried using SHSY5Y cell line expressing recombinant WT and mutated RAGE variant individually to which HiLyte Fluor labeled Aβ42 was incubated at different concentrations. Saturated binding kinetics method was adopted to determine the Kd values for Aβ42 binding to RAGE. The Kd value for Aβ42-WT and Aβ42-mutant RAGE binding were 92±40 nM (95% CI-52 to 152nM; R2-0.92) and 45±20 nM (95% CI −29 to 64nM; R2-0.93), respectively. The Kd value of <100nM observed for both variants implicates RAGE as a high-affinity receptor for Aβ42 and mutant RAGE has higher affinity compared to WT. The alteration in binding affinity is responsible for activation of the inflammatory pathway as implicated by enhanced expression of TNFα and IL6 in mutant RAGE expressing cell line which gives a mechanistic view for the G82S RAGE association with AD.

scholarly journals The Structural Changes in the Signaling Mechanism of Bacteriophytochromes in Solution Revealed by a Multiscale Computational Investigation

2021 ◽  
Author(s):  
Veronica Macaluso ◽  
Giacomo Salvadori ◽  
Lorenzo Cupellini ◽  
Benedetta Mennucci
Keyword(s):  
Structural Changes ◽  
Red Light ◽  
Underlying Mechanism ◽  
Binding Pocket ◽  
Spectroscopic Properties ◽  
Signaling Mechanism ◽  
Structure Relaxation ◽  
Light Sensing ◽  
Absorption Of Light ◽  
Dynamics Simulations

<pre>Phytochromes are red-light sensing proteins, with important light-regulatory roles in different organisms, which are capturing an increasing interest in bioimaging and optogenetics. Upon absorption of light by the embedded bilin chromophore, they undergo structural changes that extend from the chomophore to the protein and finally drive the biological function. Up to now, the underlying mechanism still has to be characterized fully. </pre> <pre>Here we investigate the Pfr activated form of a bacterial phytochrome, by combining extensive Molecular Dynamics simulations with a polarizable QM/MM description of the spectroscopic properties, revealing a large structure relaxation in solution, compared to the crystal structure, both in the chromophore-binding pocket and in the overall structure of the phytochrome. Our results indicate that the final opening of the dimeric structure is preceded by an important internal reorganization of the phytochrome specific (PHY) domain involving a bend of the helical spine connecting the PHY domain with the chromophore-binding domain, opening the way to a new understanding of the activation pathway. </pre>

scholarly journals The Structural Changes in the Signaling Mechanism of Bacteriophytochromes in Solution Revealed by a Multiscale Computational Investigation

2021 ◽  
Author(s):  
Veronica Macaluso ◽  
Giacomo Salvadori ◽  
Lorenzo Cupellini ◽  
Benedetta Mennucci
Keyword(s):  
Structural Changes ◽  
Red Light ◽  
Underlying Mechanism ◽  
Binding Pocket ◽  
Spectroscopic Properties ◽  
Signaling Mechanism ◽  
Structure Relaxation ◽  
Light Sensing ◽  
Absorption Of Light ◽  
Dynamics Simulations

<pre>Phytochromes are red-light sensing proteins, with important light-regulatory roles in different organisms, which are capturing an increasing interest in bioimaging and optogenetics. Upon absorption of light by the embedded bilin chromophore, they undergo structural changes that extend from the chomophore to the protein and finally drive the biological function. Up to now, the underlying mechanism still has to be characterized fully. </pre> <pre>Here we investigate the Pfr activated form of a bacterial phytochrome, by combining extensive Molecular Dynamics simulations with a polarizable QM/MM description of the spectroscopic properties, revealing a large structure relaxation in solution, compared to the crystal structure, both in the chromophore-binding pocket and in the overall structure of the phytochrome. Our results indicate that the final opening of the dimeric structure is preceded by an important internal reorganization of the phytochrome specific (PHY) domain involving a bend of the helical spine connecting the PHY domain with the chromophore-binding domain, opening the way to a new understanding of the activation pathway. </pre>

scholarly journals Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations

2021 ◽  
pp. 1-12
Author(s):  
Haiyan Li ◽  
Zanxia Cao ◽  
Guodong Hu ◽  
Liling Zhao ◽  
Chunling Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Binding Protein ◽  
Network Models ◽  
Md Simulations ◽  
Protein Domain ◽  
Opening Angle ◽  
Conformation Changes ◽  
Wide Range ◽  
Ribose Binding Protein

BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.

scholarly journals Motif V regulates energy transduction between the flavivirus NS3 ATPase and RNA-binding cleft

2019 ◽  
Vol 295 (6) ◽  
pp. 1551-1564 ◽  
Author(s):  
Kelly E. Du Pont ◽  
Russell B. Davidson ◽  
Martin McCullagh ◽  
Brian J. Geiss
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Rna Binding ◽  
Atp Hydrolysis ◽  
Nonstructural Protein ◽  
Binding Pocket ◽  
Energy Transduction ◽  
Helicase Domain ◽  
Genome Replication ◽  
Turnover Rates

The unwinding of dsRNA intermediates is critical for the replication of flavivirus RNA genomes. This activity is provided by the C-terminal helicase domain of viral nonstructural protein 3 (NS3). As a member of the superfamily 2 (SF2) helicases, NS3 requires the binding and hydrolysis of ATP/NTP to translocate along and unwind double-stranded nucleic acids. However, the mechanism of energy transduction between the ATP- and RNA-binding pockets is not well-understood. Previous molecular dynamics simulations conducted by our group have identified Motif V as a potential “communication hub” for this energy transduction pathway. To investigate the role of Motif V in this process, here we combined molecular dynamics, biochemistry, and virology approaches. We tested Motif V mutations in both the replicon and recombinant protein systems to investigate viral genome replication, RNA-binding affinity, ATP hydrolysis activity, and helicase-mediated unwinding activity. We found that the T407A and S411A substitutions in NS3 reduce viral replication and increase the helicase-unwinding turnover rates by 1.7- and 3.5-fold, respectively, suggesting that flaviviruses may use suboptimal NS3 helicase activity for optimal genome replication. Additionally, we used simulations of each mutant to probe structural changes within NS3 caused by each mutation. These simulations indicate that Motif V controls communication between the ATP-binding pocket and the helical gate. These results help define the linkage between ATP hydrolysis and helicase activities within NS3 and provide insight into the biophysical mechanisms for ATPase-driven NS3 helicase function.

scholarly journals All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveal Secondary and Tertiary Structural Changes and Mechanisms of Allostery

2021 ◽  
Author(s):  
Carolina Pérez Segura ◽  
Boon Chong Goh ◽  
Jodi A. Hadden-Perilla
Keyword(s):  
Small Molecules ◽  
Drug Target ◽  
Structural Changes ◽  
Salt Bridge ◽  
Md Simulations ◽  
Health Concern ◽  
Protein Dimer ◽  
B Virus ◽  
Flexible Protein ◽  
Dynamics Simulations

AbstractThe hepatitis B virus (HBV) capsid is an attractive drug target, relevant to combating viral hepatitis as a major public health concern. Among small molecules known to interfere with capsid assembly, the phenylpropenamides, including AT130, represent an important anti-viral paradigm based on disrupting the timing of genome encapsulation. Crystallographic studies of AT130-bound complexes have been essential in explaining the effects of the small molecule on HBV capsid structure; however, computational examination reveals that key changes attributed to AT130 were erroneous, likely a consequence of interpreting poor resolution arising from a highly flexible protein. Here, all-atom molecular dynamics simulations of an intact AT130-bound HBV capsid reveal that, rather than damaging spike helicity, AT130 enhances the capsid’s ability to recover it. A new conformational state is identified, which can lead to dramatic opening of the intradimer interface and disruption of communication within the spike tip. A novel salt bridge is also discovered, which can mediate contact between the spike tip and fulcrum even in closed conformations, revealing a mechanism of direct communication across these domains. Combined with dynamical network analysis, results describe a connection between the intra- and interdimer interfaces and enable mapping of allostery traversing the entire capsid protein dimer.

scholarly journals Microsecond-timescale simulations suggest 5-HT–mediated preactivation of the 5-HT3Aserotonin receptor

2019 ◽  
Vol 117 (1) ◽  
pp. 405-414 ◽  
Author(s):  
Nicholas B. Guros ◽  
Arvind Balijepalli ◽  
Jeffery B. Klauda
Keyword(s):  
Serotonin Receptor ◽  
Molecular Mechanisms ◽  
Transmembrane Domain ◽  
Allosteric Regulation ◽  
Md Simulations ◽  
Binding Pocket ◽  
Careful Examination ◽  
Dynamic Binding ◽  
Order Of Magnitude ◽  
Membrane Bound

Aided by efforts to improve their speed and efficiency, molecular dynamics (MD) simulations provide an increasingly powerful tool to study the structure–function relationship of pentameric ligand-gated ion channels (pLGICs). However, accurate reporting of the channel state and observation of allosteric regulation by agonist binding with MD remains difficult due to the timescales necessary to equilibrate pLGICs from their artificial and crystalized conformation to a more native, membrane-bound conformation in silico. Here, we perform multiple all-atom MD simulations of the homomeric 5-hydroxytryptamine 3A (5-HT3A) serotonin receptor for 15 to 20 μs to demonstrate that such timescales are critical to observe the equilibration of a pLGIC from its crystalized conformation to a membrane-bound conformation. These timescales, which are an order of magnitude longer than any previous simulation of 5-HT3A, allow us to observe the dynamic binding and unbinding of 5-hydroxytryptamine (5-HT) (i.e., serotonin) to the binding pocket located on the extracellular domain (ECD) and allosteric regulation of the transmembrane domain (TMD) from synergistic 5-HT binding. While these timescales are not long enough to observe complete activation of 5-HT3A, the allosteric regulation of ion gating elements by 5-HT binding is indicative of a preactive state, which provides insight into molecular mechanisms that regulate channel activation from a resting state. This mechanistic insight, enabled by microsecond-timescale MD simulations, will allow a careful examination of the regulation of pLGICs at a molecular level, expanding our understanding of their function and elucidating key structural motifs that can be targeted for therapeutic regulation.

scholarly journals Comparative Analyses of theβ-Tubulin Gene and Molecular Modeling Reveal Molecular Insight into the Colchicine Resistance in Kinetoplastids Organisms

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Luis Luis ◽  
María Luisa Serrano ◽  
Mariana Hidalgo ◽  
Alexis Mendoza-León
Keyword(s):  
Conformational Changes ◽  
Mammalian Cells ◽  
Structural Changes ◽  
Differential Susceptibility ◽  
Binding Pocket ◽  
Crystallographic Structure ◽  
Tubulin Gene ◽  
Colchicine Binding Site ◽  
Colchicine Resistance ◽  
Leishmania Spp

Differential susceptibility to microtubule agents has been demonstrated between mammalian cells and kinetoplastid organisms such asLeishmania spp. andTrypanosoma spp. The aims of this study were to identify and characterize the architecture of the putative colchicine binding site ofLeishmania spp. and investigate the molecular basis of colchicine resistance. We cloned and sequenced theβ-tubulin gene ofLeishmania (Viannia) guyanensisand established the theoretical 3D model of the protein, using the crystallographic structure of the bovine protein as template. We identified mutations on theLeishmania  β-tubulin gene sequences on regions related to the putative colchicine-binding pocket, which generate amino acid substitutions and changes in the topology of this region, blocking the access of colchicine. The same mutations were found in theβ-tubulin sequence of kinetoplastid organisms such asTrypanosoma cruzi,T. brucei, andT. evansi. Using molecular modelling approaches, we demonstrated that conformational changes include an elongation and torsion of anα-helix structure and displacement to the inside of the pocket of oneβ-sheet that hinders access of colchicine. We propose that kinetoplastid organisms show resistance to colchicine due to amino acids substitutions that generate structural changes in the putative colchicine-binding domain, which prevent colchicine access.

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