Cyclic Photoisomerization of Azobenzene in Atomistic Simulations: Modeling the Effect of Light on Columnar Aggregates of Azo Stars

This computational study investigates the influence of light on supramolecular aggregates of three-arm azobenzene stars. Every star contains three azobenzene (azo) moieties, each able to undergo reversible photoisomerization. In solution, the azo stars build column-shaped supramolecular aggregates. Previous experimental works report severe morphological changes of these aggregates under UV–Vis light. However, the underlying molecular mechanisms are still debated. Here we aim to elucidate how light affects the structure and stability of the columnar stacks on the molecular scale. The system is investigated using fully atomistic molecular dynamics (MD) simulations. To implement the effects of light, we first developed a stochastic model of the cyclic photoisomerization of azobenzene. This model reproduces the collective photoisomerization kinetics of the azo stars in good agreement with theory and previous experiments. We then apply light of various intensities and wavelengths on an equilibrated columnar stack of azo stars in water. The simulations indicate that the aggregate does not break into separate fragments upon light irradiation. Instead, the stack develops defects in the form of molecular shifts and reorientations and, as a result, it eventually loses its columnar shape. The mechanism and driving forces behind this order–disorder structural transition are clarified based on the simulations. In the end, we provide a new interpretation of the experimentally observed morphological changes.

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Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations

Molecules ◽

10.3390/molecules26247598 ◽

2021 ◽

Vol 26 (24) ◽

pp. 7598

Author(s):

Markus Koch ◽

Marina Saphiannikova ◽

Olga Guskova

Keyword(s):

Hydrogen Bonds ◽

Md Simulations ◽

Binding Energies ◽

Atomistic Simulations ◽

Π Interactions ◽

Different Types ◽

Non Covalent Interactions ◽

Experimental Works ◽

Supramolecular Aggregates ◽

Covalent Interactions

We present a simulation study of supramolecular aggregates formed by three-arm azobenzene (Azo) stars with a benzene-1,3,5-tricarboxamide (BTA) core in water. Previous experimental works by other research groups demonstrate that such Azo stars assemble into needle-like structures with light-responsive properties. Disregarding the response to light, we intend to characterize the equilibrium state of this system on the molecular scale. In particular, we aim to develop a thorough understanding of the binding mechanism between the molecules and analyze the structural properties of columnar stacks of Azo stars. Our study employs fully atomistic molecular dynamics (MD) simulations to model pre-assembled aggregates with various sizes and arrangements in water. In our detailed approach, we decompose the binding energies of the aggregates into the contributions due to the different types of non-covalent interactions and the contributions of the functional groups in the Azo stars. Initially, we investigate the origin and strength of the non-covalent interactions within a stacked dimer. Based on these findings, three arrangements of longer columnar stacks are prepared and equilibrated. We confirm that the binding energies of the stacks are mainly composed of π–π interactions between the conjugated parts of the molecules and hydrogen bonds formed between the stacked BTA cores. Our study quantifies the strength of these interactions and shows that the π–π interactions, especially between the Azo moieties, dominate the binding energies. We clarify that hydrogen bonds, which are predominant in BTA stacks, have only secondary energetic contributions in stacks of Azo stars but remain necessary stabilizers. Both types of interactions, π–π stacking and H-bonds, are required to maintain the columnar arrangement of the aggregates.

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Atomistic Simulations of Epitaxial Regrowth of As-doped Silicon

MRS Proceedings ◽

10.1557/proc-1070-e03-09 ◽

2008 ◽

Vol 1070 ◽

Cited By ~ 1

Author(s):

Joo Chul Yoon ◽

Scott Dunham

Keyword(s):

Crystalline Silicon ◽

Solid Phase ◽

Nearest Neighbors ◽

Surface Region ◽

Md Simulations ◽

Atomistic Simulations ◽

Dual Function ◽

Crystalline Region ◽

Kinetics Of ◽

Si Ion Implantation

ABSTRACTWe conducted molecular dynamics (MD) simulations of solid phase epitaxial growth of As-doped Si using a Tersoff potential characterized via comparison to DFT calculations, including energies of AsnV clusters. The Si:As systems were initialized by amorphizing the surface region of crystalline silicon via Si ion implantation and/or selective melting. The remaining crystalline region provides dual function of controlling temperature in system without perturbing regrowth and providing seed for recrystallization. After recrystallization, isolated As atoms occupy substitutional sites, with the average number of nearest neighbors for As changing from about 3.3 in amorphous Si to 4 after crystallization. We observe V incorporation associated with high As concentrations. A small fraction of isolated As atoms have associated vacancies, while vacancies are incorporated in the majority of cases in which there are sites with two As neighbors. These observations are consistent with our previous model developed to explain kinetics of As shallow junction formation which assumed V incorporation at sites with 2 or more As nearest neighbors to account for experimental data.

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Computational study on the molecular mechanisms of drug resistance of Narlaprevir due to V36M, R155K, V36M+R155K, T54A, and A156T mutations of HCV NS3/4A protease

Biochemistry and Cell Biology ◽

10.1139/bcb-2014-0039 ◽

2014 ◽

Vol 92 (5) ◽

pp. 357-369 ◽

Cited By ~ 8

Author(s):

Huiqun Wang ◽

Lingling Geng ◽

Bo-Zhen Chen ◽

Mingjuan Ji

Keyword(s):

Drug Resistance ◽

Free Energy ◽

Molecular Mechanism ◽

Molecular Mechanisms ◽

Computational Study ◽

Decomposition Analysis ◽

Md Simulations ◽

Free Energy Calculations ◽

Energy Decomposition Analysis ◽

Free Energy Decomposition

Narlaprevir is a novel NS3/4A protease inhibitor of hepatitis C virus (HCV), and it has been tested in a phase II clinical trial recently. However, distinct drug-resistance of Narlaprevir has been discovered. In our study, the molecular mechanisms of drug-resistance of Narlaprevir due to the mutations V36M, R155K, V36M+R155K, T54A, and A156T of NS3/4A protease have been investigated by molecular dynamics (MD) simulations, free energy calculations, and free energy decomposition analysis. The predicted binding free energies of Narlaprevir towards the wild-type and five mutants show that the mutations V36M, R155K, and T54A lead to low-level drug resistance and the mutations V36M+R155K and A156T lead to high-level drug resistance, which is consistent with the experimental data. The analysis of the individual energy terms indicates that the van der Waals contribution is important for distinguishing the binding affinities of these six complexes. These findings again show that the combination of different molecular modeling techniques is an efficient way to interpret the molecular mechanism of drug-resistance. Our work mainly elaborates the molecular mechanism of drug-resistance of Narlaprevir and further provides valuable information for developing novel, safer, and more potent HCV antiviral drugs in the near future.

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The Role of Vascular Aging in Atherosclerotic Plaque Development and Vulnerability

Current Pharmaceutical Design ◽

10.2174/1381612825666190830175424 ◽

2019 ◽

Vol 25 (29) ◽

pp. 3098-3111 ◽

Cited By ~ 6

Author(s):

Luca Liberale ◽

Giovanni G. Camici

Keyword(s):

Atherosclerotic Plaque ◽

Molecular Mechanisms ◽

Driving Forces ◽

Plaque Burden ◽

Vascular Aging ◽

Age Related ◽

Plaque Development ◽

Increased Risk ◽

The Impact ◽

Over Time

Background: The ongoing demographical shift is leading to an unprecedented aging of the population. As a consequence, the prevalence of age-related diseases, such as atherosclerosis and its thrombotic complications is set to increase in the near future. Endothelial dysfunction and vascular stiffening characterize arterial aging and set the stage for the development of cardiovascular diseases. Atherosclerotic plaques evolve over time, the extent to which these changes might affect their stability and predispose to sudden complications remains to be determined. Recent advances in imaging technology will allow for longitudinal prospective studies following the progression of plaque burden aimed at better characterizing changes over time associated with plaque stability or rupture. Oxidative stress and inflammation, firmly established driving forces of age-related CV dysfunction, also play an important role in atherosclerotic plaque destabilization and rupture. Several genes involved in lifespan determination are known regulator of redox cellular balance and pre-clinical evidence underlines their pathophysiological roles in age-related cardiovascular dysfunction and atherosclerosis. Objective: The aim of this narrative review is to examine the impact of aging on arterial function and atherosclerotic plaque development. Furthermore, we report how molecular mechanisms of vascular aging might regulate age-related plaque modifications and how this may help to identify novel therapeutic targets to attenuate the increased risk of CV disease in elderly people.

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Effect of Ionic Strength on the Aggregation Propensity of Aβ1-42 Peptide: An In-silico Study

Current Chemical Biology ◽

10.2174/2212796814999200818103157 ◽

2020 ◽

Vol 14 (3) ◽

pp. 216-226

Author(s):

Priyanka Borah ◽

Venkata S.K. Mattaparthi

Keyword(s):

Diffusion Coefficient ◽

Ionic Strength ◽

Marked Effect ◽

Computational Study ◽

Conformational Dynamics ◽

Rapid Change ◽

Md Simulations ◽

Radius Of Gyration ◽

Aggregation Propensity ◽

In Silico Study

Background: Aggregation of misfolded proteins under stress conditions in the cell might lead to several neurodegenerative disorders. Amyloid-beta (Aβ1-42) peptide, the causative agent of Alzheimer’s disease, has the propensity to fold into β-sheets under stress, forming aggregated amyloid plaques. This is influenced by factors such as pH, temperature, metal ions, mutation of residues, and ionic strength of the solution. There are several studies that have highlighted the importance of ionic strength in affecting the folding and aggregation propensity of Aβ1-42 peptide. Objective: To understand the effect of ionic strength of the solution on the aggregation propensity of Aβ1-42 peptide, using computational approaches. Materials and Methods: In this study, Molecular Dynamics (MD) simulations were performed on Aβ1-42 peptide monomer placed in (i) 0 M, (ii) 0.15 M, and (iii) 0.30 M concentration of NaCl solution. To prepare the input files for the MD simulations, we have used the Amberff99SB force field. The conformational dynamics of Aβ1-42 peptide monomer in different ionic strengths of the solutions were illustrated from the analysis of the corresponding MD trajectory using the CPPtraj tool. Results: From the MD trajectory analysis, we observe that with an increase in the ionic strength of the solution, Aβ1-42 peptide monomer shows a lesser tendency to undergo aggregation. From RMSD and SASA analysis, we noticed that Aβ1-42 peptide monomer undergoes a rapid change in conformation with an increase in the ionic strength of the solution. In addition, from the radius of gyration (Rg) analysis, we observed Aβ1-42 peptide monomer to be more compact at moderate ionic strength of the solution. Aβ1-42 peptide was also found to hold its helical secondary structure at moderate and higher ionic strengths of the solution. The diffusion coefficient of Aβ1-42 peptide monomer was also found to vary with the ionic strength of the solution. We observed a relatively higher diffusion coefficient value for Aβ1-42 peptide at moderate ionic strength of the solution. Conclusion: Our findings from this computational study highlight the marked effect of ionic strength of the solution on the conformational dynamics and aggregation propensity of Aβ1-42 peptide monomer.

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Platelet-derived lysophosphatidic acid mediated LPAR1 activation as a therapeutic target for osteosarcoma metastasis

Oncogene ◽

10.1038/s41388-021-01956-6 ◽

2021 ◽

Author(s):

Satoshi Takagi ◽

Yuki Sasaki ◽

Sumie Koike ◽

Ai Takemoto ◽

Yosuke Seto ◽

...

Keyword(s):

Platelet Activation ◽

Pulmonary Metastasis ◽

Lysophosphatidic Acid ◽

Therapeutic Intervention ◽

Molecular Mechanisms ◽

Morphological Changes ◽

Osteosarcoma Cells ◽

Invasion And Metastasis ◽

Platelet Releasate

AbstractOsteosarcoma is the most common primary malignant bone cancer, with high rates of pulmonary metastasis. Osteosarcoma patients with pulmonary metastasis have worse prognosis than those with localized disease, leading to dramatically reduced survival rates. Therefore, understanding the biological characteristics of metastatic osteosarcoma and the molecular mechanisms of invasion and metastasis of osteosarcoma cells will lead to the development of innovative therapeutic intervention for advanced osteosarcoma. Here, we identified that osteosarcoma cells commonly exhibit high platelet activation-inducing characteristics, and molecules released from activated platelets promote the invasiveness of osteosarcoma cells. Given that heat-denatured platelet releasate maintained the ability to promote osteosarcoma invasion, we focused on heat-tolerant molecules, such as lipid mediators in the platelet releasate. Osteosarcoma-induced platelet activation leads to abundant lysophosphatidic acid (LPA) release. Exposure to LPA or platelet releasate induced morphological changes and increased invasiveness of osteosarcoma cells. By analyzing publicly available transcriptome datasets and our in-house osteosarcoma patient-derived xenograft tumors, we found that LPA receptor 1 (LPAR1) is notably upregulated in osteosarcoma. LPAR1 gene KO in osteosarcoma cells abolished the platelet-mediated osteosarcoma invasion in vitro and the formation of early pulmonary metastatic foci in experimental pulmonary metastasis models. Of note, the pharmacological inhibition of LPAR1 by the orally available LPAR1 antagonist, ONO-7300243, prevented pulmonary metastasis of osteosarcoma in the mouse models. These results indicate that the LPA–LPAR1 axis is essential for the osteosarcoma invasion and metastasis, and targeting LPAR1 would be a promising therapeutic intervention for advanced osteosarcoma.

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The human EDAR 370V/A polymorphism affects tooth root morphology potentially through the modification of a reaction–diffusion system

Scientific Reports ◽

10.1038/s41598-021-84653-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Keiichi Kataoka ◽

Hironori Fujita ◽

Mutsumi Isa ◽

Shimpei Gotoh ◽

Akira Arasaki ◽

...

Keyword(s):

Molecular Mechanisms ◽

Computational Study ◽

Reaction Diffusion ◽

Human Migration ◽

Reaction Diffusion System ◽

Diffusion System ◽

Tooth Root ◽

Computed Tomography Images ◽

Diffusion Dynamics ◽

Root Morphogenesis

AbstractMorphological variations in human teeth have long been recognized and, in particular, the spatial and temporal distribution of two patterns of dental features in Asia, i.e., Sinodonty and Sundadonty, have contributed to our understanding of the human migration history. However, the molecular mechanisms underlying such dental variations have not yet been completely elucidated. Recent studies have clarified that a nonsynonymous variant in the ectodysplasin A receptor gene (EDAR370V/A; rs3827760) contributes to crown traits related to Sinodonty. In this study, we examined the association between theEDARpolymorphism and tooth root traits by using computed tomography images and identified that the effects of theEDARvariant on the number and shape of roots differed depending on the tooth type. In addition, to better understand tooth root morphogenesis, a computational analysis for patterns of tooth roots was performed, assuming a reaction–diffusion system. The computational study suggested that the complicated effects of theEDARpolymorphism could be explained when it is considered that EDAR modifies the syntheses of multiple related molecules working in the reaction–diffusion dynamics. In this study, we shed light on the molecular mechanisms of tooth root morphogenesis, which are less understood in comparison to those of tooth crown morphogenesis.

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Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Molecules ◽

10.3390/molecules26010198 ◽

2021 ◽

Vol 26 (1) ◽

pp. 198

Author(s):

Lijun Lang ◽

Alberto Perez

Keyword(s):

Bayesian Inference ◽

Virtual Screening ◽

Statistical Mechanics ◽

Small Molecules ◽

Rational Design ◽

Driving Forces ◽

Peptide Inhibitors ◽

Atomistic Simulations ◽

Binding Mechanism ◽

Intrinsically Disordered

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).

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High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs

Nature Communications ◽

10.1038/s41467-021-22628-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Betty Ha ◽

Kevin P. Larsen ◽

Jingji Zhang ◽

Ziao Fu ◽

Elizabeth Montabana ◽

...

Keyword(s):

Reverse Transcriptase ◽

Viral Entry ◽

Reverse Transcription ◽

Molecular Mechanisms ◽

Dissociation Kinetics ◽

Structural Mechanism ◽

Medium Resolution ◽

Kinetics Of ◽

Hiv 1

AbstractReverse transcription of the HIV-1 viral RNA genome (vRNA) is an integral step in virus replication. Upon viral entry, HIV-1 reverse transcriptase (RT) initiates from a host tRNALys3 primer bound to the vRNA genome and is the target of key antivirals, such as non-nucleoside reverse transcriptase inhibitors (NNRTIs). Initiation proceeds slowly with discrete pausing events along the vRNA template. Despite prior medium-resolution structural characterization of reverse transcriptase initiation complexes (RTICs), higher-resolution structures of the RTIC are needed to understand the molecular mechanisms that underlie initiation. Here we report cryo-EM structures of the core RTIC, RTIC–nevirapine, and RTIC–efavirenz complexes at 2.8, 3.1, and 2.9 Å, respectively. In combination with biochemical studies, these data suggest a basis for rapid dissociation kinetics of RT from the vRNA–tRNALys3 initiation complex and reveal a specific structural mechanism of nucleic acid conformational stabilization during initiation. Finally, our results show that NNRTIs inhibit the RTIC and exacerbate discrete pausing during early reverse transcription.

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Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment

Chemical Science ◽

10.1039/d0sc04657d ◽

2021 ◽

Author(s):

Arghadwip Paul ◽

Suman Samantray ◽

Marco Anteghini ◽

Mohammed Khaled ◽

Birgit Strodel

Keyword(s):

Amyloid Β ◽

Md Simulations ◽

Amyloid Β Peptide ◽

Intrinsically Disordered ◽

Thermodynamics And Kinetics ◽

Markov State ◽

Markov State Models ◽

State Models ◽

Kinetics Of

The convergence of MD simulations is tested using varying measures for the intrinsically disordered amyloid-β peptide (Aβ). Markov state models show that 20–30 μs of MD is needed to reliably reproduce the thermodynamics and kinetics of Aβ.

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