Chemistry Commons^™

Coevolution, Dynamics And Allostery Conspire In Shaping Cooperative Binding And Signal Transmission Of The Sars-Cov-2 Spike Protein With Human Angiotensin-Converting Enzyme 2, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Binding to the host receptor is a critical initial step for the coronavirus SARS-CoV-2 spike protein to enter into target cells and trigger virus transmission. A detailed dynamic and energetic view of the binding mechanisms underlying virus entry is not fully understood and the consensus around the molecular origins behind binding preferences of SARS-CoV-2 for binding with the angiotensin-converting enzyme 2 (ACE2) host receptor is yet to be established. In this work, we performed a comprehensive computational investigation in which sequence analysis and modeling of coevolutionary networks are combined with atomistic molecular simulations and comparative binding free energy analysis of …

Computational And Pharmacological Evaluation Of Carveol For Antidiabetic Potential, Muhammad Shabir Ahmed, Arif Ullah Khan, Lina Tariq Al Kury, Fawad Ali Shah

All Works

© Copyright © 2020 Ahmed, Khan, Kury and Shah. Background: Carveol is a natural drug product present in the essential oils of orange peel, dill, and caraway seeds. The seed oil of Carum Carvi has been reported to be antioxidant, anti-inflammatory, anti-hyperlipidemic, antidiabetic, and hepatoprotective. Methods: The antidiabetic potential of carveol was investigated by employing in-vitro, in-vivo, and in-silico approaches. Moreover, alpha-amylase inhibitory assay and an alloxan-induced diabetes model were used for in-vitro and in-vivo analysis, respectively. Results: Carveol showed its maximum energy values (≥ -7 Kcal/mol) against sodium-glucose co-transporter, aldose reductase, and sucrose-isomaltase intestinal, whereas it exhibited intermediate energy …

Allosteric Regulation At The Crossroads Of New Technologies: Multiscale Modeling, Networks, And Machine Learning, Gennady M. Verkhivker, Steve Agajanian, Guang Hu, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

Allosteric regulation is a common mechanism employed by complex biomolecular systems for regulation of activity and adaptability in the cellular environment, serving as an effective molecular tool for cellular communication. As an intrinsic but elusive property, allostery is a ubiquitous phenomenon where binding or disturbing of a distal site in a protein can functionally control its activity and is considered as the “second secret of life.” The fundamental biological importance and complexity of these processes require a multi-faceted platform of synergistically integrated approaches for prediction and characterization of allosteric functional states, atomistic reconstruction of allosteric regulatory mechanisms and discovery of …

Nobiletin Affects Circadian Rhythms And Oncogenic Characteristics In A Cell-Dependent Manner, Sujeewa S. Lellupitiyage Don, Kelly L. Robertson, Hui-Hsien Lin, Caroline Labriola, Mary E. Harrington, Stephanie R. Taylor, Michelle E. Farkas

Psychology: Faculty Publications

The natural product nobiletin is a small molecule, widely studied with regard to its therapeutic effects, including in cancer cell lines and tumors. Recently, nobiletin has also been shown to affect circadian rhythms via their enhancement, resulting in protection against metabolic syndrome. We hypothesized that nobiletin’s anti-oncogenic effects, such as prevention of cell migration and formation of anchorage independent colonies, are correspondingly accompanied by modulation of circadian rhythms. Concurrently, we wished to determine whether the circadian and anti-oncogenic effects of nobiletin differed across cancer cell lines. In this study, we assessed nobiletin’s circadian and therapeutic characteristics to ascertain whether these …

Synergistic Use Of Remote Sensing And Modeling For Estimating Net Primary Productivity In The Red Sea With Vgpm, Eppley-Vgpm, And Cbpm Models Intercomparison, Wenzhao Li, Surya Prakash Tiwari, Hesham El-Askary, Mohamed Ali Qurban, Vassilis Amiridis, K. P. Manikandan, Michael J. Garay, Olga V. Kalashnikova, Thomas C. Piechota, Daniele C. Struppa

Mathematics, Physics, and Computer Science Faculty Articles and Research

Primary productivity (PP) has been recently investigated using remote sensing-based models over quite limited geographical areas of the Red Sea. This work sheds light on how phytoplankton and primary production would react to the effects of global warming in the extreme environment of the Red Sea and, hence, illuminates how similar regions may behave in the context of climate variability. study focuses on using satellite observations to conduct an intercomparison of three net primary production (NPP) models--the vertically generalized production model (VGPM), the Eppley-VGPM, and the carbon-based production model (CbPM)--produced over the Red Sea domain for the 1998-2018 time period. …

Volume 12, Haleigh James, Hannah Meyls, Hope Irvin, Megan E. Hlavaty, Samara L. Gall, Austin J. Funk, Karyn Keane, Sarah Ghali, Antonio Harvey, Andrew Jones, Rachel Hazelwood, Madison Schmitz, Marija Venta, Haley Tebo, Jeremiah Gilmer, Bridget Dunn, Benjamin Sullivan, Mckenzie Johnson

Incite: The Journal of Undergraduate Scholarship

Introduction, Dr. Roger A. Byrne, Dean

From the Editor, Dr. Larissa "Kat" Tracy

From the Designers, Rachel English, Rachel Hanson

Immortality in the Mortal World: Otherworldly Intervention in "Lanval" and "The Wife of Bath's Tale" by Haleigh James

Analysis of Phenolic Compounds in Moroccan Olive Oils by HPLC by Hannah Meyls

Art by Hope Irvin

The Effects of Cell Phone Use on Gameplay Enjoyment and Frustration by Megan E. Hlavaty, Samara L. Gall, and Austin J. Funk

Care, No Matter What: Planned Parenthood's Use of Organizational Rhetoric to Expand its Reputation by Karyn Keane

Analysis of Petroleum Products for …

Computational Chemistry In The Cloud, Gregory Campbell

19th Annual Celebration of Undergraduate Research and Creative Activity (2020)

Computational chemistry requires expensive computers and significant computer expertise. We are remedying these issues by using cloud computing to lower costs and by developing our Server In The Cloud (SITC) script to reduce the need for local expertise. SITC implements computational chemistry engines with the user-friendly WebMO interface on Google and Amazon cloud computers. In this way, we are making computational chemistry cheaper and more accessible to a wider range of chemistry students and researchers.

Nf-Κb Inhibitors Attenuate Mcao Induced Neurodegeneration And Oxidative Stress—A Reprofiling Approach, Awais Ali, Fawad Ali Shah, Alam Zeb, Imran Malik, Arooj Mohsin Alvi, Lina Tariq Alkury, Sajid Rashid, Ishtiaq Hussain, Najeeb Ullah, Arif Ullah Khan, Phil Ok Koh, Shupeng Li

All Works

© Copyright © 2020 Ali, Shah, Zeb, Malik, Alvi, Alkury, Rashid, Hussain, Ullah, Ullah Khan, Koh and Li. Stroke is the leading cause of morbidity and mortality worldwide. About 87% of stroke cases are ischemic, which disrupt the physiological activity of the brain, thus leading to a series of complex pathophysiological events. Despite decades of research on neuroprotectants to probe for suitable therapies against ischemic stroke, no successful results have been obtained, and new alternative approaches are urgently required in order to combat this pathological torment. To address these problems, drug repositioning/reprofiling is explored extensively. Drug repurposing aims to identify …

Polyacrylamide In Glycerol Solutions From An Atomistic Perspective Of The Energetics, Structure, And Dynamics, Scott D. Hopkins, Gideon K. Gogovi, Eric Weisel, Robert A. Handler, Estela Blaisten-Barojas

VMASC Publications

All-atom molecular dynamics is used to investigate the structural, energetic, and dynamical properties of polyacrylamide (PAM) oligomers of different lengths solvated in pure glycerol, a 90:10 glycerol–water mixture, and pure water. We predict that the oligomers’ globular structure is obtained only when the modeling strategy considers the solvent as a continuous background. Meanwhile, for all-atom modeled solvents, the glycerol solutions display a strong tendency of trapping the oligomers in instantaneous elongated random coiled structures that remain locked-in over tens of nanoseconds. In pure water, the oligomers acquire considerably shorter random coiled structures of increased flexibility. The all-atom force field, generalized …

Advancement Of Predictive Modeling Of Zeta Potentials (Ζ) In Metal Oxide Nanoparticles With Correlation Intensity Index (Cii), Andrey A. Toropov, Natalia Sizochenko, Alla P. Toropova, Danuta Leszczynska, Jerzy Leszczynski

Articles

It was expected that index of the ideality of correlation (IIC) and correlation intensity index (CII) could be used as possible tools to improve the predictive power of the quantitative model for zeta potential of nanoparticles. In this paper, we test how the statistical quality of quantitative structure-activity models for zeta potentials (ζ, a common measurement that reflects surface charge and stability of nanomaterial) could be improved with the use of these two indexes. Our hypothesis was tested using the benchmark data set that consists of 87 measurements of zeta potentials in water. We used quasi-SMILES molecular representation to take …