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Articles 1 - 9 of 9
Full-Text Articles in Biochemistry
From Deep Mutational Mapping Of Allosteric Protein Landscapes To Deep Learning Of Allostery And Hidden Allosteric Sites: Zooming In On “Allosteric Intersection” Of Biochemical And Big Data Approaches, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao
From Deep Mutational Mapping Of Allosteric Protein Landscapes To Deep Learning Of Allostery And Hidden Allosteric Sites: Zooming In On “Allosteric Intersection” Of Biochemical And Big Data Approaches, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao
Mathematics, Physics, and Computer Science Faculty Articles and Research
The recent advances in artificial intelligence (AI) and machine learning have driven the design of new expert systems and automated workflows that are able to model complex chemical and biological phenomena. In recent years, machine learning approaches have been developed and actively deployed to facilitate computational and experimental studies of protein dynamics and allosteric mechanisms. In this review, we discuss in detail new developments along two major directions of allosteric research through the lens of data-intensive biochemical approaches and AI-based computational methods. Despite considerable progress in applications of AI methods for protein structure and dynamics studies, the intersection between allosteric …
Methylene Blue Inhibits Cromakalim-Activated K+ Currents In Follicle-Enclosed Oocytes, Dmytro Isaev, Keun-Hang Susan Yang, Georg Petroianu, Dietrich Ernst Lorke, Murat Oz
Methylene Blue Inhibits Cromakalim-Activated K+ Currents In Follicle-Enclosed Oocytes, Dmytro Isaev, Keun-Hang Susan Yang, Georg Petroianu, Dietrich Ernst Lorke, Murat Oz
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
The effects of methylene blue (MB) on cromakalim-induced K+ currents were investigated in follicle-enclosed Xenopus oocytes. In concentrations ranging from 3–300 μM, MB inhibited K+ currents (IC50: 22.4 μM) activated by cromakalim, which activates KATP channels. MB inhibited cromakalim-activated K+ currents in a noncompetitive and voltage-independent manner. The respective EC50 and slope values for cromakalim-activation of K+ currents were 194 ± 21 µM and 0.91 for controls, and 206 ± 24 µM and 0.87 in the presence of 30 μM MB. The inhibition of cromakalim-induced K+ currents by MB was not …
Investigating The Interactions Between Individual Calmodulin And Hiv-1 Protein Domains, Riley K. Kendall, Jerry Larue
Investigating The Interactions Between Individual Calmodulin And Hiv-1 Protein Domains, Riley K. Kendall, Jerry Larue
Student Scholar Symposium Abstracts and Posters
The World Health Organization found that 37.9 million people were living with HIV by the end of 2018. HIV is a virus that weakens the immune system through viral replication and the destruction of CD4+ T-cells, which are white blood cells that detect infection and make antibodies. A cure for HIV has not yet been discovered. HIV-1 contains a Gag polyprotein which regulates the stages of viral replication. Previous studies suggest that the myristoyl group of a matrix protein peptide found on the Gag polyprotein, MA, forms a complex with a calcium-binding, multifunctional regulatory protein called Calmodulin (CaM). CaM …
Allosteric Mechanism Of The Circadian Protein Vivid Resolved Through Markov State Model And Machine Learning Analysis, Hongyu Zhou, Zheng Dong, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao
Allosteric Mechanism Of The Circadian Protein Vivid Resolved Through Markov State Model And Machine Learning Analysis, Hongyu Zhou, Zheng Dong, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao
Mathematics, Physics, and Computer Science Faculty Articles and Research
The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an …
Curcumin Potentiates The Function Of Human Α7-Nicotinic Acetylcholine Receptors Expressed In Sh-Ep1 Cells, Eslam El Nebrisi, Lina T. Al Kury, Keun-Hang Susan Yang, Petrilla Jayaprakash, Frank Christopher Howarth, Nadine Kabbani, Murat Oz
Curcumin Potentiates The Function Of Human Α7-Nicotinic Acetylcholine Receptors Expressed In Sh-Ep1 Cells, Eslam El Nebrisi, Lina T. Al Kury, Keun-Hang Susan Yang, Petrilla Jayaprakash, Frank Christopher Howarth, Nadine Kabbani, Murat Oz
Mathematics, Physics, and Computer Science Faculty Articles and Research
Effects of curcumin, a biologically active ingredient of turmeric, were tested on the Ca2+transients induced by the activation of α7 subunit of the human nicotinic acetylcholine (α7nACh) receptor expressed in SH-EP1 cells. Curcumin caused a significant potentiation of choline (1 mM)-induced Ca2+ transients with an EC50 value of 133 nM. The potentiating effect of curcumin was not observed in Ca2+ transients induced by high K+ (60 mM) containing solutions or activation of α4β2 nACh receptors and the extent of curcumin potentiation was not altered in the presence of …
Cellular And Molecular Targets Of Menthol Actions, Murat Oz, Eslam El Nebrisi, Keun-Hang Susan Yang, Frank Christopher Howarth, Lina T. Al Kury
Cellular And Molecular Targets Of Menthol Actions, Murat Oz, Eslam El Nebrisi, Keun-Hang Susan Yang, Frank Christopher Howarth, Lina T. Al Kury
Mathematics, Physics, and Computer Science Faculty Articles and Research
Menthol belongs to monoterpene class of a structurally diverse group of phytochemicals found in plant-derived essential oils. Menthol is widely used in pharmaceuticals, confectionary, oral hygiene products, pesticides, cosmetics, and as a flavoring agent. In addition, menthol is known to have antioxidant, anti-inflammatory, and analgesic effects. Recently, there has been renewed awareness in comprehending the biological and pharmacological effects of menthol. TRP channels have been demonstrated to mediate the cooling actions ofmenthol. There has been new evidence demonstrating thatmenthol can significantly influence the functional characteristics of a number of different kinds of ligand and voltage-gated ion channels, indicating that at …
Connecting The Physiological And Behavioral Response To Heat Stress On A Warming Planet, Anastasia Kalyta
Connecting The Physiological And Behavioral Response To Heat Stress On A Warming Planet, Anastasia Kalyta
Student Scholar Symposium Abstracts and Posters
Intertidal communities are considered good models of the biological effects of climate change on ecosystems, as their resident organisms are subjected to heat spells during daytime low tides. The increasing heat exposure can elicit behavioral as well as physiological responses in intertidal organisms. We studied the relationship between these responses to heat stress in the blue-banded hermit crab, Pagurus samuelis, by inducing a “heat shock” with elevated water temperature of 29 °C for 2.5 h. The behavioral effect of heat-shock was quantified using a 30-minute feeding assay, measuring the mass of a standard squid pellet consumed by individual hermit crabs. …
Solid-Phase Organic Matter Reduction Regulates Anaerobic Decomposition In Bog Soil, Jason K. Keller, Kimberly K. Takagi
Solid-Phase Organic Matter Reduction Regulates Anaerobic Decomposition In Bog Soil, Jason K. Keller, Kimberly K. Takagi
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Peatlands store globally significant amounts of carbon and are important sources of the greenhouse gas methane (CH4) to the atmosphere. However, for reasons which are not well understood, many peatland soils produce smaller amounts of CH4 than theoretically predicted, and carbon dioxide (CO2) produced during anaerobic decomposition in peatland soils cannot be accounted for by commonly measured microbial processes. Here we show that the reduction of solid-phase organic matter (i.e., humic substances) suppresses CH4 production in a bog soil and can be responsible for 33–61% of the total carbon mineralization in this soil. These results demonstrate that the reduction of …
Pathways Of Anaerobic Carbon Cycling Across An Ombrotrophic–Minerotrophic Peatland Gradient, Jason K. Keller, Scott D. Bridgham
Pathways Of Anaerobic Carbon Cycling Across An Ombrotrophic–Minerotrophic Peatland Gradient, Jason K. Keller, Scott D. Bridgham
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Peatland soils represent globally significant stores of carbon, and understanding carbon cycling pathways in these ecosystems has important implications for global climate change. We measured aceticlastic and autotrophic methanogenesis, sulfate reduction, denitrification, and iron reduction in a bog, an intermediate fen, and a rich fen in the Upper Peninsula of Michigan for one growing season. In 3-d anaerobic incubations of slurried peat, denitrification and iron reduction were minor components of anaerobic carbon mineralization. Experiments using 14C-labeled methanogenic substrates showed that methanogenesis in these peatlands was primarily through the aceticlastic pathway, except early in the growing season in more ombrotrophic peatlands, …