Search Results - "Walker, Alice R."

Exploring the Effects of Mutagenesis on FusionRed by Using Excited‐State QM/MM Dynamics and Classical Force Field Simulations by Murphy, Ashlyn R., Hix, Mark A., Walker, Alice R.

“…Fluorescent proteins (FPs) are a powerful tool for examining tissues, cells, and subcellular components in vivo and in vitro. FusionRed is a particular FP…”
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Simulation-guided engineering of split GFPs with efficient β-strand photodissociation by Shamsudin, Yasmin, Walker, Alice R., Jones, Chey M., Martínez, Todd J., Boxer, Steven G.

“…Green fluorescent proteins (GFPs) are ubiquitous for protein tagging and live-cell imaging. Split-GFPs are widely used to study protein-protein interactions by…”
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ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding by Walker, Alice R, Silvestrov, Pavel, Müller, Tina A, Podolsky, Robert H, Dyson, Gregory, Hausinger, Robert P, Cisneros, Gerardo Andrés

“…The search for prostate cancer biomarkers has received increased attention and several DNA repair related enzymes have been linked to this dysfunction. Here we…”
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Genetically encoded green fluorescent sensor for probing sulfate transport activity of solute carrier family 26 member a2 (Slc26a2) protein by Lai, Cuixin, Yang, Lina, Pathiranage, Vishaka, Wang, Ruizhao, Subach, Fedor V., Walker, Alice R., Piatkevich, Kiryl D.

“…Genetically encoded fluorescent biosensors became indispensable tools for biological research, enabling real-time observation of physiological processes in…”
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Dimer Interface Destabilization of Photodissociative Dronpa Driven by Asymmetric Monomer Dynamics by McCulley, Christina H., Walker, Alice R.

“…Photoswitchable Dronpa (psDronpa) is a unique member of the fluorescent protein family that can undergo reversible photoinduced switching between fluorescent…”
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Rational Design and Expedient Synthesis of Heparan Sulfate Mimetics from Natural Aminoglycosides for Structure and Activity Relationship Studies by Wakpal, Joseph, Pathiranage, Vishaka, Walker, Alice R., Nguyen, Hien M.

“…Heparan sulfate (HS) contains variably repeating disaccharide units organized into high‐ and low‐sulfated domains. This rich structural diversity enables HS to…”
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AutoParams: An Automated Web-Based Tool To Generate Force Field Parameters for Molecular Dynamics Simulations by Hix, Mark A., Walker, Alice R.

“…Many research questions benefit from molecular dynamics simulations to observe the motions and conformations of molecules over time, which rely on force fields…”
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Conical Intersection Accessibility Dictates Brightness in Red Fluorescent Proteins by Pieri, Elisa, Walker, Alice R., Zhu, Mingning, Martínez, Todd J.

“…Red fluorescent protein (RFP) variants are highly sought after for in vivo imaging since longer wavelengths improve depth and contrast in fluorescence imaging…”
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Proton Transfer from a Photoacid to a Water Wire: First Principles Simulations and Fast Fluorescence Spectroscopy by Walker, Alice R, Wu, Boning, Meisner, Jan, Fayer, Michael D, Martínez, Todd J

“…Proton transfer reactions are ubiquitous in chemistry, especially in aqueous solutions. We investigate photoinduced proton transfer between the photoacid…”
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Computational Simulations of DNA Polymerases: Detailed Insights on Structure/Function/Mechanism from Native Proteins to Cancer Variants by Walker, Alice R, Cisneros, G. Andrés

“…Genetic information is vital in the cell cycle of DNA-based organisms. DNA polymerases (DNA Pols) are crucial players in transactions dealing with these…”
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LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields by Kratz, Eric G., Walker, Alice R., Lagardère, Louis, Lipparini, Filippo, Piquemal, Jean-Philip, Andrés Cisneros, G.

“…We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER–HP to enable QM/MM…”
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Unfolding Pathways of Hen Egg-White Lysozyme in Ethanol by Walker, Alice R, Baddam, Nikhil, Cisneros, G. Andrés

“…The aggregation of amyloid fibrils can lead to various diseases including Alzheimer’s, Parkinson’s disease, and transmissible spongiform encephalopathy…”
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Rational Design of the β‐Bulge Gate in a Green Fluorescent Protein Accelerates the Kinetics of Sulfate Sensing by Ong, Whitney S. Y., Ji, Ke, Pathiranage, Vishaka, Maydew, Caden, Baek, Kiheon, Villones, Rhiza Lyne E., Meloni, Gabriele, Walker, Alice R., Dodani, Sheel C.

“…Detection of anions in complex aqueous media is a fundamental challenge with practical utility that can be addressed by supramolecular chemistry. Biomolecular…”
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Proton Transfer Dynamics in the Aprotic Proton Accepting Solvent 1‑Methylimidazole by Thomaz, Joseph E, Walker, Alice R, Van Wyck, Stephen J, Meisner, Jan, Martinez, Todd J, Fayer, Michael D

“…The dynamics of proton transfer to the aprotic solvent 1-methylimidazole (MeIm, proton acceptor) from the photoacid 8-hydroxypyrene-1,3,6-trisulfonic acid…”
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Rational Design and Expedient Synthesis of Heparan Sulfate Mimetics from Natural Aminoglycosides for Structure and Activity Relationship Studies by Wakpal, Joseph, Pathiranage, Vishaka, Walker, Alice R., Nguyen, Hien M.

“…Heparan sulfate (HS) contains variably repeating disaccharide units organized into high‐ and low‐sulfated domains. This rich structural diversity enables HS to…”
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Reduced structural flexibility for an exonuclease deficient DNA polymerase III mutant by Gahlon, Hailey L, Walker, Alice R, Cisneros, G Andrés, Lamers, Meindert H, Rueda, David S

“…DNA synthesis, carried out by DNA polymerases, requires balancing speed and accuracy for faithful replication of the genome. High fidelity DNA polymerases…”
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Characterization of Nine Cancer-Associated Variants in Human DNA Polymerase κ by Antczak, Nicole M, Walker, Alice R, Stern, Hannah R, Leddin, Emmett M, Palad, Carl, Coulther, Timothy A, Swett, Rebecca J, Cisneros, G. Andrés, Beuning, Penny J

“…Specialized DNA damage-bypass Y-family DNA polymerases contribute to cancer prevention by providing cellular tolerance to DNA damage that can lead to mutations…”
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Bulky Lesion Bypass Requires Dpo4 Binding in Distinct Conformations by Liyanage, Pramodha S., Walker, Alice R., Brenlla, Alfonso, Cisneros, G. Andrés, Romano, Louis J., Rueda, David

“…Translesion DNA synthesis is an essential process that helps resume DNA replication at forks stalled near bulky adducts on the DNA. Benzo[ a ]pyrene (B[ a ]P)…”
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Rational Design of the β‐Bulge Gate in a Green Fluorescent Protein Accelerates the Kinetics of Sulfate Sensing by Ong, Whitney S. Y., Ji, Ke, Pathiranage, Vishaka, Maydew, Caden, Baek, Kiheon, Villones, Rhiza Lyne E., Meloni, Gabriele, Walker, Alice R., Dodani, Sheel C.

“…Detection of anions in complex aqueous media is a fundamental challenge with practical utility that can be addressed by supramolecular chemistry. Biomolecular…”
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Investigating carbohydrate based ligands for galectin-3 with docking and molecular dynamics studies by Walker, Alice R., Bonomi, Robin, Popov, Vadim, Gelovani, Juri G., Andrés Cisneros, G.

“…•Binding free energies of a library of galectin-3 ligands for PET have been calculated.•Docking scores are improved after MD relaxation.•Good agreement between…”
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