Explanipedia

Lithocholic acid induces T3SS-dependent formation of invasion-competent Shigella flexneri aggregates Open

J. Gibson Lanier, Freddie R. Salsbury, Volkan K. Köseoğlu · 2025

Shigella flexneri causes shigellosis, the second leading cause of diarrheal deaths worldwide. The pathogen invades colonic epithelial cells using a type III secretion system (T3SS) that delivers effector proteins to remodel host actin cyto…

K294E change in the rotavirus factory forming protein NSP2 stabilizes a rare C-terminal conformation Open

Sarah L. Nichols, Thomas Hollis, Freddie R. Salsbury, Sarah McDonald Esstman · 2025

Rotaviruses (RVs) induce the formation of cytoplasmic viral factories, termed viroplasms, which are the sites of early particle assembly and viral RNA synthesis. The RV octameric nonstructural protein 2 (NSP2) plays critical, albeit incomp…

Editorial: aims and scope update Open

Freddie R. Salsbury, Mohd Hamdan Adnan, Thomas C. Bishop, Jonathan B. Chaires, Md. Imtaiyaz Hassan · 2024

Allosteric Modulation of Thrombin by Thrombomodulin: Insights from Logistic Regression and Statistical Analysis of Molecular Dynamics Simulations Open

Dizhou Wu, Freddie R. Salsbury · 2024

Thrombomodulin (TM), a transmembrane receptor integral to the anticoagulant pathway, governs thrombin's substrate specificity via interaction with thrombin's anion-binding exosite I. Despite its established role, the precise mechanisms und…

Unraveling the Impact of W215A/E217A Mutations on Thrombin’s Dynamics and Thrombomodulin Binding through Molecular Dynamics Simulations Open

Dizhou Wu, Freddie R. Salsbury · 2023

Thrombin, a central serine protease in hemostasis, exhibits dual functionality in coagulation processes—favoring fibrinogen cleavage in its native form while shifting towards protein C activation when complexed with thrombomodulin (TM). Th…

Unraveling the Role of Hydrogen Bonds in Thrombin via Two Machine Learning Methods Open

Dizhou Wu, Freddie R. Salsbury · 2023

Hydrogen bonds play a critical role in the folding and stability of proteins, such as proteins and nucleic acids, by providing strong and directional interactions. They help to maintain the secondary and 3D structure of proteins, and struc…

Synthesis, Molecular Modeling and Anticancer Activity of New Rescinnamine Derivatives as MMR-Inducers Open

shimaa naguib, Omar M. Aly, Gamal Abourhma, Stephen B. King, Freddie R. Salsbury , et al. · 2023

Mis-match repair proteins (MMR), such as MSH2/MSH6 have DNA dual functions, repair, and death functions.Rauwolfia alkaloids such as rescinnamine is capable to induce their death conformation lead the cancer cell to the apoptotic pathway.Ce…

Compound C Inhibits Ovarian Cancer Progression via PI3K-AKT-mTOR-NFκB Pathway Open

Alia Ghoneum, Daniela Gonzalez, Hesham Afify, Junjun Shu, Abigail Hegarty , et al. · 2022

Epithelial Ovarian cancer (OvCa) is the leading cause of death from gynecologic malignancies in the United States, with most patients diagnosed at late stages. High-grade serous cancer (HGSC) is the most common and lethal subtype. Despite …

Impact of A2T and D23N mutations on C99 homodimer conformations Open

Yan Lü, Freddie R. Salsbury, Philippe Derreumaux · 2022

The proteolytic cleavage of C99 by γ-secretase is the last step in the production of amyloid-β (Aβ) peptides. Previous studies have shown that membrane lipid composition, cholesterol concentration, and mutation in the transmembrane helix m…

Simulations suggest double sodium binding induces unexpected conformational changes in thrombin Open

Dizhou Wu, Freddie R. Salsbury · 2022

Integration of Computation into mechanics at WFU Open

Freddie R. Salsbury · 2022

TREX1 as a Novel Immunotherapeutic Target Open

Wayne O. Hemphill, Sean R. Simpson, Mingyong Liu, Freddie R. Salsbury, Thomas Hollis , et al. · 2021

Mutations in the TREX1 3’ → 5’ exonuclease are associated with a spectrum of autoimmune disease phenotypes in humans and mice. Failure to degrade DNA activates the cGAS-STING DNA-sensing pathway signaling a type-I interferon (IFN) response…

Light Chain Mutation Effects on the Dynamics of Thrombin Open

Dizhou Wu, Jiajie Xiao, Freddie R. Salsbury · 2021

Thrombin plays an important role in the process of hemostasis and blood coagulation. Studies in thrombin can help us find ways to treat cancer because thrombin is able to reduce the characteristic hypercoagulability of cancer. Thrombin is …

Insights into Correlated Motions and Long-Range Interactions in CheY Derived from Molecular Dynamics Simulations Open

Michael H. Knaggs, Freddie R. Salsbury, Marshall H. Edgell, Jacquelyn S. Fetrow · 2020

CheY is a response regulator protein involved in bacterial chemotaxis. Much is known about its active and inactive conformations, but little is known about the mechanisms underlying long-range interactions or correlated motions. To investi…

Dissecting Contributions to Efficient Catalysis in the tRNA Modifying Enzyme TilS Open

Ferdiemar C. Guinto, Rebecca W. Alexander, Freddie R. Salsbury · 2020

Structure and Dynamics of tRNA<sup>Met</sup> Containing Core Substitutions Open

Ryan C. Godwin, Lindsay Macnamara, Rebecca W. Alexander, Freddie R. Salsbury · 2018

The fidelity of protein synthesis is largely dominated by the accurate recognition of transfer RNAs (tRNAs) by their cognate aminoacyl-tRNA synthetases. Aminoacylation of each tRNA with its cognate amino acid is necessary to maintain the a…

All-atom molecular dynamics comparison of disease-associated zinc fingers Open

Ryan C. Godwin, William H. Gmeiner, Freddie R. Salsbury · 2017

An important regulatory domain of NF-[Formula: see text]B Essential Modulator (NEMO) is a ubiquitin-binding zinc finger, with a tetrahedral CYS3HIS1 zinc-coordinating binding site. Two variations of NEMO's zinc finger are implicated in var…

Visualizing correlated motion with HDBSCAN clustering Open

Ryan L. Melvin, Jiajie Xiao, Ryan C. Godwin, Kenneth S. Berenhaut, Freddie R. Salsbury · 2017

Correlated motion analysis provides a method for understanding communication between and dynamic similarities of biopolymer residues and domains. The typical equal‐time correlation matrices—frequently visualized with pseudo‐colorings or he…

All-Atom MD Predicts Magnesium-Induced Hairpin in Chemically Perturbed RNA Analog of F10 Therapeutic Open

Ryan L. Melvin, William H. Gmeiner, Freddie R. Salsbury · 2017

Given their increasingly frequent usage, understanding the chemical and structural properties which allow therapeutic nucleic acids to promote the death of cancer cells is critical for medical advancement. One molecule of interest is a 10-…

MutSα's Multi-Domain Allosteric Response to Three DNA Damage Types Revealed by Machine Learning Open

Ryan L. Melvin, W. G. Thompson, Ryan C. Godwin, William H. Gmeiner, Freddie R. Salsbury · 2017

MutSα is a key component in the mismatch repair (MMR) pathway. This protein is responsible for initiating the signaling pathways for DNA repair or cell death. Herein we investigate this heterodimer's post-recognition, post-binding r…

Statistical Mechanics Examples Open

Ryan C. Godwin, Freddie R. Salsbury · 2017

This is a LabVIEW program designed to explore various problems in statistical mechanics. This suite of applications allows the user to vary input parameters and observe their influence on the output. More detailed descriptions of each prog…

Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator) Open

Ryan C. Godwin, Ryan L. Melvin, William H. Gmeiner, Freddie R. Salsbury · 2016

Zinc-finger proteins are regulators of critical signaling pathways for various cellular functions, including apoptosis and oncogenesis. Here, we investigate how binding site protonation states and zinc coordination influence protein struct…

Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge Open

Ryan L. Melvin, Ryan C. Godwin, Jiajie Xiao, W. G. Thompson, Kenneth S. Berenhaut , et al. · 2016

As the length of molecular dynamics (MD) trajectories grows with increasing computational power, so does the importance of clustering methods for partitioning trajectories into conformational bins. Of the methods available, the vast majori…

All-Atom Molecular Dynamics Reveals Mechanism of Zinc Complexation with Therapeutic F10 Open

Ryan L. Melvin, William H. Gmeiner, Freddie R. Salsbury · 2016

Advancing the use of therapeutic nucleic acids requires understanding the chemical and structural properties that allow these polymers to promote the death of malignant cells. Here we explore Zn²⁺ complexation by the fluoropyrim…

Visualizing ensembles in structural biology Open

Ryan L. Melvin, Freddie R. Salsbury · 2016

Generalized Allostery in Thrombin Open

Jiajie Xiao, Freddie R. Salsbury · 2016

Salsbury Group 2016 Research Presentation Open

Freddie R. Salsbury · 2016

Annual research overview; sort of big picture

Villin Headpiece Simulations Open

Ryan C. Godwin, Freddie R. Salsbury · 2016

3 separate simulations each of 6µs concatenated together are contained herein. Each trajectory was run with ACEMD using a CHARMM 27 force field. The proteins (2RJY) were first solvated to 0.15 mol/L of NaCL and set in a water box modeled a…

A Matlab script to perform PCA on molecular dynamics trajectories Open

Jiajie Xiao, Freddie R. Salsbury · 2016

A Matlab script to perform principal component analysis on molecular dynamics trajectories and construct free energy surfaces using predominant principal components.

Importance of long-time simulations for rare event sampling in zinc finger proteins Open

Ryan C. Godwin, William H. Gmeiner, Freddie R. Salsbury · 2015

Molecular dynamics (MD) simulation methods have seen significant improvement since their inception in the late 1950s. Constraints of simulation size and duration that once impeded the field have lessened with the advent of better algorithm…

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