Article
Biochemistry & Molecular Biology
Kim Lopez-Guell, Federica Battistini, Modesto Orozco
Summary: Traditional models of DNA flexibility, which assume local harmonic movements, fail to capture the multimodality and correlations in DNA movements. We propose a new multimodal-harmonic correlated model that provides high-quality results at a low computational cost. This model can be used to explore the dynamics of long DNA segments, approaching the chromatin range.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Ankita Tripathi, Kshatresh Dutta Dubey
Summary: This study demonstrates a method to enhance promiscuity, called allostery-driven promiscuity, using molecular dynamics simulations and hybrid QM/MM calculations. By studying the AEE enzyme, the authors show that a single site mutation can induce conformational changes in the capping loop, allowing recognition of different substrates for different functions.
CHEMISTRY-AN ASIAN JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Prateek Kumar, Taniya Bhardwaj, Ankur Kumar, Neha Garg, Rajanish Giri
Summary: The study seeks to understand the molecular interactions between hydroxychloroquine and the main protease (Mpro) of SARS-CoV-2 through one-microsecond long molecular dynamics simulations. The analysis shows that hydroxychloroquine binds to the catalytic pocket of Mpro and remains stable for approximately one-third of the simulation time but causes increased fluctuations thereafter. The lack of pre-formed hydrogen bonds or other noncovalent interactions with Mpro suggests instability in binding at the catalytic pocket, indicating that hydroxychloroquine may not inhibit Mpro.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Bharat P. Chaudhary, David L. Zoetewey, Martin J. McCullagh, Smita Mohanty
Summary: Asparagine-linked glycosylation, also known as N-linked glycosylation, is a crucial and highly conserved protein modification process in eukaryotes and some prokaryotes. Mutations in the Ost4 subunit can lead to destabilization of the OST complex and reduced activity. The point mutation in Ost4 did not impact the protein's structure, but affected its position and solvent exposure in the membrane mimetic environment, disrupting interactions with other subunits.
Article
Virology
Carolina Perez-Segura, Boon Chong Goh, Jodi A. Hadden-Perilla
Summary: The research reveals a new alternative state that can lead to a significant opening of the intradimer interface, as well as the discovery of a new salt bridge that mediates direct communication between the spike tip and fulcrum.
Article
Chemistry, Multidisciplinary
Janna N. Sloand, Theodore T. Nguyen, Scott A. Zinck, Erik C. Cook, Tawanda J. Zimudzi, Scott A. Showalter, Adam B. Glick, Julianna C. Simon, Scott H. Medina
News Item
Biophysics
Scott A. Showalter
BIOPHYSICAL JOURNAL
(2020)
Article
Biophysics
Suzette A. Pabit, Yen-Lin Chen, Emery T. Usher, Erik C. Cook, Lois Pollack, Scott A. Showalter
BIOPHYSICAL JOURNAL
(2020)
Article
Biochemistry & Molecular Biology
Emery T. Usher, Scott A. Showalter
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biology
Valerie J. Morley, Clare L. Kinnear, Derek G. Sim, Samantha N. Olson, Lindsey M. Jackson, Elsa Hansen, Grace A. Usher, Scott A. Showalter, Manjunath P. Pai, Robert J. Woods, Andrew F. Read
Article
Chemistry, Physical
Victor A. Prieto, Kevin E. W. Namitz, Scott A. Showalter
Summary: This study examines the interactions mediated by charged residues in intrinsically disordered protein sequences, specifically focusing on the role of charged regions in the binding between Fcp1 and its partner Rap74. The experimental results show both intramolecular and intermolecular interactions between oppositely charged regions in Fcp1, with hydrophobic interactions playing a key role in the formation of the complex. Mutations in charged residues support the hypothesis that they contribute to the strength of binding, as evidenced by paramagnetic relaxation enhancement data.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biophysics
Emery T. Usher, Kevin E. W. Namitz, Michael S. Cosgrove, Scott A. Showalter
Summary: Post-translational modification, particularly methylation, plays a critical role in regulating cellular processes. By studying methyltransferase function through in vitro experiments, researchers can gain insight into the complex mechanisms of regulated gene expression. The use of two-dimensional NMR to monitor methylation events shows promise in understanding the intricate processes of methyltransferases and other enzymes.
BIOPHYSICAL JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Emery T. Usher, Scott A. Showalter
Summary: PDX1 is a central regulator of insulin transcription in pancreatic beta cells, and its function is regulated by cellular cues. However, the molecular mechanisms of PDX1 in glucose response remain elusive. This review summarizes existing studies on PDX1 and provides a comprehensive resource for future research on transcriptional control.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Olivia A. Fraser, Sophia M. Dewing, Emery T. Usher, Christy George, Scott A. Showalter
Summary: Intrinsically disordered proteins are frequently regulated through post-translational modification, but the mechanistic understanding of lysine N-epsilon-acetylation is lagging behind proteomic discoveries. Here, we present a non-perturbing NMR method to monitor N-epsilon-lysine acetylation, which allows detection without the need for exogenous tags. This method has broad applications in studying various systems including intrinsically disordered proteins and lysine deacetylase enzyme assays.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemical Research Methods
Olivia A. Fraser, Kevin E. W. Namitz, Scott A. Showalter
Summary: Post-translational modifications (PTMs) are reversible chemical modifications that can affect protein structure and function. Methylation and acetylation are two well-known PTMs with important biological roles, but their specific effects on transcription factor structure and function are not well understood. This study presents a nondestructive and label-free method using nuclear magnetic resonance (NMR) to detect methylation and acetylation events on histone H3 tail. The authors introduce isotopic enrichment and 13C labeling schemes that enable efficient NMR experiments for detecting low-abundance analytes.
Meeting Abstract
Biophysics
Emery T. Usher, Scott A. Showalter
BIOPHYSICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Emery T. Usher, Nafiseh Sabri, Roman Rohac, Amie K. Boal, Tanja Mittag, Scott A. Showalter
Summary: The interaction between Pdx1 and SPOP causes SPOP relocalization from nuclear speckles to the diffuse nucleoplasm, where the ubiquitination activity of Pdx1 mediated by SPOP occurs. Efficient turnover of Pdx1 requires both SB motifs. The subnuclear localization of SPOP-substrate interactions and substrate ubiquitination may be directed by the properties of the substrate itself.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Meeting Abstract
Biophysics
Grace A. Usher, Roman Rohac, Nafiseh Sabri, Tanja Mittag, Amie K. Boal, Scott A. Showalter
BIOPHYSICAL JOURNAL
(2020)
Meeting Abstract
Biophysics
Suzette A. Pabit, Yen-Lin Chen, Grace A. Usher, Erik C. Cook, Lois Pollack, Scott A. Showalter
BIOPHYSICAL JOURNAL
(2020)
Meeting Abstract
Chemistry, Multidisciplinary
Janna Sloand, Erik Cook, Tawanda Zimudzi, Scott Zinck, Julianna Simon, Scott Showalter, Scott Medina
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2019)