Using All-Atom Potentials to Refine RNA Structure Predictions of SARS-CoV-2 Stem Loops

Autor: Christina Bergonzo, Andrea L. Szakal

Publikováno v: International Journal of Molecular Sciences, Vol 21, Iss 17, p 6188 (2020)

A considerable amount of rapid-paced research is underway to combat the SARS-CoV-2 pandemic. In this work, we assess the 3D structure of the 5′ untranslated region of its RNA, in the hopes that stable secondary structures can be targeted, interrupt

Externí odkaz: https://doaj.org/article/0837bc809807465b9aa9bfa02441d70b

Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments

Autor: Christina Bergonzo, Alexander Grishaev, Sandro Bottaro

Publikováno v: Bergonzo, C, Grishaev, A & Bottaro, S 2022, ' Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments ', RNA, vol. 28, no. 7, pp. 937-946 . https://doi.org/10.1261/rna.078888.121

We describe the conformational ensemble of the single-stranded r(UCAAUC) oligonucleotide obtained using extensive molecular dynamics (MD) simulations and Rosetta's FARFAR2 algorithm. The conformations observed in MD consist of A-form-like structures

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e121a1aa1c17f00f405005d17f2de55c
https://curis.ku.dk/portal/da/publications/conformational-heterogeneity-of-ucaauc-rna-oligonucleotide-from-molecular-dynamics-simulations-saxs-and-nmr-experiments(4c8e52ff-71e8-4c14-820b-01dd3c754034).html

Atomic Model Structure of the NIST Monoclonal Antibody (NISTmAb) Reference Material

Autor: Christina Bergonzo, D. Travis Gallagher

Publikováno v: Journal of Research of the National Institute of Standards and Technology. 126

As monoclonal antibodies have become a vital resource in medicine, knowledge of their complex molecular structures has increased in importance. Thousands of antibody components (Fab and Fc fragments) are described in the Protein Data Bank. Whole anti

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f23c2317984e42c382415e103fb20f16
https://doi.org/10.6028/jres.126.012

Structural insights into DNA-stabilized silver clusters

Autor: Danielle Schultz, Joy P. Dunkers, Nese Sari, Christina Bergonzo, Nancy J. Lin, Jeffrey A. Fagan, Robert G. Brinson

Publikováno v: Soft Matter. 15:4284-4293

Despite their great promise as fluorescent biological probes and sensors, the structure and dynamics of Ag complexes derived from single stranded DNA (ssDNA) are less understood than their double stranded counterparts. In this work, we seek new insig

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1ba59e30f48f0c1c32c29d7cc4248ad5
https://doi.org/10.1039/c9sm00198k

HDX-MS and MD Simulations Provide Evidence for Stabilization of the IgG1—FcγRIa (CD64a) Immune Complex Through Intermolecular Glycoprotein Bonds

Autor: Kyle W. Anderson, Christina Bergonzo, Kerry Scott, Ioannis L. Karageorgos, Elyssia S. Gallagher, Venkata S. Tayi, Michael Butler, Jeffrey W. Hudgens

Publikováno v: Journal of Molecular Biology. 434:167391

Previous reports present different models for the stabilization of the Fc-FcγRI immune complex. Although accord exists on the importance of L235 in IgG1 and some hydrophobic contacts for complex stabilization, discord exists regarding the existence

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5a3a618977b941671f524e80bc9270f5
https://doi.org/10.1016/j.jmb.2021.167391