Mapping conformational epitopes by NMR spectroscopy

AP Valente, M Manzano-Rendeiro - Current Opinion in Virology, 2021 - Elsevier
Antibodies recognize their target with high affinity and specificity. This is important for
pathogen neutralization, which plays a crucial role in defense against disease. Antibodies …

A dynamic overview of antimicrobial peptides and their complexes

VS De Paula, AP Valente - Molecules, 2018 - mdpi.com
In this narrative review, we comprehensively review the available information about the
recognition, structure, and dynamics of antimicrobial peptides (AMPs). Their complex …

Anomalous Dynamics in Macromolecular Liquids

MG Guenza - Polymers, 2022 - mdpi.com
Macromolecular liquids display short-time anomalous behaviors in disagreement with
conventional single-molecule mean-field theories. In this study, we analyze the behavior of …

[HTML][HTML] Conformational dynamics and kinetics of protein interactions by nuclear magnetic resonance

AH Moraes, AP Valente - Journal of Magnetic Resonance Open, 2023 - Elsevier
Structural information of protein complexes is fundamental for the rational drug design and
improvement of vaccines and biosensors. Also, protein misassembly can have severe …

[HTML][HTML] Identifying the leading dynamics of ubiquitin: A comparison between the tICA and the LE4PD slow fluctuations in amino acids' position

ER Beyerle, MG Guenza - The Journal of Chemical Physics, 2021 - pubs.aip.org
Molecular Dynamics (MD) simulations of proteins implicitly contain the information
connecting the atomistic molecular structure and proteins' biologically relevant motion …

[HTML][HTML] Kinetics analysis of ubiquitin local fluctuations with Markov state modeling of the LE4PD normal modes

ER Beyerle, MG Guenza - The Journal of chemical physics, 2019 - pubs.aip.org
Local fluctuations are important for protein binding and molecular recognition because they
provide conformational states that can be trapped through a selection mechanism of …

Universality and specificity in protein fluctuation dynamics

J Copperman, M Dinpajooh, ER Beyerle… - Physical Review Letters, 2017 - APS
We investigate the universal scaling of protein fluctuation dynamics with a site-specific
diffusive model of protein motion, which predicts an initial subdiffusive regime in the …

[HTML][HTML] Comparison between slow anisotropic LE4PD fluctuations and the principal component analysis modes of ubiquitin

ER Beyerle, MG Guenza - The Journal of Chemical Physics, 2021 - pubs.aip.org
The biological function and folding mechanisms of proteins are often guided by large-scale
slow motions, which involve crossing high energy barriers. In a simulation trajectory, these …

Nuclear spin relaxation

J Kowalewski - 2020 - books.rsc.org
The review covers the progress in the field of NMR relaxation in fluids primarily during 2019.
Since the topic is returning to this volume SPR after a break of a few years, some highlights …

Thermodynamically consistent coarse graining of polymers

MG Guenza - Coarse-Grained Modeling of Biomolecules, 2017 - taylorfrancis.com
This chapter summarizes the coarse-graining (CG) approach that is called the Integral
Equation Coarse-Grained (IECG) model. In most CG models, which are numerically solved …