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Your search keyword '"Oliveira Junior, Antonio Bento"' showing total 4 results
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4 results on '"Oliveira Junior, Antonio Bento"'

1. Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes.

Author

Freitas, Frederico Campos, Maldonado, Michelli, Oliveira Junior, Antonio Bento, Onuchic, José Nelson, and Oliveira, Ronaldo Junio de

Subjects
CARRIER proteins, PROTEINS, PROTEIN structure, PROTEIN-protein interactions, DENSITY of states, STREPTAVIDIN, AVIDIN
Abstract

Biotin-labeled proteins are widely used as tools to study protein–protein interactions and proximity in living cells. Proteomic methods broadly employ proximity-labeling technologies based on protein biotinylation in order to investigate the transient encounters of biomolecules in subcellular compartments. Biotinylation is a post-translation modification in which the biotin molecule is attached to lysine or tyrosine residues. So far, biotin-based technologies proved to be effective instruments as affinity and proximity tags. However, the influence of biotinylation on aspects such as folding, binding, mobility, thermodynamic stability, and kinetics needs to be investigated. Here, we selected two proteins [biotin carboxyl carrier protein (BCCP) and FKBP3] to test the influence of biotinylation on thermodynamic and kinetic properties. Apo (without biotin) and holo (biotinylated) protein structures were used separately to generate all-atom structure-based model simulations in a wide range of temperatures. Holo BCCP contains one biotinylation site, and FKBP3 was modeled with up to 23 biotinylated lysines. The two proteins had their estimated thermodynamic stability changed by altering their energy landscape. In all cases, after comparison between the apo and holo simulations, differences were observed on the free-energy profiles and folding routes. Energetic barriers were altered with the density of states clearly showing changes in the transition state. This study suggests that analysis of large-scale datasets of biotinylation-based proximity experiments might consider possible alterations in thermostability and folding mechanisms imposed by the attached biotins. [ABSTRACT FROM AUTHOR]

Published
2022
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4. Resolving the fine structure in the energy landscapes of repeat proteins

Author

Barcelona Supercomputing Center, Sanches, Murilo N., Parra, Rodrigo Gonzalo, Viegas, Rafael Giordano, Oliveira Junior, Antonio Bento, Wolynes, Peter, Ferreiro, Diego U., Leite, Vitor B.P., Barcelona Supercomputing Center, Sanches, Murilo N., Parra, Rodrigo Gonzalo, Viegas, Rafael Giordano, Oliveira Junior, Antonio Bento, Wolynes, Peter, Ferreiro, Diego U., and Leite, Vitor B.P.

Abstract

Ankyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein–protein interactions in a diversity of biological systems. These proteins have an elongated non-globular shape and often display complex folding mechanisms. This work investigates the energy landscape of representative proteins of this class made up of 3, 4 and 6 ANK repeats using the energy-landscape visualisation method (ELViM). By combining biased and unbiased coarse-grained molecular dynamics AWSEM simulations that sample conformations along the folding trajectories with the ELViM structure-based phase space, one finds a three-dimensional representation of the globally funnelled energy surface. In this representation, it is possible to delineate distinct folding pathways. We show that ELViMs can project, in a natural way, the intricacies of the highly dimensional energy landscapes encoded by the highly symmetric ankyrin repeat proteins into useful low-dimensional representations. These projections can discriminate between multiplicities of specific parallel folding mechanisms that otherwise can be hidden in oversimplified depictions., M.N.S. was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq; Grant 130147/2020-6). This research was supported by the Center for Theoretical Biological Physics sponsored by the NSF (Grant PHY-2019745). A.B.O. acknowledges the Robert A. Welch Postdoctoral Fellow program. P.G.W. is also supported by the D.R. Bullard-Welch Chair at Rice University (Grant C-0016). V.B.P.L. was supported by CNPq (Grant 310017/2020-3) and FAPESP (Grants 2019/22540-3 and 2018/18668-1). D.U.F. is a CONICET researcher and is supported by Grant PICT2016/1467, UBACYT, and NASA Astrobiology Institute-Enigma (Grant 80NSSC18M0093)., Peer Reviewed, Postprint (published version)

Published
2022

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