2024

Isoleucine gate blocks K+ conduction in C-type inactivation

Werner Treptow, Yichen Liu, Carlos A.Z. Bassetto, Bernardo I. Pinto, Joao Antonio Alves Nunes, Ramon Mendoza Uriarte, Christophe J. Chipot, Francisco Bezanilla, Benoit Roux 

eLife sciences

 

Unveiling Tst3, a Multi-Target Gating Modifier Scorpion α Toxin from Tityus stigmurus Venom of Northeast Brazil: Evaluation and Comparison with Well-Studied Ts3 Toxin of Tityus serrulatus

Diogo Tibery, João Antonio Alves, Daniel Oliveira, Luis Felipe Santos, Adolfo Carlos Barros, Matheus de Freitas, Werner Treptow and Elisabeth Schwartz

Toxins

 

The binding and mechanism of a positive allosteric modulator of Kv3 channels

Qiansheng Liang, Gamma Chi, Leonardo Cirqueira, Lianteng Zhi, Agistubi Marasco, Nadia Pilati, Martin Gunthorpe, Giuseppe Alvaro, Charles Large, David Sauer, Werner Treptow, Manuel Covarrubias.

Nature Communications.

 

Sequence-dependent and -independent information in a combined random energy model for protein folding and coding

Antonio F. Pereira de Araujo

Proteins: Structure, Function, and Bioinformatics

 

Occurrence and evolutionary conservation analysis of α-helical cationic amphiphilic segments in the human proteome

Igor Costa, Tiago Junot, Fernanda Silva, Wanessa Felix, José L. Cardozo, Antonio F. Pereira de Araujo, Constança Pais, Sónia Gonçalves, Nuno C. Santos, José R. Leite, Carlos Bloch Jr., Guilherme D. Brand

The FEBS Journal

 

2023

Allosteric modulation of membrane proteins by small low-affinity ligands

Werner Treptow.

J. Chem. Inf. Model.

 

α-Alkylidene δ-lactones inhibit quorum sensing phenotypes in Chromobacterium strain CV026 showing interaction with the CviR receptor

Fernanda Favero, Terezinha Tolentino, Vinicius Fernandes, Werner Treptow, Alex Leite Pereira, Angelo Henrique Machado

RSC Adv.

 

2022

Concentration-dependent thermodynamic analysis of the partition process of small ligands into proteins

Leonardo Cirqueira, Letícia Stock, Werner Treptow

Computational and Structural Biotechnology Journal

 

Constrained Layer Assignment for the Protein Burial Folding Code Accounting for Chain Connectivity

2021

Trivial and nontrivial error sources account for misidentification of protein partners in mutual information approaches

Camila Pontes, Miguel Andrade, José Fiorote,  Werner Treptow

Scientific Reports

 

2020

Donepezil Inhibits Acetylcholinesterase via Multiple Binding Modes at Room Temperature

Monica A. Silva, Alessandra Kiametis,  Werner Treptow

J. Chem. Inf. Model.

 

Nucleosome binding peptide presents laudable biophysical and in vivo effects

Kaian Teles, Vinícius Fernandes, Isabel Silva, Manuela Leite, Cesar Grisolia, Vincenzo R. Lobbia, Hugo van Ingen, Rodrigo Honorato, Paulo Lopes de Oliveira, Werner Treptow,  Guilherme Santos

Biomedicine & Pharmacotherapy

 

2019

Coevolutive, Evolutive and Stochastic Information in Protein-Protein Interactions

Miguel Andrade, Camila Pontes, Werner Treptow

Computational and Structural Biotechnology Journal

 

2018

Atomistic Model for Simulations of the Sedative Hypnotic Drug 2,2,2-Trichloroethanol

Alessandra Kiametis, Letícia Stock, Leonardo Cirqueira, Werner Treptow

ACS Omega

 

Binding of the general anesthetic sevoflurane to ion channels

Letícia Stock, Juliana Hosoume, Leonardo Cirqueira, Werner Treptow

PLOS Computational Biology

 

Fat nucleosome: role of lipids on chromatin

Vinícius Fernandes, Kaian, Teles, Camyla Ribeiro, Werner Treptow, Guilherme M Santos

Progress in Lipid Research

 

2017

Biophysical studies of cholesterol effects on chromatin

Isabel TG Silva, Vinícius Fernandes, Caio Souza, Werner Treptow, Guilherme M Santos

Journal of lipid research

 

Concentration-Dependent Binding of Small Ligands to Multiple Saturable Sites in Membrane Proteins

Letícia Stock, Juliana Hosoume, Werner Treptow    

Scientific Reports

 

2016

Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes

Diogo C Ferreira, Marx G van der Linden, Leandro C de Oliveira, José N Onuchic, Antônio FP de Araújo

Proteins

 

2015

Positive allosteric modulation of Kv channels by sevoflurane: Insights into the structural basis of inhaled anesthetic action

Qiansheng Liang, Warren D Anderson, Shelly T Jones, Caio S Souza, Juliana M Hosoume, Werner Treptow, Manuel Covarrubias

PloS one

 

Mechanistic insights into the modulation of voltage-gated ion channels by inhalational anesthetics

Manuel Covarrubias, Annika F Barber, Vincenzo Carnevale, Werner Treptow, Roderic G Eckenhoff

Biophysical journal

 

2014

Electric fingerprint of voltage sensor domains

Caio S Souza, Cristiano Amaral, Werner Treptow

Proceedings of the National Academy of Sciences

 

2013

Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure

Marx G van der Linden, Diogo C Ferreira, Leandro C de Oliveira, José N Onuchic, Antônio FP de Araújo

Proteins

 

Pore waters regulate ion permeation in a calcium release-activated calcium channel

Hao Dong, Giacomo Fiorin, Vincenzo Carnevale, Werner Treptow, Michael L Klein

Proceedings of the National Academy of Sciences

 

Conduction in a biological sodium selective channel

Letícia Stock, Lucie Delemotte, Vincenzo Carnevale, Werner Treptow, Michael L Klein

The journal of physical chemistry B

 

Structural basis for activation of voltage-gated cation channels

Letícia Stock, Caio Souza, Werner Treptow

Biochemistry

 

2012

Information-theoretic analysis and prediction of protein atomic burials: On the search for an informational intermediate between sequence and structure

Juliana R Rocha, Marx G van der Linden, Diogo C Ferreira, Paulo H Azevêdo, Antônio FP de Araújo

Bioinformatics

 

Exploring conformational states of the bacterial voltage-gated sodium channel NavAb via molecular dynamics simulations

Cristiano Amaral, Vincenzo Carnevale, Michael L Klein, Werner Treptow

Proceedings of the National Academy of Sciences

 

Hinge-bending motions in the pore domain of a bacterial voltage-gated sodium channel

Annika F Barber, Vincenzo Carnevale, SG Raju, Cristiano Amaral, Werner Treptow, Michael L Klein

Biochimica et Biophysica Acta (BBA)-Biomembranes

 

Computer simulations of voltage-gated cation channels

Werner Treptow, Michael L Klein

The journal of physical chemistry letters

 

2011

Molecular mapping of general anesthetic sites in a voltage-gated ion channel

Annika F Barber, Qiansheng Liang, Cristiano Amaral, Werner Treptow, Manuel Covarrubias

Biophysical journal

 

Sodium ion binding sites and hydration in the lumen of a bacterial ion channel from molecular dynamics simulations

Vincenzo Carnevale, Werner Treptow, Michael L Klein

American Chemical Society

 

Intermediate states of the Kv1. 2 voltage sensor from atomistic molecular dynamics simulations

Lucie Delemotte, Mounir Tarek, Michael L Klein, Cristiano Amaral, Werner Treptow

Proceedings of the National Academy of Sciences

 

2010

Effect of sensor domain mutations on the properties of voltage-gated ion channels: molecular dynamics studies of the potassium channel Kv1. 2

Lucie Delemotte, Werner Treptow, Michael L Klein, Mounir Tarek

Biophysical journal

 

Affinity of C60 neat fullerenes with membrane proteins: a computational study on potassium channels

Sebastian Kraszewski, Mounir Tarek, Werner Treptow, Christophe Ramseyer

American Chemical Society

 

The membrane-bound state of K2P potassium channels

Werner Treptow, Michael L Klein

Journal of the American Chemical Society

 

2009

A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins

Antônio FP de Araújo, José N Onuchic

Proceedings of the National Academy of Sciences

 

Self assembly of peptides near or within membranes using coarse grained MD simulations

A Khalfa, W Treptow, Bernard Maigret, M Tarek

Chemical Physics

 

Initial response of the potassium channel voltage sensor to a transmembrane potential

Werner Treptow, Mounir Tarek, Michael L Klein

Journal of the American Chemical Society

 

2008

Increasing discrepancy between absolute and effective indexes of research output in a Brazilian academic department

Antônio FP de Araújo

Scientometrics

 

Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins

Antônio FP de Araújo, Antonio LC Gomes, Alexandre A Bursztyn,  Eugene I Shakhnovich

Proteins