Characterization of the inner membrane cytochrome ImcH from Geobacter reveals its importance for extracellular electron transfer and energy conservation
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - October 2, 2023 Category: Biochemistry Authors: Andreia I. Pimenta,
Catarina M. Paquete,
Leonor Morgado,
Marcus J. Edwards,
Thomas A. Clarke,
Carlos A. Salgueiro,
In ês A. C. Pereira,
Américo G. Duarte Tags: RESEARCH ARTICLE Source Type: research
In silico protein dynamics in the human cytoplasm: partial folding, misfolding, fold switching, and non ‐native interactions
This study demonstrates that even fast-folding proteins can get stuck in non-native states in the cell, making them useful models for protein-chaperone interactions and early stages of aggregate formation relevant to cellular disease.This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - September 30, 2023 Category: Biochemistry Authors: Premila P. Samuel Russell,
Meredith M. Rickard,
Mayank Boob,
Martin Gruebele,
Taras V. Pogorelov Tags: RESEARCH ARTICLE Source Type: research
UCSF ChimeraX: Tools for Structure Building and Analysis
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - September 29, 2023 Category: Biochemistry Authors: Elaine C. Meng,
Thomas D. Goddard,
Eric F. Pettersen,
Greg S. Couch,
Zach J. Pearson,
John H. Morris,
Thomas E. Ferrin Tags: TOOLS FOR PROTEIN SCIENCE Source Type: research
CC+: A Searchable Database of Validated Coiled Coils in PDB Structures and AlphaFold2 Models
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - September 29, 2023 Category: Biochemistry Authors: Prasun Kumar,
Rokas Petrenas,
William M. Dawson,
Hugo Schweke,
Emmanuel D. Levy,
Derek N. Woolfson Tags: TOOLS FOR PROTEIN SCIENCE Source Type: research
The antimicrobial peptide database is 20 years old: Recent developments and future directions
This article highlights new database additions and findings. To facilitate antimicrobial development to combat drug-resistant pathogens, the APD has been re-annotating the data for antibacterial activity (active, inactive, and uncertain), toxicity (hemolytic and nonhemolytic AMPs), and salt tolerance (salt sensitive and insensitive). Comparison of the respective desired and undesired AMP groups produces new knowledge for peptide design. Our unification of AMPs from the six life kingdoms into “natural AMPs” enabled the first comparison with globular or transmembrane proteins. Due to the dominance of amphipathic helical ...
Source: Protein Science - September 28, 2023 Category: Biochemistry Authors: Guangshun Wang Tags: TOOLS FOR PROTEIN SCIENCE Source Type: research
Molecular mechanism of the common and opposing cosolvent effects of fluorinated alcohol and urea on a coiled coil protein
In this study, GCN4-p1 with two-stranded coiled coil helices was employed as a model protein, and molecular dynamics simulations for the helix dimer and isolated coil were conducted in aqueous solutions with 2 M TFE and urea. As 2 M cosolvent aqueous solutions did not exhibit clustering of cosolvent molecules, we were able to directly investigate the molecular origin of the excess PBP without considering the enhancement effect of PBPs arising from the concentration fluctuations. The calculated excess PBPs of TFE for the helices and those of urea for the coils were consistent with experimentally observed stabilization ...
Source: Protein Science - September 26, 2023 Category: Biochemistry Authors: Noa Nakata,
Ryuichi Okamoto,
Tomonari Sumi,
Kenichiro Koga,
Takeshi Morita,
Hiroshi Imamura Tags: RESEARCH ARTICLE Source Type: research
Iron insertion into coproporphyrin III ‐ferrochelatase complex: evidence for an intermediate distorted catalytic species
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - September 25, 2023 Category: Biochemistry Authors: Thomas Gabler,
Andrea Dali,
Federico Sebastiani,
Paul Georg Furtm üller,
Maurizio Becucci,
Stefan Hofbauer,
Giulietta Smulevich Tags: RESEARCH ARTICLE Source Type: research
Investigating protein ‐membrane interactions using native reverse micelles constructed from naturally sourced lipids
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - September 25, 2023 Category: Biochemistry Authors: Sara H. Walters,
Abdul J. Castillo,
Angela M. Develin,
Courtney L. Labrecque,
Yun Qu,
Brian Fuglestad Tags: METHODS AND APPLICATIONS Source Type: research
The variable domain from dynamin ‐related protein 1 promotes liquid–liquid phase separation that enhances its interaction with cardiolipin‐containing membranes
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - September 25, 2023 Category: Biochemistry Authors: Ammon E. Posey,
Kyle A. Ross,
Mehran Bagheri,
Elizabeth N. Lanum,
Misha A. Khan,
Christine E. Jennings,
Megan C. Harwig,
Nolan W. Kennedy,
Vincent J. Hilser,
James L. Harden,
R. Blake Hill Tags: RESEARCH ARTICLE Source Type: research
Multi ‐perspectives and challenges in identifying B ‐cell epitopes
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - September 22, 2023 Category: Biochemistry Authors: Nishant Kumar,
Nisha Bajiya,
Sumeet Patiyal,
Gajendra P. S. Raghava Tags: REVIEW ARTICLE Source Type: research
Elucidation of binding mechanism, affinity, and complex structure between mWT1 tumor ‐associated antigen peptide and HLA‐A*24:02
AbstractWe have applied our advanced computational and experimental methodologies to investigate the complex structure and binding mechanism of a modified Wilms' Tumor 1 (mWT1) protein epitope to the understudied Asian-dominant allele HLA-A*24:02 (HLA-A24) in aqueous solution. We have applied our developed multicanonical molecular dynamics (McMD)-based dynamic docking method to analyze the binding pathway and mechanism, which we verified by comparing the highest probability structures from simulation with our experimentally solved x-ray crystal structure. Subsequent path sampling MD simulations elucidated the atomic detail...
Source: Protein Science - September 20, 2023 Category: Biochemistry Authors: Gert ‐Jan Bekker,
Nobutaka Numoto,
Maki Kawasaki,
Takahiro Hayashi,
Saaya Yabuno,
Yuko Kozono,
Takeyuki Shimizu,
Haruo Kozono,
Nobutoshi Ito,
Masayuki Oda,
Narutoshi Kamiya Tags: RESEARCH ARTICLE Source Type: research
Structural Features of Thyroglobulin Linked to Protein Trafficking
This article is protected by copyright. All rights reserved. (Source: Protein Science)
Source: Protein Science - September 18, 2023 Category: Biochemistry Authors: Cintia E. Citterio,
Kookjoo Kim,
Bhavana Rajesh,
Kevin Pena,
Oliver Biggs Clarke,
Peter Arvan Tags: RESEARCH ARTICLE Source Type: research
Hydrophobicity and molecular mass ‐based separation method for autoantibody discovery from mammalian total cellular proteins
AbstractSerum autoantibody profiles are unique to individuals and reflect the level and history of autoimmunity and tumor immunity. The identification of autoantibody biomarkers is critical for the development of immune monitoring systems for immune-related disorders. Here, we present a practical method for large-scale autoantibody discovery using total cellular proteins from cultured mammalian cells. We found that nucleic acid-free and fully denatured water-soluble total cellular proteins from mammalian cells were superior, allowing precise separation by reversed-phase HPLC after preparing a large set of homogeneous total...
Source: Protein Science - September 15, 2023 Category: Biochemistry Authors: Mirei Date,
Ai Miyamoto,
Tomoko Honjo,
Tsugumi Shiokawa,
Hiroko Tada,
Nobuhiro Okada,
Junichiro Futami Tags: METHODS AND APPLICATIONS Source Type: research
Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by Electron Paramagnetic Resonance spectroscopy and simulation
AbstractThe catalytic activity of human glutathione S-transferase A1-1 (hGSTA1-1), a homodimeric detoxification enzyme, is dependent on the conformational dynamics of a key C-terminal helix α9 in each monomer. However, the structural details of how the two monomers interact upon binding of substrates is not well understood and the structure of the ligand-free state of the hGSTA1-1 homodimer has not been resolved. Here, we used a combination of electron paramagnetic resonance (EPR) di stance measurements and weighted ensemble (WE) simulations to characterize the conformational ensemble of the ligand-free state at the atom...
Source: Protein Science - September 15, 2023 Category: Biochemistry Authors: Xiaowei Bogetti,
Anthony Bogetti,
Joshua Casto,
Gordon Rule,
Lillian Chong,
Sunil Saxena Tags: RESEARCH ARTICLE Source Type: research
Hexamethylene amiloride binds the SARS ‐CoV‐2 envelope protein at the protein–lipid interface
AbstractThe SARS-CoV-2 envelope (E) protein forms a five-helix bundle in lipid bilayers whose cation-conducting activity is associated with the inflammatory response and respiratory distress symptoms of COVID-19. E channel activity is inhibited by the drug 5-(N,N-hexamethylene) amiloride (HMA). However, the binding site of HMA in E has not been determined. Here we use solid-state NMR to measure distances between HMA and the E transmembrane domain (ETM) in lipid bilayers.13C,15N-labeled HMA is combined with fluorinated or13C-labeled ETM. Conversely, fluorinated HMA is combined with13C,15N-labeled ETM. These orthogonal isoto...
Source: Protein Science - September 15, 2023 Category: Biochemistry Authors: Noah H. Somberg,
Jo ão Medeiros‐Silva,
Hyunil Jo,
Jun Wang,
William F. DeGrado,
Mei Hong Tags: RESEARCH ARTICLE Source Type: research
