Structure and gating behavior of the human integral membrane protein VDAC1 in a lipid bilayer

EE Najbauer, K Tekwani Movellan… - Journal of the …, 2022 - ACS Publications
The voltage-dependent anion channel (VDAC), the most abundant protein in the outer
mitochondrial membrane, is responsible for the transport of all ions and metabolites into and …

Modeling membrane geometries implicitly in Rosetta

H Woods, JK Leman, J Meiler - Protein Science, 2024 - Wiley Online Library
Interactions between membrane proteins (MPs) and lipid bilayers are critical for many
cellular functions. In the Rosetta molecular modeling suite, the implicit membrane energy …

Plants fighting back: to transport or not to transport, this is a structural question

M Hrmova, M Gilliham - Current opinion in plant biology, 2018 - Elsevier
Highlights•Structural information is required to fully understand the molecular basis of
transporter function.•Resolved atomic structures of transporters must put into context with …

Analyses of protein cores reveal fundamental differences between solution and crystal structures

Z Mei, JD Treado, AT Grigas, ZA Levine… - Proteins: Structure …, 2020 - Wiley Online Library
There have been several studies suggesting that protein structures solved by NMR
spectroscopy and X‐ray crystallography show significant differences. To understand the …

Core packing of well‐defined X‐ray and NMR structures is the same

AT Grigas, Z Liu, L Regan, CS O'Hern - Protein Science, 2022 - Wiley Online Library
Numerous studies have investigated the differences and similarities between protein
structures determined by solution NMR spectroscopy and those determined by X‐ray …

Is protein structure enough? A review of the role of lipids in SLC6 transporter function

A Schumann-Gillett, MT Blyth, ML O'Mara - Neuroscience Letters, 2019 - Elsevier
SLC6 neurotransmitter transporters facilitate the Na+-and Cl−-dependent uptake of amino
acids and amino acid derivatives into cells. Disrupting transport leads to a range of …

[HTML][HTML] Assessment of structural changes in proteins and surrounding water molecules in solution according to SAXS and MD data

AV Smirnov, AM Semenov, BA Fedorov - Наносистемы: физика …, 2022 - cyberleninka.ru
The SASPAR program for calculation of SAXS of proteins in solution uses trajectories of
molecular dynamics (MD) and an explicit solvent model. The program allows one to take into …

[PDF][PDF] Development of Frameworks for Computational Protein Structure Prediction Applications Challenged By Limited Training Data

H Woods - 2023 - ir.vanderbilt.edu
Membrane proteins (MPs) exist in complex and diverse membrane environments in which
they function. Cellular membranes adopt different geometries and cover a variety of different …

Computational Studies of Packing and Jamming in Biological Systems

JD Treado - 2022 - search.proquest.com
The application of coarse-grained computational models to the study of physical systems
has explodedin recent years, in part due to the relative simplicity of such models compared …

Computational Studies of Proteins: Void Analyses, NMR and X-ray Structures, Fluctuations in Protein Structure Measured Using Molecular Dynamics Simulations

Z Mei - 2021 - search.proquest.com
Although the amount of experimental and theoretical protein studies have grown
exponentially in recent years, we still do not have enough knowledge about the folding …