Cargando…

Refining amino acid hydrophobicity for dynamics simulation of membrane proteins

Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is...

Descripción completa

Detalles Bibliográficos
Autor principal:	Hills, Jr, Ronald D.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	PeerJ Inc. 2018
Materias:	Biophysics
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767086/ https://www.ncbi.nlm.nih.gov/pubmed/29340240 http://dx.doi.org/10.7717/peerj.4230

Ejemplares similares

Modelling dynamics in protein crystal structures by ensemble refinement
por: Burnley, B Tom, et al.
Publicado: (2012)

Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?
por: Larsen, Andreas H., et al.
Publicado: (2022)

Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins
por: Sanders, Joshua C., et al.
Publicado: (2021)

Unfolding of α-helical 20-residue poly-glutamic acid analyzed by multiple runs of canonical molecular dynamics simulations
por: Ogasawara, Naoki, et al.
Publicado: (2018)

The impact of curcumin derived polyphenols on the structure and flexibility COVID-19 main protease binding pocket: a molecular dynamics simulation study
por: Mulu, Aweke, et al.
Publicado: (2021)

Mass spectrometry of intact membrane proteins: shifting towards a more native-like context
por: Oluwole, Abraham, et al.
Publicado: (2023)

Assessing the dynamics and macromolecular interactions of the intrinsically disordered protein YY1
por: Donald, Heather, et al.
Publicado: (2023)

Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy
por: Lórenz-Fonfría, Víctor A., et al.
Publicado: (2014)

Hydrogen/deuterium exchange-mass spectrometry of integral membrane proteins in native-like environments: current scenario and the way forward
por: Javed, Waqas, et al.
Publicado: (2023)

Rethinking the use of finite element simulations in comparative biomechanics research
por: Tseng, Z. Jack
Publicado: (2021)

Perspectives on Membrane Protein Insertion, Protein–Bilayer Interactions, and Amino Acid Side Hydrophobicity
por: Andersen, Olaf Sparre
Publicado: (2007)

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps
por: Singharoy, Abhishek, et al.
Publicado: (2016)

Musculoskeletal simulations to examine the effects of accentuated eccentric loading (AEL) on jump height
por: Su, Eric Yung-Sheng, et al.
Publicado: (2023)

Characterization of C-ring component assembly in flagellar motors from amino acid coevolution
por: dos Santos, Ricardo Nascimento, et al.
Publicado: (2018)

Dynamic regulation of RAS and RAS signaling
por: Kolch, Walter, et al.
Publicado: (2023)

The biological function of an insect antifreeze protein simulated by molecular dynamics
por: Kuiper, Michael J, et al.
Publicado: (2015)

Ligand-bound Structures Provide Atomic Snapshots for the Catalytic Mechanism of d-Amino Acid Deacylase
por: Bhatt, Tarun Kumar, et al.
Publicado: (2010)

NMR insights into dynamic, multivalent interactions of intrinsically disordered regions: from discrete complexes to condensates
por: Ahmed, Rashik, et al.
Publicado: (2022)

Relationships between Structural Dynamics and Functional Kinetics in Oligomeric Membrane Receptors
por: Edelstein, Stuart J., et al.
Publicado: (2010)

Modeling the effects of cyclodextrin on intracellular membrane vesicles from Cos-7 cells prepared by sonication and carbonate treatment
por: Kilbride, Peter, et al.
Publicado: (2015)

Automated cryo-EM structure refinement using correlation-driven molecular dynamics
por: Igaev, Maxim, et al.
Publicado: (2019)

Antimicrobial peptide CGA-N12 decreases the Candida tropicalis mitochondrial membrane potential via mitochondrial permeability transition pore
por: Li, Ruifang, et al.
Publicado: (2020)

Uncovering protein structure
por: Stollar, Elliott J, et al.
Publicado: (2020)

The hydrophobic nature of a novel membrane interface regulates the enzyme activity of a voltage-sensing phosphatase
por: Kawanabe, Akira, et al.
Publicado: (2018)

The biophysics of disordered proteins from the point of view of single-molecule fluorescence spectroscopy
por: Cubuk, Jasmine, et al.
Publicado: (2022)

Protein interactions: anything new?
por: Barrera-Vilarmau, Susana, et al.
Publicado: (2022)

Live imaging approach of dynamic multicellular responses in ERK signaling during vertebrate tissue development
por: Hirashima, Tsuyoshi
Publicado: (2022)

How phosphorylation impacts intrinsically disordered proteins and their function
por: Newcombe, Estella A., et al.
Publicado: (2022)

Not Just an Oil Slick: How the Energetics of Protein-Membrane Interactions Impacts the Function and Organization of Transmembrane Proteins
por: Mondal, Sayan, et al.
Publicado: (2014)

Protein signatures using electrostatic molecular surfaces in harmonic space
por: Carvalho, C. Sofia, et al.
Publicado: (2013)

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry
por: Vivoli, Mirella, et al.
Publicado: (2014)

Eisosomes Are Dynamic Plasma Membrane Domains Showing Pil1-Lsp1 Heteroligomer Binding Equilibrium
por: Olivera-Couto, Agustina, et al.
Publicado: (2015)

Identification of AtHsp90.6 involved in early embryogenesis and its structure prediction by molecular dynamics simulations
por: Luo, An, et al.
Publicado: (2019)

Classifying acoustic signals into phoneme categories: average and dyslexic readers make use of complex dynamical patterns and multifractal scaling properties of the speech signal
por: Hasselman, Fred
Publicado: (2015)

Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT
por: Zhao, Huaying, et al.
Publicado: (2015)

DySCo: Quantitating Associations of Membrane Proteins Using Two-Color Single-Molecule Tracking
por: Dunne, Paul D., et al.
Publicado: (2009)

A new function for the xanthophyll zeaxanthin: glueing chlorophyll biosynthesis to thylakoid protein assembly
por: Bassi, Roberto
Publicado: (2021)

Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus
por: Yadav, Mohini, et al.
Publicado: (2021)

Protein–ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI)
por: Grøftehauge, Morten K., et al.
Publicado: (2015)

Too packed to change: side-chain packing and site-specific substitution rates in protein evolution
por: Marcos, María Laura, et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_st79lsv6ugdgbqbr8q1i3q5ld6