Biomembranes research using thermal and cold neutrons

Heberle, Frederick A.; Myles, Dean A. A.; Katsaras, John

doi:10.1016/j.chemphyslip.2015.07.020

Cited by 8 publications

(4 citation statements)

References 120 publications

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“…The basic principle behind neutron diffraction is similar to X-ray diffraction, but it uses a beam of thermal or cold neutrons to obtain a diffraction pattern, which is then used to solve the structure without any radiation damage [ 181 ]. Exchange of H 2 O with D 2 O (deuterium oxide, heavy water) may provide information on the water content of peptide–membrane structure [ 182 ] and to investigate the water defects in the membranes during peptide translocation [ 183 , 184 ].…”

Section: Structural Analysismentioning

confidence: 99%

Membrane Active Peptides and Their Biophysical Characterization

2018

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In the last 20 years, an increasing number of studies have been reported on membrane active peptides. These peptides exert their biological activity by interacting with the cell membrane, either to disrupt it and lead to cell lysis or to translocate through it to deliver cargos into the cell and reach their target. Membrane active peptides are attractive alternatives to currently used pharmaceuticals and the number of antimicrobial peptides (AMPs) and peptides designed for drug and gene delivery in the drug pipeline is increasing. Here, we focus on two most prominent classes of membrane active peptides; AMPs and cell-penetrating peptides (CPPs). Antimicrobial peptides are a group of membrane active peptides that disrupt the membrane integrity or inhibit the cellular functions of bacteria, virus, and fungi. Cell penetrating peptides are another group of membrane active peptides that mainly function as cargo-carriers even though they may also show antimicrobial activity. Biophysical techniques shed light on peptide–membrane interactions at higher resolution due to the advances in optics, image processing, and computational resources. Structural investigation of membrane active peptides in the presence of the membrane provides important clues on the effect of the membrane environment on peptide conformations. Live imaging techniques allow examination of peptide action at a single cell or single molecule level. In addition to these experimental biophysical techniques, molecular dynamics simulations provide clues on the peptide–lipid interactions and dynamics of the cell entry process at atomic detail. In this review, we summarize the recent advances in experimental and computational investigation of membrane active peptides with particular emphasis on two amphipathic membrane active peptides, the AMP melittin and the CPP pVEC.

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Section: Structural Analysismentioning

confidence: 99%

Membrane Active Peptides and Their Biophysical Characterization

2018

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“…Experimental techniques are getting more and more sophisticated to reveal lateral membrane organization and the principles driving it. Experimental advances include improved methods for single-particle tracking, fluorescence correlation spectroscopy, super-resolved imaging, scattering, solid-state NMR, and mass spectrometry, as well as methods to prepare asymmetric model membranes and real cell membrane extracts. − However, the detailed membrane organization proves difficult to probe at the molecular level, despite progress in experimental techniques that can directly probe living cells . Computer simulations, in principle, can provide this detail.…”

Section: Introductionmentioning

confidence: 99%

Computational Modeling of Realistic Cell Membranes

Marrink¹,

Corradi

Souza³

et al. 2019

Chem. Rev.

585

488

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Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.

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“…Accompanying the advance of membrane simulations is the development of experimental techniques to study membrane lateral organizations, − the arrival of the single-particle cryo-EM era to reveal thousands of membrane protein structures, , and the maturing of simulation force fields (FFs) and membrane system modeling protocols, − as well as the shifting focus on membrane proteins as the drug targets . The recent revolution of structure-predicting tools such as AlphaFold2 and RoseTTAFold further adds to the modeling arsenal expanding the scope of protein targets for MD simulations. , In the pharmaceutical industry, drug discovery is more than ever “structurally enabled”, meaning structure-based pharmacology discovery with computer-aided drug discovery (CADD) techniques including docking and free energy calculations …”

Section: Introductionmentioning

confidence: 99%

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

Feng

Park

Choi

et al. 2023

J. Chem. Theory Comput.

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Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drugbinding and dynamics, protein−lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.

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Biomembranes research using thermal and cold neutrons

Cited by 8 publications

References 120 publications

Membrane Active Peptides and Their Biophysical Characterization

Membrane Active Peptides and Their Biophysical Characterization

Computational Modeling of Realistic Cell Membranes

CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

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