MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

Michaud-Agrawal, Naveen; Denning, Elizabeth J.; Woolf, Thomas B.; Beckstein, Oliver

doi:10.1002/jcc.21787

Cited by 2,752 publications

(2,596 citation statements)

References 21 publications

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“…All simulations have been performed using the MD code NAMD 67 . For visual inspection, VMD 68 was used and most of the analysis was performed using the Python library MDAnalysis 69 .…”

Section: Methodsmentioning

confidence: 99%

Water-induced correlation between single ions imaged at the solid–liquid interface

2014

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When immersed into water, most solids develop a surface charge, which is neutralized by an accumulation of dissolved counterions at the interface. Although the density distribution of counterions perpendicular to the interface obeys well-established theories, little is known about counterions' lateral organization at the surface of the solid. Here we show, by using atomic force microscopy and computer simulations, that single hydrated metal ions can spontaneously form ordered structures at the surface of homogeneous solids in aqueous solutions. The structures are laterally stabilized only by water molecules with no need for specific interactions between the surface and the ions. The mechanism, studied here for several systems, is controlled by the hydration landscape of both the surface and the adsorbed ions. The existence of discrete ion domains could play an important role in interfacial phenomena such as charge transfer, crystal growth, nanoscale self-assembly and colloidal stability.

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“…All simulations have been performed using the MD code NAMD 67 . For visual inspection, VMD 68 was used and most of the analysis was performed using the Python library MDAnalysis 69 .…”

Section: Methodsmentioning

confidence: 99%

Water-induced correlation between single ions imaged at the solid–liquid interface

2014

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“…A further test simulation was carried out in which a Fe 2ϩ ion was pulled from the outer environment into the C3WT channel to study its effect on the Fe 2ϩ aqua ions located in the C3 channel (a Fe 2ϩ ion was pulled for about 20 Å along the C3 channel to reach the internal cavity using a rate of 2 Å/ns and a spring force constant of 5 kcal/mol Å 2 ). Trajectories were analyzed with the HOLE program (37) and in-house codes written using the MDAnalysis library (38). Channel radius was estimated considering only the heavy atoms of residues shaping the pore.…”

Section: Methodsmentioning

confidence: 99%

Electrostatic and Structural Bases of Fe2+ Translocation through Ferritin Channels

Chandramouli

Bernacchioni

Maio

et al. 2016

Journal of Biological Chemistry

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Edited by F. Peter GuengerichFerritin molecular cages are marvelous 24-mer supramolecular architectures that enable massive iron storage (>2000 iron atoms) within their inner cavity. This cavity is connected to the outer environment by two channels at C3 and C4 symmetry axes of the assembly. Ferritins can also be exploited as carriers for in vivo imaging and therapeutic applications, owing to their capability to effectively protect synthetic non-endogenous agents within the cage cavity and deliver them to targeted tissue cells without stimulating adverse immune responses. Recently, X-ray crystal structures of Fe 2؉ -loaded ferritins provided important information on the pathways followed by iron ions toward the ferritin cavity and the catalytic centers within the protein. However, the specific mechanisms enabling Fe 2؉ uptake through wild-type and mutant ferritin channels is largely unknown. To shed light on this question, we report extensive molecular dynamics simulations, site-directed mutagenesis, and kinetic measurements that characterize the transport properties and translocation mechanism of Fe 2؉ through the two ferritin channels, using the wild-type bullfrog Rana catesbeiana H protein and some of its variants as case studies. We describe the structural features that determine Fe 2؉ translocation with atomistic detail, and we propose a putative mechanism for Fe 2؉ transport through the channel at the C3 symmetry axis, which is the only iron-permeable channel in vertebrate ferritins. Our findings have important implications for understanding how ion permeation occurs, and further how it may be controlled via purposely engineered channels for novel biomedical applications based on ferritin.Twenty-four-mer ferritins are ubiquitous iron storage proteins that share a common architecture: a protein nanocage (see Fig. 1A) assembled from subunits made up by a 4-helix bundle (helices H1-H4) structure completed by a short C-terminal helix, H5, and a long loop connecting helices H2 and H3. This protein shell surrounds an 8-nm inner cage connected to the external environment by two different types of channels: eight channels in correspondence with the four 3-fold (C3, see Fig. 1B) symmetry axes and six channels in correspondence with the three 4-fold (C4, see Fig. 1C) symmetry axes of the octahedral point symmetry of the cage (1, 2). Despite many similarities across ferritins expressed in different species, the interiors of the C3 and C4 channels are quite variable, showing substantial differences in terms of hydrophobicity/hydrophilicity and electric charge distributions when comparing vertebrate ferritins with those from plants, bacteria, or archaea (3, 4). In turn, the specific chemical nature of these channels directly affects their transport properties and determines the preferred pathways followed by ferrous ions from the exterior of the cage to the catalytic ferroxidase center within the internal cavity. In vertebrate ferritins, for example, the C4 channels (about 12 Å in length) are relatively narrow and mai...

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“…Analysis was done by GROMACS tools, the MDAnalysis package [22] and in-house Python scripts. We demonstrate conformational changes by the distances between the center of mass of the two NBDs.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Molecular dynamics of the cryo-EM CFTR structure

Tordai

Leveles

Hegedüs

2017

Biochemical and Biophysical Research Communications

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Cystic fibrosis (CF), a lethal monogenic disease, is caused by mutant variants of the CF transmembrane conductance regulator (CFTR). Recent advances in single molecule cryo-EM methods enabled structural determination of full-length human and zebrafish CFTR, achieving an important milestone for CF drug development. To relate these structures to the gating cycle, we examined its dynamic features using molecular dynamics simulations. Our results show that the nucleotide binding domains (NBDs) in this bottom-open apo conformation exhibit motions related to dimerization and the bottom-closed apo CFTR model indicates opening of NBDs in contrast to transporters. These observations help in understanding the properties of CFTR chloride channel distinct from transporters and in proper interpretation of available structural information on this ABC protein.

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MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

Cited by 2,752 publications

References 21 publications

Water-induced correlation between single ions imaged at the solid–liquid interface

Water-induced correlation between single ions imaged at the solid–liquid interface

Electrostatic and Structural Bases of Fe2+ Translocation through Ferritin Channels

Molecular dynamics of the cryo-EM CFTR structure

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