Molecular dynamics simulations of membrane proteins

Baştuğ, Turgut; Kuyucak, Serdar

doi:10.1007/s12551-012-0084-9

Cited by 11 publications

(5 citation statements)

References 69 publications

(64 reference statements)

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“… 19 Thus, longer simulations are desirable for GPCRs and other membrane proteins. 31 – 33 Activation that was shown experimentally to occur on millisecond timescales 34 has not been observed in the longest cMD simulations. 25 …”

Section: Introductionmentioning

confidence: 83%

Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics

Miao

Nichols

McCammon

2014

Phys. Chem. Chem. Phys.

103

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Section: Introductionmentioning

confidence: 83%

Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics

Miao

Nichols

McCammon

2014

Phys. Chem. Chem. Phys.

103

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“…For details of the basic formalism of MD simulations, we refer to the monographs [41,42,43]. A recent review of MD simulations of membrane proteins can be found in [44]. …”

Section: Methodsmentioning

confidence: 99%

Computational Studies of Marine Toxins Targeting Ion Channels

2013

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Toxins from marine animals offer novel drug leads for treatment of diseases involving ion channels. Computational methods could be very helpful in this endeavour in several ways, e.g., (i) constructing accurate models of the channel-toxin complexes using docking and molecular dynamics (MD) simulations; (ii) determining the binding free energies of toxins from umbrella sampling MD simulations; (iii) predicting the effect of mutations from free energy MD simulations. Using these methods, one can design new analogs of toxins with improved affinity and selectivity properties. Here we present a review of the computational methods and discuss their applications to marine toxins targeting potassium and sodium channels. Detailed examples from the potassium channel toxins—ShK from sea anemone and κ-conotoxin PVIIA—are provided to demonstrate capabilities of the computational methods to give accurate descriptions of the channel-toxin complexes and the energetics of their binding. An example is also given from sodium channel toxins (µ-conotoxin GIIIA) to illustrate the differences between the toxin binding modes in potassium and sodium channels.

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“…The first protein has a shorter hydrophobic section (namely, KALP 19, 36 The anchoring groups (that is, lysine) at the extremities of the three different protein models are the same to ensure physical consistency. 37 The models for the three proteins are validated through measurements of the tilt of each protein in a membrane along with its impact on the structural characteristics of the bilayer in its vicinity. These measurements require the substitution of four phospholipid molecules in a bilayer (see SI for details) with a single protein.…”

Section: Coarse-grained Model For Proteinsmentioning

confidence: 99%

Self-Organization of Alpha Helical Proteins in Bioinspired Membranes and Vesicles

Banerjee¹,

Finkel²,

Dutt³

2020

Preprint

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ABSTRACTA fundamental understanding of protein-protein and protein-lipid interactions under various conditions can reveal the energy pathways in photosynthetic bacterial membranes. In this study, we examine the role of key factors such as bilayer curvature, the concentration, helical separation and hydrophobic mismatch of proteins on their self-organization in bilayers. We also develop an understanding of the physical factors underlying the aggregation of proteins. We determine the impact of bilayer curvature by comparing the aggregation of proteins in membranes and vesicles. We identify a threshold helical separation below which small, stable aggregates are observed. Large, unstable protein aggregates are observed above the threshold separation. We examine the effect of the deformations incurred by the proteins via their concentration, and show the aggregation of the proteins to arise from their deformation-induced displacement. We demonstrate the negative hydrophobic mismatch condition to favor a higher degree of protein aggregation. We adopt the Molecular Dynamics simulation technique along with a coarse-grained force field to capture the behavior spanning extensive spatiotemporal scales. Our results can guide experimental studies of bioinspired materials with structure-function properties mimicking those of photosynthetic bacterial membranes, or assist in understanding the organization of inclusions in polymeric matrices.

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Molecular dynamics simulations of membrane proteins

Cited by 11 publications

References 69 publications

Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics

Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics

Computational Studies of Marine Toxins Targeting Ion Channels

Self-Organization of Alpha Helical Proteins in Bioinspired Membranes and Vesicles

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