Functional and structural characterization of interactions between opposite subunits in HCN pacemaker channels

ABSTRACTHyperpolarization-activated and cyclic nucleotide (HCN) modulated channels are tetrameric cation channels. In each of the four subunits, the intracellular cyclic nucleotide-binding domain (CNBD) is coupled to the transmembrane domain via a helical structure, the C-linker. High-resolution channel structures suggest that the C-linker enables functionally relevant interactions with the opposite subunit, which might be critical for coupling the conformational changes in the CNBD to the channel pore. We combined mutagenesis, patch-clamp technique, confocal patch-clamp fluorometry, and molecular dynamics simulations to show that residue K464 of the C-linker is essential for stabilizing the closed state of the mHCN2 channel by forming interactions with the opposite subunit. MD simulations revealed that both cAMP and K464E induce a rotation of the intracellular domain relative to the channel pore, weakening the autoinhibitory effect of the unoccupied CL-CNBD region. The adopted poses are in excellent agreement with structural results.

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An improved open-channel structure of MscL determined from FRET confocal microscopy and simulation

The Journal of General Physiology ◽

10.1085/jgp.200910376 ◽

2010 ◽

Vol 136 (4) ◽

pp. 483-494 ◽

Cited By ~ 64

Author(s):

Ben Corry ◽

Annette C. Hurst ◽

Prithwish Pal ◽

Takeshi Nomura ◽

Paul Rigby ◽

...

Keyword(s):

Patch Clamp ◽

Conformational Changes ◽

Brownian Dynamics ◽

Resonance Energy Transfer ◽

Resonance Energy ◽

Channel Structure ◽

Paramagnetic Resonance ◽

Physiological Processes ◽

Lipid Environment ◽

Dynamics Simulations

Mechanosensitive channels act as molecular transducers of mechanical force exerted on the membrane of living cells by opening in response to membrane bilayer deformations occurring in physiological processes such as touch, hearing, blood pressure regulation, and osmoregulation. Here, we determine the likely structure of the open state of the mechanosensitive channel of large conductance using a combination of patch clamp, fluorescence resonance energy transfer (FRET) spectroscopy, data from previous electron paramagnetic resonance experiments, and molecular and Brownian dynamics simulations. We show that structural rearrangements of the protein can be measured in similar conditions as patch clamp recordings while controlling the state of the pore in its natural lipid environment by modifying the lateral pressure distribution via the lipid bilayer. Transition to the open state is less dramatic than previously proposed, while the N terminus remains anchored at the surface of the membrane where it can either guide the tilt of or directly translate membrane tension to the conformation of the pore-lining helix. Combining FRET data obtained in physiological conditions with simulations is likely to be of great value for studying conformational changes in a range of multimeric membrane proteins.

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Molecular structure of azobenzene-containing systems from classical MD simulations

10.14293/p2199-8442.1.sop-matsci.pwghsh.v1 ◽

2015 ◽

Author(s):

Olga Guskova ◽

Vladimir Toshchevikov ◽

Jaroslav Ilnytskyi ◽

Marina Saphiannikova

Keyword(s):

Molecular Structure ◽

Conformational Changes ◽

Md Simulations ◽

Chem Phys ◽

Polymer Chains ◽

Gyration Radius ◽

Light Illumination ◽

Molecular Glasses ◽

Mesoscopic Level ◽

Dynamics Simulations

Azobenzene-containing side chain polymers [1,2] and molecular glasses based on propeller-like C3-symmetric azobenzene mesogenes [3] are investigated in classical molecular dynamics simulations. Two length scales are considered: (i) the molecular level with atomistic resolution, where reversible conformational changes of azobenzene chromophores upon light illumination lead to contractions/extensions of low amplitudes due to a limited size of mesogene groups, and (ii) the mesoscopic level, where light-induced molecular movements are observed over larger distances, comparable with the gyration radius of polymer chains. The influence of isomerization and orientation mechanisms on molecular structure and light-induced deformation is elucidated. [1] J. Ilnytskyi et al., J. Chem. Phys. 135, 044901 (2011). [2] M Saphiannikova et al., Proceedings of SPIE "Optical Materials and Biomaterials in Security and Defence Systems Technology X", 8901, 890138 (2013). [3] N.S. Jadavalli et al., Appl. Phys. Lett. 105, 051601 (2014).

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Molecular Basis Explanation of Imatinib Resistance of Bcr-Abl Due to T315I and P-Loop Mutations from Molecular Dynamics Simulations.

Blood ◽

10.1182/blood.v110.11.2917.2917 ◽

2007 ◽

Vol 110 (11) ◽

pp. 2917-2917

Author(s):

Tai-Sung Lee ◽

Steven Potts ◽

Hagop Kantarjian ◽

Jorge Cortes ◽

Francis Giles ◽

...

Keyword(s):

Molecular Dynamics ◽

Conformational Changes ◽

Electrostatic Interactions ◽

Large Scale ◽

Resistance Mechanism ◽

Md Simulations ◽

Resistance Mechanisms ◽

Static Structure ◽

Imatinib Resistance ◽

Dynamics Simulations

Abstract Molecular dynamics (MD) simulations on the complex of imatinib with the wild-type, T315I, and other 10 P-loop mutants of the tyrosine kinase Bcr-Abl have been performed to study the imatinib resistance mechanism at the atomic level. MD simulations show that large scale computational simulations could offer insight information that a static structure or simple homology modeling methods cannot provide for studying the Bcr-Abl imatinib resistance problem, especially in the case of conformational changes due to remote mutations. By utilizing the Molecular Mechanics/Poisson-Boltzmann surface area (MM-PBSA) techniques and analyzing the interactions between imatinib and individual residues, imatinib resistance mechanisms not previously thought have been revealed. Non-directly contacted P-loop mutations either unfavorably change the direct electrostatic interactions with imatinib, or cause the conformational changes influencing the contact energies between imatinib and other non-P-loop residues. We demonstrate that imatinib resistance of T315I mainly comes from the breakdown of the interactions between imatinib and E286 and M290, contradictory to previously suggested that the missing hydrogen bonding is the main contribution. We also demonstrate that except for the mutations of the direct contact residues, such as L248 and Y253, the unfavorable electrostatic interaction between P-loop and imatinib is the main reason for resistance for the P-loop mutations. Furthermore, in Y255H, protonation of the histidin is essential for rendering this mutation resistant to Gleevec. Our results demonstrate that MD is a powerful way to verify and predict clinical response or resistance to imatinib and other potential drugs.

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Effects of number of parallel runs and frequency of bias-strength replacement in generalized ensemble molecular dynamics simulations

10.7717/peerj-pchem.4 ◽

2019 ◽

Vol 1 ◽

pp. e4 ◽

Cited By ~ 1

Author(s):

Takuya Shimato ◽

Kota Kasahara ◽

Junichi Higo ◽

Takuya Takahashi

Keyword(s):

Molecular Dynamics ◽

Potential Energy ◽

Molecular Dynamics Simulations ◽

Conformational Changes ◽

High Frequency ◽

Md Simulations ◽

Energy Space ◽

Bias Potential ◽

Ensemble Approach ◽

Dynamics Simulations

Background The generalized ensemble approach with the molecular dynamics (MD) method has been widely utilized. This approach usually has two features. (i) A bias potential, whose strength is replaced during a simulation, is applied. (ii) Sampling can be performed by many parallel runs of simulations. Although the frequency of the bias-strength replacement and the number of parallel runs can be adjusted, the effects of these settings on the resultant ensemble remain unclear. Method In this study, we performed multicanonical MD simulations for a foldable mini-protein (Trp-cage) and two unstructured peptides (8- and 20-residue poly-glutamic acids) with various settings. Results As a result, running many short simulations yielded robust results for the Trp-cage model. Regarding the frequency of the bias-potential replacement, although using a high frequency enhanced the traversals in the potential energy space, it did not promote conformational changes in all the systems.

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HIV-1 Env gp41 Transmembrane Domain Dynamics are Modulated by Lipid, Water, and Ion Interactions

10.1101/292326 ◽

2018 ◽

Author(s):

L.R. Hollingsworth ◽

J.A. Lemkul ◽

D.R. Bevan ◽

A.M. Brown

Keyword(s):

Host Cell ◽

Conformational Changes ◽

Electrostatic Interactions ◽

Transmembrane Domain ◽

Chloride Ions ◽

Viral Envelope ◽

Membrane Properties ◽

Viral Fusion ◽

Network Of Hydrogen Bonds ◽

Dynamics Simulations

AbstractThe gp41 transmembrane domain (TMD) of the envelope glycoprotein (Env) of the human immunodeficiency virus (HIV) modulates the conformation of the viral envelope spike, the only druggable target on the surface of the virion. Understanding of TMD dynamics is needed to better probe and target Env with small molecule and antibody therapies. However, little is known about TMD dynamics due to difficulties in describing native membrane properties. Here, we performed atomistic molecular dynamics simulations of a trimeric, prefusion TMD in a model, asymmetric viral membrane that mimics the native viral envelope. We found that water and chloride ions permeated the membrane and interacted with the highly conserved arginine bundle, (R696)3, at the center of the membrane and influenced TMD stability by creating a network of hydrogen bonds and electrostatic interactions. We propose that this (R696)3- water - anion network plays an important role in viral fusion with the host cell by modulating protein conformational changes within the membrane. Additionally, R683 and R707 at the exofacial and cytofacial membrane-water interfaces, respectively, are anchored in the lipid headgroup region and serve as a junction point for stabilization of the termini. The membrane thins as a result of the tilting of the TMD trimer, with nearby lipids increasing in volume, leading to an entropic driving force for TMD conformational change. These results provide additional detail and perspective on the influence of certain lipid types on TMD dynamics and rationale for targeting key residues of the TMD for therapeutic design. These insights into the molecular details of TMD membrane anchoring will build towards a greater understanding of dynamics that lead to viral fusion with the host cell.

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Molecular dynamics simulations disclose early stages of the photo-activation of cryptochrome 4

10.1101/324962 ◽

2018 ◽

Cited By ~ 1

Author(s):

D. R. Kattnig ◽

C. Nielsen ◽

I. A. Solov’yov

Keyword(s):

Molecular Dynamics ◽

Conformational Changes ◽

Large Scale ◽

Conformational Dynamics ◽

Md Simulations ◽

Quantum Processes ◽

Helical Segment ◽

High Betweenness ◽

Dynamics Simulations ◽

Fad Binding

AbstractBirds appear to be equipped with a light-dependent, radical-pair-based magnetic compass that relies on truly quantum processes. While the identity of the sensory protein has remained speculative, cryptochrome 4 has recently been identified as the most auspicious candidate. Here, we report on allatom molecular dynamics (MD) simulations addressing the structural reorganisations that accompany the photoreduction of the flavin cofactor in a model of the European robin cryptochrome 4 (ErCry4). Extensive MD simulations reveal that the photo-activation of ErCry4 induces large-scale conformational changes on short (hundreds of nanoseconds) timescales. Specifically, the photo-reduction is accompanied with the release of the C-terminal tail, structural rearrangements in the vicinity of the FAD-binding site, and the noteworthy formation of an α-helical segment at the N-terminal part. Some of these rearrangements appear to expose potential phosphorylation sites. We describe the conformational dynamics of the protein using a graph-based approach that is informed by the adjacency of residues and the correlation of their local motions. This approach reveals densely coupled reorganisation communities, which facilitate an efficient signal transduction due to a high density of hubs. These communities are interconnected by a small number of highly important residues characterized by high betweenness centrality. The network approach clearly identifies the sites restructuring upon photoactivation, which appear as protrusions or delicate bridges in the reorganisation network. We also find that, unlike in the homologous cryptochrome from D. melanogaster, the release of the C-terminal domain does not appear to be correlated with the transposition of a histidine residue close to the FAD cofactor.

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An equilibrium constant pH molecular dynamics method for accurate prediction of pH-dependence in protein systems: Theory and application

10.1101/2020.11.23.394015 ◽

2020 ◽

Author(s):

Ekaterina Kots ◽

Derek M. Shore ◽

Harel Weinstein

Keyword(s):

Molecular Dynamics ◽

Equilibrium Constant ◽

Conformational Changes ◽

Ph Dependence ◽

Md Simulations ◽

Water Soluble ◽

Conformational Sampling ◽

Ph Change ◽

Constant Ph ◽

Dynamics Simulations

ABSTRACTComputational modeling and simulation of biomolecular systems at their functional pH ranges requires an accurate approach to exploring the pH dependence of conformations and interactions. Here we present a new approach – the Equilibrium Constant pH (ECpH) method – to perform conformational sampling of protein systems in the framework of molecular dynamics simulations in an N, P, T-thermodynamic ensemble. The performance of ECpH is illustrated for two proteins with experimentally determined conformational responses to pH change: the small globular water-soluble bovine b-lactoglobulin (BBL), and the dimer transmembrane antiporter CLC-ec1 Cl−/H+. We show that with computational speeds comparable to equivalent canonical MD simulations we performed, the ECpH trajectories reproduce accurately the pH-dependent conformational changes observed experimentally in these two protein systems, some of which were not seen in the corresponding canonical MD simulations.Abstract FigureTable of Contents artwork

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Molecular Dynamics Simulations of HLA-CW4-Β2M-KIR2DL1 Protein and Homology Modeling of a Complex Associated with Psoriasis Disease (HLA-CW6-Β 2M-KIR2DS1)

10.1101/2021.12.20.473468 ◽

2021 ◽

Author(s):

Mansour H Almatarneh ◽

Ahmad M Alqaisi ◽

Enas K Ibrahim ◽

Ghada G Kayed ◽

Joshua W Hollett

Keyword(s):

Molecular Dynamics ◽

Conformational Changes ◽

Complex Structure ◽

3D Structure ◽

Md Simulations ◽

Salt Bridges ◽

Small Peptide ◽

Β2 Microglobulin ◽

Dynamics Simulations ◽

The Right

Molecular dynamics (MD) simulation was used to study the interactions of two immune proteins of HLA-Cw4-β2m-KIR2DL1 complex with small peptide QYDDAVYKL (nine amino acids) in an aqueous solution. This study aims to gain a detailed information about the conformational changes and the dynamics of the complex. The right parameters and force field for performing the MD simulations that was needed to calibrate the complex structure were determined. The non-bonded interactions (Electrostatic and van der Waals contributions), H-bond formation, and salt bridges between the ligand HLA-Cw4 and the receptor KIR2DL1 were estimated using the obtained MD trajectories. The buried surface area due to binding was calculated to get insight into the causes of specificity of receptor to ligand and explains mutations experiment. The study concluded that β2-microglobulin, one part of the complex, is not directly interacting with the peptide at the groove; therefore, it could be neglected from simulation. Our results showed that β2-microglobulin does not have any significant effect on the dynamics of the 3D-structure of the complex. This project will help in understanding to optimize candidate drug design, a small peptide that disrupts the interaction, for the optimal biological effect.

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Exploring the Early Stages of the Amyloid Aβ(1–42) Peptide Aggregation Process: An NMR Study

Pharmaceuticals ◽

10.3390/ph14080732 ◽

2021 ◽

Vol 14 (8) ◽

pp. 732

Author(s):

Angelo Santoro ◽

Manuela Grimaldi ◽

Michela Buonocore ◽

Ilaria Stillitano ◽

Anna Maria D’Ursi

Keyword(s):

Conformational Changes ◽

Amyloid Fibrils ◽

Structural Model ◽

Conformational Transition ◽

Helical Structure ◽

Aggregation Process ◽

Nmr Study ◽

Aβ Aggregation ◽

Dynamics Simulations ◽

Β Sheet

Alzheimer’s disease (AD) is a neurodegenerative pathology characterized by the presence of neurofibrillary tangles and amyloid plaques, the latter mainly composed of Aβ(1–40) and Aβ(1–42) peptides. The control of the Aβ aggregation process as a therapeutic strategy for AD has prompted the interest to investigate the conformation of the Aβ peptides, taking advantage of computational and experimental techniques. Mixtures composed of systematically different proportions of HFIP and water have been used to monitor, by NMR, the conformational transition of the Aβ(1–42) from soluble α-helical structure to β-sheet aggregates. In the previous studies, 50/50 HFIP/water proportion emerged as the solution condition where the first evident Aβ(1–42) conformational changes occur. In the hypothesis that this solvent reproduces the best condition to catch transitional helical-β-sheet Aβ(1–42) conformations, in this study, we report an extensive NMR conformational analysis of Aβ(1–42) in 50/50 HFIP/water v/v. Aβ(1–42) structure was solved by us, giving evidence that the evolution of Aβ(1–42) peptide from helical to the β-sheet may follow unexpected routes. Molecular dynamics simulations confirm that the structural model we calculated represents a starting condition for amyloid fibrils formation.

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Conformational Changes of the Wild-Type hIAPP and the S20P Mutant in Water Revealed by Molecular Dynamics Simulations

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.396-398.1554 ◽

2011 ◽

Vol 396-398 ◽

pp. 1554-1557

Author(s):

Mian Wang ◽

Jian Yi Wang

Keyword(s):

Molecular Dynamics ◽

Hydrogen Bond ◽

Conformational Changes ◽

Amyloid Fibrils ◽

Helical Structure ◽

Wild Type ◽

Hydrogen Bond Interaction ◽

Hydrogen Bond Networks ◽

Α Helix ◽

Dynamics Simulations

Conformational changes of wild-type (WT) hIAPP and the S20P mutant in explicit water are investigated using molecular dynamics. In the whole simulation, WT shows compacter structure and has more hydrogen-bond networks than S20P. The residues 14-18 in WT is always maintained as a helical structure which is stabilized by the hydrogen bond between Ser20 and NH group of His18, and the other regions in WT partially loosen from α-helix structures into the coil structures. The S20P mutant in a shortage of hydrogen-bond interaction unfolds faster than WT. This work provides insight into the specific conformation of IAPP which is associated with the generation of amyloid fibrils.

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