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14 results for “complex spike”
Simple structural views of the SARS spike glycoprotein complex with human angiotensin-converting enzyme 2 (ACE2)
<p>A set of 5 screenshots of UnityMol running the first example system. Three screenshots are from a multi-user virtual reality session with 3 participants, two screenshots illustrate a custom menu to drive the example more efficiently and make it simple for the end user.</p>
Simulation of Receptor Binding Domain of SARS-CoV-2 spike protein (WT and variants) in complex with neutralizing antibodies.
<p>This repository contains the molecular dynamics trajectories of the SARS-CoV-2 Spike RBD bound to BD23 and B38 monoclonal antibodies. The simulations for the RBD only systems are also provided. The trajectories are available for the WT spike protein as well as for four different variants (alpha, beta, kappa and delta). The simulations of the RBD only system are propagated for 300 ns and for the RBD-Antibody complex for 500 ns. The trajectories are saved at 100 ps interval. The Steered MD simulation trajectories (WT_RBD_B38_SMD_1.dcd etc.) and collective variables files are also included (WT_RBD_B38_SMD_1.colvars.traj etc.). There are 5 SMD trajectories for each RBD antibody pair. The details of the simulation can be obtained from the preprint: https://doi.org/10.1101/2021.08.13.456317</p>
SIRAH-CoV2 initiative: SARS-Cov2 Spike´s RBD / ACE2-B0AT1 complex (PDB id:6M17)
<p>This dataset contains the trajectory of a 3 microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. Zinc ions were parameterized as reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.0c00160">Klein et al. 2020</a>.</p> <p>The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, and 6M17_SIRAHcg_rawdata_2-3.tar contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p> <p>Additionally, the file 6M17_SIRAHcg_3us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_3us_prot_skip10ns.tar contains one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6M17_SIRAHcg_10us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD 1.9.3 using the command line:</p> <p>vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot.ncrst 6M17_SIRAHcg_3us_prot_skip10ns.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV2 initiative.</p> <p>For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
SIRAH-CoV2 initiative: UPDATED TRAJECTORY of SARS-Cov2 Spike´s RBD / ACE2-B0AT1 complex (PDB id:6M17)
<p>This dataset contains an updated trajectory of a four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). It substitutes the previous one on the same system, which was performed in the absence of disulfide bridges.</p> <p>Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. Zinc ions were parameterized as reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.0c00160">Klein et al. 2020</a>.</p> <p>The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, 6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tar contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p> <p>Additionally, the file 6M17_SIRAHcg_4us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6M17_SIRAHcg_4us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD 1.9.3 using the command line:</p> <p>vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot.ncrst 6M17_SIRAHcg_4usprot_skip.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV2 initiative.</p> <p>For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
Data from: Cerebellar complex spikes multiplex complementary behavioral information
<p><span>Purkinje<b> </b>cell (PC) discharge, the only output of cerebellar cortex, involves two types of action potentials, high-frequency simple spikes (SSs) and low-frequency complex spikes (CSs). While there is consensus that SSs convey information needed to optimize movement kinematics, the function of CSs, determined by the PC´s climbing fibre input, remains controversial. While initially thought to be specialized in reporting information on motor error for the subsequent amendment of behavior, CSs seem to contribute to other aspects of motor behavior as well. When faced with the bewildering diversity of findings and views unraveled by highly specific tasks one may wonder if there is just one true function with all the other attributions wrong? Or is the diversity of findings a reflection of distinct pools of PCs, each processing specific streams of information conveyed by climbing fibres? With these questions in mind, we recorded CSs from the monkey oculomotor vermis deploying a repetitive saccade task that entailed sizable motor errors as well as small amplitude saccades, correcting them. We demonstrate that in addition to carrying error-related information, CSs carry information on the metrics of both primary and small corrective saccades in a time-specific manner, with changes in CS firing probability coupled with changes in CS duration. Furthermore, we also found CS activity that seemed to predict the upcoming events. </span>Hence PCs receive a multiplexed climbing fibre input that merges complementary streams of information on the behavior, separable by the recipient PC because they are staggered in time.</p>
SARS-CoV-2 spike protein complexes and their contacts
<p>This archive contains protein complex structures containing SARS-CoV-2 spike protein as well as derived data.</p>
Data from: Cerebellar complex spikes multiplex complementary behavioral information
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Trajectories of all MD simulations performed of Spike RBD/hACE2 complexes (WT, Delta, BA.1 to BA.4)
<p>Trajectories (.dcd) of the molecular dynamics simulations performed on Spike RBD / hACE2 complexes</p> <p>Protein structure files (.psf) prepared with Charmm36m topology / parameters</p> <p>For the WT (SARS-CoV-2 original strain), 6 additional replicas were uploaded, 3 including all glycans present on both spike and hACE2 et 3 replicas without glycan as control simulations.</p> <p> </p>
Supplementary Structural Models (SARS-CoV-2 Spike-RBD:ACE2 complex and TMPRSS2) - SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals
<p>Structural Models (PDB) of SARS-CoV-2 Spike RBD bound to ACE2 receptors of 215 animals.</p> <p>Structural model of Human TMPRSS2.</p> <p>Modelled using the FunMod pipeline and referenced in the preprint</p> <p><a href="https://www.biorxiv.org/content/10.1101/2020.05.01.072371v5">SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals</a></p> <p> </p>
SARS-CoV-2 spike binding to ACE2-B0AT1 complex
<p>Cryo-EM maps and models of SARS-CoV-2 spike (EMD:21457) and ACE2-B0AT1 (EMD:30039) are illustrated. Membranes are shown around the B0AT1 and approximated around the spike, which is lacking the trans-membrane domain. The binding of the spike to the ACE2 receptor is shown based on the model RBD built into the ACE2-B0AT1 map. The appears to attain a sharp angle wrt. the membrane surface to allow this binding.</p>
Data from: Complex spike synchrony dependent modulation of rat deep cerebellar nuclear activity
The rules determining cerebellar output are not fully understood, but must involve Purkinje cell activity (PCs), as PCs are the major input to deep cerebellar nuclear (DCN) cells (which form the majority of cerebellar output). Here, the influence of PC complex spikes (CSs) was investigated by simultaneously recording DCN activity with CSs from PC arrays in anesthetized rats. Crosscorrelograms were used to identify PCs that were presynaptic to recorded DCN cells (presynaptic PCs). Such PCs were located within rostrocaudal cortical strips and displayed synchronous CS activity. CS-associated modulation of DCN activity included a short-latency post-CS inhibition and long-latency excitations before and after the CS. The amplitudes of the post-CS responses correlated with the level of synchronization among presynaptic PCs. A temporal precision of {less than or equal to} 10 ms was generally required for CSs to be maximally effective. The results suggest that CS synchrony is a key control parameter of cerebellar output.Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
Exploring Conformational Landscapes and Binding Mechanisms of Convergent Evolition for the SARS-CoV-2 Spike Omicron Variant Complexes with the ACE2 Receptor Using AlphaFold2-Based Structural Ensembles and Molecular Dynamics Simulations
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Data from: Complex spike synchrony dependent modulation of rat deep cerebellar nuclear activity
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The Set1 complex is dimeric and acts with Proof Only Jhd2 demethylation to convey symmetrical H3K4 trimethylation [Spike-in-ChIP-seq]
GEO Series GSE127841. Saccharomyces cerevisiae; Schizosaccharomyces pombe. 36 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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