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22 results for “self-assembling peptide”
Research data supporting: "Self-assembly of cyclic peptide monolayers by hydrophobic supramolecular hinges"
<p>This repository contains the set of modelling data shown in the paper:<strong> "Self-assembly of cyclic peptide monolayers by hydrophobic supramolecular hinges"</strong>, published on Chemical Science (DOI: 10.1039/d3sc03930g)</p>
Self-Assembled Proteomimetic (SAP) with Antibody-like Binding from Short PNA-Peptide Conjugates
<p><span><span>Affinity proteins </span><span>based on </span><span>a </span><span>three-helix </span><span>bundle</span> <span>(</span><span>affibodies, </span><span>alphabodies</span><span> and computationally </span></span><span><span>de novo</span></span><span> <span>designed</span><span> ones)</span><span> have shown to be a general platform to discover binders with properties reminiscent of </span><span>antibodies</span><span>, combining </span><span>high </span><span>target </span><span>specificity</span><span> with </span><span>affinities reaching well below</span> <span>the </span><span>nanomolar</span><span>.</span> <span>Herein</span><span>,</span><span> we report a new strategy</span><span>, coined self-assembled proteomimetic (SAP)</span><span>,</span><span> to mimic </span><span>such</span><span> three-helix bundle</span><span> architecture with a hybridization-enforced two-helix </span><span>coiled</span> <span>coil</span><span> that is obtained by templated</span> <span>native chemical ligation (</span><span>T-</span><span>NCL) of PNA-peptide conjugates.</span> <span>This SAP </span><span>strategy</span> <span>stands out by</span><span> its</span><span> synthetic accessibility reducing the length on the longest </span><span>synthetic</span><span> peptide to </span><span>less than 30 amino acids, readily attainable by standard SPPS methodologies</span><span>. We show that the </span><span>T</span><span>-NCL dramatically accelerates the </span><span>ligation</span><span>, enabling this chemistry to </span><span>proceed</span> <span>in a combinatorial fashion </span><span>at</span><span> low</span> <span>micromolar</span><span> concentration</span><span>s</span><span>.</span> <span>We </span><span>demonstrate</span> <span>that small </span><span>combinatorial </span><span>libraries of </span><span>SAP</span><span>s</span><span> can be prepared in one operation and used directly in </span><span>affinity selection</span><span>s</span><span> against a target of interest </span><span>with an</span><span> LC-MS </span><span>analysis</span><span> of the fittest binders</span><span>.</span> <span>Moreover, we </span><span>show</span><span> that </span><span>the underlying</span> <span>design</span><span> paradigm</span><span> is functional for</span><span> SAPs based on structurally distinct three-helix peptides </span><span>aimed at</span><span> different </span><span>therapeutic </span><span>targets, namely</span> <span>HER2 </span><span>and</span><span> spike’s RBD</span><span>,</span></span> <span><span>reaching picomolar </span><span>affinities</span></span><span><span>. We further </span><span>illustrate </span><span>that the</span> <span>affinity </span><span>of the </span><span>S</span><span>AP</span><span> can be allosterically regulated using a toehold displacement</span><span> of the hybridizing PNAs</span><span> to disrupt the </span><span>coiled coil</span><span> stabilization.</span> <span>Finally, w</span><span>e show that </span><span>an RBD-targeting </span><span>SAP effectively inhibits viral </span><span>entry </span><span>of SARS-CoV-2</span> <span>with an IC</span></span><span><span>50</span></span><span><span> of </span><span>2.8</span> <span>nM</span><span>.</span></span><span> </span></p>
Supporting data for: "Hybrid Computational-Experimental Data-Driven Design of Self-Assembling π-Conjugated Peptides"
<p>This repository contains supporting data and code for the paper titled "Hybrid Computational-Experimental Data-Driven Design of Self-Assembling π-Conjugated Peptides" by Kirill Shmilovich, Sayak Subhra Panda, Anna Stouffer, John D. Tovar, and Andrew L. Ferguson.</p>
Data for publication "Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism"
<p>The data provided refer to our published article:</p> <p>T. John,* S. Piantavigna, T. J. A. Dealey, B. Abel, H. J. Risselada, L. L. Martin*, Lipid oxidation controls peptide self-assembly near<br>membranes through a surface attraction mechanism, Chem. Sci. 14 (2023), 3730-3741. <a href="https://doi.org/10.1039/d3sc00159h">https://doi.org/10.1039/d3sc00159h</a>.</p>
Data regarding "Development and evaluation of RADA-PDGF2 self-assembling peptide hydrogel for enhanced skin wound healing"
<p>Raw data for data published in Development and evaluation of RADA-PDGF2 self-assembling peptide hydrogel for enhanced skin wound healing, Front. Pharmacol. Sec. Experimental Pharmacology and Drug Discovery Volume 14 - 2023 | <a href="https://doi.org/10.3389/fphar.2023.1293647">doi: 10.3389/fphar.2023.1293647</a></p>
Comparing natural hydrogels to self-assembling peptides in spinal cord injury treatment: a systematic review
<p><strong>Abstract</strong></p> <p><em><strong>Background:</strong></em><em> </em>In many cases, central nervous system (CNS) injury is unchanging due to the absence of neuronal regeneration and repair capabilities.<strong> </strong>In recent years, regenerative medicine, and especially hydrogels, have reached a significant amount of attention for their promising results for the treatment of spinal cord injury (SCI) currently considered permanent. Hydrogels are categorized based on their foundation: synthetic, natural, and combination. The objective of this study was to compare the properties and efficacy of commonly used hydrogels, like collagen, and other natural peptides with synthetic self-assembling peptide hydrogels in the treatment of SCI. </p> <p><em><strong>Methods</strong></em><em>:</em><em> </em>Articles were searched in PubMed, Scopus, Web of Science, and Embase. All studies from 1985 until January 2020 were included in the primary search. Eligible articles were included based on the following criteria: administering hydrogels (both natural and synthetic) for SCI treatment, soley foucsing on spinal cord injury treatment, and published in a peer-reviewd journal. Data surronding xonal regeneration, revascularization, elasticity, drug delivery efficacy, and porosity were extracted.</p> <p><em><strong>Results:</strong></em> A total of 24 articles were included for full-text review and data extraction. There were only one experimental study directly comparing Collagen I (as natural hydorgel) and PEG (as synthetic hydrogels) in an <em>in vitro </em>setting. The included study suggested PEG’s cell behavior is more expectable in the injury site, which makes it a more reliable scaffold.</p> <p><em><strong>Conclusions:</strong></em> There is limited research comparing and evaluating both types of natural and self-assembling peptides (SAPs) in the same animal or <em>in vitro</em> study, despite its importance. Although we assume that the remodeling of natural scaffolds may lead to a stable hydrogel, there was not a definitive conclusion that synthetic hydrogels are more beneficial than natural hydrogels in neuronal regeneration.</p>
Research data supporting "Residue-Specific Solvation Directed Thermodynamic and Kinetic Control over Peptide Self-Assembly with 1D/2D Structure Selection"
<p>Experimental research raw data supporting the publication by Lin, Y. et al, 2019, "Residue-Specific Solvation Directed Thermodynamic and Kinetic Control over Peptide Self-Assembly with 1D/2D Structure Selection", ACS Nano. DOI: 10.1021/acsnano.8b08117.</p> <p>Molecular simulation data is available upon reasonable request from irene.yarovsky@rmit.edu.au.</p>
Molecular modeling of self-assembling peptides MELD structures
<p>Top 10 MELD structures for each system used in the "Molecular modeling of self-assembling peptides" paper.</p>
Simulation Data for Design of Peptides that Fold and Self-Assemble on Graphite
<p>This data set for the manuscript entitled "Design of Peptides that Fold and Self-Assemble on Graphite" includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or Amber prmtop format), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included.</p> <p>Version: 2.0</p> <p>Changes versus version 1.0 are the addition of the free energy of folding, adsorption, and pairing calculations (Sim_Figure-7) and shifting of the figure numbers to accommodate this addition.</p> <p><br> Conventions Used in These Files<br> ===============================</p> <p>Structure Files<br> ----------------<br> - graph_*.psf or sol_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.)</p> <p>- graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)<br> - repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl)<br> - freeTop_*.pdb (same as the above pdb files, but the carbons of the lower graphene layer have been placed at a single z value and marked for restraints in NAMD)<br> - amber_*.prmtop (combined topology and parameter files for Amber force field simulations)<br> - repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd)</p> <p>Force Field Parameters<br> ----------------------<br> CHARMM format parameter files:<br> - par_all36m_prot.prm (CHARMM36m FF for proteins)<br> - par_all36_cgenff_no_nbfix.prm (CGenFF v4.4 for graphene) The NBFIX parameters are commented out since they are only needed for aromatic halogens and we use only the CG2R61 type for graphene.<br> - toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)</p> <p>Template NAMD Configuration Files<br> ---------------------------------<br> These contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):<br> - template_min.namd (minimization)<br> - template_eq.namd (NPT equilibration with lower graphene fixed)<br> - template_abf.namd (for adaptive biasing force)</p> <p>Minimization<br> -------------<br> - namd/min_*.0.namd</p> <p>Equilibration<br> -------------<br> - namd/eq_*.0.namd</p> <p>Adaptive biasing force calculations<br> -----------------------------------<br> - namd/eabfZRest7_graph_chp1404.0.namd<br> - namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)</p> <p>Log Files<br> ---------<br> For each NAMD configuration file given in the last two sections, there is a log file with the same prefix, which gives the text output of NAMD. For instance, the output of namd/eabfZRest7_graph_chp1404.0.namd is eabfZRest7_graph_chp1404.0.log.</p> <p>Simulation Output<br> -----------------<br> The simulation output files (which match the names of the NAMD configuration files) are in the output/ directory. Files with the extensions .coor, .vel, and .xsc are coordinates in NAMD binary format, velocities in NAMD binary format, and extended system information (including cell size) in text format. Files with the extension .dcd give the trajectory of the atomic coorinates over time (and also include system cell information). Due to storage limitations, large DCD files have been omitted or replaced with new DCD files having the prefix stride50_ including only every 50 frames. The time between frames in these files is 50 * 50000 steps/frame * 4 fs/step = 10 ns. The system cell trajectory is also included for the NPT runs are output/eq_*.xst.</p> <p>Scripts<br> -------<br> Files with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. If there are scripts with step1_*.sh and step2_*.sh, they are intended to be run in order, with step1_*.sh first.</p> <p><br> CONTENTS<br> ========</p> <p>The directory contents are as follows. The directories Sim_Figure-1 and Sim_Figure-8 include README.txt files that describe the files and naming conventions used throughout this data set.</p> <p>Sim_Figure-1: Simulations of N-acetylated C-amidated amino acids (Ac-X-NHMe) at the graphite–water interface.</p> <p>Sim_Figure-2: Simulations of different peptide designs (including acyclic, disulfide cyclized, and N-to-C cyclized) at the graphite–water interface.</p> <p>Sim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.</p> <p>Sim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.</p> <p>Sim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 295 K.</p> <p>Sim_Figure-5_replica: Temperature replica exchange molecular dynamics simulations for the peptide cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) with 20 replicas for temperatures from 295 to 454 K.</p> <p>Sim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).</p> <p>Sim_Figure-7: Free energy calculations for folding, adsorption, and pairing for the peptide CHP1404 (sequence: cyc(GTGSGTG-GPGG-GCGTGTG-SGPG)). For folding, we calculate the PMF as function of RMSD by replica-exchange umbrella sampling (in the subdirectory Folding_CHP1404_Graphene/). We make the same calculation in solution, which required 3 seperate replica-exchange umbrella sampling calculations (in the subdirectory Folding_CHP1404_Solution/). Both PMF of RMSD calculations for the scrambled peptide are in Folding_scram1404/. For adsorption, calculation of the PMF for the orientational restraints and the calculation of the PMF along z (the distance between the graphene sheet and the center of mass of the peptide) are in Adsorption_CHP1404/ and Adsorption_scram1404/. The actual calculation of the free energy is done by a shell script ("doRestraintEnergyError.sh") in the 1_free_energy/ subsubdirectory. Processing of the PMFs must be done first in the 0_pmf/ subsubdirectory. Finally, files for free energy calculations of pair formation for CHP1404 are found in the Pair/ subdirectory.</p> <p>Sim_Figure-8: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) where the peptides are far above the graphene–water interface in the initial configuration.</p> <p>Sim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite–water interface at 370 K.</p> <p>Sim_Figure-9_scrambled: Two replicates of a simulation of nine peptide molecules with the control sequence cyc(GGTPTTGGGGGGSGGPSGTGGC) at the graphite–water interface at 370 K.</p> <p>Sim_Figure-10: Adaptive biasing for calculation of the free energy of the folded peptide as a function of the angle between its long axis and the zigzag directions of the underlying graphene sheet.</p> <p> </p>
Self-assembling peptide nanofiber HIV vaccine elicits robust vaccine-induced antibody functions and modulates Fc glycosylation.
<p>To develop vaccines for certain key global pathogens such as HIV, it is crucial to elicit both neutralizing and non-neutralizing Fc-mediated effector antibody functions. Clinical evidence indicates that non-neutralizing antibody functions including antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP) contribute to protection against several pathogens. In this study, we demonstrated that conjugation of HIV Envelop (Env) antigen gp120 to a self-assembling nanofiber material named Q11 induced antibodies with higher breadth and functionality when compared to soluble gp120. Immunization with Q11-conjugated gp120 vaccine (gp120-Q11) demonstrated higher tier 1 neutralization, ADCP and ADCC as compared to soluble gp120. Moreover, Q11 conjugation altered the Fc N-glycosylation profile of antigen-specific antibodies, leading to a phenotype associated with increased ADCC in animals immunized with gp120-Q11. Thus, this nanomaterial vaccine strategy can enhance non-neutralizing antibody functions possibly through modulation of IgG Fc N-glycosylation.</p>
Treatment of Postsphincterotomy Bleeding With a Novel Self-assembling Peptide Hemostatic Gel.
ClinicalTrials.gov study NCT05886127. IPD Sharing: YES. Countries: 1. Publications: 5.
Remineralization of White Spot Lesions Using Self-Assembling Peptide P11-4 in Primary Anterior Teeth A Randomized Clinical Trial
ClinicalTrials.gov study NCT03927794. IPD Sharing: NO. Countries: 1. Publications: 4.
Data from: Self-assembly behaviors of peptide-drug conjugates: influence of multiple factors on aggregate morphology and potential self-assembly mechanism
Open the record for dataset details and reuse information.
Evaluation of Self-assembling Peptides Versus Amorphous Calcium Phosphate in the Treatment of White Spot Lesions
ClinicalTrials.gov study NCT07146464. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Effect of Self-Assembling Peptides on the Progression of Non-Cavitated Proximal Caries
ClinicalTrials.gov study NCT04776785. IPD Sharing: Not stated. Countries: 1. Publications: 0.
"Clinical Evaluation of Self-Assembling Peptides Versus Tri-Calcium Phosphate Based Varnish in Treatment of White Spot Lesions; Split-Mouth Randomized Clinical Trial"
ClinicalTrials.gov study NCT07289932. IPD Sharing: YES. Countries: 1. Publications: 0.
SVF Combined With Functional Self-assembling Peptide Nanofiber Hydrogels in the Treatment of Spinal Cord Injury
ClinicalTrials.gov study NCT05967325. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Self-assembling Peptide With Sodium Fluoride in Treating White Spot Lesionss in Primary Teeth
ClinicalTrials.gov study NCT05721586. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Remineralization Capacity and Patient Satisfaction of Self-Assembling Peptide With Fluoride Versus Tooth Protective Coating With Surface Pre-Reacted Glass on White Spot Lesions
ClinicalTrials.gov study NCT07086235. IPD Sharing: NO. Countries: 1. Publications: 0.
Evaluation of the Effect of Self-Assembling Peptide P11-4
ClinicalTrials.gov study NCT05667545. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
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OpenNeuro
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