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8 results for “proline-rich”
Data From: Exploring Gelatin-A and Mouse Proline-Rich Protein 5 as Probes for Wine Polyphenols analysis by Quartz Crystal Microbalance with Dissipation Monitoring
<p>Polyphenols are essential in winemaking, affecting the wine's quality, color, astringency, bitterness, and chemical stability. Conventional methods for assessing polyphenolic content are both expensive and time-intensive, underscoring the need for new, efficient techniques.</p> <p>The Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D) sensor is recognized for its speed and reliability as a label-free detection tool. This study applies QCM-D to evaluate Gelatin Type A (Gel-A) from porcine skin and Mouse Proline-Rich Protein 5 (MP5) for polyphenol analysis in red wines without pre-treatment. MP5 notably exhibited a linear dissipation signal response with both total polyphenol and hydroxybenzoic acid concentrations. These findings highlight the potential for creating a stand-alone sensor platform for real-time polyphenol monitoring in winemaking.</p>
Fluorine NMR study of proline-rich sequences using fluoroprolines
<p>Experimental NMR dataset related to the publication in Magnetic Resonance 2021 entitled:</p> <p>"Fluorine NMR study of proline-rich sequences using fluoroprolines"</p> <p>by</p> <p>Davy Sinnaeve, Abir Ben Bouzayene, Emile Ottoy, Gert-Jan Hofman, Eva Erdmann,<br> Bruno Linclau, Ilya Kuprov, José C. Martins, Vladimir Torbeev and Bruno Kieffer</p> <p><strong>Abstract.</strong> Proline homopolymer motifs are found in many proteins; their peculiar conformational and dynamic properties are often directly involved in those proteins' functions. However, the dynamics of proline homopolymers is hard to study by NMR due to lack of amide protons and small chemical shift dispersion. Exploiting the spectroscopic properties of fluorinated prolines opens interesting perspectives to address these issues. Fluorinated prolines are already widely used in protein structure engineering – they introduce conformational and dynamical biases – but their use as <sup>19</sup>F NMR reporters of proline conformation has not yet been explored. In this work, we look at model peptides where Cγ-fluorinated prolines with opposite configurations of the chiral Cγ centre have been introduced at two postions in distinct polyproline segments. By looking at the effects of swapping these (4<em>R</em>)- and (4<em>S</em>)-4-fluoroprolines within the polyproline segments, we were able to separate the intrinsic conformational properties of the polyproline sequence from the conformational alterations instilled by fluorination. We assess the fluoroproline <sup>19</sup>F relaxation properties, and exploit the latter in elucidating binding kinetics to the SH3 domain</p> <p>CONTENT OF THE REDEPOSITORY</p> <p><strong>Peptide assignment </strong></p> <p>To assign MpRS and MpSR peptides we recorded at 298 K the following experiments:</p> <ul> <li>H-<sup>13</sup>C HSQC. Recorded at 700MHz. The corresponding data are in the following datasets: MpRS_HSQC and MpSR_HSQC</li> <li>H-<sup>1</sup>H TOCSY. Recorded at 600MHz. The corresponding data are in the following datasets: MpRS_TOCSY and MpSR_TOCSY</li> <li>H-<sup>13</sup>C HSQC-NOESY. Recorded at 700MHz. The corresponding data are in the following datasets: MpRS_HSQC_NOESY and MpSR_HSQC_NOESY</li> <li>H-<sup>1</sup>H NOESY. Recorded at 600MHz. The corresponding data are in the following datasets: MpRS_NOESY and MpSR_NOESY</li> </ul> <p> </p> <p><strong>Homonuclear scalar coupling constants </strong></p> <p>Homonuclear <sup>3</sup>J<sub>H-H </sub>scalar couplings were measured using SERF experiments on a 700MHz spectrometer at 298 K. The corresponding data can be examined in the followed datasets: MpRS_SERF and MpSR_SERF for both MpRS and MpSR peptides, respectively.</p> <p> </p> <p><strong><sup>1</sup></strong><strong>D <sup>19</sup>F spectra </strong></p> <p> </p> <p><sup>1</sup>D <sup>19</sup>F spectra of MpRS and MpSR peptides were recorded on a 600MHz spectrometer at 298 K, with samples dissolved in D2O. 3mm tubes were used. The data are stored in the following datasets: MpRS_1D_F and MpSR_1D_F for both MpRS and MpSR peptides respectively.</p> <p> </p> <p><strong><sup>19</sup></strong><strong>F Relaxation </strong></p> <p>Longitudinal and transverse relaxation rates of fluorine were measured for both MpRS and MpSR peptides. Standard inversion recovery, spin-echo and CPMG experiments were collected for both MpSR and MpRS peptides on a 600MHz at 298 K. The corresponding data may be examined in these datasets:</p> <p>For MpRS: MpRS_R1, MpRS_R2_spin_echo, MpRS_R2_CPMG</p> <p>For MpSR: MpSR_R1, MpSR_R2_spin_echo, MpSR_R2_CPMG</p> <p> </p> <p><sup>1</sup>HG-<sup>19</sup>F heteronuclear-nOes were measured using nOe buildup experiments recorded on a 600MHz spectrometer at 298 K. The experimental data of both peptides are in the following datasets: MpRS_HGF_NOE and MpSR_HGF_NOE</p> <p> </p> <p><strong>Titration experiments with Vinexin SH3.3 domain</strong></p> <p>Titration experiments were performed on a 600MHz spectrometer at 298K using 3 mm tubes. The respective volumes of peptide and SH3 protein are given in the title file. The 1D <sup>19</sup>F spectra of MpRS and MpSR peptides are stored in titrMpRS_1D_F and titrMpSR_1D_F, respectively. The <sup>1</sup>H-<sup>15</sup>N HSQC spectra are stored in titrMpRS_HSQC and titrMpSR_HSQC datasets.</p> <p>Stock solutions were:</p> <p>SH3: 314 µM</p> <p>MpRS S0: 5.67 mM</p> <p>MpSR S0: 5.1 mM</p> <p>S1 stocks resulted from S0 by a factor 2 dilution.</p>
Simulated complex structures of the h-FBP21 tandem WW domain with proline-rich ligand extracted from SmB/B' core-splicing protein
<p>The tandem WW domain of the human formin-binding protein 21 (h-FBP21 tWW) consists of two WW domains separated by a flexible linker. It can bind target sequences in two different orientations and the flexibility of the linker additionally allows the two WW domains to adopt various relative orientations to each other. As consequence, the elucidation of possible complex structures for the h-FBP21 tWW is very challenging.</p> <p>Here, we present two complex structures for the h-FBP21 tWW and a proline-rich sequence from its natural binding partner, the core-splicing protein SmB/B’. Showing parallel (‘6’) and antiparallel (’14’) binding orientation, the two structures also differ in the relative positioning of the WW domains.</p> <p>For further instructions regarding the files, please refer to ‘README’.</p>
Isothermal Titration Calorimetry Data - Intramolecular autoinhibition regulates the selectivity of PRPF40A tandem WW domains for proline-rich motifs
<p>This is the repository of all ITC data related to the paper:</p> <p><strong><span>Intramolecular autoinhibition regulates the selectivity of PRPF40A tandem WW domains for proline-rich motifs</span></strong></p> <p><span>Santiago Martínez-Lumbreras<sup>1,2,*</sup>, Lena K. Träger<sup>2</sup>, Miriam M. Mulorz<sup>3</sup>, Marco Payr<sup>2</sup>, Varvara Dikaya<sup>2</sup>, Clara Hipp<sup>1,2</sup>, Julian König<sup>3</sup> and Michael Sattler<sup>1,2,*</sup></span><strong><span> </span></strong></p> <p><sup><span>1</span></sup><span> <span> </span>Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany</span></p> <p><sup><span>2</span></sup><span><span> </span>Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Lichtenbergstrasse 4, 85747 Garching, Germany</span></p> <p><sup><span>3</span></sup><span> Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128 Mainz, </span><span>Germany</span></p> <p><span>* Correspondence should be addressed to: </span></p> <p><span>Santiago Martínez Lumbreras <a href="mailto:santiago.martinez@tum.de">santiago.martinez@tum.de</a> or</span></p> <p><span>Michael Sattler </span><span><a href="mailto:michael.sattler@helmholtz-munich.de"><span>michael.sattler@helmholtz-munich.de</span></a></span></p>
data for "An unbound proline-rich signaling peptide frequently samples cis conformations in Gaussian accelerated molecular dynamics simulations"
<p>Disordered proline-rich motifs are common across the proteomes of many species and are often involved in protein-protein interactions. Proline is a unique amino acid due to the covalent bond between the backbone nitrogen and the proline side chain. The resulting five-membered ring allows proline to sample the <em>cis</em> state about its peptide bond, which other residues cannot do as readily. Because proline-rich disordered sequences exist as ensembles that likely include structures with the proline peptide bond in <em>cis</em>, a robust methodology to accurately account for these conformations in the overall ensemble is crucial. Observing the <em>cis </em>conformations of proline in a disordered sequence is challenging both experimentally and computationally. Nitrogen-hydrogen NMR spectroscopy cannot directly observe proline residues, which lack an amide bond, and computational methods struggle to overcome the large kinetic barrier between the <em>cis </em>and <em>trans </em>states, since isomerization usually occurs on the order of seconds. In the current work, Gaussian accelerated molecular dynamics was used to overcome this free energy barrier and simulate proline isomerization in a tetrapeptide (KPTP) and in the 12-residue proline-rich SH3 binding peptide, ArkA. We found that Gaussian accelerated molecular dynamics, when combined with a lowered peptide bond dihedral angle potential energy barrier (15 kcal/mol), allowed sufficient sampling of the proline <em>cis </em>and <em>trans </em>states on a microsecond timescale. All ArkA prolines spend a significant fraction of time in <em>cis</em>, leading to a more compact ensemble with less polyproline II helix structure than an ArkA ensemble with all peptide bonds in <em>trans</em>. The ensemble containing <em>cis</em> prolines also matches more closely to <em>in vitro</em> circular dichroism data than the all-<em>trans</em> ensemble. The ability of the ArkA prolines to isomerize likely affects the peptide’s ability to bind its partner SH3 domain, and should be studied further. This is the first molecular dynamics simulation study of proline isomerization in a biologically relevant proline-rich sequence that we know of, and a similar protocol could be applied to study multi-proline isomerization in other proline-containing proteins to improve conformational diversity and agreement with <em>in vitro</em> data.</p>
Role of the proline-rich disordered domain of DROSHA in intronic microRNA processing
GEO Series GSE230544. Homo sapiens. 20 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Small proline-rich proteins 1 and 2 function as antimicrobial proteins in the skin
GEO Series GSE182756. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
A Missense Variant in CASKIN1's Proline-Rich Region Segregates with Psychosis in a Three-Generation Family
GEO Series GSE268384. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
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