Search results for: PSBC

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When a protein misfolds from its native structure, the machinery will malfunction and lead to misfolding diseases. Although in vitro experiments are able to conclude that the mutations of the amino acid sequence lead to incorrectly folded protein structures, these experiments are unable to decipher the folding process. Therefore, molecular dynamic (MD) simulations are employed to simulate the folding process so that our improved understanding of the folding process will enable us to contemplate better treatments for misfolding diseases. MD simulations make use of force fields to simulate the folding process of peptides. Secondary structures are formed via the hydrogen bonds formed between the backbone atoms (C, O, N, H). It is important that the hydrogen bond energy computed during the MD simulation is accurate in order to direct the folding process to the native structure. Since the atoms involved in a hydrogen bond possess very dissimilar electronegativities, the more electronegative atom will attract greater electron density from the less electronegative atom towards itself. This is known as the polarization effect. Since the polarization effect changes the electron density of the two atoms in close proximity, the atomic charges of the two atoms should also vary based on the strength of the polarization effect. However, the fixed atomic charge scheme in force fields does not account for the polarization effect. In this study, we introduce the polarized structure-specific backbone charge (PSBC) model. The PSBC model accounts for the polarization effect in MD simulation by updating the atomic charges of the backbone hydrogen bond atoms according to equations derived between the amount of charge transferred to the atom and the length of the hydrogen bond, which are calculated from quantum-mechanical calculations. Compared to other polarizable models, the PSBC model does not require quantum-mechanical calculations of the peptide simulated at every time-step of the simulation and maintains the dynamic update of atomic charges, thereby reducing the computational cost and time while accounting for the polarization effect dynamically at the same time. The PSBC model is applied to two different 尾-peptides, namely the Beta3s/GS peptide, a de novo designed three-stranded 尾-sheet whose structure is folded in vitro and studied by NMR, and the trpzip peptides, a double-stranded 尾-sheet where a correlation is found between the type of amino acids that constitute the 尾-turn and the 尾-propensity. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=hydrogen%20bond" title="hydrogen bond">hydrogen bond</a>, <a href="https://publications.waset.org/abstracts/search?q=polarization%20effect" title=" polarization effect"> polarization effect</a>, <a href="https://publications.waset.org/abstracts/search?q=protein%20folding" title=" protein folding"> protein folding</a>, <a href="https://publications.waset.org/abstracts/search?q=PSBC" title=" PSBC"> PSBC</a> </p> <a href="https://publications.waset.org/abstracts/45837/folding-of-v-structures-via-the-polarized-structure-specific-backbone-charge-psbc-model" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/45837.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">275</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">1</span> Phylogenetic Analysis and a Review of the History of the Accidental Phytoplankter, Phaeodactylum tricornutum Bohlin (Bacillariophyta)</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Jamal%20S.%20M.%20Sabir">Jamal S. M. Sabir</a>, <a href="https://publications.waset.org/abstracts/search?q=Edward%20C.%20Theriot"> Edward C. Theriot</a>, <a href="https://publications.waset.org/abstracts/search?q=Schonna%20R.%20Manning"> Schonna R. Manning</a>, <a href="https://publications.waset.org/abstracts/search?q=Abdulrahman%20L.%20Al-Malki"> Abdulrahman L. Al-Malki</a>, <a href="https://publications.waset.org/abstracts/search?q=Mohammad"> Mohammad</a>, <a href="https://publications.waset.org/abstracts/search?q=Mumdooh%20J.%20Sabir"> Mumdooh J. Sabir</a>, <a href="https://publications.waset.org/abstracts/search?q=Dwight%20K.%20Romanovicz"> Dwight K. Romanovicz</a>, <a href="https://publications.waset.org/abstracts/search?q=Nahid%20H.%20Hajrah"> Nahid H. Hajrah</a>, <a href="https://publications.waset.org/abstracts/search?q=Robert%20K.%20Jansen"> Robert K. Jansen</a>, <a href="https://publications.waset.org/abstracts/search?q=Matt%20P.%20Ashworth"> Matt P. Ashworth</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The diatom Phaeodactylum tricornutum has been used as a model for cell biologists and ecologists for over a century. We have incorporated several new raphid pennates into a three-gene phylogenetic dataset (SSU, rbcL, psbC), and recover Gomphonemopsis sp. as sister to P. tricornutum with 100% BS support. This is the first time a close relative has been identified for P. tricornutum with robust statistical support. We test and reject a succession of hypotheses for other relatives. Our molecular data are statistically significantly incongruent with placement of either or both species among the Cymbellales, an order of diatoms with which both have been associated. We believe that further resolution of the phylogenetic position of P. tricornutum will rely more on increased taxon sampling than increased genetic sampling. Gomphonemopsis is a benthic diatom, and its phylogenetic relationship with P. tricornutum is congruent with the hypothesis that P. tricornutum is a benthic diatom with specific adaptations that lead to active recruitment into the plankton. We hypothesize that other benthic diatoms are likely to have similar adaptations and are not merely passively recruited into the plankton. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=benthic" title="benthic">benthic</a>, <a href="https://publications.waset.org/abstracts/search?q=diatoms%3B%20ecology" title=" diatoms; ecology"> diatoms; ecology</a>, <a href="https://publications.waset.org/abstracts/search?q=Phaeodactylum%20tricornutum" title=" Phaeodactylum tricornutum"> Phaeodactylum tricornutum</a>, <a href="https://publications.waset.org/abstracts/search?q=phylogeny" title=" phylogeny"> phylogeny</a>, <a href="https://publications.waset.org/abstracts/search?q=tychoplankton" title=" tychoplankton "> tychoplankton </a> </p> <a href="https://publications.waset.org/abstracts/91315/phylogenetic-analysis-and-a-review-of-the-history-of-the-accidental-phytoplankter-phaeodactylum-tricornutum-bohlin-bacillariophyta" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/91315.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">244</span> </span> </div> </div> </div> </main> <footer> <div id="infolinks" class="pt-3 pb-2"> <div class="container"> <div style="background-color:#f5f5f5;" class="p-3"> <div class="row"> <div class="col-md-2"> <ul class="list-unstyled"> About <li><a href="https://waset.org/page/support">About Us</a></li> <li><a href="https://waset.org/page/support#legal-information">Legal</a></li> <li><a target="_blank" rel="nofollow" href="https://publications.waset.org/static/files/WASET-16th-foundational-anniversary.pdf">WASET celebrates its 16th foundational anniversary</a></li> </ul> </div> <div class="col-md-2"> <ul class="list-unstyled"> Account <li><a href="https://waset.org/profile">My Account</a></li> </ul> </div> <div class="col-md-2"> 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Search results for: PSBC