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首页> 外文期刊>Journal of Physical Organic Chemistry >Examination of ethanol interactions with Trp‐cage peptide through MD simulations and intermolecular nuclear Overhauser effects
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Examination of ethanol interactions with Trp‐cage peptide through MD simulations and intermolecular nuclear Overhauser effects

机译：通过MD仿真和分子间核传输效应检查与TRP笼肽的乙醇相互作用

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Abstract > Molecular dynamic (MD) simulations of the model protein Trp‐cage dissolved in 35% ethanol‐water at 298?K have been carried out using conventional force fields. The goal was to develop a better understanding of experimental intermolecular nuclear Overhauser effects (NOEs) that arise from interactions of ethanol methyl groups with hydrogens of the peptide. Cross‐relaxation terms ( <mat:math display="inline" overflow="scroll" altimg="urn:x-wiley:08943230:media:poc3809:poc3809-math-0002" wiley:location="equation/poc3809-math-0002.png"> <mat:msubsup> <mat:mi>σ</mat:mi> <mat:mi>ETH</mat:mi> <mat:mi>NOE</mat:mi> </mat:msubsup> </mat:math> ) for peptide N‐H hydrogens and several side chain groups were calculated from the MD trajectories. The simulations indicate that water preferentially solvates hydrogens at the peptide termini while ethanol preferentially accumulates at the other hydrogens of the peptide. Most of a calculated NOE arises from interaction of ethanol molecules in the first solvent layer with a peptide hydrogen. Calculated <mat:math display="inline" overflow="scroll" altimg="urn:x-wiley:08943230:media:poc3809:poc3809-math-0003" wiley:location="equation/poc3809-math-0003.png"> <mat:msubsup> <mat:mi>σ</mat:mi> <mat:mi>ETH</mat:mi> <mat:mi>NOE</mat:mi> </mat:msubsup> </mat:math> are qualitatively consistent with experimental values but are not in quantitative agreement. Results from MD trajectories calculated by using modified force fields for ethanol intended to reduce peptide‐methyl group interactions do not lead to better agreement between observed and calculated <mat:math display="inline" overflow="scroll" altimg="urn:x-wiley:08943230:media:poc3809:poc3809-math-0004 </span> <span class="z_kbtn z_kbtnclass hoverxs" style="display: none;">展开▼</span> </div> <div class="translation abstracttxt"> <span class="zhankaihshouqi fivelineshidden" id="abstract"> <span>机译：</span><abstract type =“main”xml：lang =“en”> <标题类型=“main”>抽象</ title> >分子动力学（MD）模拟溶解在35％乙醇中的模型蛋白质Trp-笼的模拟 - 使用常规力场进行了298 k的水。目标是更好地了解产生由乙醇甲基与肽的氢的相互作用产生的实验分子间核传承效应（NOES）。交叉放松术语（<mat：数学显示=“内联”overflow =“滚动”Altimg =“URN：X-Wiley：08943230：Media：PoC3809：PoC3809-Math-0002”Wiley：Location =“等式/ PoC3809-Math -0002.png“> <mat：msubsup> <may：mi>σ</ mat：mi> <mat：mi> eth </ mat：mi> <mat：mi> noe </ mat：mi> </ mat ：用于肽N-H氢的msubsup> </ mat：数学>）从MD轨迹计算几个侧链组。模拟表明水优先在肽末端溶剂化液体，而乙醇优先积聚在肽的其他氢。大多数计算的NOE产生乙醇分子在第一溶剂层中的相互作用与肽氢。计算<mat：数学显示=“内联”overflow =“滚动”Altimg =“URN：X-Wiley：08943230：Media：PoC3809：PoC3809-Math-0003”Wiley：Location =“等式/ PoC3809-Math-0003.png “> <mat：msubsup> <mat：mi>σ</ mat：mi> <mat：mi> eth </ mat：mi> <mat：mi> noe </ mat：mi> </ mat：msubsup> < / MAT：数学>与实验值质量符合，但不是量化协议。 MD轨迹通过使用用于减少肽 - 甲基相互作用的乙醇的修改力场计算的MD轨迹不会导致观察和计算的<mat：数学显示=“inline”overflow =“滚动”altimg =“urn：x之间更好地协议-Wiley：08943230：媒体：POC3809：POC3809-MATH-0004 </span> <span class="z_kbtn z_kbtnclass hoverxs" style="display: none;">展开▼</span> </div> </div> <div class="record"> <h2 class="all_title" id="enpatent33" >著录项</h2> <ul> <li> <span class="lefttit">来源</span> <div style="width: 86%;vertical-align: text-top;display: inline-block;"> <a href='/journal-foreign-35546/'>《Journal of Physical Organic Chemistry》</a> <b style="margin: 0 2px;">|</b><span>2018年第8期</span><b style="margin: 0 2px;">|</b><span>共14页</span> </div> </li> <li> <div class="author"> <span class="lefttit">作者</span> <p id="fAuthorthree" class="threelineshidden zhankaihshouqi"> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Gerig John T.&option=202" target="_blank" rel="nofollow">Gerig John T.;</a> </p> <span class="z_kbtnclass z_kbtnclassall hoverxs" id="zkzz" style="display: none;">展开▼</span> </div> </li> <li> <div style="display: flex;"> <span class="lefttit">作者单位</span> <div style="position: relative;margin-left: 3px;max-width: 639px;"> <div class="threelineshidden zhankaihshouqi" id="fOrgthree"> <p>Department of Chemistry and BiochemistryUniversity of California Santa BarbaraSanta Barbara CA USA;</p> </div> <span class="z_kbtnclass z_kbtnclassall hoverxs" id="zhdw" style="display: none;">展开▼</span> </div> </div> </li> <li > <span class="lefttit">收录信息</span> <span style="width: 86%;vertical-align: text-top;display: inline-block;"></span> </li> <li> <span class="lefttit">原文格式</span> <span>PDF</span> </li> <li> <span class="lefttit">正文语种</span> <span>eng</span> </li> <li> <span class="lefttit">中图分类</span> <span><a href="https://www.zhangqiaokeyan.com/clc/4796.html" title="有机化学一般性问题">有机化学一般性问题;</a></span> </li> <li class="antistop"> <span class="lefttit">关键词</span> <p style="width: 86%;vertical-align: text-top;"> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=ethanol‐water mixtures&option=203" rel="nofollow">ethanol‐water mixtures;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=force field adjustment&option=203" rel="nofollow">force field adjustment;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=intermolecular NOE&option=203" rel="nofollow">intermolecular NOE;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=MD simulation&option=203" rel="nofollow">MD simulation;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=peptide&option=203" rel="nofollow">peptide;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Trp‐cage peptide&option=203" rel="nofollow">Trp‐cage peptide;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=solvent structure and dynamics&option=203" rel="nofollow">solvent structure and dynamics;</a> </p> <div class="translation"> 机译：乙醇 - 水混合物;力场调整;分子间NOE;MD模拟;肽;TRP-笼肽;溶剂结构和动力学; 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