Development of more accurate molecular dynamics simulation method by combining ab initio all electron calculation method for proteins

结合蛋白质从头算全电子计算方法开发更精确的分子动力学模拟方法

基本信息

  • 批准号:
    17510156
  • 负责人:
  • 金额:
    $ 1.6万
  • 依托单位:
  • 依托单位国家:
    日本
  • 项目类别:
    Grant-in-Aid for Scientific Research (C)
  • 财政年份:
    2005
  • 资助国家:
    日本
  • 起止时间:
    2005 至 2006
  • 项目状态:
    已结题

项目摘要

There are two important calculation methods for proteins, molecular dynamics (MD) simulation method and ab initio all electron calculation method. Our purpose was the improvement of the MD simulation method by combining ab initio all electron calculation method with it. The coworker is one of the authors of ab initio all electron calculation program (ProteinDF) and the head investigator is the author of a MD simulation program (COSMOS90). We improved the MD simulation method using precise atomic charges calculated by ProteinDF every thousands steps of MD. There are two methods calculating atomic charges based on (1)the Mulliken population analysis and (2)the electrostatic potentials (ESP) on the molecular surface. The ESP method is more reliable than the Mulliken method which depends on the basis sets used for expanding the wave functions. However, it is difficult to directly apply the ESP method to proteins, because we can not calculate the electrostatic potentials on the molecular surface for the buried amino acids of a protein. We overcame such difficulty by developing a new ESP method based on the localized orbital (LO). We checked that our method (so called ESPLO) give the precise atomic charges for a-helix and β-sheet. Next, we successfully performed MD simulations for a peptide consisting of 12 Gly residues in water. The ESPLO charges for the peptide were calculated every 1 ps using ProteinDF, where the water molecules around the peptide were represented by point charges. In principle, our methodology is applicable to a protein in water, but for the practical use we should accelerate the procedure making LO from MO.
蛋白质的计算方法主要有两种,分子动力学模拟方法和从头算全电子计算方法。我们的目的是将从头计算全电子计算方法与分子动力学模拟方法相结合,改进分子动力学模拟方法,我们的合作者是从头计算全电子计算程序(ProteinDF)的作者之一,我们的主要研究者是分子动力学模拟程序(COSMOS 90)的作者。我们改进了分子动力学模拟方法,使用精确的原子电荷计算的蛋白质DF每数千步的分子动力学。计算原子电荷的方法主要有两种:(1)Mulliken布居分析法和(2)分子表面静电势法。ESP方法比Mulliken方法更可靠,Mulliken方法依赖于用于展开波函数的基组。然而,将ESP方法直接应用于蛋白质是困难的,因为我们无法计算蛋白质中埋藏的氨基酸在分子表面的静电势。我们克服了这样的困难,开发了一种新的ESP方法的基础上的本地化轨道(LO)。我们检查了我们的方法(所谓的ESPLO)给出了α-螺旋和β-折叠的精确原子电荷。接下来,我们成功地进行了MD模拟的肽组成的12个甘氨酸残基在水中。使用ProteinDF每1 ps计算肽的ESPLO电荷,其中肽周围的水分子由点电荷表示。原则上,我们的方法适用于水中的蛋白质,但为了实际应用,我们应该加速从MO制备LO的过程。

项目成果

期刊论文数量(5)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
地球シミュレータによる蛋白質の大規模シミュレーション:ベクトル化と並列化による加速性能
使用地球模拟器进行大规模蛋白质模拟:通过矢量化和并行化实现加速性能
A 45-ns molecular dynamics simulation of hemoglobin in water by vectorizing and parallelizing COSMOS90 on the Earth Simulator : dynamics of tertiary and quaternary structures
通过地球模拟器上的 COSMOS90 矢量化和并行化对水中血红蛋白进行 45 纳秒分子动力学模拟:三级和四级结构的动力学
  • DOI:
  • 发表时间:
    2007
  • 期刊:
  • 影响因子:
    0
  • 作者:
    M.Saito;I.Okazaki
  • 通讯作者:
    I.Okazaki
地球シミコ-レータによる蛋白質の大規模シミュレーション : ベクトル化と並列化による加速性能
使用地球模拟器进行大规模蛋白质模拟:通过矢量化和并行化实现加速性能
Large Scale Simulations of Proteins on the Earth Simulator : Acceleration Performance by Vectorization and Parallelization
地球模拟器上蛋白质的大规模模拟:矢量化和并行化的加速性能
{{ item.title }}
{{ item.translation_title }}
  • DOI:
    {{ item.doi }}
  • 发表时间:
    {{ item.publish_year }}
  • 期刊:
  • 影响因子:
    {{ item.factor }}
  • 作者:
    {{ item.authors }}
  • 通讯作者:
    {{ item.author }}

数据更新时间:{{ journalArticles.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ monograph.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ sciAawards.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ conferencePapers.updateTime }}

{{ item.title }}
  • 作者:
    {{ item.author }}

数据更新时间:{{ patent.updateTime }}

SAITO Minoru其他文献

A STUDY ON THE SHAPE OF A STRUCTURE FOR MITIGATING THE IMPACT OF LONG-TERM HYPOXIA OCCURRING IN ALL LAYERS ON <i>TRIDENTIGER OBSCURUS</i>
缓解<i>TRIDENTIGER OBSCURUS各层长期缺氧影响的结构形状研究
COMPARISONS OF FISH DETECTION AMONG ENVIRONMENTAL DNA METABARCODING FROM THREE DIFFERENT GLASS-FIBER FILTER PORE SIZES AND CONVENTIONAL COLLECTION SURVEYS
三种不同玻璃纤维过滤器孔径的环境 DNA 宏编码与常规收集调查的鱼类检测比较

SAITO Minoru的其他文献

{{ item.title }}
{{ item.translation_title }}
  • DOI:
    {{ item.doi }}
  • 发表时间:
    {{ item.publish_year }}
  • 期刊:
  • 影响因子:
    {{ item.factor }}
  • 作者:
    {{ item.authors }}
  • 通讯作者:
    {{ item.author }}

{{ truncateString('SAITO Minoru', 18)}}的其他基金

Estimation of fishway installation sites suitable for diadromous species based on species distribution models and food web evaluation
基于物种分布模型和食物网评估估算适合产鱼鱼类的鱼道设置地点
  • 批准号:
    20K15545
  • 财政年份:
    2020
  • 资助金额:
    $ 1.6万
  • 项目类别:
    Grant-in-Aid for Early-Career Scientists
Development of odor sensors and odor sensing system mimicking biological olfactory system
模仿生物嗅觉系统的气味传感器和气味传感系统的开发
  • 批准号:
    22560348
  • 财政年份:
    2010
  • 资助金额:
    $ 1.6万
  • 项目类别:
    Grant-in-Aid for Scientific Research (C)
Large scale MD simulation studies on quaternary structural changes of hemoglobin
血红蛋白四级结构变化的大规模MD模拟研究
  • 批准号:
    20500268
  • 财政年份:
    2008
  • 资助金额:
    $ 1.6万
  • 项目类别:
    Grant-in-Aid for Scientific Research (C)
Prediction and control of base sequence recognition ability for nucleic acid binding proteins by using computer experiments.
利用计算机实验预测和控制核酸结合蛋白的碱基序列识别能力。
  • 批准号:
    14598001
  • 财政年份:
    2002
  • 资助金额:
    $ 1.6万
  • 项目类别:
    Grant-in-Aid for Scientific Research (C)
Prediction and control of protein stability using computer experiments
使用计算机实验预测和控制蛋白质稳定性
  • 批准号:
    12680650
  • 财政年份:
    2000
  • 资助金额:
    $ 1.6万
  • 项目类别:
    Grant-in-Aid for Scientific Research (C)
Comparative Scientific Research about the traditional Consciousness of Liberal Arts (jiyugakugei), Way of Arts (geido) and Six Arts (rikugei) in the East and the West
东西方传统文雅意识、艺道意识、六艺意识的比较科学研究
  • 批准号:
    10610049
  • 财政年份:
    1998
  • 资助金额:
    $ 1.6万
  • 项目类别:
    Grant-in-Aid for Scientific Research (C)

相似海外基金

Determination of atomic charge in protein molecule by electron diffraction
通过电子衍射测定蛋白质分子中的原子电荷
  • 批准号:
    20K15764
  • 财政年份:
    2020
  • 资助金额:
    $ 1.6万
  • 项目类别:
    Grant-in-Aid for Early-Career Scientists
Accurate energy evaluation at atomic level and establishing NMR chemical shifts as reliable reporters of atomic charge distributions
在原子水平上进行准确的能量评估,并建立 NMR 化学位移作为原子电荷分布的可靠报告者
  • 批准号:
    2481046
  • 财政年份:
    2020
  • 资助金额:
    $ 1.6万
  • 项目类别:
    Studentship
Atomic Charge Exchange and Stripping Reactions
原子电荷交换和剥离反应
  • 批准号:
    6930213
  • 财政年份:
    1969
  • 资助金额:
    $ 1.6万
  • 项目类别:
Atomic Charge Exchange and Stripping Reactions
原子电荷交换和剥离反应
  • 批准号:
    6800221
  • 财政年份:
    1969
  • 资助金额:
    $ 1.6万
  • 项目类别:
    Standard Grant
{{ showInfoDetail.title }}

作者:{{ showInfoDetail.author }}

知道了