Multiscale Simulations of Biological Systems and Processes

生物系统和过程的多尺度模拟

• 批准号: 10709506
• 负责人: ARIEH WARSHEL
• 金额: $ 66.04万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-05-01 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10709506
• 关键词: ATP phosphohydrolase; Active Sites; Biochemical Reaction; Biological Process; COVID-19 pandemic; Catalysis; Cells; Charge; Clustered Regularly Interspaced Short Palindromic Repeats; Collaborations; Complex; Computer Assisted; Computer Simulation; Computing Methodologies; Coupled; Development; Directed Molecular Evolution; Disease; Drug Design; Drug resistance; Electrodes; Electrolytes; Electron Transport; Entropy; Enzymes; Experimental Designs; Free Energy; G-Protein-Coupled Receptors; Grain; Ion Channel Gating; Ions; Life; Medical; Membrane; Methods; Microscopic; Modeling; Molecular; Pharmaceutical Preparations; Process; Proteins; Protons; Structure; Surface; System; biological systems; complex biological systems; cytochrome c oxidase; design; experimental group; experimental study; fighting; improved; multi-scale modeling; screening; simulation; trend; voltage

Project Summary In order to advance the understanding of life processes at the molecular level, we developed multiscale computer simulations that can treat complex biological systems. We intend to apply such strategies to systems which are to important medical problems. Our proposed projects are listed below. A.1 Enzymatic Processes: By exploiting our advances in multiscale modeling, we intend to progress in the following directions: (a) Quantifying computer-aided enzyme design by: (i) reproducing the observed trend in experiments of directed evolution using automatic configuration generator coupled with EVB simulations; (ii) reproducing the catalytic activity of experimentally designed enzymes; (iii) improving the action of promiscuous enzymes; (iv) destroying and rebuilding active sites. Our studies will be done in collaboration with key experimental groups. (b) Continuing to advance the quantitative computational methods, including: (i) using our PD QM(ai)/MM method in for evaluating the ab initio free energy surfaces of enzymatic reactions; (ii) Advancing a maximum entropy approach for fast screening (iii) Quantifying the relationship between folding and catalysis; (c) Conducting studies on important classes of enzymes; (d) Exploring the relations of our findings to medical problems such as the Covid-19 pandemic, drug resistance and other topics like CRISPR. A.2 Multiscale Modeling of the energetics and functions of complex biological systems: Basic functions of living cells are underpinned by proteins that guide the transport of electrons, protons, and ions. Thus, it is crucial to quantitatively explore and exploit the structure-function correlations using computer simulation approaches. We have made a major progress in developing microscopic and coarse grained (CG) approaches for such systems, and we will advance them in the following directions: (a) Simulating the proton transfer (PTR) gating mechanism of cytochrome c oxidase (CcO) and extending our recent studies of FO-ATPase. (b) Exploiting our advances in modeling voltage-gated ion channels for the following purposes: (i) to quantify the interplay between the electrode potential and the protein/membrane energy landscape, (ii) to reproduce the gating voltage and the subsequent ion current and its selectivity using both CG and explicit MC electrolyte models, (iii) to simulating the action of GPCRs and transporters by CG approach, (iv) to explore the relations between our finding and various diseases.

项目摘要 为了在分子水平上推进对生命过程的理解，我们发展了多尺度计算机 可以处理复杂生物系统的模拟。我们打算将这些策略应用于以下系统 重要的医疗问题。我们建议的项目如下所示。 A.1酶过程：通过利用我们在多尺度建模方面的进展，我们打算在 以下方向：(A)量化计算机辅助酶设计：(I)重现观察到的趋势 利用自动配置生成器和EVB模拟相结合的定向进化实验；(Ii) 重现实验设计的酶的催化活性；(Iii)改善杂乱的作用 酶；(Iv)破坏和重建活性部位。我们的研究将与KEY合作完成 试验组。(B)继续推进量化计算方法，包括：(I)使用我们的 酶反应从头算自由能面的Pd QM(Ai)/MM方法；(Ii)进展 快速筛选的最大熵方法(III)量化折叠与催化之间的关系； (C)对重要类别的酶进行研究；。(D)探索我们的研究结果与医学的关系。 新冠肺炎疫情、抗药性等问题以及CRISPR等话题。 A.2复杂生物系统的能量和功能的多尺度建模：基本功能 活细胞的基础是指导电子、质子和离子运输的蛋白质。因此，它是 利用计算机模拟定量探索和开发结构-功能相关性的关键 接近了。我们在开发微观和粗粒度(CG)方法方面取得了重大进展 对于这类体系，我们将朝着以下方向发展：(A)模拟质子转移 细胞色素c氧化酶(CcO)的门控机制和我们最近对FO-ATPase的研究。(B)剥削 我们在为以下目的建模电压门控离子通道方面的进展：(I)量化相互作用 在电极电位和蛋白质/膜能量格局之间，(Ii)重现门控电压 以及使用CG和显式MC电解液模型的后续离子电流及其选择性，(Iii)到 用CG方法模拟GPCRs和转运体的作用，(Iv)探索我们的 以及各种疾病的发现。

项目成果

Enhancing computational enzyme design by a maximum entropy strategy.

• DOI: 10.1073/pnas.2122355119
• 发表时间: 2022-02-15
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1
• 作者: Xie WJ;Asadi M;Warshel A
• 通讯作者: Warshel A

Electrostatic influence on IL-1 transport through the GSDMD pore.

• DOI: 10.1073/pnas.2120287119
• 发表时间: 2022-02-08
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1
• 作者: Xie WJ;Xia S;Warshel A;Wu H
• 通讯作者: Wu H

Enhancing Luciferase Activity and Stability through Generative Modeling of Natural Enzyme Sequences.

通过天然酶序列的生成模型增强荧光素酶活性和稳定性。

• DOI: 10.1101/2023.09.18.558367
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Xie,WenJun;Liu,Dangliang;Wang,Xiaoya;Zhang,Aoxuan;Wei,Qijia;Nandi,Ashim;Dong,Suwei;Warshel,Arieh
• 通讯作者: Warshel,Arieh

ZnT2 is an electroneutral proton-coupled vesicular antiporter displaying an apparent stoichiometry of two protons per zinc ion

• DOI: 10.1371/journal.pcbi.1006882
• 发表时间: 2019-03-01
• 期刊: PLOS COMPUTATIONAL BIOLOGY
• 影响因子: 4.3
• 作者: Golan, Yarden;Alhadeff, Raphael;Assaraf, Yehuda G.
• 通讯作者: Assaraf, Yehuda G.

Natural Evolution Provides Strong Hints about Laboratory Evolution of Designer Enzymes.

• DOI: 10.1073/pnas.2207904119
• 发表时间: 2022-08-02
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1