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Simulation of Multi-Protein systems

多蛋白系统的模拟

基本信息

批准号：
10491046
负责人：
Dmytro Kozakov
金额：
$ 31.08万
依托单位：
STATE UNIVERSITY NEW YORK STONY BROOK
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-09-20 至 2025-08-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10491046
关键词：
3-Dimensional Algorithms Alzheimer&apos s disease model Aprotinin Area Award Binding Biological Models Biological Products Bovine Serum Albumin Capsid Cell physiology Cells Cellular biology Collaborations Complex Crowding Data Development Disease Erythrocytes Evaluable Disease Evaluation Formulation Fourier Transform Goals Grant Hemoglobin Image Compression Liquid substance Mass Spectrum Analysis Memory Methods Minor Modeling Molecular Conformation Multiprotein Complexes Mycoplasma genitalium National Institute of General Medical Sciences Nucleosome Core Particle Pathway interactions Peptides Performance Pharmaceutical Preparations Property Protein Conformation Proteins Resolution Rest Rotation Sampling Speed Structure Sum System Validation Variant Writing base experimental group experimental study flexibility gamma-Crystallins improved innovation insight method development molecular assembly/self assembly molecular modeling mouse model multicatalytic endopeptidase complex novel strategies particle protein aggregation self assembly simulation therapeutic development

项目摘要

Simulation of large multi-component molecular assemblies with atomistic details is an important step toward understanding cellular processes. The goal of this proposal is to develop an efficient method for the simulation of multi-protein systems consisting of many copies of a few types of proteins, each in a number of discrete conformations. The basis for our approach is the observation that the interaction energy between two proteins (or discrete protein conformations within an ensemble) – can be efficiently calculated over the entire rotational-translational space using the fast Manifold Fourier transform (FMFT) correlation approach. Given any conformation of a complex multi-particle system, its energy can be easily obtained by summing the pairwise interaction energies extracted from the lookup tables. The key innovation to efficiently implement this method is our ability to compress and store the interaction energy lookup tables in memory using wavelet sets. We will apply the method in two application. The first is simulation of multi-protein assemblies and their association pathways, possibly in conjunction with low resolution Mass Spectrometry (MS) and EM data, providing mechanistic insight into cellular function. The second is simulation of protein aggregation and crowding, which is important for the fundamental understanding of cell biology and therapeutic development.

具有原子细节的大型多组分分子组装的模拟是一个重要的研究方向