Sequence and Environmental Determinants of the Protein Energy Landscape

蛋白质能量景观的序列和环境决定因素

• 批准号: 10623527
• 负责人: SUSAN MARQUSEE
• 金额: $ 38.28万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-06-01 至 2028-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10623527
• 关键词: Amino Acid Sequence; Area; Biophysics; Cells; Cellular Stress; Complex; Crowding; Data; Disease; Environment; Free Energy; Goals; Health; In Vitro; Kinetics; Link; Modification; Molecular; Molecular Conformation; Mutation; Nature; Pathology; Population; Post-Translational Protein Processing; Protein Biosynthesis; Protein Dynamics; Proteins; Quality Control; Ribosomes; Sampling; Signaling Protein; Structural Models; Structure; Technology; Testing; Tube; Variant; biophysical analysis; career; experimental study; in vivo; non-Native; protein degradation; protein folding; protein purification; proteostasis; single molecule

All proteins sample a diverse array of conformations (folded, unfolded, and excited states) with differing free energies and dynamics depending on the environmental conditions. We can now predict a structural model for the folded state given the amino acid sequence. The sequence of a protein, however, encodes much more than just this native structure – it encodes the entire energy landscape – an ensemble of conformations whose populations (energetics) and dynamics are finely tuned and critical for proper function and cellular health. A major hurdle in going from sequence to function is our lack of understanding of the non-native regions of the landscape. These high-energy conformations are important for directing the stability, dynamics and folding of a protein, and modulations of this ensemble play a role in misfolding, protein signaling, catalytic activity, and allostery. A compromised landscape, due to either changes in the cellular milieu, intrinsic genetic defects, or the cumulative effects of cellular stresses, has been linked to disruption of proteostasis, resulting in varying misfolding diseases and pathologies. Rare and transient conformations are, by their very nature, difficult to study. For decades, biophysical chemists (including the PI) have been probing these fluctuations with high-level technologies using purified proteins in a test tube. The test tube, however, is very different from the cell. In vivo, proteins live in a crowded cellular environment, subject to quality control machinery, cellular modifications and subject to non-equilibrium effects such as protein synthesis and degradation. In order to take full advantage of the wealth of detailed, quantitative biophysical data available from in vitro studies, we need to understand how cellular factors and the cellular environment modulate the energetics and dynamics. Such complex settings, however, are inaccessible to the standard toolbox used for quantitative biophysical studies. The PI is an expert in the area of protein folding and dynamics, having devoted most of her career to developing and utilizing sophisticated technologies to probe rare and transient conformations, both at the single molecule and ensemble level. This current proposal focuses on: 1) understanding how these states are modulated by features in the cell, such as co-translational folding, post-translational modifications, and 2) understanding how the dynamics of conformational changes are controlled at the sequence level. The long- term goal is a is a molecular, quantitative, and predictive understanding of the relationship between sequence and the energy landscape, together with a predictive understanding of how the environment modulates this landscape.

所有的蛋白质样品具有不同的构象（折叠，未折叠和激发态）， 自由能和动力学取决于环境条件。我们现在可以预测一个结构模型 对于给定氨基酸序列的折叠状态。然而，蛋白质的序列编码的 不仅仅是这种天然结构-它编码了整个能量景观-一种构象的集合， 种群（能量学）和动力学是微调的，对正常功能和细胞健康至关重要。一 从序列到功能的一个主要障碍是我们缺乏对非天然区域的了解。 景观这些高能构象对于指导蛋白质的稳定性、动力学和折叠是重要的。 蛋白质，并且该整体的调节在错误折叠、蛋白质信号传导、催化活性和 变构一个妥协的景观，由于细胞环境的变化，内在的遗传缺陷，或 细胞应激的累积效应与蛋白质稳态的破坏有关，导致不同的 错误折叠的疾病和病理。 罕见的和短暂的构象，就其本质而言，很难研究。几十年来，生物物理 化学家（包括PI）一直在用高水平的技术探测这些波动， 试管中的蛋白质然而，试管与细胞非常不同。在体内，蛋白质生活在一个拥挤的 细胞环境，受到质量控制机制，细胞修饰和非平衡 影响，如蛋白质的合成和降解。为了充分利用丰富的细节， 从体外研究中获得的定量生物物理数据，我们需要了解细胞因子和细胞周期是如何变化的。 细胞环境调节能量学和动力学。然而，这种复杂的环境是无法进入的， 用于定量生物物理研究的标准工具箱。 PI是蛋白质折叠和动力学领域的专家，她的大部分职业生涯都致力于 开发和利用先进的技术来探测罕见和短暂的构象，无论是在单一的 分子和系综水平。目前的建议侧重于：1）了解这些国家是如何 由细胞中的特征调节，例如共翻译折叠、翻译后修饰，和2） 了解构象变化的动力学是如何在序列水平上控制的。很长的- 术语目标是一个是分子的，定量的，和预测性的理解序列之间的关系 和能源格局，以及对环境如何调节能源格局的预测性理解 景观