Reweighting Methods for Elucidation of Conformational Ensembles of Proteins

Abstract

This dissertation explores the application and advancement of reweighting methods in computational biology, focusing on increasing their ability to provide reliable solutions for understanding the conformational states of biological systems. We begin by introducing reweighting methods, discussing their different categories, available implementations, and the various types of input data they use. We review applications of these methods in biological systems, showing their use in understanding complex molecular systems and we discuss the limitations and challenges faced by reweighting methods, setting the foundation for the methodology proposed in this work.The second chapter outlines the methodology we developed to increase the reliability of reweighting methods. An important contribution of this work is the incorporation of multiple experimental data to improve the robustness of the solutions. This methodology is applied to the ubiquitin dimer system, where we used two reweighting methods, SES and BME, in combination with a variety of experimental data: PCS, RDC, PRE, Diamagnetic RDC, and SANS. The combination of different data types increases the accuracy of the results, with each dataset deconvoluting specific information of the system. We fully discuss the limitations of each type of experimental data and the importance of their proper integration. The third chapter shifts focus to the application of reweighting methods using only SANS data, which is often the most accessible experimental data for many systems. This section details how SANS data can reliably be used to predict the pH dependence of conformations in the ubiquitin dimer and explores the potential for studying larger systems, such as trimer and tetramer ubiquitin. Additionally, we address the critical issue of ensemble generation, proposing methods to assess and ensure that the initial ensemble adequately covers the conformational space. Finally, we suggest future directions for reweighting methods, including their integration with molecular dynamics, emphasizing the potential for these approaches to transform the study of complex biological systems.