Deciphering structure-function relationship in large protein complexes by modeling

Ibm Thomas J. Watson Research Center, Yorktown Heights NY

Investigators

Linked publications & trials

Abstract

Project Summary Most biological systems consist of many components (proteins, RNAs) that work together in a cooperative manner to carry out specific functions, for example the ribosome for protein synthesis and the bacterial flagellar motor for locomotion. One of the most important questions in biology is how “structure determines function”. As the structural information for these complexes becomes available thanks to the recent development of high resolution techniques such as Cryo-electron microscopy and tomography, the challenge is how this structural information can be used to understand functions of these large complexes. The overall goal of this project is to address this challenge by developing structure-based models to bridge the gap between structure and function for large biological complexes. The structure-based mathematical models, which explicitly include interactions of different components in the complex based on the complex structure, will be used to study/understand the emergent dynamic properties of the complex and its input-output relationship in wildtype complex and different mutants. In the next funding period, we will focus on studying the structure, function, and dynamics of two large protein complexes that are ubiquitous in the bacteria kingdom. The first functional complex we will study is the bacterial MCP chemoreceptor cluster, which serve important cellular functions such as signal amplification and enhancing adaptation. The fine structure of the MCP cluster is solved by cryo-EM studies, which show that the core functional unit consists of 2 trimers of dimer (TOD) of the MCP receptors connected by two CheW molecules and one CheA dimer and these basic units connect with each other through interactions between CheW and CheA to form a regular two dimension lattice with six-fold symmetry. In this project, we plan to develop a model of the chemorecptor cluster that include all pair-wise interactions among the key proteins (MCP receptor, CheW, and CheA) based on the fine structure of the chemoreceptor clsuter, and use it to investigate the molecular mechanism underlying signal amplification, the functional role of the coupling protein CheW, and statistics of the stochastic switching dynamics of the MCP cluster in single cells. The second functional complex we plan to study is the bacterial flagellar motor (BFM) complex, which drives the motility and chemotaxis motion of bacteria. Recent cryo-EM studies of the BFM stator structure showed that the power generating stator unit consists of a MotB dimer surrounded by a MotA pentamer ring, which suggested a new mechanism for how proton-motive-force(PMF) is used to generate rotation of the rotor and how BFM switch between clockwise (CW) and counter clockwise (CCW) rotations. In this project, we plan to develop a structure-based model that describes the interactions between MotA and MotB in the stator unit and those between MotA and FliG subunits of the rotor as well as the proton-assisted conformational changes in the stator unit based on the stucture of the BFM complex. We will use the struture-based model to understand/explain all the relevant BFM behaviors which include the PMF-driven rotational dynamics, the CW- CCW switching dynamics, and the mechano-adaptation in BFM within the same unified modeling framework. Although we will initially focus on the MCP cluster and the BFM complex, we will look out for other opportunities in modeling functions and dynamics of other protein complexes. Throughout our study, results from our models will be compared with exsiting experimental data to guide the model development, and the predictions from our models will be tested in our collaborators’ labs to further verifiy and refine/improve them. Combined with quantitative functional measurements, the structure-based models can be used to explain expeirmental observations under different external and internal conditions within an unified structure-based framework, and they may also reveal possible new molecular mechanisms underlying the structure-function relation in large multicomponent complexes. This general approach should be applicable to study other large biomolecular complexes.