An Integrated Framework Advancing Membrane Protein Modeling and Design

Abstract

Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures. Computational tools are therefore instrumental to membrane protein structure prediction, consequently increasing our understanding of membrane protein function and their role in disease. Here, we describe a general framework facilitating membrane protein modeling and design that combines the scientific principles for membrane protein modeling with the flexible software architecture of Rosetta3. This new framework, called RosettaMP, provides a general membrane representation that interfaces with scoring, conformational sampling, and mutation routines that can be easily combined to create new protocols. To demonstrate the capabilities of this implementation, we developed four proof-of-concept applications for (1) prediction of free energy changes upon mutation; (2) high-resolution structural refinement; (3) protein-protein docking; and (4) assembly of symmetric protein complexes, all in the membrane environment. Preliminary data show that these algorithms can produce meaningful scores and structures. The data also suggest needed improvements to both sampling routines and score functions. Importantly, the applications collectively demonstrate the potential of combining the flexible nature of RosettaMP with the power of Rosetta algorithms to facilitate membrane protein modeling and design.

Author Summary

Over 30% of the human proteome consists of proteins embedded in biological membranes. These proteins are critical in many processes such as transport of materials in and out of the cell and transmitting signals to other cells in the body. They are implicated in a large number of diseases; in fact, they are targeted by over 50% of pharmaceutical drugs on the market. Since the membrane environment makes experimental structure determination extremely difficult, there is a need for alternative, computational approaches. Here, we describe a new framework, RosettaMP, for computational modeling and design of membrane protein structures, integrated in the Rosetta3 software suite. This framework includes a set of tools for representing the membrane bilayer, moving the protein, altering its sequence, and estimating free energies. We demonstrate tools to predict the effects of mutations, refine atomic details of protein structures, simulate protein binding, and assemble symmetric complexes, all in the membrane bilayer. Taken together, these applications demonstrate the potential of RosettaMP to facilitate membrane protein structure prediction and design, enabling us to understand the function of these proteins and their role in human disease.