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.

Outer membrane protein design

“…The energy functions provided produce reasonable correlation for predicted vs. experimental ΔΔG values for mutations in OmpLA though the calculations produce a less strong correlation for predicted vs. experimental ΔΔG values for mutations in OmpA. [58] Finally, TmSIP which was used to stabilize β-barrels [20,23] has been updated. This computational potential is now more powerful and includes intrastrand side-chain interactions and an asymmetric membrane.…”

Coarse-Grained Protein Models and Their Applications

“…A versatile method for modeling membrane proteins is also available in the RosettaMP framework. 585 RosettaMP allows the prediction of free energy changes upon mutation, high-resolution structural refinement, protein−protein docking and assembly of symmetric protein complexes in the membrane environment.…”

Systematic evaluation of CS-Rosetta for membrane protein structure prediction with sparse NOE restraints

“…16–18 Additional details, including Rosetta commands and flag files, can be found in Supporting Information. Recently, Alford and co‐workers reported a general framework for MP modeling with Rosetta3 (RosettaMP) and applied it for structural refinement, free energy changes upon mutation, and protein‐protein docking. In the present work, we focus on the different topic of de novo structure prediction.…”