Computational design of a modular protein sense-response system

Abstract

Sensing and responding to signals is a fundamental ability of living systems, but despite substantial progress in the computational design of new protein structures, there is no general approach for engineering arbitrary new protein sensors. Here, we describe a generalizable computational strategy for designing sensor-actuator proteins by building binding sites de novo into heterodimeric protein-protein interfaces and coupling ligand sensing to modular actuation through split reporters. Using this approach, we designed protein sensors that respond to farnesyl pyrophosphate, a metabolic intermediate in the production of valuable compounds. The sensors are functional in vitro and in cells, and the crystal structure of the engineered binding site closely matches the design model. Our computational design strategy opens broad avenues to link biological outputs to new signals.

Amino acid interacting network in the receptor-binding domain of SARS-CoV-2 spike protein

“…This new concept and method of AABP for interaction between amino acids is clearly one step beyond the simpler interatomic interactions in proteins. 12 More importantly, the method can be readily applied to and play a crucial role in large-scale computation for protein design [34][35][36][37] and understanding the mutation process [38][39][40] leading to effective vaccine and therapeutic drug design [41][42][43] in combating COVID-19 pandemics. This is because such urgent research topics require the information on the details of the interaction under different environments, involving a single amino acid or clusters of multiple amino acids.…”

Driving Protein Conformational Cycles in Physiology and Disease: “Frustrated” Amino Acid Interaction Networks Define Dynamic Energy Landscapes

“…[ 23,53,54 ] Such proteins could be used for a multitude of purposes including as biosensors and biocatalysts. [ 55,56 ] Within this dynamic energy landscape framework, it is not just important to design a thermostable 3Dl structure, but it will also be important to control desired fluctuations away from the structure. Progress is being made in this area.…”

New computational protein design methods for de novo small molecule binding sites

“…QacR variants were experimentally validated in an in vitro transcription-translation system where two designs possessed sensitivity to vanillin. Design methods in the Rosetta Macromolecular Modeling Suite [ 18 ] such as the RosettaMatch application [ 19 ] have been used to reengineer proteins to bind digoxigenin [ 20 ], fentanyl [ 21 ], and 17a-hydroxylprogesterone [ 4 ] and to create a new binding site for the metabolic intermediate farnesyl pyrophosphate in a protein-protein interface to build synthetic sense/response systems [ 22 ]. The Rotamer Interaction Field algorithm was used to place a binding site for (Z)-4-(3,5- difluoro-4-hydroxybenzylidene)-1,2-dimethyl-1H-imidazol-5(4H)-one (DFHBI) into the cavity of a de novo designed beta-barrel [ 23 ].…”

“…Despite previously demonstrated success of these protocols [ 20 , 22 ], there are still several limitations that prevent generalizable de novo design of ligand binding sites. First, binding site geometries need to be predefined for a target ligand.…”