title: Subdomain interactions foster the design of two protein pairs with ∼80% sequence identity but different folds.
abstract: Metamorphic proteins, including proteins with high levels of sequence identity but different folds, are exceptions to the long-standing rule-of-thumb that proteins with as little as 30% sequence identity adopt the same fold. Which topologies can be bridged by these highly identical sequences remains an open question. Here we bridge two 3-α-helix bundle proteins with two radically different folds. Using a straightforward approach, we engineered the sequences of one subdomain within maltose binding protein (MBP, α/β/α-sandwich) and another within outer surface protein A (OspA, β-sheet) to have high sequence identity (80 and 77%, respectively) with engineered variants of protein G (GA, 3-α-helix bundle). Circular dichroism and nuclear magnetic resonance spectra of all engineered variants demonstrate that they maintain their native conformations despite substantial sequence modification. Furthermore, the MBP variant (80% identical to GA) remained active. Thermodynamic analysis of numerous GA and MBP variants suggests that the key to our approach involved stabilizing the modified MBP and OspA subdomains via external interactions with neighboring substructures, indicating that subdomain interactions can stabilize alternative folds over a broad range of sequence variation. These findings suggest that it is possible to bridge one fold with many other topologies, which has implications for protein folding, evolution, and misfolding diseases.
authors.affiliation: Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland; Potomac Affinity Proteins, Rockville, Maryland. Electronic address: llporter@umd.edu.
authors.forename: Lauren L
authors.initials: LL
authors.lastname: Porter
authors.affiliation: Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland.
authors.forename: Yanan
authors.initials: Y
authors.lastname: He
authors.affiliation: Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland.
authors.forename: Yihong
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland; Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland.
authors.forename: John
authors.initials: J
authors.lastname: Orban
authors.affiliation: Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland; Potomac Affinity Proteins, Rockville, Maryland.
authors.forename: Philip N
authors.initials: PN
authors.lastname: Bryan
mesh_terms: D000954:Antigens, Surface / Q000737:chemistry* / Q000235:genetics; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000235:genetics; D001428:Bacterial Vaccines / Q000737:chemistry* / Q000235:genetics; D002942:Circular Dichroism; D008074:Lipoproteins / Q000737:chemistry* / Q000235:genetics; D058619:Maltose-Binding Proteins / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D009154:Mutation; D019906:Nuclear Magnetic Resonance, Biomolecular; D017510:Protein Folding; D055550:Protein Stability; D017433:Protein Structure, Secondary; D017386:Sequence Homology, Amino Acid; D013816:Thermodynamics
chemical_list: D000954:Antigens, Surface; D001425:Bacterial Outer Membrane Proteins; D001428:Bacterial Vaccines; D008074:Lipoproteins; D058619:Maltose-Binding Proteins; C072045:OspA protein