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Ruan B, He Y, Chen Y, Choi EJ, Chen Y, Motabar D, Solomon T, Simmerman R, Kauffman T, Gallagher DT, Orban J, Bryan PN. Design and characterization of a protein fold switching network. Nat Commun 2023; 14:431. [PMID: 36702827 PMCID: PMC9879998 DOI: 10.1038/s41467-023-36065-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/13/2023] [Indexed: 01/27/2023] Open
Abstract
To better understand how amino acid sequence encodes protein structure, we engineered mutational pathways that connect three common folds (3α, β-grasp, and α/β-plait). The structures of proteins at high sequence-identity intersections in the pathways (nodes) were determined using NMR spectroscopy and analyzed for stability and function. To generate nodes, the amino acid sequence encoding a smaller fold is embedded in the structure of an ~50% larger fold and a new sequence compatible with two sets of native interactions is designed. This generates protein pairs with a 3α or β-grasp fold in the smaller form but an α/β-plait fold in the larger form. Further, embedding smaller antagonistic folds creates critical states in the larger folds such that single amino acid substitutions can switch both their fold and function. The results help explain the underlying ambiguity in the protein folding code and show that new protein structures can evolve via abrupt fold switching.
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Affiliation(s)
- Biao Ruan
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
| | - Yanan He
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - Yingwei Chen
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
| | - Eun Jung Choi
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
| | - Yihong Chen
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - Dana Motabar
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA.,Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Tsega Solomon
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.,Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Richard Simmerman
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
| | - Thomas Kauffman
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.,Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - D Travis Gallagher
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.,National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - John Orban
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA. .,Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
| | - Philip N Bryan
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA. .,Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.
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A malaria parasite subtilisin propeptide-like protein is a potent inhibitor of the egress protease SUB1. Biochem J 2020; 477:525-540. [PMID: 31942933 PMCID: PMC6993865 DOI: 10.1042/bcj20190918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/23/2022]
Abstract
Subtilisin-like serine peptidases (subtilases) play important roles in the life cycle of many organisms, including the protozoan parasites that are the causative agent of malaria, Plasmodium spp. As with other peptidases, subtilase proteolytic activity has to be tightly regulated in order to prevent potentially deleterious uncontrolled protein degradation. Maturation of most subtilases requires the presence of an N-terminal propeptide that facilitates folding of the catalytic domain. Following its proteolytic cleavage, the propeptide acts as a transient, tightly bound inhibitor until its eventual complete removal to generate active protease. Here we report the identification of a stand-alone malaria parasite propeptide-like protein, called SUB1-ProM, encoded by a conserved gene that lies in a highly syntenic locus adjacent to three of the four subtilisin-like genes in the Plasmodium genome. Template-based modelling and ab initio structure prediction showed that the SUB1-ProM core structure is most similar to the X-ray crystal structure of the propeptide of SUB1, an essential parasite subtilase that is discharged into the parasitophorous vacuole (PV) to trigger parasite release (egress) from infected host cells. Recombinant Plasmodium falciparum SUB1-ProM was found to be a fast-binding, potent inhibitor of P. falciparum SUB1, but not of the only other essential blood-stage parasite subtilase, SUB2, or of other proteases examined. Mass-spectrometry and immunofluorescence showed that SUB1-ProM is expressed in the PV of blood stage P. falciparum, where it may act as an endogenous inhibitor to regulate SUB1 activity in the parasite.
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Serine Proteases of Malaria Parasite Plasmodium falciparum: Potential as Antimalarial Drug Targets. Interdiscip Perspect Infect Dis 2014; 2014:453186. [PMID: 24799897 PMCID: PMC3988940 DOI: 10.1155/2014/453186] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/02/2014] [Accepted: 01/07/2014] [Indexed: 01/08/2023] Open
Abstract
Malaria is a major global parasitic disease and a cause of enormous mortality and morbidity. Widespread drug resistance against currently available antimalarials warrants the identification of novel drug targets and development of new drugs. Malarial proteases are a group of molecules that serve as potential drug targets because of their essentiality for parasite life cycle stages and feasibility of designing specific inhibitors against them. Proteases belonging to various mechanistic classes are found in P. falciparum, of which serine proteases are of particular interest due to their involvement in parasite-specific processes of egress and invasion. In P. falciparum, a number of serine proteases belonging to chymotrypsin, subtilisin, and rhomboid clans are found. This review focuses on the potential of P. falciparum serine proteases as antimalarial drug targets.
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