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Boone K, Cloyd AK, Derakovic E, Spencer P, Tamerler C. Designing Collagen-Binding Peptide with Enhanced Properties Using Hydropathic Free Energy Predictions. APPLIED SCIENCES (BASEL, SWITZERLAND) 2023; 13:3342. [PMID: 38037603 PMCID: PMC10686322 DOI: 10.3390/app13053342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Collagen is fundamental to a vast diversity of health functions and potential therapeutics. Short peptides targeting collagen are attractive for designing modular systems for site-specific delivery of bioactive agents. Characterization of peptide-protein binding involves a larger number of potential interactions that require screening methods to target physiological conditions. We build a hydropathy-based free energy estimation tool which allows quick evaluation of peptides binding to collagen. Previous studies showed that pH plays a significant role in collagen structure and stability. Our design tool enables probing peptides for their collagen-binding property across multiple pH conditions. We explored binding features of currently known collagen-binding peptides, collagen type I alpha chain 2 sense peptide (TKKTLRT) and decorin LRR-10 (LRELHLNNN). Based on these analyzes, we engineered a collagen-binding peptide with enhanced properties across a large pH range in contrast to LRR-10 pH dependence. To validate our predictions, we used a quantum-dots-based binding assay to compare the coverage of the peptides on type I collagen. The predicted peptide resulted in improved collagen binding. Hydropathy of the peptide-protein pair is a promising approach to finding compatible pairings with minimal use of computational resources, and our method allows for quick evaluation of peptides for binding to other proteins. Overall, the free-energy-based tool provides an alternative computational screening approach that impacts protein interaction search methods.
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Affiliation(s)
- Kyle Boone
- Institute for Bioengineering Research, University of Kansas, 5109 Learned Hall 1530 W, 15th Street, Lawrence, KS 66045-7609, USA
- Department of Mechanical Engineering, University of Kansas, Lawrence, KS 66045-7609, USA
| | - Aya Kirahm Cloyd
- Institute for Bioengineering Research, University of Kansas, 5109 Learned Hall 1530 W, 15th Street, Lawrence, KS 66045-7609, USA
- Bioengineering Program, University of Kansas, 1132 Learned Hall 1530 W, 15th Street, Lawrence, KS 66045-7609, USA
| | - Emina Derakovic
- Department of Mechanical Engineering, University of Kansas, Lawrence, KS 66045-7609, USA
| | - Paulette Spencer
- Institute for Bioengineering Research, University of Kansas, 5109 Learned Hall 1530 W, 15th Street, Lawrence, KS 66045-7609, USA
- Department of Mechanical Engineering, University of Kansas, Lawrence, KS 66045-7609, USA
- Bioengineering Program, University of Kansas, 1132 Learned Hall 1530 W, 15th Street, Lawrence, KS 66045-7609, USA
| | - Candan Tamerler
- Institute for Bioengineering Research, University of Kansas, 5109 Learned Hall 1530 W, 15th Street, Lawrence, KS 66045-7609, USA
- Department of Mechanical Engineering, University of Kansas, Lawrence, KS 66045-7609, USA
- Bioengineering Program, University of Kansas, 1132 Learned Hall 1530 W, 15th Street, Lawrence, KS 66045-7609, USA
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Miller AD. Sense–antisense (complementary) peptide interactions and the proteomic code; potential opportunities in biology and pharmaceutical science. Expert Opin Biol Ther 2015; 15:245-67. [DOI: 10.1517/14712598.2015.983069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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