Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition
Abstract The use of designed antimicrobial peptides as drugs has been impeded by the absence of simple sequence-structure–function relationships and design rules. The likely cause is that many of these peptides permeabilize membranes via highly disordered, heterogeneous mechanisms, fo...
| Main Authors: | , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
Springer US
2021
|
| Online Access: | https://hdl.handle.net/1721.1/132037 |
| _version_ | 1811084823818665984 |
|---|---|
| author | Chen, Charles H. Starr, Charles G. Guha, Shantanu Wimley, William C. Ulmschneider, Martin B. Ulmschneider, Jakob P. |
| author2 | Massachusetts Institute of Technology. Synthetic Biology Center |
| author_facet | Massachusetts Institute of Technology. Synthetic Biology Center Chen, Charles H. Starr, Charles G. Guha, Shantanu Wimley, William C. Ulmschneider, Martin B. Ulmschneider, Jakob P. |
| author_sort | Chen, Charles H. |
| collection | MIT |
| description | Abstract
The use of designed antimicrobial peptides as drugs has been impeded by the absence of simple sequence-structure–function relationships and design rules. The likely cause is that many of these peptides permeabilize membranes via highly disordered, heterogeneous mechanisms, forming aggregates without well-defined tertiary or secondary structure. We suggest that the combination of high-throughput library screening with atomistic computer simulations can successfully address this challenge by tuning a previously developed general pore-forming peptide into a selective pore-former for different lipid types. A library of 2916 peptides was designed based on the LDKA template. The library peptides were synthesized and screened using a high-throughput orthogonal vesicle leakage assay. Dyes of different sizes were entrapped inside vesicles with varying lipid composition to simultaneously screen for both pore size and affinity for negatively charged and neutral lipid membranes. From this screen, nine different LDKA variants that have unique activity were selected, sequenced, synthesized, and characterized. Despite the minor sequence changes, each of these peptides has unique functional properties, forming either small or large pores and being selective for either neutral or anionic lipid bilayers. Long-scale, unbiased atomistic molecular dynamics (MD) simulations directly reveal that rather than rigid, well-defined pores, these peptides can form a large repertoire of functional dynamic and heterogeneous aggregates, strongly affected by single mutations. Predicting the propensity to aggregate and assemble in a given environment from sequence alone holds the key to functional prediction of membrane permeabilization.
Graphic Abstract |
| first_indexed | 2024-09-23T12:57:50Z |
| format | Article |
| id | mit-1721.1/132037 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T12:57:50Z |
| publishDate | 2021 |
| publisher | Springer US |
| record_format | dspace |
| spelling | mit-1721.1/1320372023-12-12T16:09:09Z Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition Chen, Charles H. Starr, Charles G. Guha, Shantanu Wimley, William C. Ulmschneider, Martin B. Ulmschneider, Jakob P. Massachusetts Institute of Technology. Synthetic Biology Center Massachusetts Institute of Technology. Research Laboratory of Electronics Abstract The use of designed antimicrobial peptides as drugs has been impeded by the absence of simple sequence-structure–function relationships and design rules. The likely cause is that many of these peptides permeabilize membranes via highly disordered, heterogeneous mechanisms, forming aggregates without well-defined tertiary or secondary structure. We suggest that the combination of high-throughput library screening with atomistic computer simulations can successfully address this challenge by tuning a previously developed general pore-forming peptide into a selective pore-former for different lipid types. A library of 2916 peptides was designed based on the LDKA template. The library peptides were synthesized and screened using a high-throughput orthogonal vesicle leakage assay. Dyes of different sizes were entrapped inside vesicles with varying lipid composition to simultaneously screen for both pore size and affinity for negatively charged and neutral lipid membranes. From this screen, nine different LDKA variants that have unique activity were selected, sequenced, synthesized, and characterized. Despite the minor sequence changes, each of these peptides has unique functional properties, forming either small or large pores and being selective for either neutral or anionic lipid bilayers. Long-scale, unbiased atomistic molecular dynamics (MD) simulations directly reveal that rather than rigid, well-defined pores, these peptides can form a large repertoire of functional dynamic and heterogeneous aggregates, strongly affected by single mutations. Predicting the propensity to aggregate and assemble in a given environment from sequence alone holds the key to functional prediction of membrane permeabilization. Graphic Abstract 2021-09-20T17:41:35Z 2021-09-20T17:41:35Z 2021-02-10 2021-03-07T05:40:22Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/132037 en https://doi.org/10.1007/s00232-021-00174-1 Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. The Author(s), under exclusive licence to Springer Science+Business Media, LLC part of Springer Nature application/pdf Springer US Springer US |
| spellingShingle | Chen, Charles H. Starr, Charles G. Guha, Shantanu Wimley, William C. Ulmschneider, Martin B. Ulmschneider, Jakob P. Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition |
| title | Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition |
| title_full | Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition |
| title_fullStr | Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition |
| title_full_unstemmed | Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition |
| title_short | Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition |
| title_sort | tuning of a membrane perforating antimicrobial peptide to selectively target membranes of different lipid composition |
| url | https://hdl.handle.net/1721.1/132037 |
| work_keys_str_mv | AT chencharlesh tuningofamembraneperforatingantimicrobialpeptidetoselectivelytargetmembranesofdifferentlipidcomposition AT starrcharlesg tuningofamembraneperforatingantimicrobialpeptidetoselectivelytargetmembranesofdifferentlipidcomposition AT guhashantanu tuningofamembraneperforatingantimicrobialpeptidetoselectivelytargetmembranesofdifferentlipidcomposition AT wimleywilliamc tuningofamembraneperforatingantimicrobialpeptidetoselectivelytargetmembranesofdifferentlipidcomposition AT ulmschneidermartinb tuningofamembraneperforatingantimicrobialpeptidetoselectivelytargetmembranesofdifferentlipidcomposition AT ulmschneiderjakobp tuningofamembraneperforatingantimicrobialpeptidetoselectivelytargetmembranesofdifferentlipidcomposition |