Conformations of peptoids in nanosheets result from the interplay of backbone energetics and intermolecular interactions
The conformations adopted by the molecular constituents of a supramolecular assembly influence its large-scale order. At the same time, the interactions made in assemblies by molecules can influence their conformations. Here we study this interplay in extended flat nanosheets made from nonnatural se...
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| Published in | Proceedings of the National Academy of Sciences - PNAS Vol. 115; no. 22; pp. 5647 - 5651 |
|---|---|
| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
National Academy of Sciences
29.05.2018
Proceedings of the National Academy of Sciences |
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| Abstract | The conformations adopted by the molecular constituents of a supramolecular assembly influence its large-scale order. At the same time, the interactions made in assemblies by molecules can influence their conformations. Here we study this interplay in extended flat nanosheets made from nonnatural sequence-specific peptoid polymers. Nanosheets exist because individual polymers can be linear and untwisted, by virtue of polymer backbone elements adopting alternating rotational states whose twists oppose and cancel. Using molecular dynamics and quantum mechanical simulations, together with experimental data, we explore the design space of flat nanostructures built from peptoids. We show that several sets of peptoid backbone conformations are consistent with their being linear, but the specific combination observed in experiment is determined by a combination of backbone energetics and the interactions made within the nanosheet. Our results provide a molecular model of the peptoid nanosheet consistent with all available experimental data and show that its structure results from a combination of intraand intermolecular interactions. |
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| AbstractList | The conformations adopted by the molecular constituents of a supramolecular assembly influence its large-scale order. At the same time, the interactions made in assemblies by molecules can influence their conformations. Here we study this interplay in extended flat nanosheets made from nonnatural sequence-specific peptoid polymers. Nanosheets exist because individual polymers can be linear and untwisted, by virtue of polymer backbone elements adopting alternating rotational states whose twists oppose and cancel. Using molecular dynamics and quantum mechanical simulations, together with experimental data, we explore the design space of flat nanostructures built from peptoids. We show that several sets of peptoid backbone conformations are consistent with their being linear, but the specific combination observed in experiment is determined by a combination of backbone energetics and the interactions made within the nanosheet. Our results provide a molecular model of the peptoid nanosheet consistent with all available experimental data and show that its structure results from a combination of intraand intermolecular interactions. The conformations adopted by the molecular constituents of a supramolecular assembly influence its large-scale order. At the same time, the interactions made in assemblies by molecules can influence their conformations. Here we study this interplay in extended flat nanosheets made from nonnatural sequence-specific peptoid polymers. Nanosheets exist because individual polymers can be linear and untwisted, by virtue of polymer backbone elements adopting alternating rotational states whose twists oppose and cancel. Using molecular dynamics and quantum mechanical simulations, together with experimental data, we explore the design space of flat nanostructures built from peptoids. We show that several sets of peptoid backbone conformations are consistent with their being linear, but the specific combination observed in experiment is determined by a combination of backbone energetics and the interactions made within the nanosheet. Our results provide a molecular model of the peptoid nanosheet consistent with all available experimental data and show that its structure results from a combination of intra- and intermolecular interactions. Significance Commonly observed secondary structures of proteins, such as α -helices and β -sheets, are built from a trans- amide backbone with residues sampling a single region of the Ramachandran plot. Here we report a secondary structure displayed by biomimetic peptoid polymers in which the backbone exhibits the cis conformation and alternating residues display rotational states of opposed (pseudo)chirality. This structure is linear and untwisted and enables strands to pack densely into extended bilayer nanosheets. The conformations adopted by the molecular constituents of a supramolecular assembly influence its large-scale order. At the same time, the interactions made in assemblies by molecules can influence their conformations. Here we study this interplay in extended flat nanosheets made from nonnatural sequence-specific peptoid polymers. Nanosheets exist because individual polymers can be linear and untwisted, by virtue of polymer backbone elements adopting alternating rotational states whose twists oppose and cancel. Using molecular dynamics and quantum mechanical simulations, together with experimental data, we explore the design space of flat nanostructures built from peptoids. We show that several sets of peptoid backbone conformations are consistent with their being linear, but the specific combination observed in experiment is determined by a combination of backbone energetics and the interactions made within the nanosheet. Our results provide a molecular model of the peptoid nanosheet consistent with all available experimental data and show that its structure results from a combination of intra- and intermolecular interactions. Commonly observed secondary structures of proteins, such as α -helices and β -sheets, are built from a trans- amide backbone with residues sampling a single region of the Ramachandran plot. Here we report a secondary structure displayed by biomimetic peptoid polymers in which the backbone exhibits the cis conformation and alternating residues display rotational states of opposed (pseudo)chirality. This structure is linear and untwisted and enables strands to pack densely into extended bilayer nanosheets. The conformations adopted by the molecular constituents of a supramolecular assembly influence its large-scale order. At the same time, the interactions made in assemblies by molecules can influence their conformations. Here we study this interplay in extended flat nanosheets made from nonnatural sequence-specific peptoid polymers. Nanosheets exist because individual polymers can be linear and untwisted, by virtue of polymer backbone elements adopting alternating rotational states whose twists oppose and cancel. Using molecular dynamics and quantum mechanical simulations, together with experimental data, we explore the design space of flat nanostructures built from peptoids. We show that several sets of peptoid backbone conformations are consistent with their being linear, but the specific combination observed in experiment is determined by a combination of backbone energetics and the interactions made within the nanosheet. Our results provide a molecular model of the peptoid nanosheet consistent with all available experimental data and show that its structure results from a combination of intra- and intermolecular interactions. |
| Author | Edison, John R. Hochbaum, Allon I. Hudson, Benjamin C. Spencer, Ryan K. Zuckermann, Ronald N. Paravastu, Anant K. Whitelam, Stephen Butterfoss, Glenn L. |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29760077$$D View this record in MEDLINE/PubMed https://www.osti.gov/biblio/1437093$$D View this record in Osti.gov |
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| Copyright | Volumes 1–89 and 106–114, copyright as a collective work only; author(s) retains copyright to individual articles Copyright National Academy of Sciences May 29, 2018 2018 |
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| Keywords | peptoid secondary structure biomimetic sequence-specific polymers cis-amide 2D supramolecular assembly |
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| Snippet | The conformations adopted by the molecular constituents of a supramolecular assembly influence its large-scale order. At the same time, the interactions made... Significance Commonly observed secondary structures of proteins, such as α -helices and β -sheets, are built from a trans- amide backbone with residues... Commonly observed secondary structures of proteins, such as α -helices and β -sheets, are built from a trans- amide backbone with residues sampling a single... |
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| SubjectTerms | Backbone BASIC BIOLOGICAL SCIENCES Bioenergetics Biological Sciences Biomimetic Materials - chemistry Computer simulation Experimental data MATERIALS SCIENCE Molecular biology Molecular dynamics Molecular Dynamics Simulation Molecular structure Nanosheets Nanostructure Nanostructures - chemistry Nanostructures - ultrastructure Peptides Peptoids - chemistry Physical Sciences Polymers Protein Structure, Secondary Quantum mechanics Quantum physics Rotational states |
| Title | Conformations of peptoids in nanosheets result from the interplay of backbone energetics and intermolecular interactions |
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