Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations

Torkelson, Kaylyn; Pfaendtner, Jim

doi:10.1021/acs.biomac.4c00527

Title: Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations

Journal Article · 17 September 2024 · Biomacromolecules

DOI: https://doi.org/10.1021/acs.biomac.4c00527 · OSTI ID:2512404

^[1];

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University of Washington, Seattle, WA (United States)
North Carolina State University, Raleigh, NC (United States)

Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. Here, we present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.

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Research Organization:: University of Washington, Seattle, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: SC0019288

OSTI ID:: 2512404

Journal Information:: Biomacromolecules, Journal Name: Biomacromolecules Journal Issue: 10 Vol. 25; ISSN 1525-7797

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (46)

Peptide Folding: When Simulation Meets Experiment Daura, Xavier; Gademann, Karl; Jaun, Bernhard Angewandte Chemie International Edition, Vol. 38, Issue 1-2 https://doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M	journal	January 1999
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields Vanommeslaeghe, K.; Hatcher, E.; Acharya, C. Journal of Computational Chemistry https://doi.org/10.1002/jcc.21367	journal	January 2009
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data Huang, Jing; MacKerell, Alexander D. Journal of Computational Chemistry, Vol. 34, Issue 25 https://doi.org/10.1002/jcc.23354	journal	July 2013
Development and use of an atomistic CHARMM-based forcefield for peptoid simulation Mirijanian, Dina T.; Mannige, Ranjan V.; Zuckermann, Ronald N. Journal of Computational Chemistry, Vol. 35, Issue 5 https://doi.org/10.1002/jcc.23478	journal	November 2013
A CGenFF‐based force field for simulations of peptoids with both cis and trans peptide bonds Weiser, Laura J.; Santiso, Erik E. Journal of Computational Chemistry, Vol. 40, Issue 22 https://doi.org/10.1002/jcc.25850	journal	May 2019
Peptoids and polypeptoids: biomimetic and bioinspired materials for biomedical applications Ganesh, Shimoga D.; Saha, Nabanita; Zandraa, Oyunchimeg Polymer Bulletin, Vol. 74, Issue 8 https://doi.org/10.1007/s00289-016-1902-1	journal	January 2017
VMD: Visual molecular dynamics Humphrey, William; Dalke, Andrew; Schulten, Klaus Journal of Molecular Graphics, Vol. 14, Issue 1 https://doi.org/10.1016/0263-7855(96)00018-5	journal	February 1996
Chiral N-substituted glycines can form stable helical conformations Armand, Philippe; Kirshenbaum, Kent; Falicov, Alexis Folding and Design, Vol. 2, Issue 6 https://doi.org/10.1016/S1359-0278(97)00051-5	journal	December 1997
PLUMED 2: New feathers for an old bird Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide Computer Physics Communications, Vol. 185, Issue 2 https://doi.org/10.1016/j.cpc.2013.09.018	journal	February 2014
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Abraham, Mark James; Murtola, Teemu; Schulz, Roland SoftwareX, Vol. 1-2 https://doi.org/10.1016/j.softx.2015.06.001	journal	September 2015
Design, Synthesis, Assembly, and Engineering of Peptoid Nanosheets Robertson, Ellen J.; Battigelli, Alessia; Proulx, Caroline Accounts of Chemical Research, Vol. 49, Issue 3 https://doi.org/10.1021/acs.accounts.5b00439	journal	January 2016
Hierarchical Self-Assembly Pathways of Peptoid Helices and Sheets Zhao, Mingfei; Lachowski, Kacper J.; Zhang, Shuai Biomacromolecules, Vol. 23, Issue 3 https://doi.org/10.1021/acs.biomac.1c01385	journal	January 2022
Computational and Experimental Determination of the Properties, Structure, and Stability of Peptoid Nanosheets and Nanotubes Zhao, Mingfei; Zhang, Shuai; Zheng, Renyu Biomacromolecules, Vol. 24, Issue 6 https://doi.org/10.1021/acs.biomac.3c00107	journal	May 2023
Rational Design of Novel Biomimetic Sequence-Defined Polymers for Mineralization Applications Torkelson, Kaylyn; Naser, Nada Y.; Qi, Xin Chemistry of Materials, Vol. 36, Issue 2 https://doi.org/10.1021/acs.chemmater.3c02216	journal	January 2024
Hierarchical Nanomaterials Assembled from Peptoids and Other Sequence-Defined Synthetic Polymers Li, Zhiliang; Cai, Bin; Yang, Wenchao Chemical Reviews, Vol. 121, Issue 22 https://doi.org/10.1021/acs.chemrev.1c00024	journal	August 2021
Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction Shao, Li; Ma, Jinrong; Prelesnik, Jesse L. Chemical Reviews, Vol. 122, Issue 24 https://doi.org/10.1021/acs.chemrev.2c00220	journal	October 2022
Peptoids and Polypeptoids at the Frontier of Supra- and Macromolecular Engineering Gangloff, Niklas; Ulbricht, Juliane; Lorson, Thomas Chemical Reviews, Vol. 116, Issue 4 https://doi.org/10.1021/acs.chemrev.5b00201	journal	December 2015
Using Enhanced Sampling Simulations to Study the Conformational Space of Chiral Aromatic Peptoid Monomers Jain, Rakshit Kumar; Hall, Carol K.; Santiso, Erik E. Journal of Chemical Theory and Computation, Vol. 19, Issue 24 https://doi.org/10.1021/acs.jctc.3c00803	journal	November 2023
MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids Zhao, Mingfei; Sampath, Janani; Alamdari, Sarah The Journal of Physical Chemistry B, Vol. 124, Issue 36 https://doi.org/10.1021/acs.jpcb.0c04567	journal	August 2020
Evaluating the Conformations and Dynamics of Peptoid Macrocycles Eastwood, James R. B.; Jiang, Linhai; Bonneau, Richard The Journal of Physical Chemistry B, Vol. 126, Issue 28 https://doi.org/10.1021/acs.jpcb.2c01669	journal	July 2022
Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains Alamdari, Sarah; Torkelson, Kaylyn; Wang, Xiaoqian The Journal of Physical Chemistry B, Vol. 127, Issue 27 https://doi.org/10.1021/acs.jpcb.3c01913	journal	June 2023
Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N-1-Phenylethyl Sidechains Alamdari, Sarah; Pfaendtner, Jim The Journal of Physical Chemistry B, Vol. 127, Issue 27 https://doi.org/10.1021/acs.jpcb.3c02576	journal	June 2023
Control over Conformational Landscapes of Polypeptoids by Monomer Sequence Patterning DeStefano, Audra J.; Mengel, Shawn D.; Bates, Morgan W. Macromolecules, Vol. 57, Issue 4 https://doi.org/10.1021/acs.macromol.3c02338	journal	February 2024
Sequence-Defined Synthetic Polymers for New-Generation Functional Biomaterials Deng, Zhengyu; Shi, Qiangqiang; Tan, Jiajia ACS Materials Letters, Vol. 3, Issue 9 https://doi.org/10.1021/acsmaterialslett.1c00358	journal	August 2021
Influence of Peptoid Sequence on the Mechanisms and Kinetics of 2D Assembly Yadav Schmid, Sakshi; Ma, Xiang; Hammons, Joshua A. ACS Nano, Vol. 18, Issue 4 https://doi.org/10.1021/acsnano.3c10810	journal	January 2024
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges Vanommeslaeghe, K.; Raman, E. Prabhu; MacKerell, A. D. Journal of Chemical Information and Modeling, Vol. 52, Issue 12 https://doi.org/10.1021/ci3003649	journal	November 2012
Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning Hopkins, Chad W.; Le Grand, Scott; Walker, Ross C. Journal of Chemical Theory and Computation, Vol. 11, Issue 4 https://doi.org/10.1021/ct5010406	journal	March 2015
A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1 Pietrucci, Fabio; Laio, Alessandro Journal of Chemical Theory and Computation, Vol. 5, Issue 9 https://doi.org/10.1021/ct900202f	journal	August 2009
Peptoid Oligomers with α-Chiral, Aromatic Side Chains: Effects of Chain Length on Secondary Structure Wu, Cindy W.; Sanborn, Tracy J.; Zuckermann, Ronald N. Journal of the American Chemical Society, Vol. 123, Issue 13 https://doi.org/10.1021/ja003153v	journal	April 2001
Folding a Nonbiological Polymer into a Compact Multihelical Structure Lee, Byoung-Chul; Zuckermann, Ronald N.; Dill, Ken A. Journal of the American Chemical Society, Vol. 127, Issue 31 https://doi.org/10.1021/ja0514904	journal	August 2005
New Peptidomimetic Polymers for Antifouling Surfaces Statz, Andrea R.; Meagher, Robert J.; Barron, Annelise E. Journal of the American Chemical Society, Vol. 127, Issue 22 https://doi.org/10.1021/ja0522534	journal	June 2005
Extraordinarily Robust Polyproline Type I Peptoid Helices Generated via the Incorporation of α-Chiral Aromatic N -1-Naphthylethyl Side Chains Stringer, Joseph R.; Crapster, J. Aaron; Guzei, Ilia A. Journal of the American Chemical Society, Vol. 133, Issue 39 https://doi.org/10.1021/ja204755p	journal	October 2011
A Peptoid “Antibody Surrogate” That Antagonizes VEGF Receptor 2 Activity Udugamasooriya, D. Gomika; Dineen, Sean P.; Brekken, Rolf A. Journal of the American Chemical Society, Vol. 130, Issue 17 https://doi.org/10.1021/ja711193x	journal	April 2008
Biomimetic Nanostructures: Creating a High-Affinity Zinc-Binding Site in a Folded Nonbiological Polymer Lee, Byoung-Chul; Chu, Tammy K.; Dill, Ken A. Journal of the American Chemical Society, Vol. 130, Issue 27 https://doi.org/10.1021/ja802125x	journal	July 2008
Oligo( N- aryl glycines): A New Twist on Structured Peptoids Shah, Neel H.; Butterfoss, Glenn L.; Nguyen, Khanh Journal of the American Chemical Society, Vol. 130, Issue 49 https://doi.org/10.1021/ja804580n	journal	December 2008
Homogeneous and Robust Polyproline Type I Helices from Peptoids with Nonaromatic α-Chiral Side Chains Roy, Olivier; Dumonteil, Geoffrey; Faure, Sophie Journal of the American Chemical Society, Vol. 139, Issue 38 https://doi.org/10.1021/jacs.7b07475	journal	September 2017
Impact of Hydrophobic Sequence Patterning on the Coil-to-Globule Transition of Protein-like Polymers Murnen, Hannah K.; Khokhlov, Alexei R.; Khalatur, Pavel G. Macromolecules, Vol. 45, Issue 12 https://doi.org/10.1021/ma300707t	journal	June 2012
Peptoid Polymers: A Highly Designable Bioinspired Material Sun, Jing; Zuckermann, Ronald N. ACS Nano, Vol. 7, Issue 6 https://doi.org/10.1021/nn4015714	journal	May 2013
Peptoid nanosheets exhibit a new secondary-structure motif Mannige, Ranjan V.; Haxton, Thomas K.; Proulx, Caroline Nature, Vol. 526, Issue 7573 https://doi.org/10.1038/nature15363	journal	October 2015
Promoting transparency and reproducibility in enhanced molecular simulations Nature Methods, Vol. 16, Issue 8, p. 670-673 https://doi.org/10.1038/s41592-019-0506-8	journal	July 2019
Martinoid: the peptoid martini force field Swanson, Hamish W. A.; van Teijlingen, Alexander; Lau, King Hang Aaron Physical Chemistry Chemical Physics, Vol. 26, Issue 6 https://doi.org/10.1039/D3CP05907C	journal	January 2024
Comparison of simple potential functions for simulating liquid water Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. The Journal of Chemical Physics, Vol. 79, Issue 2 https://doi.org/10.1063/1.445869	journal	July 1983
Molecular dynamics with coupling to an external bath Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F. The Journal of Chemical Physics, Vol. 81, Issue 8 https://doi.org/10.1063/1.448118	journal	October 1984
Peptoids that mimic the structure, function, and mechanism of helical antimicrobial peptides Chongsiriwatana, N. P.; Patch, J. A.; Czyzewski, A. M. Proceedings of the National Academy of Sciences, Vol. 105, Issue 8 https://doi.org/10.1073/pnas.0708254105	journal	February 2008
Sequence-specific polypeptoids: A diverse family of heteropolymers with stable secondary structure Kirshenbaum, K.; Barron, A. E.; Goldsmith, R. A. Proceedings of the National Academy of Sciences, Vol. 95, Issue 8 https://doi.org/10.1073/pnas.95.8.4303	journal	April 1998
Surface-immobilised antimicrobial peptoids Statz, Andrea R.; Park, Jong Pil; Chongsiriwatana, Nathaniel P. Biofouling, Vol. 24, Issue 6 https://doi.org/10.1080/08927010802331829	journal	August 2008

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