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Piskorz T, Perez-Chirinos L, Qiao B, Sasselli IR. Tips and Tricks in the Modeling of Supramolecular Peptide Assemblies. ACS OMEGA 2024; 9:31254-31273. [PMID: 39072142 PMCID: PMC11270692 DOI: 10.1021/acsomega.4c02628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/30/2024]
Abstract
Supramolecular peptide assemblies (SPAs) hold promise as materials for nanotechnology and biomedicine. Although their investigation often entails adapting experimental techniques from their protein counterparts, SPAs are fundamentally distinct from proteins, posing unique challenges for their study. Computational methods have emerged as indispensable tools for gaining deeper insights into SPA structures at the molecular level, surpassing the limitations of experimental techniques, and as screening tools to reduce the experimental search space. However, computational studies have grappled with issues stemming from the absence of standardized procedures and relevant crystal structures. Fundamental disparities between SPAs and protein simulations, such as the absence of experimentally validated initial structures and the importance of the simulation size, number of molecules, and concentration, have compounded these challenges. Understanding the roles of various parameters and the capabilities of different models and simulation setups remains an ongoing endeavor. In this review, we aim to provide readers with guidance on the parameters to consider when conducting SPA simulations, elucidating their potential impact on outcomes and validity.
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Affiliation(s)
| | - Laura Perez-Chirinos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Baofu Qiao
- Department
of Natural Sciences, Baruch College, City
University of New York, New York, New York 10010, United States
| | - Ivan R. Sasselli
- Centro
de Física de Materiales (CFM), CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
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2
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Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
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3
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Co NT, Li MS, Krupa P. Computational Models for the Study of Protein Aggregation. Methods Mol Biol 2022; 2340:51-78. [PMID: 35167070 DOI: 10.1007/978-1-0716-1546-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein aggregation has been studied by many groups around the world for many years because it can be the cause of a number of neurodegenerative diseases that have no effective treatment. Obtaining the structure of related fibrils and toxic oligomers, as well as describing the pathways and main factors that govern the self-organization process, is of paramount importance, but it is also very difficult. To solve this problem, experimental and computational methods are often combined to get the most out of each method. The effectiveness of the computational approach largely depends on the construction of a reasonable molecular model. Here we discussed different versions of the four most popular all-atom force fields AMBER, CHARMM, GROMOS, and OPLS, which have been developed for folded and intrinsically disordered proteins, or both. Continuous and discrete coarse-grained models, which were mainly used to study the kinetics of aggregation, are also summarized.
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Affiliation(s)
- Nguyen Truong Co
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Pawel Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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Nobile MS, Fontana F, Manzoni L, Cazzaniga P, Mauri G, Saracino GAA, Besozzi D, Gelain F. HyperBeta: characterizing the structural dynamics of proteins and self-assembling peptides. Sci Rep 2021; 11:7783. [PMID: 33833280 PMCID: PMC8032683 DOI: 10.1038/s41598-021-87087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 03/17/2021] [Indexed: 11/10/2022] Open
Abstract
Self-assembling processes are ubiquitous phenomena that drive the organization and the hierarchical formation of complex molecular systems. The investigation of assembling dynamics, emerging from the interactions among biomolecules like amino-acids and polypeptides, is fundamental to determine how a mixture of simple objects can yield a complex structure at the nano-scale level. In this paper we present HyperBeta, a novel open-source software that exploits an innovative algorithm based on hyper-graphs to efficiently identify and graphically represent the dynamics of \documentclass[12pt]{minimal}
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\begin{document}$$\beta$$\end{document}β-sheets formation. Differently from the existing tools, HyperBeta directly manipulates data generated by means of coarse-grained molecular dynamics simulation tools (GROMACS), performed using the MARTINI force field. Coarse-grained molecular structures are visualized using HyperBeta ’s proprietary real-time high-quality 3D engine, which provides a plethora of analysis tools and statistical information, controlled by means of an intuitive event-based graphical user interface. The high-quality renderer relies on a variety of visual cues to improve the readability and interpretability of distance and depth relationships between peptides. We show that HyperBeta is able to track the \documentclass[12pt]{minimal}
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\begin{document}$$\beta$$\end{document}β-sheets formation in coarse-grained molecular dynamics simulations, and provides a completely new and efficient mean for the investigation of the kinetics of these nano-structures. HyperBeta will therefore facilitate biotechnological and medical research where these structural elements play a crucial role, such as the development of novel high-performance biomaterials in tissue engineering, or a better comprehension of the molecular mechanisms at the basis of complex pathologies like Alzheimer’s disease.
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Affiliation(s)
- Marco S Nobile
- Department of Industrial Engineering and Innovation Sciences, Eindhoven University of Technology, Eindhoven, The Netherlands.,Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy.,SYSBIO/ISBE.IT Centre of Systems Biology, Milan, Italy.,Bicocca Bioinformatics, Biostatistics and Bioimaging Centre (B4), Monza, Italy
| | - Federico Fontana
- Fondazione IRCCS Casa Sollievo della Sofferenza, Unità Ingegneria Tissutale, Viale Cappuccini 1, San Giovanni Rotondo, 71013, Foggia, Italy
| | - Luca Manzoni
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
| | - Paolo Cazzaniga
- SYSBIO/ISBE.IT Centre of Systems Biology, Milan, Italy.,Bicocca Bioinformatics, Biostatistics and Bioimaging Centre (B4), Monza, Italy.,Department of Human and Social Sciences, University of Bergamo, Bergamo, Italy
| | - Giancarlo Mauri
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy.,SYSBIO/ISBE.IT Centre of Systems Biology, Milan, Italy.,Bicocca Bioinformatics, Biostatistics and Bioimaging Centre (B4), Monza, Italy
| | - Gloria A A Saracino
- Center for Nanomedicine and Tissue Engineering (CNTE), A.S.S.T. Grande Ospedale Metropolitano Niguarda, Piazza dell'Ospedale Maggiore 3, 20162, Milan, Italy
| | - Daniela Besozzi
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy. .,SYSBIO/ISBE.IT Centre of Systems Biology, Milan, Italy. .,Bicocca Bioinformatics, Biostatistics and Bioimaging Centre (B4), Monza, Italy.
| | - Fabrizio Gelain
- Fondazione IRCCS Casa Sollievo della Sofferenza, Unità Ingegneria Tissutale, Viale Cappuccini 1, San Giovanni Rotondo, 71013, Foggia, Italy. .,Center for Nanomedicine and Tissue Engineering (CNTE), A.S.S.T. Grande Ospedale Metropolitano Niguarda, Piazza dell'Ospedale Maggiore 3, 20162, Milan, Italy.
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Fontana F, Gelain F. Probing mechanical properties and failure mechanisms of fibrils of self-assembling peptides. NANOSCALE ADVANCES 2020; 2:190-198. [PMID: 36133966 PMCID: PMC9416940 DOI: 10.1039/c9na00621d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/16/2019] [Indexed: 05/08/2023]
Abstract
Self-assembling peptides (SAPs) are a promising class of biomaterials amenable to easy molecular design and functionalization. Despite their increasing usage in regenerative medicine, a detailed analysis of their biomechanics at the nanoscale level is still missing. In this work, we propose and validate, in all-atom dynamics, a coarse-grained model to elucidate strain distribution, failure mechanisms and biomechanical effects of functionalization of two SAPs when subjected to both axial stretching and bending forces. We highlight different failure mechanisms for fibril seeds and fibrils, as well as the negligible contribution of the chosen functional motif to the overall system rupture. This approach could lay the basis for the development of "more" coarse-grained models in the long pathway connecting SAP sequences and hydrogel mechanical properties.
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Affiliation(s)
- Federico Fontana
- Fondazione IRCCS Casa Sollievo della Sofferenza, Unità Ingegneria Tissutale Viale Cappuccini 1, San Giovanni Rotondo 71013 Foggia Italy
| | - Fabrizio Gelain
- Fondazione IRCCS Casa Sollievo della Sofferenza, Unità Ingegneria Tissutale Viale Cappuccini 1, San Giovanni Rotondo 71013 Foggia Italy
- Center for Nanomedicine and Tissue Engineering (CNTE), ASST Ospedale Metropolitano Niguarda Piazza dell'Ospedale Maggiore 3 20162 Milan Italy
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