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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes pp 541–558Cite as

Explicit-Solvent All-Atom Molecular Dynamics of Peptide Aggregation

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Part of the book series: Springer Series on Bio- and Neurosystems ((SSBN,volume 8))

Abstract

Recent advances in computational technology have allowed us to simulate biomolecular processes on timescales that begin to reach the rates of peptide aggregation phenomena. Molecular dynamics simulations have evolved into a mature technique to the extent that they can be employed as a highly productive tool to gain meaningful insights into the structure, dynamics and molecular mechanisms of protein aggregation. In this chapter, we describe the basics of explicit solvent all-atom molecular dynamics simulations and its applications for studying early stages of aggregation processes of two short pentapeptides: KLVFF and FVFLM, related to Alzheimer’s disease and preeclampsia, respectively. We focus on certain important problems in the field of protein aggregation that explicit solvent all-atom molecular dynamics simulation studies could resolve. This includes how fibril formation rates depend on a number of factors such as the presence of short peptides and population of fibril-prone conformations. Specific applications of atomistic simulations in explicit solvent to address these two issues are discussed.

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Acknowledgements

The authors thank Girik Malik for critical reading of the manuscript. M. K. acknowledges the Polish Ministry of Science and Higher Education for financial support through “Mobilnosc Plus” Program No. 1287/MOB/IV/2015/0. A. Kol. and M. K. would like to acknowledge support from the National Science Center grant [MAESTRO 2014/14/A/ST6/00088]. IAB acknowledges support from the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) R01HD084628 and The Research Institute at Nationwide Children’s Hospital’s John E. Fisher Endowed Chair for Neonatal and Perinatal Research. A. Klo. acknowledges support from National Science Foundation grant DBI 1661391, and Bridge funds provided by The Research Institute at Nationwide Children’s Hospital. This research was supported in part by the High Performance Computing Facility at The Research Institute at Nationwide Children’s Hospital.

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Authors and Affiliations

  1. Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland

    Maksim Kouza & Andrzej Kolinski

  2. Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA

    Andrzej Kloczkowski

  3. Center for Perinatal Research, The Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA

    Irina Alexandra Buhimschi

  4. Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43215, USA

    Irina Alexandra Buhimschi & Andrzej Kloczkowski

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  1. Maksim Kouza
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  2. Andrzej Kolinski
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  3. Irina Alexandra Buhimschi
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  4. Andrzej Kloczkowski
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Correspondence to Maksim Kouza .

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  1. Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland

    Adam Liwo

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Kouza, M., Kolinski, A., Buhimschi, I.A., Kloczkowski, A. (2019). Explicit-Solvent All-Atom Molecular Dynamics of Peptide Aggregation. In: Liwo, A. (eds) Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer Series on Bio- and Neurosystems, vol 8. Springer, Cham. https://doi.org/10.1007/978-3-319-95843-9_16

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