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Water Contribution to the Protein Folding and Its Relevance in Protein Design and Protein Aggregation

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Soft Matter Systems for Biomedical Applications

Part of the book series: Springer Proceedings in Physics ((SPPHY,volume 266))

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Abstract

Water plays a fundamental role in protein stability. However, the effect of the properties of water on the behaviour of proteins is only partially understood. Several theories have been proposed to give insight into the mechanisms of cold and pressure denaturation, or the limits of temperature and pressure above which no protein has a stable, functional state, or how unfolding and aggregation are related. Here we review our results based on a theoretical approach that can rationalize the water contribution to protein solutions’ free energy. We show, using Monte Carlo simulations, how we can explain experimental data with our recent results. We discuss how our findings can help in developing new strategies for the design of novel synthetic biopolymers or new possible approaches for mitigating neurodegenerative pathologies.

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Abbreviations

2D:

two-dimensional

3D:

three-dimensional

b:

bulk

f:

folding

GPU:

graphics processing unit

h:

hydration

HB:

hydrogen bond

IFP:

inverse folding problem

IU:

internal units

MD:

molecular dynamics

R:

residue

SR:

stability region

u:

unfolding

w:

water

C p :

isobaric heat capacity

C p :

isobaric heat capacity

F :

effective free energy

H :

enthalpy

k :

factor of compressibility

k B :

Boltzmann constant

N :

number of cells

P :

pressure

r :

distance

S :

entropy

T :

temperature

V :

volume

v :

proper volume

α :

thermal expansivity factor

b :

isothermal compressibility factor

ϵ :

depth of the potential well

∆x :

difference in magnitude x between final and initial state

σ :

bonding index

Φ :

hydrophobic amino acid

ζ :

hydrophilic amino acid

χ :

mixed amino acids

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Acknowledgements

G.F. acknowledges the support of the Spanish Grant N. PGC2018-099277-B-C22 (MCIU/AEI/ERDF) and the support by ICREA Foundation (ICREA Academia prize). I.C. acknowledges the support of the Maria de Maeztu Units of Excellence Programme – Grant No. MDM-2017-0720 Spanish Ministry of Science, Innovation and Universities, the Austrian Science Fund (FWF) project 26253-N27, the Spanish Ministerio de Economià y Competitividad (MINECO) Grant. N. FIS2017-89471-R, the Programa Red Guipuzcoana de Ciencia, Tecnología y Informacion SN 2019-CIEN-000051-01, the BIKAINTEK program (grant No. 008- B1/2020), the COST Action CA17139.

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Authors and Affiliations

  1. Secció de Física Estadística i Interdisciplinària–Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain

    Giancarlo Franzese & Joan Àguila Rojas

  2. Institute of Nanoscience and Nanotechnology (IN2UB), Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain

    Giancarlo Franzese & Joan Àguila Rojas

  3. Faculty of Chemistry, Chemical Physics Department, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, 28040, Madrid, Spain

    Valentino Bianco

  4. Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia San Sebastián, Spain

    Ivan Coluzza

  5. Basque Foundation for Science, IKERBASQUE, 48013, Bilbao, Spain

    Ivan Coluzza

Authors
  1. Giancarlo Franzese
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  2. Joan Àguila Rojas
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  3. Valentino Bianco
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  4. Ivan Coluzza
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Correspondence to Giancarlo Franzese .

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Editors and Affiliations

  1. Taras Shevchenko National University of Kyiv, Kyiv, Ukraine

    Leonid Bulavin

  2. National Academy of Science of Ukraine, Biocolloidal Chemistry Institute named after F.D. Ovharenko, Kyiv, Ukraine

    Nikolai Lebovka

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Franzese, G., Rojas, J.À., Bianco, V., Coluzza, I. (2022). Water Contribution to the Protein Folding and Its Relevance in Protein Design and Protein Aggregation. In: Bulavin, L., Lebovka, N. (eds) Soft Matter Systems for Biomedical Applications. Springer Proceedings in Physics, vol 266. Springer, Cham. https://doi.org/10.1007/978-3-030-80924-9_1

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