The dynamics of biological polymers, including proteins, RNA, and DNA, occur in very high-dimensional spaces. Many naturally occurring polymers can navigate a vast phase space and rapidly find their lowest free energy (folded) state. Thus, although the search process is stochastic, it is not completely random. Instead, it is best described in terms of diffusion along a downhill energy landscape. In this context, there have been many efforts to use simplified representations of the energetics, for which the potential energy is chosen to be a relatively smooth function with a global minimum that corresponds to the folded state. That is, instead of including every type of physical interaction, the broad characteristics of the landscape are encoded in approximate energy functions. We describe a particular class of models, called structure-based models, that can be used to explore the diffusive properties of biomolecular folding and conformational rearrangements. These energy functions may be regarded as the spherical cow for modeling molecular biophysics. We discuss the physical principles underlying these models and provide an entry-level tutorial, which may be adapted for use in curricula for physics and non-physics majors.
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March 2022
COMPUTATIONAL PHYSICS|
March 01 2022
Quantifying biomolecular diffusion with a “spherical cow” model
Frederico Campos Freitas;
Frederico Campos Freitas
a)
1
Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro
, Uberaba, MG, Brazil
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Sandra Byju;
Sandra Byju
b)
2
Department of Physics and Center for Theoretical Biological Physics, Northeastern University
, 360 Huntington Avenue, Boston, Massachusetts 02115
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Asem Hassan;
Asem Hassan
2
Department of Physics and Center for Theoretical Biological Physics, Northeastern University
, 360 Huntington Avenue, Boston, Massachusetts 02115
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Ronaldo Junio de Oliveira;
Ronaldo Junio de Oliveira
c)
1
Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro
, Uberaba, MG, Brazil
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Paul C. Whitford
Paul C. Whitford
d)
2
Department of Physics and Center for Theoretical Biological Physics, Northeastern University
, 360 Huntington Avenue, Boston, Massachusetts 02115
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a)
ORCID: 0000-0001-9195-9900.
b)
ORCID: 0000-0003-0220-195X.
c)
ORCID: 0000-0003-4860-309X.
d)
Author to whom correspondence should be addressed: p.whitford@northeastern.edu, ORCID: 0000-0001-7104-2265.
Am. J. Phys. 90, 225–238 (2022)
Article history
Received:
October 20 2021
Accepted:
October 20 2021
Citation
Frederico Campos Freitas, Sandra Byju, Asem Hassan, Ronaldo Junio de Oliveira, Paul C. Whitford; Quantifying biomolecular diffusion with a “spherical cow” model. Am. J. Phys. 1 March 2022; 90 (3): 225–238. https://doi.org/10.1119/5.0075952
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