Spontaneous dimensional reduction and ground state degeneracy in a simple chain model

Škrbić, Tatjana; Hoang, Trinh Xuan; Giacometti, Andrea; Maritan, Amos; Banavar, Jayanth R.

doi:10.1103/physreve.104.l012101

Cited by 6 publications

(3 citation statements)

References 22 publications

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“…There is nevertheless a preferred axis at the location of each main chain sphere corresponding to the tangent along the chain or the direction along which the chain is oriented at that location. Replacing the spheres with objects such as unidirectional coins, uniaxial discs, allowing neighboring spheres to overlap, or adding side chains to the spheres along the main chain are all steps that break the spherical symmetry and yield ground state structures, which resemble protein structures to varying degrees [50][51][52][53][54][55][56][57][58][59][60][61]. To avoid clouding the issue by studying an approximate model for proteins, we resort instead to a careful analysis of experimental data of over 4,000 protein native state structures (see Materials and Methods).…”

Section: Introductionmentioning

confidence: 99%

A Tale of Two Chains: Geometries of a Chain Model and Protein Native State Structures

Škrbić,

Giacometti,

Hoang

et al. 2024

Preprint

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Linear chain molecules play a central role in polymer physics with innumerable industrial applications. They are also ubiquitous constituents of living cells. Here we highlight the similarities and differences between two distinct ways of viewing a linear chain. We do this, on the one hand, through the lens of simulations for a standard polymer chain of tethered spheres at low and high temperatures and, on the other hand, through published experimental data on an important class of biopolymers, proteins. We present detailed analyses of their local and non-local structures as well as the maps of their closest contacts. We seek to reconcile the startlingly different behaviors of the two types of chains based on symmetry considerations.

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Section: Introductionmentioning

confidence: 99%

A Tale of Two Chains: Geometries of a Chain Model and Protein Native State Structures

Škrbić,

Giacometti,

Hoang

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…There is, nevertheless, a preferred axis at the location of each main chain sphere corresponding to the tangent along the chain or the direction along which the chain is oriented at that location. Replacing the spheres with objects such as unidirectional coins and uniaxial discs, allowing neighboring spheres to overlap, or adding side chains to the spheres along the main chain are all steps that break the spherical symmetry and yield ground state structures, which resemble protein structures to varying degrees [ 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 ]. To avoid clouding the issue by studying an approximate model for proteins, we resort instead to a careful analysis of experimental data of over 4000 protein native state structures (see Section 2 ).…”

Section: Introductionmentioning

confidence: 99%

A Tale of Two Chains: Geometries of a Chain Model and Protein Native State Structures

Škrbić,

Giacometti,

Hoang

et al. 2024

Polymers

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Linear chain molecules play a central role in polymer physics with innumerable industrial applications. They are also ubiquitous constituents of living cells. Here, we highlight the similarities and differences between two distinct ways of viewing a linear chain. We do this, on the one hand, through the lens of simulations for a standard polymer chain of tethered spheres at low and high temperatures and, on the other hand, through published experimental data on an important class of biopolymers, proteins. We present detailed analyses of their local and non-local structures as well as the maps of their closest contacts. We seek to reconcile the startlingly different behaviors of the two types of chains based on symmetry considerations.

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“…Second, the side chains must fill the space in the interior of the protein, packing tightly against each other, maximizing favorable self-interactions in the hydrophobic interior, and minimizing empty space [29] (see Figure 1). Interestingly, even in toy chain models [32][33][34][35][36][37][38], adding side chain spheres to the canonical tangent sphere model and permitting adjoining spheres to overlap, destabilizes the disordered compact globular phase and results in novel structured phases with effectively reduced dimensionalities.…”

Section: Introductionmentioning

confidence: 99%

Amino acid characteristics in protein native state structures

Škrbić,

Giacometti,

Hoang

et al. 2023

Preprint

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We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We find that when the amino acids are grouped based on chemical similarity, the resulting groups equally well fit the geometrical attributes in a harmonious manner. Our analysis underscores the role of minimal frustration in the evolution of protein sequences that fit within a pre-sculpted menu of putative native state folds.

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Spontaneous dimensional reduction and ground state degeneracy in a simple chain model

Cited by 6 publications

References 22 publications

A Tale of Two Chains: Geometries of a Chain Model and Protein Native State Structures

A Tale of Two Chains: Geometries of a Chain Model and Protein Native State Structures

A Tale of Two Chains: Geometries of a Chain Model and Protein Native State Structures

Amino acid characteristics in protein native state structures

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