Hydropathic wave ordering of alpha crystallin—Membrane interactions enhances human lens transparency and resists cataracts

Moret, Marcelo A.; Zebende, Gilney Figueira; Phillips, J. C.

doi:10.1016/j.physa.2018.09.128

Cited by 2 publications

(3 citation statements)

References 22 publications

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“…Furthermore, we uncover the topology and sequence bases of the evolutionary trend of proteins. Such an evolutionary trend is consistent with what has been suggested by previous studies (76–80). Besides enhancing the functional sensitivity of proteins, such evolutionary trends can also prevent the dysfunctional aggregation of proteins (80).…”

Section: Discussionsupporting

confidence: 93%

“…Our topological and sequence analyses show that higher organismal complexity correlates with the assortativity of the residue contact networks and the hydrophilic-hydrophobic segregation in protein sequences. These correlations are consistent with what has been suggested by previous evolutionary studies (Phillips 2009; Phillips 2012; Hemery and Rivoire 2015; Foy et al 2019; Moret et al 2019; Phillips 2020), and may guide the design or modification of proteins. For example, one may enhance the flexibility or functional sensitivity of a protein by greater segregation of hydrophobic and hydrophilic amino acids in the sequence.…”

Section: Discussionsupporting

confidence: 91%

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The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database

Tang

Ren²,

Wang

et al. 2022

Preprint

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The relationship between species evolution and protein evolution has been remaining as a mystery. The recent development of artificial intelligence provides us with new and powerful tools for studying the evolution of proteins and species. In this work, based on the AlphaFold Protein Structure Database (AlphaFold DB), we perform comparative analyses of the protein structures of different species. The statistics of AlphaFold-predicted structures show that, as species evolve from prokaryotes to eukaryotes, from unicellular to multicellular organisms, from invertebrates to vertebrates, and so on, the proteins within them evolve towards larger radii of gyration, higher coil fractions, higher modularity, and slower relaxations, indicating that the average flexibility of proteins gradually increases in the species evolution. With the scaling analyses, the size dependence of proteins' shape, topology, and dynamics suggest a decreasing fractal dimension of the proteins in species evolution. This evolutionary trend is accompanied by the increasing eigengaps in the vibration spectra of proteins, implying that the proteins are statistically evolving towards higher functional specificity and lower dimensionality in the equilibrium dynamics. Furthermore, we also uncover the topology and sequence bases of this evolutionary trend. The residue contact networks of the proteins are evolving towards higher assortativity, and the hydrophobic and hydrophilic amino acid residues are evolving to have increasing segregations in the sequences. This study provides new insights into how the diversity in the functionality of the proteins increases and their plasticity grows in evolution. The evolutionary laws implied by these statistical results may also shed light on the study of protein design.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionsupporting

confidence: 91%

The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database

Tang

Ren²,

Wang

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Our topological and sequence analyses show that higher organismal complexity correlates with the assortativity of the residue contact networks and the hydrophilic–hydrophobic segregation in protein sequences. These correlations are consistent with what has been suggested by previous evolutionary studies ( Phillips 2009 , 2012 , 2020 ; Hemery and Rivoire 2015 ; Foy et al 2019 ; Moret et al 2019 ), and may guide the design or modification of proteins. For example, one may enhance the flexibility or functional sensitivity of a protein by greater segregation of hydrophobic and hydrophilic amino acids in the sequence.…”

Section: Discussionsupporting

confidence: 91%

The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database

Tang

Ren

Wang

et al. 2022

Molecular Biology and Evolution

View full text Add to dashboard Cite

The recent development of artificial intelligence provides us with new and powerful tools for studying the mysterious relationship between organism evolution and protein evolution. In this work, based on the AlphaFold Protein Structure Database (AlphaFold DB), we perform comparative analyses of the proteins of different organisms. The statistics of AlphaFold-predicted structures show that, for organisms with higher complexity, their constituent proteins will have larger radii of gyration, higher coil fractions, and slower vibrations, statistically. By conducting normal mode analysis and scaling analyses, we demonstrate that higher organismal complexity correlates with lower fractal dimensions in both the structure and dynamics of the constituent proteins, suggesting that higher functional specialization is associated with higher organismal complexity. We also uncover the topology and sequence bases of these correlations. As the organismal complexity increases, the residue contact networks of the constituent proteins will be more assortative, and these proteins will have a higher degree of hydrophilic–hydrophobic segregation in the sequences. Furthermore, by comparing the statistical structural proximity across the proteomes with the phylogenetic tree of homologous proteins, we show that, statistical structural proximity across the proteomes may indirectly reflect the phylogenetic proximity, indicating a statistical trend of protein evolution in parallel with organism evolution. This study provides new insights into how the diversity in the functionality of proteins increases and how the dimensionality of the manifold of protein dynamics reduces during evolution, contributing to the understanding of the origin and evolution of lives.

show abstract

Hydropathic wave ordering of alpha crystallin—Membrane interactions enhances human lens transparency and resists cataracts

Cited by 2 publications

References 22 publications

The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database

The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database

The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database

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